Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2083
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: 66767
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2772 original size:12 final size:12
Alignment explanation
Indices: 2755--2779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2745 ACAAATACTT
2755 ATGTATCGATAC
1 ATGTATCGATAC
2767 ATGTATCGATAC
1 ATGTATCGATAC
2779 A
1 A
2780 AAATTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:2789 original size:30 final size:32
Alignment explanation
Indices: 2735--2797 Score: 112
Period size: 30 Copynumber: 2.0 Consensus size: 32
2725 AGTACTAATT
2735 ATGTATCGATACAAATACTTATGTATCGATAC
1 ATGTATCGATACAAATACTTATGTATCGATAC
2767 ATGTATCGATACAAA-A-TTATGTATCGATAC
1 ATGTATCGATACAAATACTTATGTATCGATAC
2797 A
1 A
2798 AATCTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 15 0.48
31 1 0.03
32 15 0.48
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (32 bp):
ATGTATCGATACAAATACTTATGTATCGATAC
Found at i:2868 original size:22 final size:20
Alignment explanation
Indices: 2831--2931 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 20
2821 ACCGTTGACC
*
2831 TGTATCGATACATTTGTAGCC
1 TGTATCGATACATTTGT-GCA
2852 TGTATCGATAACATTTGTGCA
1 TGTATCGAT-ACATTTGTGCA
*
2873 TGTATCGACTACCATTTGTGAA
1 TGTATCGA-TA-CATTTGTGCA
* *
2895 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTGC--A
2916 TGTATCGATACATTTG
1 TGTATCGATACATTTG
2932 GAATTTTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.04
20 2 0.03
21 35 0.51
22 28 0.41
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTGTGCA
Found at i:3641 original size:56 final size:54
Alignment explanation
Indices: 3549--4279 Score: 623
Period size: 56 Copynumber: 13.3 Consensus size: 54
3539 GGAGTAACAA
* * *
3549 GTGCCACCACCTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAG
1 GTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTGAAAG
* * *
3604 GTGCCACCAAACTTATGTGGGCTTTGAAAGGTGTCCTGCT-TCTTGGGGAATGAAAG
1 GTGCCACC-AACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCT-TTGAGGACTGAAAG
*
3660 TTGCACACCAACTTGTGTGGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACTGGAAA-
1 GTGC-CACCAACTTGTGTGGGCTTTAA-A-GGT-GTCCTGCTCTTTGAGGACT-GAAAG
* * *
3717 ATGCCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTC-TTGACGGACGGAAA-
1 GTG-CCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGA-GGACTGAAAG
*
3772 --GCCACCACCTTGTGTGGGCTTTAAGAGGGTGTCCTGCTC-TTGAGGTACTGGAAA-
1 GTGCCACCAACTTGTGTGGGCTTTAA-A-GGTGTCCTGCTCTTTGAGG-ACT-GAAAG
* * * * * * * *
3826 ATGCCACCCACTTGGGTGGG-TTGAACTGTTGTCCTGCTATTTGGGGACTG-AAG
1 GTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTGAAAG
* *
3879 GTTGCCACCAACTTGTGTTGGGCTTTAAGAGGTTTCCTGCTCTTTGAGTACTGGAAA-
1 G-TGCCACCAACTTGTG-TGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAG
* * *
3936 ATGCCACCAACTTGGGTGGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGGA-TGAAAG
1 GTGCCACCAACTTGTGTGGGC--TTT-AAAGGTGTCCTGCTCTTTGAGGACTGAAAG
*
3992 GTGCCACCAA-TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGCGGGAAAAA
1 GTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACT----G-AAAG
*
4051 ATGCCACC-ACTTTGTGTGGGCTTTGAAAGGTGT-CTGGCTCTTTGAGGACTGGGAAA-
1 GTGCCACCAAC-TTGTGTGGGCTTT-AAAGGTGTCCT-GCTCTTTGAGGACT--GAAAG
* * * *
4107 ATGCC-CCACCTTGTGTGGGCTTTAGAGG-GTCCTGCTCTTTGAGGA-TGGAAG
1 GTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAG
* *
4158 GCGCCACCCAACTTGTGTGGGCTTTAGAGGTGTCC-GCTCTTTG-GTGACTGAAAG
1 GTGCCA-CCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAG-GACTGAAAG
* *
4212 GTGCCACCAAACTTG-GTGGGCTTTAAGATGTGTCCTGCTCTTTGAGGA--GCAAG
1 GTGCCACC-AACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTGAAAG
4265 GTGCCA-CAACTTGTG
1 GTGCCACCAACTTGTG
4280 GCGGCTTCTT
Statistics
Matches: 567, Mismatches: 57, Indels: 107
0.78 0.08 0.15
Matches are distributed among these distances:
50 3 0.01
51 11 0.02
52 31 0.05
53 110 0.19
54 64 0.11
55 82 0.14
56 132 0.23
57 62 0.11
58 25 0.04
59 12 0.02
60 33 0.06
61 2 0.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.29
Consensus pattern (54 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAG
Found at i:3730 original size:113 final size:110
Alignment explanation
Indices: 3549--4259 Score: 759
Period size: 113 Copynumber: 6.4 Consensus size: 110
3539 GGAGTAACAA
* * * *
3549 GTGCCACCACCTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACC
1 GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACC
* *
3612 AAACTTATGTGGGCTTTGAAAGGTGTCCTGCT-TCTTGGGGAATGAAAG
64 -AACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT-TTGGGGACTGAAAG
*
3660 TTGCACACCAACTTGTGTGGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACTGGAAAATGCCCA
1 GTGC-CACCAACTTGTGTGGGCTTTAAGA-GGT-GTCCTGCTCTTTGAGGACTGGAAAATG-CCA
* * *
3724 CCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTC-TTGACGGACGGAAA-
62 CCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTG-GGGACTGAAAG
*
3772 --GCCACCACCTTGTGTGGGCTTTAAGAGGGTGTCCTGCTC-TTGAGGTACTGGAAAATGCCACC
1 GTGCCACCAACTTGTGTGGGCTTTAAGA-GGTGTCCTGCTCTTTGAGG-ACTGGAAAATGCCACC
* * * * *
3834 CACTTGGGTGGG--TTGAACTGTTGTCCTGCTATTTGGGGACTG-AAG
64 AACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACTGAAAG
* *
3879 GTTGCCACCAACTTGTGTTGGGCTTTAAGAGGTTTCCTGCTCTTTGAGTACTGGAAAATGCCACC
1 G-TGCCACCAACTTGTG-TGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACC
*
3944 AACTTGGGTGGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGGA-TGAAAG
64 AACTTGTGTGGGC--TTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAG
3992 GTGCCACCAA-TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGCGGGAAAAAATGCC
1 GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT---GG--AAAATGCC
*
4056 ACC-ACTTTGTGTGGGCTTTGAAAGGTGT-CTGGCTCTTTGAGGACTGGGAAA-
61 ACCAAC-TTGTGTGGGCTTTGAAAGGTGTCCT-GCTCTTTGGGGACT--GAAAG
* * ***
4107 ATGCC-CCACCTTGTGTGGGCTTT-AGAGG-GTCCTGCTCTTTGAGGA-TGGAAGGCGCCACCCA
1 GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCA-CCA
* *
4168 ACTTGTGTGGGCTTT-AGAGGTGTCC-GCTCTTTGGTGACTGAAAG
65 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAG
*
4212 GTGCCACCAAACTTG-GTGGGCTTTAAGATGTGTCCTGCTCTTTGAGGA
1 GTGCCACC-AACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
4260 GCAAGGTGCC
Statistics
Matches: 517, Mismatches: 41, Indels: 87
0.80 0.06 0.13
Matches are distributed among these distances:
104 4 0.01
105 4 0.01
106 30 0.06
107 36 0.07
108 65 0.13
109 42 0.08
110 85 0.16
111 27 0.05
112 36 0.07
113 114 0.22
114 33 0.06
115 37 0.07
116 4 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (110 bp):
GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
CTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAG
Found at i:3957 original size:166 final size:161
Alignment explanation
Indices: 3549--4259 Score: 620
Period size: 166 Copynumber: 4.3 Consensus size: 161
3539 GGAGTAACAA
* * * *
3549 GTGCCACCACCTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACC-
* * * * *
3613 AACTTATGTGGGCTTTGAAAGGTGTCCTGCT-TCTTGGGGAAT-GAAAGTTGCACACCAACTTGT
64 ACCTTGTGTGGGCTTT-AGAGGTGTCCTGCTCT-TTGAGG-ATGGAAAG-TGC-CACCCACTTGT
*
3676 GTGGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACTGGAAA-
124 GTGGGCTTT-A-A-GGT-GTCCTGCTCTTTGGGGACT-GAAAG
* *
3717 ATGCCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTC-TTGACGGAC-GG-AAA-GCCACC
1 GTG-CCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA-GGACTGGAAAATGCCACC
* *
3778 ACCTTGTGTGGGCTTTAAGAGGGTGTCCTGCTC-TTGAGGTACTGGAAAATGCCACCCACTTGGG
64 ACCTTGTGTGGGCTTT-AGA-GGTGTCCTGCTCTTTGAGG-A-TGGAAAGTGCCACCCACTTGTG
* * *
3842 TGGG-TTGAACTGTTGTCCTGCTATTTGGGGACTG-AAG
125 TGGGCTTTAA--GGTGTCCTGCTCTTTGGGGACTGAAAG
* *
3879 GTTGCCACCAACTTGTGTTGGGCTTT-AAGAGGTTTCCTGCTCTTTGAGTACTGGAAAATGCCAC
1 G-TGCCACCAACTTGTG-TGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
* * * * *
3943 CAACTTGGGTGGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGGAT-GAAAGGTGCCA-CCAATTGT
63 CACCTTGTGTGGGC--TTT-AGAGGTGTCCTGCTCTTTGAGGATGGAAA-GTGCCACCCACTTGT
* *
4006 GTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGCGGGAAAAA
124 GTGGGCTTT-A-AGGTGTCCTGCTCTTTGGGGACT----G-AAAG
*
4051 ATGCCACC-ACTTTGTGTGGGCTTTGAAAGGTGT-CTGGCTCTTTGAGGACTGGGAAAATGCC-C
1 GTGCCACCAAC-TTGTGTGGGCTTTGAAAGGTGTCCT-GCTCTTTGAGGACT-GGAAAATGCCAC
* *
