Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold432
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: 253078
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 16258 characters in sequence are not A, C, G, or T
Found at i:3272 original size:38 final size:37
Alignment explanation
Indices: 3201--3281 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
3191 AAATTCAGAT
* *
3201 TTCAATTCAAATTCATCTTTTTCACTTTCAATCACA-A
1 TTCAATCCAAATTCATCTTTTCCACTTTCAATCA-ATA
3238 TTCAATCCAAAATTCA-CTTTTCCA-TTCTCAAATCAATA
1 TTCAATCC-AAATTCATCTTTTCCACTT-TC-AATCAATA
3276 TTCAAT
1 TTCAAT
3282 TTAATTCCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
36 2 0.05
37 17 0.45
38 19 0.50
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.41
Consensus pattern (37 bp):
TTCAATCCAAATTCATCTTTTCCACTTTCAATCAATA
Found at i:6173 original size:16 final size:18
Alignment explanation
Indices: 6152--6197 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
6142 ATTTTCGAGC
6152 TAAAAAGCTAACCC-GA-
1 TAAAAAGCTAACCCAGAT
6168 TAAAAAGCTCAACCCAGAT
1 TAAAAAGCT-AACCCAGAT
*
6187 TAAAATGCTAA
1 TAAAAAGCTAA
6198 ACTCAAGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 5 0.19
18 4 0.15
19 8 0.31
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (18 bp):
TAAAAAGCTAACCCAGAT
Found at i:6915 original size:23 final size:23
Alignment explanation
Indices: 6879--6942 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
6869 TCGTTTATGT
6879 TCATTTGAAA-CTTGTTTAAT-AGA
1 TCATTT-AAAGCTTGTTTAATGA-A
*
6902 TTATTTAAAGCTTGTTTAATGAA
1 TCATTTAAAGCTTGTTTAATGAA
*
6925 TCATTCAAAGCTTGTTTA
1 TCATTTAAAGCTTGTTTA
6943 TTGTTCCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.89
24 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (23 bp):
TCATTTAAAGCTTGTTTAATGAA
Found at i:9177 original size:21 final size:21
Alignment explanation
Indices: 9135--9177 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9125 ACAAAATATA
* **
9135 AAAAAATAGAAATTATTTTGT
1 AAAAAATAGAAAATATAGTGT
*
9156 AAAAAATATAAAATATAGTGT
1 AAAAAATAGAAAATATAGTGT
9177 A
1 A
9178 GCCTTTAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAAAATAGAAAATATAGTGT
Found at i:13067 original size:23 final size:24
Alignment explanation
Indices: 13037--13091 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
13027 AATTCACAAA
13037 AAAAAATCAAAAGCAAAA-AAAAG
1 AAAAAATCAAAAGCAAAACAAAAG
* *
13060 AAAAAATCAAAATCAAAATCAAAAT
1 AAAAAATCAAAAGCAAAA-CAAAAG
13085 AAAAAAT
1 AAAAAAT
13092 AATAATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.61
25 11 0.39
ACGTcount: A:0.76, C:0.09, G:0.04, T:0.11
Consensus pattern (24 bp):
AAAAAATCAAAAGCAAAACAAAAG
Found at i:14660 original size:176 final size:176
Alignment explanation
Indices: 14366--17500 Score: 6216
Period size: 176 Copynumber: 17.8 Consensus size: 176
14356 GTAGCGGAGC
* * * * * *
14366 AGGTTGAAAATAACAAATCTTCCCTTCCTATACTGACGGCGAAGCAAATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
14431 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
14496 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
14542 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
14607 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
14672 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
14718 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
14783 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
14848 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
14894 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
14959 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15024 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15070 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
15135 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15200 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15246 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
15311 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15376 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15422 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
15487 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15552 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15598 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
15663 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15728 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15774 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
15839 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
15904 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
15950 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16015 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16080 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
16126 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16191 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16256 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
16302 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16367 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16432 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
16478 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16543 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16608 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
16654 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16719 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16784 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
16830 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
16895 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
16960 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
17006 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
17071 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
17136 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
17182 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
17247 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
17312 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
131 AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
17358 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
1 AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
17423 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
17488 AGCAAATTGAAGA
131 AGCAAATTGAAGA
17501 AATCTTCCCT
Statistics
Matches: 2953, Mismatches: 6, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 2953 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (176 bp):
AGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGATCGAAGATTGTAAGTCC
TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
AGCAAATTGAAGACCCCAACCTTGTCTCCCTGAGCAGCAGTGGAAT
Found at i:17541 original size:124 final size:124
Alignment explanation
Indices: 17388--17624 Score: 456
Period size: 124 Copynumber: 1.9 Consensus size: 124
17378 TGCCTTCCTG
* *
17388 TACTGACGGCGAAGTAGATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
1 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
17453 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
66 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
17512 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
1 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
17577 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGA
66 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGA
17625 CCCCAACCTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (124 bp):
TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
Found at i:17771 original size:44 final size:44
Alignment explanation
Indices: 17708--17802 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
17698 GAAGTAGATC
*
17708 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
1 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAAGTT
*
17752 GAAGATTGTGAA-TTCTATCTCCCTGGTCAGCAGTGGAATAAGTT
1 GAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTGGAATAAGTT
17796 GAAGATT
1 GAAGATT
17803 ACAGATCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (44 bp):
GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAAGTT
Found at i:17773 original size:300 final size:300
Alignment explanation
Indices: 17212--17758 Score: 1067
Period size: 300 Copynumber: 1.8 Consensus size: 300
17202 TGCCTTCCTG
* *
17212 TACTGACGGCGAAGTAGATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
1 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
17277 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGACCCCAACCTTGTCTCCC
66 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGACCCCAACCTTGTCTCCC
17342 TGAGCAGCAGTGGAATAGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGAT
131 TGAGCAGCAGTGGAATAGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGAT
*
17407 CGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCTTATCT
196 CGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTACAGATCTTATCT
17472 CCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