4113 CACCTTGTGTGGGCTTTAGAGG-GTCCTGCTCTTTGAGGATGGAAGGCGCCACCCAACTTGTGTG
63 CACCTTGTGTGGGCTTTAGAGGTGTCCTGCTCTTTGAGGATGGAAAGTGCCACCC-ACTTGTGTG
*
4177 GGCTTTAGAGGTGTCC-GCTCTTTGGTGACTGAAAG
127 GGCTTTA-AGGTGTCCTGCTCTTTGGGGACTGAAAG
*
4212 GTGCCACCAAACTTG-GTGGGCTTT-AAGATGTGTCCTGCTCTTTGAGGA
1 GTGCCACC-AACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGA
4260 GCAAGGTGCC
Statistics
Matches: 451, Mismatches: 51, Indels: 89
0.76 0.09 0.15
Matches are distributed among these distances:
160 2 0.00
161 38 0.08
162 31 0.07
163 38 0.08
164 8 0.02
165 54 0.12
166 99 0.22
167 37 0.08
168 36 0.08
169 40 0.09
170 42 0.09
171 24 0.05
172 2 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (161 bp):
GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAC
CTTGTGTGGGCTTTAGAGGTGTCCTGCTCTTTGAGGATGGAAAGTGCCACCCACTTGTGTGGGCT
TTAAGGTGTCCTGCTCTTTGGGGACTGAAAG
Found at i:3965 original size:220 final size:221
Alignment explanation
Indices: 3551--4259 Score: 645
Period size: 220 Copynumber: 3.2 Consensus size: 221
3541 AGTAACAAGT
* * *
3551 GCCACCACCTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAA
1 GCCACCACCTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGATGCCACCAA
*
3614 ACTTATGTGGGCTTTGAAAGGTGTCCTGCTTCTTGGGGAATGAAAGTTGCACACCAACTTGTGTG
65 ACTTAGGTGGGC-TTGAAAGGTGTCCTGCTTCTTGGGGAATGAAAGTTGCACACCAACTTGTGTG
*
3679 GGCTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGTGTGGGCTTTGA
129 GGCTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGGGTGGGCTTTGA
*
3744 AAGGTGTCCTGTTC-TTGACGGACGGAAA-
194 AAGGTGTCCTGCTCTTTG-CGGA-GGAAAG
3772 GCCACCACCTTGTGTGGGCTTTAAGAGGGTGTCCTGCTC-TTGAGGTACTGGAAA-ATGCCACC-
1 GCCACCACCTTGTGTGGGCTTTAAGA-GGTGTCCTGCTCTTTGAGG-ACTGGAAAGATGCCACCA
* * * * * *
3834 CACTTGGGTGGG-TTGAACTGTTGTCCTGCTAT-TTGGGGACTGAAGGTTGC-CACCAACTTGTG
64 AACTTAGGTGGGCTTGAA-AGGTGTCCTGCT-TCTTGGGGAATGAAAGTTGCACACCAACTTGTG
* *
3896 TTGGGCTTTAAGA-GGT-TTCCTGCTCTTTGAGTACTGGAAAATG-CCACCAACTTGGGTGGGCT
127 -TGGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACTGGAAAATGCCCACCAACTTGGGTGGGC-
* *
3958 TTTTGAAAGGTGTCCTGCTCTTTGGGGATGAAAGG
189 -TTTGAAAGGTGTCCTGCTCTTTGCGGAGGAAA-G
* *
3993 TGCCACCA-ATTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGCGGGAAAAAATGCCA
1 -GCCACCACCTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT---GG-AAAGATGCCA
* * * *
4057 CC--ACTTTGTGTGGGCTTTGAAAGGTGT-CTGGC-TCTTTGAGGACTGGGAAA-ATGC-C-CCA
61 CCAAACTTAG-GTGGGC-TTGAAAGGTGTCCT-GCTTC-TTGGGGAAT--GAAAGTTGCACACCA
* *
4115 CCTTGTGTGGGCTTT-AGA--G-GGTCCTGCTCTTTGAGGA-TGG--AAGGCGCCACCCAACTTG
120 ACTTGTGTGGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACTGGAAAATGC-CCA-CCAACTTG
* * *
4173 TGTGGGCTTT-AGAGGTGTCC-GCTCTTTG-GTGACTGAAAGG
182 GGTGGGCTTTGAAAGGTGTCCTGCTCTTTGCG-GA-GGAAA-G
* *
4213 TGCCACCAAACTTG-GTGGGCTTTAAGATGTGTCCTGCTCTTTGAGGA
1 -GCCACC-ACCTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGA
4260 GCAAGGTGCC
Statistics
Matches: 421, Mismatches: 31, Indels: 72
0.80 0.06 0.14
Matches are distributed among these distances:
218 25 0.06
219 51 0.12
220 102 0.24
221 100 0.24
222 37 0.09
223 36 0.09
224 12 0.03
225 23 0.05
226 23 0.05
227 9 0.02
228 3 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (221 bp):
GCCACCACCTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGATGCCACCAAA
CTTAGGTGGGCTTGAAAGGTGTCCTGCTTCTTGGGGAATGAAAGTTGCACACCAACTTGTGTGGG
CTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGGGTGGGCTTTGAAA
GGTGTCCTGCTCTTTGCGGAGGAAAG
Found at i:4312 original size:333 final size:331
Alignment explanation
Indices: 3550--4286 Score: 812
Period size: 333 Copynumber: 2.2 Consensus size: 331
3540 GAGTAACAAG
* * * *
3550 TGCCACCACCTCGTG-TGGGCTTTGAA-AGGCGTCCTGCTCTTTGAGGACTG-AAAGGTGCCACC
1 TGCCACCAACTTGTGTTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGAC-GCAAA-ATGCCACC
** * *
3612 AAACTTATGTGGGC--TTTGAAAGGTGTCCTGCT-TCTTGGGGAATGAAAGTTGCACACCAACTT
63 -AACTTGGGTCGGCTTTTTGAAAGGTGTCCTGCTCT-TTGGGGAATGAAAGGTGCACACCAACTT
3674 GTGTGGGCTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGTGTGGGC
126 GTGTGGGCTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGTGTGGGC
*
3739 TTTGAAAGGTGTCCTGTTCTTGACGGACGGAAAGCCACCACCTTGTGTGGGCTTTAAGAGGGTGT
191 TTTGAAAGGTGTCCTGCTCTTGACGGACGGAAAGCCACCACCTTGTGTGGGCTTTAAGAGGGTGT
* *
3804 CCTGCTCTTGAGGTACTGGAAAATGCCACCCACTTGGGTGGGTTGAACTGTTGTCCTGCTATTTG
256 CCTGCTCTTGAGGTACTGGAAAACGCCACCCACTTGGGTGGGTTGAAC-GGTGTCCTGCTATTTG
3869 GGGACTGAAGGT
320 GGGACTGAAGGT
* * *
3881 TGCCACCAACTTGTGTTGGGCTTTAAGAGGTTTCCTGCTCTTTGAGTACTGGAAAATGCCACCAA
1 TGCCACCAACTTGTGTTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGAC-GCAAAATGCCACCAA
*
3946 CTTGGGTGGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGG-ATGAAAGGTGC-CACCAA-TTGTGT
65 CTTGGGTCGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGGAATGAAAGGTGCACACCAACTTGTGT
4008 GGGCTTTAAGA-GGT-GTCCTGCTCTTTGAGGACTGCGGGAAAAAATG-CCACC-ACTTTGTGTG
130 GGGCTTTAAGAGGGTGGTCCTGCT-TTTGAGGACT---GG--AAAATGCCCACCAAC-TTGTGTG
4069 GGCTTTGAAAGGTGT-CTGGCTCTTTGA-GGACTGGGAAAATGCC-CCACCTTGTGTGGGCTTT-
188 GGCTTTGAAAGGTGTCCT-GCTC-TTGACGGAC--GG-AAA-GCCACCACCTTGTGTGGGCTTTA
** * *
4130 AGA-GG-GTCCTGCTCTTTGAGG-A-TGGAAGGCGCCACCCAACTTGTGTGGGCTTTAGA-GGTG
247 AGAGGGTGTCCTGCTC-TTGAGGTACTGGAAAACGCCACCC-ACTTGGGTGGG-TTGA-ACGGTG
* *
4190 TCC-GCTCTTTGGTGACTGAAAGG-
308 TCCTGCTATTTGGGGACTG-AAGGT
* **
4213 TGCCACCAAACTTG-G-TGGGCTTTAAGATGTGTCCTGCTCTTTGAGGA-GCAAGGTGCCA-CAA
1 TGCCACC-AACTTGTGTTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACGCAAAATGCCACCAA
4274 CTTGTGG-CGGCTT
65 CTTG-GGTCGGCTT
4287 CTTTAAGAGG
Statistics
Matches: 355, Mismatches: 25, Indels: 55
0.82 0.06 0.13
Matches are distributed among these distances:
328 20 0.06
329 23 0.06
330 17 0.05
331 61 0.17
332 85 0.24
333 97 0.27
334 22 0.06
335 6 0.02
336 21 0.06
337 3 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (331 bp):
TGCCACCAACTTGTGTTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACGCAAAATGCCACCAAC
TTGGGTCGGCTTTTTGAAAGGTGTCCTGCTCTTTGGGGAATGAAAGGTGCACACCAACTTGTGTG
GGCTTTAAGAGGGTGGTCCTGCTTTTGAGGACTGGAAAATGCCCACCAACTTGTGTGGGCTTTGA
AAGGTGTCCTGCTCTTGACGGACGGAAAGCCACCACCTTGTGTGGGCTTTAAGAGGGTGTCCTGC
TCTTGAGGTACTGGAAAACGCCACCCACTTGGGTGGGTTGAACGGTGTCCTGCTATTTGGGGACT
GAAGGT
Found at i:5349 original size:11 final size:10
Alignment explanation
Indices: 5327--5380 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
5317 CTTTTCTCTC
5327 TTTTTCTTTTG
1 TTTTT-TTTTG
5338 TTTGTTTTTTG
1 TTT-TTTTTTG
**
5349 TTTTTTTTCC
1 TTTTTTTTTG
5359 TCTTTTTTTTG
1 T-TTTTTTTTG
5370 CTTTTTTTTTG
1 -TTTTTTTTTG
5381 AAGAGAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 6 0.17
11 27 0.75
12 3 0.08
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:17848 original size:78 final size:78
Alignment explanation
Indices: 17732--17939 Score: 231
Period size: 78 Copynumber: 2.7 Consensus size: 78
17722 GAGATAATAA
* * * ** * * *
17732 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGACTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
17797 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAG
* *
17810 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** *
17875 TTTGGGAATAAAG
66 TTAGAAAAAAAAG
*
17888 CTGGGGTTGGAGTATCCCCTC-AGAAGTAACGGGGTTGGAGTATCCCCGATTA
1 C-GGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTA
17940 AATAACAAGG
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
77 1 0.01
78 63 0.58
79 45 0.41
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAG
Found at i:18044 original size:52 final size:53
Alignment explanation
Indices: 17983--18123 Score: 173
Period size: 52 Copynumber: 2.7 Consensus size: 53
17973 AATTGGTATT
* * *
17983 TTTG-GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTGGTG
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
**
18034 TTTCGA-AAATAAAACCGGGGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTG
1 TTT-GAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
* * *
18086 TTTTAGCAATAAAACCGGGGTTGGAATATCCCCGATTA
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTA
18124 TGAAAAATCA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
51 6 0.08
52 71 0.92
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (53 bp):
TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
Found at i:18251 original size:54 final size:51