261 CCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
17512 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
1 TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
17577 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGACCCCAACCTTGTCTCCC
66 AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGACCCCAACCTTGTCTCCC
17642 TGAGCAGCAGTGGAATAGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGAT
131 TGAGCAGCAGTGGAATAGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGAT
17707 CGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
196 CGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
17759 GTGAATTCTA
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
300 244 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (300 bp):
TACTGACGGCGAAGCAAATCGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATGGGTTG
AAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATTGAAGACCCCAACCTTGTCTCCC
TGAGCAGCAGTGGAATAGGTTGAAAATAATAGATCTTGCCTTCCTGTACTGACGGCGAAGTAGAT
CGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTACAGATCTTATCT
CCTTAAGCAGTAGTGGAGCAAATTGAAGAAATCTTCCCTA
Found at i:17815 original size:44 final size:44
Alignment explanation
Indices: 17547--17819 Score: 136
Period size: 44 Copynumber: 6.2 Consensus size: 44
17537 TTGTAAGTCC
**
17547 TATCTCCCTGGTCAGCAGTGGAATGGGTTGAAGATTACAGATCT
1 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
* * * ** * *** *
17591 TATCTCCTTAAG-CAGTAGTGGAGCAAATTGAAGACCCCA-ACCT
1 TATCTCCCT-GGTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
* * * * *
17634 TGTCTCCCTGAG-CAGCAGTGGAATAGGTTGAAAATAATAGATCT
1 TATCTCCCTG-GTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
** * * * *
17678 TGCCTTCCT-GTACTG-ACG-GCGAAGT-AGATCGAAGATTGTA-AG-TCC
1 TATCTCCCTGGT-CAGCA-GTG-GAA-TAAG-TTGAAGA-T-TACAGATCT
* **
17723 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT-GTGAAT-T
1 TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAG-ATCT
17766 CTATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
1 -TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
17811 TATCTCCCT
1 TATCTCCCT
17820 AAGCAGTAGT
Statistics
Matches: 163, Mismatches: 45, Indels: 42
0.65 0.18 0.17
Matches are distributed among these distances:
42 3 0.02
43 31 0.19
44 97 0.60
45 24 0.15
46 7 0.04
47 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAGATCT
Found at i:17831 original size:44 final size:44
Alignment explanation
Indices: 17783--17919 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 44
17773 CCTGGTCAGC
17783 AGTGGAATAAGTTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAAGTTGAAGATTACAGATCTTATCTCCCTAAGCAGT
** * *** * * * *
17827 AGTGG-AGCAGATCGAAGACCCCAG-CCTTGTCTCCCTGAGCAGC
1 AGTGGAATAAG-TTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * * * *
17870 AGTGGAGTAGGTTGAAAATTACAGATCTTATCTCGCTAAACAGT
1 AGTGGAATAAGTTGAAGATTACAGATCTTATCTCCCTAAGCAGT
17914 AGTGGA
1 AGTGGA
17920 GCAAATCGAA
Statistics
Matches: 65, Mismatches: 25, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
43 31 0.48
44 34 0.52
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
AGTGGAATAAGTTGAAGATTACAGATCTTATCTCCCTAAGCAGT
Found at i:17891 original size:87 final size:87
Alignment explanation
Indices: 17769--17941 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 87
17759 GTGAATTCTA
* *
17769 TCTCCCTGGTCAGCAGTGGAATAAGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTGGTCAGCAGTGGAATAAGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGAG
* *
17834 CAGATCGAAGACCCCAGCCTTG
66 CAAATCGAAGACACCAGCCTTG
* * *
17856 TCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCGCTAAACAGTAGTGGA
1 TCTCCCTG-GTCAGCAGTGGAATAAGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGA
17920 GCAAATCGAAGACACCAGCCTT
65 GCAAATCGAAGACACCAGCCTT
17942 ACCTCTCTGG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 77 0.99
88 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
TCTCCCTGGTCAGCAGTGGAATAAGTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGAG
CAAATCGAAGACACCAGCCTTG
Found at i:17969 original size:87 final size:87
Alignment explanation
Indices: 17793--17973 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 87
17783 AGTGGAATAA
* * * * **
17793 GTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGCCTTGTC
1 GTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCGAAGACACCAGCCTTACC
* *
17858 TCCCTGAGCAGCAGTGGAGTAG
66 TCCCTGAGCAGCAGCGGAGCAG
*
17880 GTTGAAAATTACAGATCTTATCTCGCTAAACAGTAGTGGAGCAAATCGAAGACACCAGCCTTACC
1 GTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCGAAGACACCAGCCTTACC
* * ** *
17945 TCTCTGGGTTGTAGCGGAGCAG
66 TCCCTGAGCAGCAGCGGAGCAG
17967 GTTGAAA
1 GTTGAAA
17974 GCACCAGATC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (87 bp):
GTTGAAAATTACAGATCTTATCTCCCTAAACAGTAGTGGAGCAAATCGAAGACACCAGCCTTACC
TCCCTGAGCAGCAGCGGAGCAG
Found at i:18379 original size:45 final size:45
Alignment explanation
Indices: 18328--18484 Score: 146
Period size: 44 Copynumber: 3.5 Consensus size: 45
18318 ATCACATCAG
* * *
18328 GTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTCAAGAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACCAA
*
18373 GTCTTATC-CCCTTGAAGTTGCAGTGG-GACAGACTGAAGAAACCAA
1 GTCTTATCTCCC-TGAAGTTGCAGTGGAG-CAGACTCAAGAAACCAA
** * * *
18418 -TCCCATCTCCCTGAAGTTACAGTGGAGC-GAAT-TA-AAACCACA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACCA-A
*
18460 GATCTTATCTCTCTGAAGTTGCAGT
1 G-TCTTATCTCCCTGAAGTTGCAGT
18485 AGAACAGATC
Statistics
Matches: 92, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
41 6 0.07
42 2 0.02
43 3 0.03
44 42 0.46
45 39 0.42
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAACCAA
Found at i:18430 original size:218 final size:218
Alignment explanation
Indices: 18020--18444 Score: 627
Period size: 218 Copynumber: 1.9 Consensus size: 218
18010 AGATCGGAGC
* *
18020 CATTAATCCAATCTCCTTGAGATTGCAGCGGAACGGATTAAAATAATAGATCTTATCACTCTGAA
1 CATTAATCCAATCTCCCTGAGATTGCAACGGAACGGATTAAAATAATAGATCTTATCACTCTGAA
* * *
18085 GTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAAACTGAGTAA
66 GTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAAACTAAGAAA
* * **** *** *
18150 GCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGTAGATTTTACCTCCCTGAG
131 GCAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACTGAAGAAACCAGATCCCACCTCCCTGAA
18215 GTTACAGTGGAGTTTATTGAAGT
196 GTTACAGTGGAGTTTATTGAAGT
* * * * *
18238 CATTAATCCTATCTCCCTGAGGTTGCAACTGAGCGGATTAAAATAATAGATCTTATCTCTCTGAA
1 CATTAATCCAATCTCCCTGAGATTGCAACGGAACGGATTAAAATAATAGATCTTATCACTCTGAA
*
18303 GTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTCAAGAA
66 GTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAAACT-AAGAA
* *
18368 AGCAAGTCTTATCCCCTTGAAGTTGCAGTGGGACAGACTGAAGAAACCA-ATCCCATCTCCCTGA
130 AGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACTGAAGAAACCAGATCCCACCTCCCTGA
18432 AGTTACAGTGGAG
195 AGTTACAGTGGAG
18445 CGAATTAAAA
Statistics
Matches: 183, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
218 138 0.75
219 45 0.25
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (218 bp):
CATTAATCCAATCTCCCTGAGATTGCAACGGAACGGATTAAAATAATAGATCTTATCACTCTGAA
GTTGCAGTAGAGTGGATCACATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAAACTAAGAAA
GCAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACTGAAGAAACCAGATCCCACCTCCCTGAA
GTTACAGTGGAGTTTATTGAAGT
Found at i:18441 original size:44 final size:46
Alignment explanation
Indices: 18333--18442 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 46
18323 ATCAGGTCTT
* * * **
18333 ATCTCCCTGAGGTTGCAG-CGGAGCAGACTCAAGAAAGCAAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGGAGCAGACTCAAGAAACCAAGTCCC
*
18378 ATC-CCCTTGAAGTTGCAGTGGGA-CAGACTGAAGAAACCAA-TCCC
1 ATCTCCC-TGAAGTTGCAGTGGGAGCAGACTCAAGAAACCAAGTCCC
*
18422 ATCTCCCTGAAGTTACAGTGG
1 ATCTCCCTGAAGTTGCAGTGG
18443 AGCGAATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
44 21 0.38
45 31 0.56
46 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (46 bp):
ATCTCCCTGAAGTTGCAGTGGGAGCAGACTCAAGAAACCAAGTCCC
Found at i:19058 original size:22 final size:23
Alignment explanation
Indices: 19014--19058 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19004 AGATATTATA
*
19014 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
19037 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
19059 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:19496 original size:3 final size:3
Alignment explanation
Indices: 19488--19839 Score: 704
Period size: 3 Copynumber: 117.3 Consensus size: 3
19478 TTATGTGGCA
19488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19536 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19584 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19632 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19680 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19728 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19776 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19824 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