Alignment explanation
Indices: 18184--18314 Score: 174
Period size: 51 Copynumber: 2.5 Consensus size: 51
18174 AAATAACGGG
* *
18184 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
*
18238 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGA
*
18289 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
18315 TTGAGAAACT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
51 36 0.52
52 4 0.06
53 10 0.14
54 19 0.28
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:18293 original size:133 final size:131
Alignment explanation
Indices: 18049--18302 Score: 323
Period size: 133 Copynumber: 1.9 Consensus size: 131
18039 AAAATAAAAC
* *
18049 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAATA
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
* * * * *
18114 TCCCCGATTATGAAAAATCAATATTTTGGAAACAAAGTTGGGGTTGGAGTATCCCCTCGGAAATA
66 TCCCCGATTATGAAAAATCAATATTTTGAAAACAAAATCGGAGTTGGAATATCCCCTCGGAAATA
18179 A
131 A
* * *
18180 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGA
1 CGGGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGTG--TTTTAGAAATAAAACCGGAGTTGGA
* * * * *
18244 GTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
63 ATATCCCCGATTATGA-AAAATCAATATTTTGAAAACAAAATCGGAGTTGGAATATCCCC
18303 GATTGTGGAG
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
130 3 0.03
131 32 0.31
132 1 0.01
133 68 0.65
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
TCCCCGATTATGAAAAATCAATATTTTGAAAACAAAATCGGAGTTGGAATATCCCCTCGGAAATA
A
Found at i:20761 original size:19 final size:18
Alignment explanation
Indices: 20737--20804 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
20727 CAGTAGCTAA
20737 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
20756 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
20771 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
20788 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
20805 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:20777 original size:13 final size:13
Alignment explanation
Indices: 20759--20783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20749 ACAATACTTA
20759 TGTATCGATACAT
1 TGTATCGATACAT
20772 TGTATCGATACA
1 TGTATCGATACA
20784 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20781 original size:32 final size:32
Alignment explanation
Indices: 20740--20802 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
20730 TAGCTAATTA
*
20740 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
20772 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
20803 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:21207 original size:29 final size:29
Alignment explanation
Indices: 21165--21222 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
21155 GCCTCGACTG
21165 CCTTTACTGGAAGAAGGAACGATTCGGAT
1 CCTTTACTGGAAGAAGGAACGATTCGGAT
21194 CCTTTACTGGAAGAAGGAACGATTCGGAT
1 CCTTTACTGGAAGAAGGAACGATTCGGAT
21223 ACCTATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (29 bp):
CCTTTACTGGAAGAAGGAACGATTCGGAT
Found at i:24861 original size:11 final size:11
Alignment explanation
Indices: 24845--24877 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
24835 ACCCAATCCT
24845 AAAAAAAAAAC
1 AAAAAAAAAAC
*
24856 AAAAAAAAACC
1 AAAAAAAAAAC
24867 AAAAAAAAAAC
1 AAAAAAAAAAC
24878 CTTTTCACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:24877 original size:12 final size:12
Alignment explanation
Indices: 24845--24878 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
24835 ACCCAATCCT
24845 AAAAAAAAAA-C
1 AAAAAAAAAACC
24856 -AAAAAAAAACC
1 AAAAAAAAAACC
24867 AAAAAAAAAACC
1 AAAAAAAAAACC
24879 TTTTCACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
12 11 0.52
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACC
Found at i:25947 original size:28 final size:27
Alignment explanation
Indices: 25891--26196 Score: 441
Period size: 27 Copynumber: 11.1 Consensus size: 27
25881 AGTGTGACCT
* *
25891 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
25918 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
25946 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