19840 GTTCTTGATC
Statistics
Matches: 349, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 349 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20326 original size:30 final size:29
Alignment explanation
Indices: 20209--20320 Score: 127
Period size: 30 Copynumber: 3.8 Consensus size: 29
20199 AAAAATTAAA
* * *
20209 AAAATTGCATTTTGACCCCTATACTTTTC
1 AAAATTTCATTTTAACCCCTAAACTTTTC
20238 AAAATTTACATTTTAA-CCCTAAACTTTTC
1 AAAATTT-CATTTTAACCCCTAAACTTTTC
* * *
20267 TAAAATTACATTTCAACCCTTAAACTTTCTC
1 -AAAATTTCATTTTAACCCCTAAACTTT-TC
*
20298 AAAATTTCACTTTAACCCCTAAA
1 AAAATTTCATTTTAACCCCTAAA
20321 GTTTCTAGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 25 0.36
30 42 0.61
31 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTTCATTTTAACCCCTAAACTTTTC
Found at i:20333 original size:30 final size:28
Alignment explanation
Indices: 20209--20333 Score: 101
Period size: 30 Copynumber: 4.2 Consensus size: 28
20199 AAAAATTAAA
* * *
20209 AAAATTGCATTTTGACCCCTATACTTT-T
1 AAAATTTCA-TTTAACCCCTAAACTTTCT
20237 CAAAATTTACATTTTAA-CCCTAAACTTTTCT
1 -AAAATTT-CA-TTTAACCCCTAAAC-TTTCT
* *
20268 AAAATTACATTTCAACCCTTAAACTTTCT
1 AAAATTTCATTT-AACCCCTAAACTTTCT
*
20297 CAAAATTTCACTTTAACCCCTAAAGTTTCT
1 -AAAATTTCA-TTTAACCCCTAAACTTTCT
20327 AGAAATT
1 A-AAATT
20334 ACCCTTTAGC
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
28 3 0.04
29 23 0.29
30 50 0.62
31 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTTCATTTAACCCCTAAACTTTCT
Found at i:20341 original size:30 final size:29
Alignment explanation
Indices: 20223--20369 Score: 95
Period size: 30 Copynumber: 5.0 Consensus size: 29
20213 TTGCATTTTG
* **
20223 ACCCCTATACTTT-TCAAAATTTACATTTTA
1 ACCCCTAAACTTTCT-AAAA-TTACCCTTTA
*
20253 A-CCCTAAACTTTTCTAAAATTA-CATTTCA
1 ACCCCTAAAC-TTTCTAAAATTACCCTTT-A
* * *
20282 ACCCTTAAACTTTCTCAAAATTTCACTTTA
1 ACCCCTAAACTTTCT-AAAATTACCCTTTA
*
20312 ACCCCTAAAGTTTCTAGAAATTACCCTTT-
1 ACCCCTAAACTTTCTA-AAATTACCCTTTA
* * * *
20341 AGCCCTATATTTTCCTAAAATTACACTTT
1 ACCCCTAAACTTT-CTAAAATTACCCTTT
20370 TGCCCCAGAA
Statistics
Matches: 94, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.03
29 39 0.41
30 48 0.51
31 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.39
Consensus pattern (29 bp):
ACCCCTAAACTTTCTAAAATTACCCTTTA
Found at i:21094 original size:11 final size:11
Alignment explanation
Indices: 21076--21131 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 11
21066 AGAAGAAAGG
21076 AGAAAGAAAAA
1 AGAAAGAAAAA
*
21087 AGAGAG-AAAA
1 AGAAAGAAAAA
21097 AGAAAG-AAAA
1 AGAAAGAAAAA
21107 AGAAA-AAAAA
1 AGAAAGAAAAA
*
21117 A-ACAATAAAAA
1 AGA-AAGAAAAA
21128 AGAA
1 AGAA
21132 CAAAAGTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 1 0.03
10 25 0.64
11 12 0.31
12 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:21117 original size:21 final size:21
Alignment explanation
Indices: 21076--21136 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
21066 AGAAGAAAGG
* *
21076 AGAAAGAAAAA-AGAGAGAAAA
1 AGAAAGAAAAAGA-AAAAAAAA
21097 AGAAAGAAAAAGAAAAAAAAA
1 AGAAAGAAAAAGAAAAAAAAA
* *
21118 ACAATA-AAAAAGAACAAAA
1 AGAA-AGAAAAAGAAAAAAA
21137 GTAGCAGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAAAGAAAAAGAAAAAAAAA
Found at i:21241 original size:27 final size:27
Alignment explanation
Indices: 21206--21279 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
21196 AAAATCTGCA
*
21206 GCAGGCCAGCCCAGGCCCGTTCCAGCG
1 GCAGCCCAGCCCAGGCCCGTTCCAGCG
21233 GCAGCCCAGCCCAGGCCCGTTCCAGCG
1 GCAGCCCAGCCCAGGCCCGTTCCAGCG
21260 GCAGCCCAGCACCCAGGCCC
1 GCAGCCCAG--CCCAGGCCC
21280 AAATTTGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 35 0.80
29 9 0.20
ACGTcount: A:0.16, C:0.49, G:0.30, T:0.05
Consensus pattern (27 bp):
GCAGCCCAGCCCAGGCCCGTTCCAGCG
Found at i:21705 original size:17 final size:18
Alignment explanation
Indices: 21670--22142 Score: 183
Period size: 18 Copynumber: 25.8 Consensus size: 18
21660 GTTAAATACG
21670 GTGTTTTCAAAAA---TC
1 GTGTTTTCAAAAATTTTC
21685 GTG-TTTCAAAAATTTTC
1 GTGTTTTCAAAAATTTTC
*
21702 GTGTTTTCAGAAAAATTTC
1 GTGTTTTCA-AAAATTTTC
*
21721 TTGTGTTTCAAAAA-TTTC
1 GTGT-TTTCAAAAATTTTC
* *
21739 AGGGTTTTTAAAAATTTTC
1 -GTGTTTTCAAAAATTTTC
*
21758 GTGTTTTCAAAAATTCTC
1 GTGTTTTCAAAAATTTTC
* *
21776 ATGTTTT-AAAAATCTTC
1 GTGTTTTCAAAAATTTTC
*
21793 GTGTTTTC-AAAA-TTCC
1 GTGTTTTCAAAAATTTTC
*
21809 GGTGTTTTCAAAAAATTTCCC
1 -GTGTTTTC-AAAAATTT-TC
* **
21830 TTGTTTTCAAAAATTCCC
1 GTGTTTTCAAAAATTTTC
* * *
21848 ATATTTT-GAAAATTTTC
1 GTGTTTTCAAAAATTTTC
* ***
21865 TTGTAAAATTTTC--GTGTTTTC
1 --GT---GTTTTCAAAAATTTTC
* *
21886 GTATTTTCAAAAAATTCTC
1 GTGTTTTC-AAAAATTTTC
21905 GTG-TTTCAAAAAATTTTC
1 GTGTTTTC-AAAAATTTTC
21923 GTGTTTTCAAAATTTTCATGTTTTC
1 GTGTTTTCAAAA-----A--TTTTC
* *
21948 GGGTTTTCAAAAAAAATTCTC
1 GTGTTTTC---AAAAATTTTC
* ***
21969 GTGTTTTTAAAAAAAAATC
1 GTG-TTTTCAAAAATTTTC
* **
21988 GTATTTT-AAAAAAATTC
1 GTGTTTTCAAAAATTTTC
* *
22005 ATGTTTTC-GAAATTTTC
1 GTGTTTTCAAAAATTTTC
* *
22022 GTATTTTCAAAATTTTTC
1 GTGTTTTCAAAAATTTTC
*
22040 GTG---TCAAAAAATTCTC
1 GTGTTTTC-AAAAATTTTC
* * * *
22056 ATG-TATCGAAAATTTCC
1 GTGTTTTCAAAAATTTTC
* * *
22073 TTGTTTTCAAAAAAATTCC
1 GTGTTTTC-AAAAATTTTC
22092 GTGTTTTCAAAAAATTTTC
1 GTGTTTTC-AAAAATTTTC
*
22111 GTG-TTTCAAAAATCTTC
1 GTGTTTTCAAAAATTTTC
22128 GTGTTTTCAAAAATT
1 GTGTTTTCAAAAATT
22143 ATTATTGTGT
Statistics
Matches: 350, Mismatches: 65, Indels: 83
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.03
15 5 0.01
16 18 0.05
17 85 0.24
18 98 0.28
19 81 0.23
20 14 0.04
21 13 0.04
22 9 0.03
23 2 0.01
25 12 0.03
28 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (18 bp):
GTGTTTTCAAAAATTTTC
Found at i:21854 original size:18 final size:18
Alignment explanation
Indices: 21759--21859 Score: 82
Period size: 17 Copynumber: 5.6 Consensus size: 18
21749 AAAATTTTCG
*
21759 TGTTTTCAAAAATTCTCA
1 TGTTTTCAAAAATTCCCA
* *
21777 TGTTTT-AAAAA-TCTTCG
1 TGTTTTCAAAAATTC-CCA
**
21794 TGTTTTC-AAAATTCCGG
1 TGTTTTCAAAAATTCCCA
*
21811 TGTTTTCAAAAAATTTCCCT
1 TGTTTTC-AAAAA-TTCCCA
21831 TGTTTTCAAAAATTCCCA
1 TGTTTTCAAAAATTCCCA
* *
21849 TATTTTGAAAA
1 TGTTTTCAAAA
21860 TTTTCTTGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.03
17 25 0.36
18 22 0.32
19 9 0.13
20 11 0.16
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.44
Consensus pattern (18 bp):
TGTTTTCAAAAATTCCCA
Found at i:22131 original size:36 final size:38
Alignment explanation
Indices: 22073--22158 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 38
22063 GAAAATTTCC
22073 TTGT-TTTCAAAAAAATTCCGTGTTTTCAAAAA-ATT-
1 TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
**
22108 TTCGTGTTTCAAAAATCTT-CGTGTTTTCAAAAATTATTA
1 TT-GTGTTTCAAAAAAATTCCGTGTTTTCAAAAA-TATTA
22147 TTGTGTTTCAAA
1 TTGTGTTTCAAA
22159 GTTCTCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 2 0.05
36 16 0.36
37 11 0.25
38 13 0.30
39 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (38 bp):
TTGTGTTTCAAAAAAATTCCGTGTTTTCAAAAATATTA
Found at i:26148 original size:21 final size:21
Alignment explanation
Indices: 26124--26172 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
26114 CTCTGAAGAG
**
26124 AGAAATTGGAAGTGAAAGTGA
1 AGAAATTGGAAGAAAAAGTGA
* *
26145 AGAAAATGGTAGAAAAAGTGA
1 AGAAATTGGAAGAAAAAGTGA
*
26166 GGAAATT
1 AGAAATT
26173 AAAGAGACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (21 bp):
AGAAATTGGAAGAAAAAGTGA
Found at i:27668 original size:19 final size:19
Alignment explanation
Indices: 27644--27696 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
27634 TTCAATTATG
27644 AATGATTGATAATTACTGA
1 AATGATTGATAATTACTGA
* *
27663 AATGATGTGAT-ATTAGTTA
1 AATGAT-TGATAATTACTGA
27682 AATG-TTGATGAATTA
1 AATGATTGAT-AATTA
27697 TTGTTCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 1 0.03
19 20 0.69
20 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (19 bp):
AATGATTGATAATTACTGA
Found at i:29758 original size:22 final size:22
Alignment explanation
Indices: 29713--29758 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
29703 GTTAACAAAA
* **
29713 TAAAAAAATAGAAATTATTTTG
1 TAAAAAAATAGAAAATATAGTG
*
29735 TAAAAAAATATAAAATATAGTG
1 TAAAAAAATAGAAAATATAGTG
29757 TA
1 TA
29759 GCATTTAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (22 bp):
TAAAAAAATAGAAAATATAGTG
Found at i:34224 original size:14 final size:15
Alignment explanation
Indices: 34205--34242 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
34195 GCTTCATAAC
34205 TTTCTTTTCTTT-TA
1 TTTCTTTTCTTTCTA
*
34219 TTTCTTTTCTTTCTT
1 TTTCTTTTCTTTCTA
34234 TTTCTTTTC
1 TTTCTTTTC
34243 ATGTTGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTCTTTCTA
Found at i:36369 original size:24 final size:23
Alignment explanation
Indices: 36328--36373 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
36318 TCCTCCTGTT
**
36328 TTTCTTTTCTTTTTTTTTGTTTG
1 TTTCTTTTCTTTGATTTTGTTTG