25973 CTTTTAAAGTCCACAACTCCGTAGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
26001 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
26028 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
26056 CTTTTAAGACCACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
26083 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
26110 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
26138 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
26165 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
26193 CTTT
1 CTTT
26197 CAAAGCCCAC
Statistics
Matches: 252, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
27 128 0.51
28 124 0.49
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:25977 original size:55 final size:55
Alignment explanation
Indices: 25891--26196 Score: 447
Period size: 55 Copynumber: 5.6 Consensus size: 55
25881 AGTGTGACCT
* *
25891 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
25946 CTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAAGTCCACAACTCCGTAGCAT-T
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCATCC
26001 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * *
26056 CTTTTAAGACCACAACTCTGTAGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
* * * *
26110 CTTTTAAGTCCATAACTCTGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCA-CC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCC
26165 CTTTTAAAGTCCACAACTCCGTGGCACCCTTT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTT
26197 CAAAGCCCAC
Statistics
Matches: 226, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
54 44 0.19
55 144 0.64
56 38 0.17
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.29
Consensus pattern (55 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
Found at i:26079 original size:82 final size:82
Alignment explanation
Indices: 25891--26196 Score: 461
Period size: 82 Copynumber: 3.7 Consensus size: 82
25881 AGTGTGACCT
* * *
25891 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
25956 CACAACTTCGTGGCAT-C
65 CACAACTCCGTGGCATCC
**
25973 CTTTTAAAGTCCACAACTCCGTAGCATTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
26038 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCATCC
* *
26056 CTTTTAAGACCACAACTCTGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
26121 ATAACTCTGTGGCATCT
66 ACAACTCCGTGGCATCC
* *
26138 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
1 CTTTTAAGTCCACAACTCCGTAGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTT
26197 CAAAGCCCAC
Statistics
Matches: 206, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
82 131 0.64
83 75 0.36
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.29
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCATCC
Found at i:26219 original size:30 final size:28
Alignment explanation
Indices: 25891--26494 Score: 397
Period size: 28 Copynumber: 21.5 Consensus size: 28
25881 AGTGTGACCT
* *
25891 CTTT-AAAGCCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
25918 CTTT-TAAGTCCACAACTCCGTGGCATCC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
25946 CTTT-TAAGTCCACAACTTC-GTGGCATC
1 CTTTCAAAGCCCACAA-GTCAGTGGCACC
* * * * * **
25973 CTTTTAAAGTCCACAACTCCGTAGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
26001 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
26028 CTTT-TAAGTCCACAACTCCGTGGCATCC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * * *
26056 CTTT-TAAGACCACAACTCTGTAGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
26083 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * * * *
26110 CTTT-TAAGTCCATAACTCTGTGGCATCT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
26138 CTTT-TAAGTCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
26165 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
26193 CTTTCAAAGCCCACACAAGTCAGTGGCACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCAC-C
*
26224 CTTTCAAAGCCCACGCAAGTCAGTGGCACA
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
* * * *
26254 TTTTCAAAGCCCACGAGTCAATGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
26282 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