36351 TTTCTTTTCCTTTGATTTTGTTT
1 TTTCTTTT-CTTTGATTTTGTTT
36374 TAAGATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (23 bp):
TTTCTTTTCTTTGATTTTGTTTG
Found at i:43983 original size:21 final size:21
Alignment explanation
Indices: 43959--44002 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
43949 GAATCTTTAG
*
43959 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
43980 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
44001 TA
1 TA
44003 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:47207 original size:18 final size:18
Alignment explanation
Indices: 47184--47219 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47174 ATTTCGATAA
47184 TTTTTTTAAAAAATTAGC
1 TTTTTTTAAAAAATTAGC
* *
47202 TTTTTTTGATAAATTAGC
1 TTTTTTTAAAAAATTAGC
47220 CTACCATCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (18 bp):
TTTTTTTAAAAAATTAGC
Found at i:58833 original size:16 final size:16
Alignment explanation
Indices: 58797--58836 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
58787 AAAGTTCAAA
58797 AAAAAATATATTTAAT
1 AAAAAATATATTTAAT
* *
58813 AAAAAGTATATTTGAT
1 AAAAAATATATTTAAT
*
58829 TAAAAATA
1 AAAAAATA
58837 AAATATAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
AAAAAATATATTTAAT
Found at i:59240 original size:9 final size:9
Alignment explanation
Indices: 59226--59283 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
59216 TTTGGTTAAA
*
59226 AATTAACTG
1 AATTAACCG
*
59235 AATTAACCA
1 AATTAACCG
*
59244 AATTACCCG
1 AATTAACCG
59253 AATTAACCG
1 AATTAACCG
*
59262 AATTACCCG
1 AATTAACCG
*
59271 AATTAACCA
1 AATTAACCG
59280 AATT
1 AATT
59284 GAATCACTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:59248 original size:18 final size:18
Alignment explanation
Indices: 59234--59283 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
59224 AAAATTAACT
59234 GAATTAACCAAATTACCC
1 GAATTAACCAAATTACCC
*
59252 GAATTAACCGAATTACCC
1 GAATTAACCAAATTACCC
59270 GAATTAACCAAATT
1 GAATTAACCAAATT
59284 GAATCACTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (18 bp):
GAATTAACCAAATTACCC
Found at i:60116 original size:13 final size:13
Alignment explanation
Indices: 60098--60122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60088 AGCCAAGCGA
60098 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
60111 AAAAAGGAAAAA
1 AAAAAGGAAAAA
60123 CAATAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:60659 original size:45 final size:45
Alignment explanation
Indices: 60610--60761 Score: 148
Period size: 45 Copynumber: 3.3 Consensus size: 45
60600 CTAAATTTAG
60610 ATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAAC
1 ATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAAC
* * ** ** ** *
60655 ATATTAGAGTATATTCTGGATAAATTAT--TATTATTTGGTTAAATTTAG
1 ATATTAGAATATATT-T-GA-AAATT-TGGAATT-TTTAATTTTATAAAC
60703 ATA-TAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAAC
1 ATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAAC
*
60747 ATATTAGAGTATATT
1 ATATTAGAATATATT
60762 CTGGATAAAT
Statistics
Matches: 80, Mismatches: 19, Indels: 16
0.70 0.17 0.14
Matches are distributed among these distances:
43 1 0.01
44 16 0.20
45 29 0.36
46 2 0.03
47 15 0.19
48 16 0.20
49 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (45 bp):
ATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAAC
Found at i:60718 original size:92 final size:93
Alignment explanation
Indices: 60601--60789 Score: 371
Period size: 92 Copynumber: 2.0 Consensus size: 93
60591 AAAAAAGGGC
60601 TAAATTTAGATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAACATATTAGAGTA
1 TAAATTTAGATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAACATATTAGAGTA
60666 TATTCTGGATAAATTATTATTATTTGGT
66 TATTCTGGATAAATTATTATTATTTGGT
60694 TAAATTTAGATA-TAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAACATATTAGAGTA
1 TAAATTTAGATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAACATATTAGAGTA
60758 TATTCTGGATAAATTATTATTATTTGGT
66 TATTCTGGATAAATTATTATTATTTGGT
60786 TAAA
1 TAAA
60790 CTATGCCAGT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 84 0.88
93 12 0.12
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (93 bp):
TAAATTTAGATATTAGAATATATTTGAAAATTTGGAATTTTTAATTTTATAAACATATTAGAGTA
TATTCTGGATAAATTATTATTATTTGGT
Found at i:65691 original size:37 final size:37
Alignment explanation
Indices: 65639--65711 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
65629 TCTGATTGTT
*
65639 CTTGTCTTATTTGTTGTTCCTTGGTTTCTAATATGTC
1 CTTGTCTTATGTGTTGTTCCTTGGTTTCTAATATGTC
65676 CTTGTCTTATGTGTTGTTCCTTGGTTTCTAATATGT
1 CTTGTCTTATGTGTTGTTCCTTGGTTTCTAATATGT
65712 GTTTGTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.11, C:0.15, G:0.18, T:0.56
Consensus pattern (37 bp):
CTTGTCTTATGTGTTGTTCCTTGGTTTCTAATATGTC
Found at i:68692 original size:2 final size:2
Alignment explanation
Indices: 68685--68714 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
68675 CAAACGTAAC
68685 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
68715 TACAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70767 original size:21 final size:22
Alignment explanation
Indices: 70720--70767 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
70710 AAATTTTGGA
*
70720 AAATTATTTTTATAAACATTTT
1 AAATTATTTTTATAAACAGTTT
* **
70742 GAATTATTTTT-TAAAGGGTTT
1 AAATTATTTTTATAAACAGTTT
70763 AAATT
1 AAATT
70768 GCACATTTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (22 bp):
AAATTATTTTTATAAACAGTTT
Found at i:71192 original size:22 final size:22
Alignment explanation
Indices: 71167--71208 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
71157 ATAAAAGTTC
71167 ATTTT-TAATAAAAATACATAAA
1 ATTTTATAA-AAAAATACATAAA
71189 ATTTTATAAAAAAATACATA
1 ATTTTATAAAAAAATACATA
71209 TAAAATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTTTATAAAAAAATACATAAA
Found at i:74817 original size:28 final size:26
Alignment explanation
Indices: 74768--74831 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
74758 AAAATATATA
74768 TTTATATTATTATTTTAATATTTAATAAT
1 TTTATA-TATTATTTTAATA-TTAA-AAT
*
74797 TTTATATATT-TTTTATTTATTAAAAT
1 TTTATATATTATTTTA-ATATTAAAAT
74823 TTTATATAT
1 TTTATATAT
74832 AATTATCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 12 0.36
27 9 0.27
28 6 0.18
29 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATATATTATTTTAATATTAAAAT
Found at i:85523 original size:18 final size:17
Alignment explanation
Indices: 85502--85537 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
85492 TGTATTTGAA
85502 TCATACTAAGAATTTTTT
1 TCATACTAAG-ATTTTTT
*
85520 TCATATTAAGATTTTTT
1 TCATACTAAGATTTTTT
85537 T
1 T
85538 TATATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (17 bp):
TCATACTAAGATTTTTT
Found at i:85538 original size:18 final size:18
Alignment explanation
Indices: 85502--85542 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
85492 TGTATTTGAA
*
85502 TCATACTAAGAATTTTTT
1 TCATATTAAGAATTTTTT
85520 TCATATTAAG-ATTTTTT
1 TCATATTAAGAATTTTTT
*
85537 TTATAT
1 TCATAT
85543 CATTTGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (18 bp):
TCATATTAAGAATTTTTT
Found at i:86005 original size:13 final size:13
Alignment explanation
Indices: 85987--86013 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
85977 ATTTTGTTAA
85987 AATTTTTGGGTAT
1 AATTTTTGGGTAT
86000 AATTTTTGGGTAT
1 AATTTTTGGGTAT
86013 A
1 A
86014 CAAAAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (13 bp):
AATTTTTGGGTAT
Found at i:87699 original size:181 final size:178
Alignment explanation
Indices: 87337--87710 Score: 494
Period size: 181 Copynumber: 2.1 Consensus size: 178
87327 GCATTAGATT
87337 CAAAACCCTAAACCTAAAACACAATAGTTAATGCCGAAGATAATGTCAAAAAGCACGGTGGGGAC
1 CAAAACCCTAAACCTAAAACACAATAGTTAATGCCGAAGATAATGTCAAAAAGCACGGTGGGGAC
87402 CTTGTTCCAGCATGGAGATCCAAAACCCTAAACTCTAAAACACAGTGGTTAACACTTAACACATG
66 CTTGTTCCAGCATGGAGATCCAAAACCCTAAACTCTAAAACACAGTGGTTAACA--TAACACA-G
87467 AGATAATATAAAAAAACTGGTCGTGAAGGACCTTGTTTTGGCCTGAAAATC
128 AGATAATATAAAAAAACTGGTCGTGAAGGACCTTGTTTTGGCCTGAAAATC
* * * *
87518 CAAAACCCTAAACCCTAAAATACAGTAGTTAATGCC-AGAGAT-ATGTCGAAAAGCACGGTGGTG
1 CAAAACCCTAAA-CCTAAAACACAATAGTTAATGCCGA-AGATAATGTCAAAAAGCACGGTGGGG
* * * *
87581 ACCTTGTTCCGGCATGGAGATCCAGAACCTTAAACTCTAAAACACAGTGGTTAACA-AGA-GC-G
64 ACCTTGTTCCAGCATGGAGATCCAAAACCCTAAACTCTAAAACACAGTGGTTAACATA-ACACAG
* * * * * *
87643 -G-TAATGTAAAAAACCTGGTCGTGACGGACCTTGTTTTGGCTTGGAGATC
128 AGATAATATAAAAAAACTGGTCGTGAAGGACCTTGTTTTGGCCTGAAAATC
87692 CAAAATCCC-AAACCCTAAA
1 CAAAA-CCCTAAA-CCTAAA
87711 TCTAGCCCTA
Statistics
Matches: 175, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
174 57 0.33
175 4 0.02
176 1 0.01
178 2 0.01
179 1 0.01
181 85 0.49
182 25 0.14
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (178 bp):
CAAAACCCTAAACCTAAAACACAATAGTTAATGCCGAAGATAATGTCAAAAAGCACGGTGGGGAC
CTTGTTCCAGCATGGAGATCCAAAACCCTAAACTCTAAAACACAGTGGTTAACATAACACAGAGA
TAATATAAAAAAACTGGTCGTGAAGGACCTTGTTTTGGCCTGAAAATC
Found at i:88262 original size:12 final size:12
Alignment explanation
Indices: 88247--88277 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
88237 TCAAGAACAT
88247 GAACAAGATGAA
1 GAACAAGATGAA
88259 GAACAAGATGAA
1 GAACAAGATGAA
88271 GAACAAG
1 GAACAAG
88278 TCAATTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.10, G:0.26, T:0.06
Consensus pattern (12 bp):
GAACAAGATGAA
Found at i:97636 original size:22 final size:22
Alignment explanation
Indices: 97595--97641 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
97585 GGATGGAATT
***
97595 AAATTTTAAATATTTGAATAAA
1 AAATTTTAAATATCAAAATAAA
97617 AAATTTTAAATATCAAAATAAA
1 AAATTTTAAATATCAAAATAAA
97639 AAA
1 AAA
97642 AGTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAATTTTAAATATCAAAATAAA
Found at i:100014 original size:39 final size:39
Alignment explanation
Indices: 99781--100025 Score: 260
Period size: 39 Copynumber: 6.3 Consensus size: 39
99771 TGGAATACCA
* * * *
99781 ATTATACTAAATGTTTGCTCATACGAGCATTATCCACTA
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* * * *
99820 ATTATA-TTAATTGCTTGCTCAAACGAGCAATATCCATTA
1 ATTATACTGAA-TGCTTGCTCAAACGAGCATTATCCACTG
* * * * *
99859 ATCATACTAAATGCTTGTTCAAACGAGCATTATTCATTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* * *
99898 ATTATACTGAATGCTTGCTCAAAAGAGCAATATTCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* * *
99937 ATTATACCGAATGCTTGTTC-AACGAACATTATCCACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
* * *
99975 ATTATACTGAATGCTTACACAAACGAGCATTATCTACTG
1 ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
*
100014 ATTCTACTGAAT
1 ATTATACTGAAT
100026 AAGATTTTCT
Statistics
Matches: 173, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
38 33 0.19
39 137 0.79
40 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (39 bp):
ATTATACTGAATGCTTGCTCAAACGAGCATTATCCACTG
Found at i:101187 original size:20 final size:21
Alignment explanation
Indices: 101136--101194 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
101126 TGCAAATTTG
101136 TTTTAGCAGTTACAAACCATTA
1 TTTTA-CAGTTACAAACCATTA
**
101158 TTTTCAACAGTTACAAACTGTT-
1 TTTT--ACAGTTACAAACCATTA
101180 TTTTACAGTTACAAA
1 TTTTACAGTTACAAA
101195 AATATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 11 0.33
22 8 0.24
23 13 0.39
24 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (21 bp):
TTTTACAGTTACAAACCATTA
Found at i:102726 original size:13 final size:14
Alignment explanation
Indices: 102691--102729 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
102681 CAACCATTTT
*
102691 ATAAAAAAATAAAA
1 ATAAAAAAGTAAAA
102705 ATAAAAAAGTAAAA
1 ATAAAAAAGTAAAA
*
102719 A-GAAAAAGTAA
1 ATAAAAAAGTAA
102730 TTTGTACGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (14 bp):
ATAAAAAAGTAAAA
Found at i:104477 original size:16 final size:16
Alignment explanation
Indices: 104447--104494 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
104437 TAATTTTATC
* *
104447 ATTATTAATTTAAAAT
1 ATTATAAATTAAAAAT
* *
104463 TTTATAAATTAAAAAA
1 ATTATAAATTAAAAAT
*
104479 AGTATAAATTAAAAAT
1 ATTATAAATTAAAAAT
104495 CTACCATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTATAAATTAAAAAT
Found at i:105996 original size:234 final size:234
Alignment explanation
Indices: 105450--106199 Score: 1175
Period size: 234 Copynumber: 3.1 Consensus size: 234
105440 GAAGATATGT
* * *
105450 ATCGAGAACGGTATCTAAACTCCGAATCCGGATTCGTCCTTCAATATTTTAACATAGGAGAAACA
1 ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
* *
105515 AGGAACGAACATATGCATCGAGAACGACAATACAAGACATTTTAAGATAAGCAAAGCATCAAATG
66 AGGAACGAACATATGCATTGAGAACGACAACACAAGACATTTTAAGATAAGCAAAG---C--ATG
*
105580 AACATATGTATCGAGAACGGAATCTGAACTCGCAACCTGGATTTGTCCATT-GAAA--CTGCATC
126 AACATATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCC-TTCGAAACTCTGCATC
* **
105642 ATGTCAATAAAAAGACTCGATATTTTAACATAGGAGAACCAAGGAATGAACATAGGC
190 ATGTC---------A--C-ATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
105699 ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
1 ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
105764 AGGAACGAACATATGCATTGAGAACGACAACACAAGACATTTTAAGATAAGCAAAGCATGAACAT
66 AGGAACGAACATATGCATTGAGAACGACAACACAAGACATTTTAAGATAAGCAAAGCATGAACAT
105829 ATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCCTTCGAAACTCTGCATCATGTCA
131 ATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCCTTCGAAACTCTGCATCATGTCA
105894 CATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
196 CATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
105933 ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
1 ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
* * *
105998 AGGAACGAACATATGTATTGAGAGCGACAACAGAAGACATTTTAAGATAAGCAAAGCATGAACAT
66 AGGAACGAACATATGCATTGAGAACGACAACACAAGACATTTTAAGATAAGCAAAGCATGAACAT
106063 ATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCCTTCGAAACTCTGCATCATGTCA
131 ATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCCTTCGAAACTCTGCATCATGTCA
106128 CATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
196 CATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
* *
106167 ATCGAGAACGGTAT-TGAGACTCCGAACCTGGAT
1 ATCGAGAACGGTATCT-AAACTCCGAACCCGGAT
106200 TCGTCCTAAA
Statistics
Matches: 483, Mismatches: 14, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
233 1 0.00
234 295 0.61
235 1 0.00
237 1 0.00
243 2 0.00
244 54 0.11
246 13 0.03
249 116 0.24
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (234 bp):
ATCGAGAACGGTATCTAAACTCCGAACCCGGATCCATCCTTCAATATTTTAACATAGGAGAAACA
AGGAACGAACATATGCATTGAGAACGACAACACAAGACATTTTAAGATAAGCAAAGCATGAACAT
ATGTATCGAGAACGGAATCTGAACTCGCAACCCGGATTTGTCCTTCGAAACTCTGCATCATGTCA
CATATTTTAACATAGGAGAAACAAGGAACAAACATAGGC
Found at i:108995 original size:16 final size:16
Alignment explanation
Indices: 108960--109006 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
108950 CCAAGTGTTT
* * *
108960 TAATTTTAAAAGATAC
1 TAATTTTTAAAGAAAA
108976 TAATTTTTAAAGAAAA
1 TAATTTTTAAAGAAAA
108992 TAATATTTT-AAGAAA
1 TAAT-TTTTAAAGAAA
109007 GACATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATTTTTAAAGAAAA
Found at i:111571 original size:14 final size:15
Alignment explanation
Indices: 111552--111580 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
111542 TAAAAAAAAC
111552 TCATACTA-AATATA
1 TCATACTATAATATA
111566 TCATACTATAATATA
1 TCATACTATAATATA
111581 AAACATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (15 bp):
TCATACTATAATATA
Found at i:114458 original size:35 final size:35
Alignment explanation
Indices: 114412--114482 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
114402 AGAAACAAAG
*
114412 TCTTCTAGGAAAAGTAAAAGGAAAATCATCCTCAC
1 TCTTCTAGGAAAAGTAAAAGAAAAATCATCCTCAC
*
114447 TCTTCTAGGAAAAGTACAAGAAAAATCATCCTCAC
1 TCTTCTAGGAAAAGTAAAAGAAAAATCATCCTCAC
114482 T
1 T
114483 TTTGGATGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (35 bp):
TCTTCTAGGAAAAGTAAAAGAAAAATCATCCTCAC
Found at i:116064 original size:28 final size:28
Alignment explanation
Indices: 116032--116088 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
116022 GCAATAAAGC
116032 ACATAAATAATCAAATAATTCCTTCTAG
1 ACATAAATAATCAAATAATTCCTTCTAG
*
116060 ACATATATAATCAAATAATTCCTTCTAG
1 ACATAAATAATCAAATAATTCCTTCTAG
116088 A
1 A
116089 GCACAGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.33
Consensus pattern (28 bp):
ACATAAATAATCAAATAATTCCTTCTAG
Found at i:120374 original size:2 final size:2
Alignment explanation
Indices: 120367--120392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
120357 AAGTTTCATG
120367 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
120393 GAACACAATT
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):
AT
Found at i:121071 original size:26 final size:26
Alignment explanation
Indices: 121042--121097 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
121032 TAAAATAGGG
121042 CTTTTGAATGTGGTACCTCAGTTTTA
1 CTTTTGAATGTGGTACCTCAGTTTTA
121068 CTTTTGAATGTGGTACCTCAGTTTTA
1 CTTTTGAATGTGGTACCTCAGTTTTA
121094 CTTT
1 CTTT
121098 AATATTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (26 bp):
CTTTTGAATGTGGTACCTCAGTTTTA
Found at i:125549 original size:16 final size:17
Alignment explanation
Indices: 125522--125553 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
125512 ACCCGGCCTG
125522 TTTTTAATTAAAATTAT
1 TTTTTAATTAAAATTAT
125539 TTTTTAA-TAAAATTA
1 TTTTTAATTAAAATTA
125554 AACTAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAAATTAT
Found at i:126623 original size:16 final size:16
Alignment explanation
Indices: 126602--126643 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
126592 AATAATTTGA
*
126602 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
126618 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
126634 TAGTTTTAAT
1 TAATTTTAAT
126644 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:126642 original size:22 final size:22
Alignment explanation
Indices: 126617--126671 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