26310 CTTTC-AAGCCCACGAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
26337 TTTTCAAAGCCCA-GAGTCAGTGGCA-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
26363 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
26391 CTTTCCAAGCCCACGAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
26419 CTTTCGAAGCCCACGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
* **
26449 CTTTTAAAGCCCACGCAAGTCAGTAACACTC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCAC-C
*
26480 TTTTCAAAGCCCACA
1 CTTTCAAAGCCCACA
26495 TGTGTCAGTG
Statistics
Matches: 501, Mismatches: 58, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.03
27 174 0.35
28 205 0.41
29 7 0.01
30 66 0.13
31 36 0.07
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:27120 original size:20 final size:20
Alignment explanation
Indices: 27092--27166 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
27082 TTTTACCTTG
27092 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
27112 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
27132 ATGCATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
27152 ATGTATCGATACATT
1 ATGTATCGATACATT
27167 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:28114 original size:22 final size:22
Alignment explanation
Indices: 28080--28133 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
28070 AGCCTTTGAC
28080 CATGCA-TTTTTTATTATGTTA
1 CATGCATTTTTTTATTATGTTA
*
28101 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTA
28123 CATGCATTTTT
1 CATGCATTTTT
28134 AACATGTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTA
Found at i:32060 original size:19 final size:19
Alignment explanation
Indices: 32014--32060 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
32004 CGTTTTATTC
32014 AATTTAAATAATATTTTTA
1 AATTTAAATAATATTTTTA
*
32033 AATTAAAATAATATATTTT-
1 AATTTAAATAATAT-TTTTA
*
32052 TATTTAAAT
1 AATTTAAAT
32061 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTAAATAATATTTTTA
Found at i:32065 original size:21 final size:21
Alignment explanation
Indices: 32006--32065 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
31996 GAATAGCTCG
*
32006 TTTTATTCAATTTAAATAATAT
1 TTTTATTAAATTT-AATAATAT
*
32028 TTTTAAATTAAA-ATAAT-ATAT
1 TTTT--ATTAAATTTAATAATAT
32049 TTTTATTTAAATTTAAT
1 TTTTA-TTAAATTTAAT
32066 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 12 0.39
22 7 0.23
23 1 0.03
24 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTAAATTTAATAATAT
Found at i:33404 original size:20 final size:20
Alignment explanation
Indices: 33358--33394 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
33348 CGGTTTAATT
33358 TAAAT-TATTATTTAAATAA
1 TAAATATATTATTTAAATAA
33377 TAAATATATTATTTAAAT
1 TAAATATATTATTTAAAT
33395 TTTAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATATTATTTAAATAA
Found at i:34124 original size:28 final size:25
Alignment explanation
Indices: 34080--34145 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 25
34070 TATATATAAT
*
34080 TATTTAATTTATTTTTATAAATTTAAA
1 TATTTAA-TTATTTTTAT-AACTTAAA
34107 TATTATAATTATTATTTATAACTTAAA
1 TATT-TAATTATT-TTTATAACTTAAA
34134 TATTT-ATTATTT
1 TATTTAATTATTT
34146 AAATTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 1 0.03
25 6 0.17
26 1 0.03
27 20 0.56
28 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTAATTATTTTTATAACTTAAA
Found at i:34230 original size:25 final size:24
Alignment explanation
Indices: 34202--34251 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
34192 TATTTAAAAT
34202 TATTTTA-TAAAATATTAAAATTTTA
1 TATTTTAGTAAAA-ATT-AAATTTTA
34227 TATTTTATGTAAAAATTAAATTTTA
1 TATTTTA-GTAAAAATTAAATTTTA
34252 ACTTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.65
26 3 0.13
27 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTTAGTAAAAATTAAATTTTA
Found at i:34296 original size:17 final size:17
Alignment explanation
Indices: 34274--34324 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
34264 TGTATTTTTT
34274 ATAAATTTAAATATTTA
1 ATAAATTTAAATATTTA
34291 ATAAA--TAATATTATTTA
1 ATAAATTTAA-A-TATTTA
34308 ATCAAATTTAAAT-TTTA
1 AT-AAATTTAAATATTTA
34325 TTATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 17 0.59