126607 TTACTAACAA
* * *
126617 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
126639 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
126661 TTAATTTTAAT
1 TTAATTTTAAT
126672 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:137768 original size:11 final size:12
Alignment explanation
Indices: 137744--137776 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
137734 ACTTTTTTTA
*
137744 TAATATATAAAT
1 TAATATAAAAAT
137756 TAA-ATAAAAAT
1 TAATATAAAAAT
137767 TAATATAAAA
1 TAATATAAAA
137777 TTTATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATAAAAAT
Found at i:141111 original size:31 final size:30
Alignment explanation
Indices: 141073--141130 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
141063 ATTATACATG
141073 TGAAACTTAAATTATGATTCATATATATTCA
1 TGAAACTTAAATTATGATTCA-ATATATTCA
* * *
141104 TGAAACTTTAGTTTTGATTCAATATAT
1 TGAAACTTAAATTATGATTCAATATAT
141131 CGACACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (30 bp):
TGAAACTTAAATTATGATTCAATATATTCA
Found at i:148686 original size:40 final size:40
Alignment explanation
Indices: 148642--148724 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
148632 CATTTTTAAG
148642 CAAAAAATACAAAATATACCACAGAATGTTTTTTCAAACT
1 CAAAAAATACAAAATATACCACAGAATGTTTTTTCAAACT
*
148682 CAAAAAATACAAAATATACTACAGAATGTTTTTTCAAACT
1 CAAAAAATACAAAATATACCACAGAATGTTTTTTCAAACT
148722 CAA
1 CAA
148725 TTCAAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.28
Consensus pattern (40 bp):
CAAAAAATACAAAATATACCACAGAATGTTTTTTCAAACT
Found at i:150654 original size:22 final size:22
Alignment explanation
Indices: 150622--150663 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
150612 ATGGTCGTAA
150622 TTTTATAAATACACATAAATTAT
1 TTTTATAAATACA-ATAAATTAT
*
150645 TTTTAT-AATATAATAAATT
1 TTTTATAAATACAATAAATT
150664 TTTAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTATAAATACAATAAATTAT
Found at i:162560 original size:20 final size:17
Alignment explanation
Indices: 162535--162584 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
162525 ACATTGATTA
162535 AAATATATTATATGTTTTT
1 AAATATATTA-AT-TTTTT
162554 CAAATATCATTAATTTTTT
1 -AAATAT-ATTAATTTTTT
162573 AAATA-ATTAATT
1 AAATATATTAATT
162585 AATTTAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.24
18 5 0.17
19 5 0.17
20 8 0.28
21 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATATATTAATTTTTT
Found at i:171172 original size:3 final size:3
Alignment explanation
Indices: 171164--171190 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
171154 GTATTTGGCA
171164 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
171191 AAACTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:176769 original size:132 final size:132
Alignment explanation
Indices: 176532--177032 Score: 799
Period size: 132 Copynumber: 3.8 Consensus size: 132
176522 TCCCTACTAC
* * * * *
176532 CTTGGGAAGATAAGATTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAT-AAAGAATCTAC
1 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGG-TGACAGAATCTGC
** * * * * *
176596 AATCTTTGATCTACTCCACTACTGCTTATGGAGATAGGACTAATGGCTTAAATTCGCTTCTCCAT
65 AATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATTCGCTTCTCCAC
176661 TGT
130 TGT
176664 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
1 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
* * *
176729 ATTTTTAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCCGCTTCTCCACT
66 ATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATTCGCTTCTCCACT
176794 GT
131 GT
176796 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
1 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
*
176861 ATTTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAA-TCTGCTTCTCCAC
66 ATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATTC-GCTTCTCCAC
176925 TGT
130 TGT
* *
176928 ATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
*
176993 ATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAAGACT
66 ATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACT
177033 GGATGCGATC
Statistics
Matches: 348, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.01
132 346 0.99
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (132 bp):
CTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCA
ATCTTCAACCTACTCCCCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATTCGCTTCTCCACT
GT
Found at i:177015 original size:44 final size:44
Alignment explanation
Indices: 176829--177025 Score: 127
Period size: 44 Copynumber: 4.5 Consensus size: 44
176819 CTTCGATCTG
* * *
176829 CTCCACTACTACTTAGGGTGACAGAATCTGCAATTTTCAACCTA
1 CTCCCCTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * *
176873 CTCCCCTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTG
1 CTCCCCTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAACCTA
* * * * * * * * * *
176916 CTTCTCC-ACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTG
1 C-TCCCCTACTGCT-TAGGG-TGA-CAGAATCTGCAATCTTCAACCTA
*
176961 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCCCTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
177005 CTCCCCTACTGCTTAGGGTGA
1 CTCCCCTACTGCTTAGGGTGA
177026 TAAGACTGGA
Statistics
Matches: 112, Mismatches: 29, Indels: 24
0.68 0.18 0.15
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 22 0.20
44 63 0.56
45 19 0.17
46 2 0.02
47 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (44 bp):
CTCCCCTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
Found at i:177168 original size:50 final size:50
Alignment explanation
Indices: 177114--177936 Score: 440
Period size: 50 Copynumber: 16.5 Consensus size: 50
177104 CGGAGAAATT
* * * * * *
177114 AGATTCACCGTCGTAGCTTCAATCTATTTCATTACACCGCCAGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * * *
177164 AGATTCGCTGTTGTAGCTTCAATCTATTTAACCGCAATGTCAGGGAAGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * *** * * * *
177214 AGATTCACCGTTCTAGCTTCAATCTGTTCCGCTACACCGCCTGGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * * * **
177264 AGATTCGCCGTTGTAGCTTCAATCTTTTTAATTGTAATGTC-GAGGAAACA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAG-GGAAGTA
* * ** * * *
177314 ATATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * * * * *
177364 AGATTCGTCATTGTAGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTATTT-AACTGCAACGCCAGGGAAGTA
* * * * * *
177414 AGATTCGCCGTCGTAGCTTCAATCTATTCT-GCCGCATCACCTGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATT-TAACTGCAACGCCAGGGAAGTA
* * * * * **
177464 AGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTT-AACTGCAACGCCAGGGAAGTA
* * *** * * * *
177514 AGATTCGCCGTTGTAACTTCAATCTGTTCCGCTGCATCACCTGGGAAATA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * *** * * * *
177564 AGATTCGCCGTTGTGGCTTCAATCTGTTCCGCCGCATCACCTGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * * * **
177614 AGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTT-AACTGCAACGCCAGGGAAGTA
* * * * * * *
177664 AGATTCACCGTTGT-GACTTCAATCTGTTCT-GCTACATCGCCTGGGAAATA
1 AGATTCGCCGTTGTAG-CTTCAATCTATT-TAACTGCAACGCCAGGGAAGTA
* * * * * *
177714 AGATTCGCCGTTGTAGCTTCAATCT-TTTAATTGTAATGTCGGGGAA-AA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * ** * * *
177762 CGAGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCACCGCCTGGAAAGTA
1 --AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * * * * *
177814 AGATTCGCTGTTGTAGCTTCAATCTATTCAACCGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
* * * *** * ** *
177864 AGATTCACCGTCGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
*
177914 AGATTCGCCGTTGTGGCTTCAAT
1 AGATTCGCCGTTGTAGCTTCAAT
177937 ATTTTGAATT
Statistics
Matches: 574, Mismatches: 181, Indels: 36
0.73 0.23 0.05
Matches are distributed among these distances:
48 3 0.01
49 19 0.03
50 529 0.92
51 20 0.03
52 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (50 bp):
AGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAACGCCAGGGAAGTA
Found at i:177263 original size:100 final size:100
Alignment explanation
Indices: 177148--177588 Score: 546
Period size: 100 Copynumber: 4.4 Consensus size: 100
177138 TATTTCATTA
* * * ** *
177148 CACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTT-AACCGCAATGTCAGGGAAG
1 CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAG
* *
177212 CAAGATTCACCGTTCTAGCTTCAATCTGTTCCGCTA
65 CAAGATTCGCCGTTCTAGCTTCAATCTGTTCCGCTG
* * * *
177248 CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATTGTAATGTCGAGGAAAC
1 CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
* * *
177313 AATATTCGCCGTTGTAGCTTCAATCTGTTCCACTG
66 AAGATTCGCCGTTCTAGCTTCAATCTGTTCCGCTG
* * *
177348 CACCGCCTGGAAAGTAAGATTCGTCATTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGT
1 CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
* * * *
177413 GAGATTCGCCG-TCGTAGCTTCAATCTATTCTGCCG
66 AAGATTCGCCGTTC-TAGCTTCAATCTGTTCCGCTG
* * * *
177448 CATCACCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
1 CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
* * *
177513 GAGATTCGCCGTTGTAACTTCAATCTGTTCCGCTG
66 AAGATTCGCCGTTCTAGCTTCAATCTGTTCCGCTG
* * *
177548 CATCACCTGGGAAA-TAAGATTCGCCGTTGTGGCTTCAATCT
1 CACCGCCT-GGAAAGTAAGATTCGCCGTTGTAGCTTCAATCT
177589 GTTCCGCCGC
Statistics
Matches: 296, Mismatches: 41, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
99 4 0.01
100 287 0.97
101 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (100 bp):
CACCGCCTGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
AAGATTCGCCGTTCTAGCTTCAATCTGTTCCGCTG
Found at i:177889 original size:200 final size:201
Alignment explanation
Indices: 177564--177947 Score: 549
Period size: 200 Copynumber: 1.9 Consensus size: 201
177554 CTGGGAAATA
* * * * *
177564 AGATTCGCCGTTGTGGCTTCAATCTGTTCCGCCGCATCACCTGGGAAGTAAGATTCGCCGTTGTG
1 AGATTCACCGTTGTAGCTTCAATCTGTTCCGCCGCACCACCTGGAAAGTAAGATTCGCCGTTGTA
* ** * *
177629 GCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTGACTTCAATCTGTTCT
66 GCTTCAATCTATTAAACCGCAATGTCGGGGAAGCGAGATTCACCGTCGTGACTTCAATCTGTTCC
*
177694 GCTACATCGCCTGGGAAA-TAAGATTCGCCGTTGTAGCTTCAATCTTTT-AATTGTAATGTCGGG
131 GCTACATCG-CTGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATATTTTGAATTGTAATGTCGGG
177757 GAAAACG
195 GAAAACG
* * * *
177764 AGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCACCGCCTGGAAAGTAAGATTCGCTGTTGTA
1 AGATTCACCGTTGTAGCTTCAATCTGTTCCGCCGCACCACCTGGAAAGTAAGATTCGCCGTTGTA
* *
177829 GCTTCAATCTATTCAACCGCAATGTCGGGGAAGTGAGATTCACCGTCGT-AGCTTCAATCTGTTC
66 GCTTCAATCTATTAAACCGCAATGTCGGGGAAGCGAGATTCACCGTCGTGA-CTTCAATCTGTTC
* * *
177893 CGCTGCATCGCTTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATATTTTGAATTG
130 CGCTACATCGCTGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATATTTTGAATTG
177948 CTGCAAACTA
Statistics
Matches: 161, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
199 8 0.05
200 148 0.92
201 5 0.03
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (201 bp):
AGATTCACCGTTGTAGCTTCAATCTGTTCCGCCGCACCACCTGGAAAGTAAGATTCGCCGTTGTA
GCTTCAATCTATTAAACCGCAATGTCGGGGAAGCGAGATTCACCGTCGTGACTTCAATCTGTTCC
GCTACATCGCTGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATATTTTGAATTGTAATGTCGGGG
AAAACG
Found at i:177910 original size:150 final size:150
Alignment explanation
Indices: 177083--177941 Score: 532
Period size: 150 Copynumber: 5.7 Consensus size: 150
177073 CTGCCATCTC
* * * * * * * ***
177083 CAATCTGTTTAACTGCGAT-GTCGGAGAAATTAGATTCACCGTCGTAGCTTCAATCTATTTCATT
1 CAATCTGTTCAACTGC-ATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCC
* * * * * * * * * *
177147 ACACCGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTT-AACCGCAATGTCAGGG-A
65 GCATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAACTGCAACG-CCGGGAA
* *
177210 AGCAAGATTCACCGTTCTAGCTT
128 AGCAAGATTCGCCGTTGTAGCTT
** * * * * * *****
177233 CAATCTGTTCCGCTACACCGCC-TGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAATT
1 CAATCTGTTCAACTGCATCGCCGGGGAAA-TAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCC
* ** ** * * * * ** * *
177297 GTAATGTCGAGGAAA-CAATATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAA
65 G-CATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAACTGCAACGCCGGGAAA
* * *
177361 GTAAGATTCGTCATTGTAGCTT
129 GCAAGATTCGCCGTTGTAGCTT
* * * * * * * *
177383 CAATCTTTTAAATTGCAAT-GTCGGGGAAGTGAGATTCGCCGTCGTAGCTTCAATCTATTCTGCC
1 CAATCTGTTCAACTGC-ATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCC
* * * * *
177447 GCATCACCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAG
65 GCATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAACTGCAACGCCGGGAAAG
* *
177512 CGAGATTCGCCGTTGTAACTT
130 CAAGATTCGCCGTTGTAGCTT
** * * * *
177533 CAATCTGTTCCGCTGCATCACCTGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTGTTCCGCCG
1 CAATCTGTTCAACTGCATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCCG
* * * * *
177598 CATCACCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGC
66 CATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAACTGCAACGCCGGGAAAGC
* *
177663 GAGATTCACCGTTGT-GACTT
131 AAGATTCGCCGTTGTAG-CTT
** * * * *****
177683 CAATCTGTTCTGCTACATCGCCTGGGAAATAAGATTCGCCGTTGTAGCTTCAATCT-TTTAATTG
1 CAATCTGTTCAACTGCATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCCG
* ** ** *** * * ** * *
177747 TAATGTCGGGGAAAACGAGATTCACCGTTGTAGCTTCAATCTGTTT-CGCTGCACCGCCTGGAAA
66 -CATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAACTGCAACGCCGGGAAA
* *
177811 GTAAGATTCGCTGTTGTAGCTT
129 GCAAGATTCGCCGTTGTAGCTT
* * * * * * *
177833 CAATCTATTCAACCGCAAT-GTCGGGGAAGTGAGATTCACCGTCGTAGCTTCAATCTGTTCCGCT
1 CAATCTGTTCAACTGC-ATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCC
* * *
177897 GCATCGCTTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATATTTT
65 GCATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTT
177942 GAATTGCTGC
Statistics
Matches: 544, Mismatches: 150, Indels: 31
0.75 0.21 0.04
Matches are distributed among these distances:
149 25 0.05
150 497 0.91
151 22 0.04
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (150 bp):
CAATCTGTTCAACTGCATCGCCGGGGAAATAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCCG
CATCACCTGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAACTGCAACGCCGGGAAAGC
AAGATTCGCCGTTGTAGCTT
Found at i:180466 original size:5 final size:6
Alignment explanation
Indices: 180451--180489 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
180441 TGACCTCTCA
180451 TTTTTC TTTTTC TTTTTC TTTTTTC TTATTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC -TTTTTC TT-TTTC TTTTTC T
180490 CCTATTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 19 0.61
7 12 0.39
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:180467 original size:7 final size:7
Alignment explanation
Indices: 180451--180487 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
180441 TGACCTCTCA
180451 TTTTTC-
1 TTTTTCT
180457 TTTTTC-
1 TTTTTCT
180463 TTTTTCT
1 TTTTTCT
180470 TTTTTCT
1 TTTTTCT
*
180477 TATTTCT
1 TTTTTCT
180484 TTTT
1 TTTT
180488 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:180473 original size:13 final size:13
Alignment explanation
Indices: 180451--180487 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
180441 TGACCTCTCA
180451 TTTTTC-TTTTTC
1 TTTTTCTTTTTTC
180463 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
180476 TTATTTCTTTTT
1 TT-TTTCTTTTT
180488 CTCCTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 8 0.35
14 9 0.39
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:180488 original size:13 final size:12
Alignment explanation
Indices: 180451--180489 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
180441 TGACCTCTCA
180451 TTTTTCTTTTTC
1 TTTTTCTTTTTC
180463 TTTTTCTTTTTTC
1 TTTTTC-TTTTTC
180476 TTATTTCTTTTTC
1 TT-TTTCTTTTTC
180489 T
1 T
180490 CCTATTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 15 0.60
14 4 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:180533 original size:21 final size:21
Alignment explanation
Indices: 180502--180548 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
180492 TATTTTTGAC
180502 TTTGATTTTTTTCGATTTTTTT
1 TTTGATTTTTTT-GATTTTTTT
*
180524 TTTG-TTTTTTTGTTTTTTTT
1 TTTGATTTTTTTGATTTTTTT
180544 TTTGA
1 TTTGA
180549 ATCTGAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 7 0.30
22 4 0.17
ACGTcount: A:0.06, C:0.02, G:0.11, T:0.81
Consensus pattern (21 bp):
TTTGATTTTTTTGATTTTTTT
Found at i:181440 original size:15 final size:14
Alignment explanation
Indices: 181412--181438 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
181402 TAAATGAACA
181412 AAAAAAATAAAAAG
1 AAAAAAATAAAAAG
181426 AAAAAAATAAAAA
1 AAAAAAATAAAAA
181439 AGGGTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (14 bp):
AAAAAAATAAAAAG
Found at i:182413 original size:26 final size:28
Alignment explanation
Indices: 182369--182423 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
182359 TAAAGAGATG
* *
182369 TATATGTATATTTTAAAATTGTGAAATA
1 TATATGTATATTATAAAATTGTAAAATA
182397 TATATGTATA-TAT-AAATTGTAAAATA
1 TATATGTATATTATAAAATTGTAAAATA
182423 T
1 T
182424 GTGTACATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.52
27 2 0.08
28 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (28 bp):
TATATGTATATTATAAAATTGTAAAATA
Found at i:196268 original size:21 final size:21
Alignment explanation
Indices: 196242--196287 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
196232 AATAATAATT
* *
196242 TTATTAATAAATAATTAAAAG
1 TTATTAATAAATAAGTAAAAA
* *
196263 TTATTACTATATAAGTAAAAA
1 TTATTAATAAATAAGTAAAAA
196284 TTAT
1 TTAT
196288 ACACGTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TTATTAATAAATAAGTAAAAA
Found at i:196528 original size:29 final size:30
Alignment explanation
Indices: 196495--196565 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
196485 AAATACAAAT
196495 TTTATGTATAAAATTACACA-AAATCA-ATA
1 TTTATGTATAAAATTACACATAAATCATA-A
* *
196524 TTTATGTATACAATTGCACATTAAATCATAA
1 TTTATGTATAAAATTACACA-TAAATCATAA
*
196555 TTAATGTATAA
1 TTTATGTATAA
196566 TTTTGATCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
31 16 0.46
32 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTATGTATAAAATTACACATAAATCATAA
Found at i:197366 original size:103 final size:101
Alignment explanation
Indices: 197202--197393 Score: 255
Period size: 103 Copynumber: 1.9 Consensus size: 101
197192 TATAATGATT
* ** * **
197202 AAAAAAATATTTAAGACTTCATCAAAACTAATAAAATAGAAAAAAATGAACTTTTGGATAGGT-A
1 AAAAAAATATTTAAGACTCCATCAAAACTAATAAAATAGAAAAAAAACAACATTTCAATAGGTCA
*
197266 TAATTTTATATAATAATTTATATTACAATTAATTACA
66 -AATTCTATATAATAATTTATATTACAATTAATTACA
197303 AAAAGAAATTATTTAAGACTCCATCAAAACTAATAAAA-A-AAAACAACAACAACATTTCAATAG
1 AAAA-AAA-TATTTAAGACTCCATCAAAACTAATAAAATAGAAAA-AA-AACAACATTTCAATAG
197366 GTCAAATTCTATATAATAATTTATATTA
62 GTCAAATTCTATATAATAATTTATATTA
197394 GTTAGTAGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
101 8 0.10
102 6 0.08
103 64 0.81
104 1 0.01
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.32
Consensus pattern (101 bp):
AAAAAAATATTTAAGACTCCATCAAAACTAATAAAATAGAAAAAAAACAACATTTCAATAGGTCA
AATTCTATATAATAATTTATATTACAATTAATTACA
Found at i:198524 original size:14 final size:14
Alignment explanation
Indices: 198505--198533 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
198495 ACAATTTGTC
198505 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
198519 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
198533 T
1 T
198534 AATTTCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:198527 original size:13 final size:13
Alignment explanation
Indices: 198509--198533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198499 TTTGTCTTCT
198509 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
198522 TTTTTTTTTTTT
1 TTTTTTTTTTTT
198534 AATTTCAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:199558 original size:18 final size:18
Alignment explanation
Indices: 199498--199558 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
199488 ACTATTATTT
*
199498 TATTGTTAATTTTGTTAC
1 TATTGTTAATTTTGCTAC
**
199516 TATT-TTATCAGTATTTGCTTT
1 TATTGTTA--A-T-TTTGCTAC
199537 TATTGTTAATTTTGCTAC
1 TATTGTTAATTTTGCTAC
199555 TATT
1 TATT
199559 TTATGTGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 3 0.09
18 14 0.42
19 2 0.06
20 2 0.06
21 9 0.27
22 3 0.09
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.61
Consensus pattern (18 bp):
TATTGTTAATTTTGCTAC
Found at i:205265 original size:73 final size:73
Alignment explanation
Indices: 205156--205375 Score: 440
Period size: 73 Copynumber: 3.0 Consensus size: 73
205146 TTAAAATAAC
205156 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
1 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
205221 AATGTCTT
66 AATGTCTT
205229 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
1 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
205294 AATGTCTT
66 AATGTCTT
205302 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
1 AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
205367 AATGTCTT
66 AATGTCTT
205375 A
1 A
205376 CTCGAGGCTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 147 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (73 bp):
AAAAAAATAAACTTTTTTTTGCCATTTAGTGAATTCGGGCTGGGTTGAGTCAGGCTCGGGCCAAA
AATGTCTT
Found at i:212417 original size:43 final size:41
Alignment explanation
Indices: 212343--212431 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 41
212333 AATAAAAAAT
*
212343 AAATTAGTTTTTATTAAAGTTTTATTCATTTTTACAATTAA
1 AAATTAGTTTTTATTAAAGTTTCATTCATTTTTACAATTAA
*
212384 AAATTAGTTTTTTTATTAAAGTTTCATTTATTTTTACAATTAA
1 AAATTAG--TTTTTATTAAAGTTTCATTCATTTTTACAATTAA
212427 AAATT
1 AAATT
212432 GACGTGATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 7 0.16
43 37 0.84
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (41 bp):
AAATTAGTTTTTATTAAAGTTTCATTCATTTTTACAATTAA
Found at i:212425 original size:24 final size:23
Alignment explanation
Indices: 212355--212427 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 23
212345 ATTAGTTTTT
*
212355 ATTAAAGTTTTATTCATTTTTACA
1 ATTAAAG-TTTATTTATTTTTACA
** *
212379 ATTAAAAATTAGTT-TTTTT---
1 ATTAAAGTTTATTTATTTTTACA
212398 ATTAAAGTTTCATTTATTTTTACA
1 ATTAAAGTTT-ATTTATTTTTACA
212422 ATTAAA
1 ATTAAA
212428 AATTGACGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 8 0.22
20 3 0.08
21 5 0.14
22 5 0.14
23 4 0.11
24 12 0.32
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTAAAGTTTATTTATTTTTACA
Found at i:220423 original size:15 final size:16
Alignment explanation
Indices: 220391--220424 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
220381 TATTTTTGTC
*
220391 CACACGGGCAGAGTGA
1 CACACGGCCAGAGTGA
220407 CACACGGCCAG-GTGA
1 CACACGGCCAGAGTGA
220422 CAC
1 CAC
220425 GGCCTTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.32, G:0.32, T:0.06
Consensus pattern (16 bp):
CACACGGCCAGAGTGA
Found at i:221926 original size:6 final size:6
Alignment explanation
Indices: 221910--221939 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
221900 ATATGTTAAA
221910 ATATATT ATATTT ATATTT ATATTT ATATT
1 ATAT-TT ATATTT ATATTT ATATTT ATATT
221940 GTTAGAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:232360 original size:11 final size:10
Alignment explanation
Indices: 232344--232382 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
232334 CATATTCCTT
232344 AATTTTTTTA
1 AATTTTTTTA
232354 GAATTTTTTTA
1 -AATTTTTTTA
*
232365 AATTTTTATA
1 AATTTTTTTA
232375 AATATTTT
1 AAT-TTTT
232383 GAATTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:232365 original size:20 final size:19
Alignment explanation
Indices: 232342--232409 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
232332 CACATATTCC
* *
232342 TTAATTTTTTTAGAATTTTT
1 TTAATTTTTATA-AATATTT
232362 TTAAATTTTTATAAATATTT
1 TT-AATTTTTATAAATATTT
* * *
232382 TGAATTTTCAAAAATTATTT
1 TTAATTTTTATAAA-TATTT
*
232402 TGAATTTT
1 TTAATTTT
232410 ATTTTATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.24
20 22 0.54
21 9 0.22
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (19 bp):
TTAATTTTTATAAATATTT
Found at i:232382 original size:19 final size:20
Alignment explanation
Indices: 232355--232409 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
232345 ATTTTTTTAG
* * * *
232355 AATTTTTTTAAATTTTTATA
1 AATTATTTTGAATTTTCAAA
232375 AA-TATTTTGAATTTTCAAA
1 AATTATTTTGAATTTTCAAA
232394 AATTATTTTGAATTTT
1 AATTATTTTGAATTTT
232410 ATTTTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
AATTATTTTGAATTTTCAAA
Found at i:233330 original size:20 final size:20
Alignment explanation
Indices: 233301--233338 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
233291 TTGCACATAT
233301 GAAATATATTTTAAAAATGG
1 GAAATATATTTTAAAAATGG
*
233321 GAAATGTATTTTAAAAAT
1 GAAATATATTTTAAAAAT
233339 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
GAAATATATTTTAAAAATGG
Found at i:233345 original size:20 final size:20
Alignment explanation
Indices: 233302--233354 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
233292 TGCACATATG
***
233302 AAATATATTTTAAAAATGGG
1 AAATATATTTTAAAAATAAA
*
233322 AAATGTATTTTAAAAATAAA
1 AAATATATTTTAAAAATAAA
233342 AAATATATATTTA
1 AAATATAT-TTTA
233355 TTATATTCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
AAATATATTTTAAAAATAAA
Found at i:234706 original size:22 final size:23
Alignment explanation
Indices: 234678--234732 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
234668 TAGTATAGTC
234678 TTGAGACTTGCT-ACCTTATGTA
1 TTGAGACTTGCTAACCTTATGTA
*
234700 TTGAGACTTGTTAACCTTATGTA
1 TTGAGACTTGCTAACCTTATGTA
234723 TTGAGACTTG
1 TTGAGACTTG
234733 ACCTTGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (23 bp):
TTGAGACTTGCTAACCTTATGTA
Found at i:235123 original size:30 final size:30
Alignment explanation
Indices: 235064--235123 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
235054 GAAACCTCCT
* * **
235064 AACCCACCACCTCCGCCAGCTCCTCCACCA
1 AACCCACCACCGCCACCAGCTCCAACACCA
*
235094 AACCCACCACCGGCACCAGCTCCAACACCA
1 AACCCACCACCGCCACCAGCTCCAACACCA
235124 CCCCCAAGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.57, G:0.08, T:0.07
Consensus pattern (30 bp):
AACCCACCACCGCCACCAGCTCCAACACCA
Found at i:246401 original size:68 final size:68
Alignment explanation
Indices: 246327--246465 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
246317 CATTTTTTAG
*
246327 TAGATGAGGGAAAATGCAAACTAACTTCTAGTACAAGGGCCTCCATGGTACTTTTACCATTTTAG
1 TAGATGAGGGAAAATACAAACTAACTTCTAGTACAAGGGCCTCCATGGTACTTTTACCATTTTAG
246392 TTC
66 TTC
*
246395 TAGATGAGGGAAAATACAAACTAACTTCTAGTACAAGGGCCTCTATGGTACTTTTACCATTTTAG
1 TAGATGAGGGAAAATACAAACTAACTTCTAGTACAAGGGCCTCCATGGTACTTTTACCATTTTAG
246460 TTC
66 TTC
246463 TAG
1 TAG
246466 TTGATCTTAC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (68 bp):
TAGATGAGGGAAAATACAAACTAACTTCTAGTACAAGGGCCTCCATGGTACTTTTACCATTTTAG
TTC
Done.