18 4 0.14
19 1 0.03
20 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTTAAATATTTA
Found at i:34352 original size:19 final size:18
Alignment explanation
Indices: 34316--34358 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
34306 TAATCAAATT
* *
34316 TAAATTTTATTATTAATATA
1 TAAA-TTTAATATAAATA-A
34336 TAAATTTAATATAAATAA
1 TAAATTTAATATAAATAA
34354 TAAAT
1 TAAAT
34359 AAATTCAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTTAATATAAATAA
Found at i:35670 original size:16 final size:15
Alignment explanation
Indices: 35625--35670 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
35615 TTTGTTTTGA
*
35625 TCATTTTTCATTTAAG
1 TCATTTTTGATTT-AG
*
35641 TCATTTTAGATTTAG
1 TCATTTTTGATTTAG
35656 TCATTTTTGAGTTTA
1 TCATTTTTGA-TTTA
35671 AATTAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (15 bp):
TCATTTTTGATTTAG
Found at i:35932 original size:22 final size:20
Alignment explanation
Indices: 35889--35932 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
35879 TAGTTTAGTT
**
35889 AAAATAATTTAAATTATCTA
1 AAAATAATTTAAATTAAATA
35909 AAAATAATGTTAATATTAAATA
1 AAAATAAT-TTAA-ATTAAATA
35931 AA
1 AA
35933 TATTAGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATAATTTAAATTAAATA
Found at i:36011 original size:29 final size:32
Alignment explanation
Indices: 35979--36039 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
35969 TACTTATGGT
35979 TTTAAATAT-A-AAATTAAAAAAATT-ATAAA
1 TTTAAATATCATAAATTAAAAAAATTAATAAA
* *
36008 TTTAAATATCATCACTTAAAAAAATTAATAAA
1 TTTAAATATCATAAATTAAAAAAATTAATAAA
36040 AAATATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 9 0.33
30 1 0.04
31 12 0.44
32 5 0.19
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAATATCATAAATTAAAAAAATTAATAAA
Found at i:36408 original size:30 final size:30
Alignment explanation
Indices: 36363--36468 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
36353 AAATTTTATA
36363 TTAATATAA-AAAATAAATTTTTAATATTTT
1 TTAA-ATAATAAAATAAATTTTTAATATTTT
*
36393 TTAAATAATAAAATAAA---ATAA-ATTTT
1 TTAAATAATAAAATAAATTTTTAATATTTT
* *
36419 TATTAATATATAAAATAAAATTTTAATATTTT
1 T-TAAATA-ATAAAATAAATTTTTAATATTTT
*
36451 TTAATTAATAAAATAAAT
1 TTAAATAATAAAATAAAT
36469 CATCAAACTA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
26 6 0.10
27 8 0.13
28 10 0.16
29 4 0.06
30 22 0.35
31 7 0.11
32 6 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTAAATAATAAAATAAATTTTTAATATTTT
Found at i:36418 original size:24 final size:24
Alignment explanation
Indices: 36391--36444 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
36381 TTTTAATATT
36391 TTTTAAATAATAAAATAAAAT-AAA
1 TTTTAAATAAT-AAATAAAATAAAA
* * *
36415 TTTTTATTAATATATAAAATAAAA
1 TTTTAAATAATAAATAAAATAAAA
36439 TTTTAA
1 TTTTAA
36445 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTAAATAATAAATAAAATAAAA
Found at i:36426 original size:58 final size:59
Alignment explanation
Indices: 36352--36467 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 59
36342 ATATTTTATT
*
36352 TAAATTTTATATTAATATAAAAAATAAATTTTTAATATTTTTTAAATAATAAAATAAAA
1 TAAATTTTATATTAATATAAAAAATAAAATTTTAATATTTTTTAAATAATAAAATAAAA
* *
36411 TAAATTTT-TATTAATATATAAAATAAAATTTTAATATTTTTTAATTAATAAAATAAA
1 TAAATTTTATATTAATATAAAAAATAAAATTTTAATATTTTTTAAATAATAAAATAAA
36468 TCATCAAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 46 0.85
59 8 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (59 bp):
TAAATTTTATATTAATATAAAAAATAAAATTTTAATATTTTTTAAATAATAAAATAAAA
Found at i:36624 original size:19 final size:18
Alignment explanation
Indices: 36600--36635 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
36590 AAACTATTAA
36600 TTTATATATTTATATTATT
1 TTTATATATTT-TATTATT
36619 TTTATATATTTTATTAT
1 TTTATATATTTTATTAT
36636 ATTATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATATATTTTATTATT
Found at i:41709 original size:36 final size:36
Alignment explanation
Indices: 41640--41710 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
41630 TCAAAATAAT
*
41640 ATAAAAATATTTTATATTATTTATAATTAAATTTAA
1 ATAAAAATATTTTATATTATTTATAATAAAATTTAA
*
41676 ATAAAAATATTTTTTATTATTTA-AATAATAATTTA
1 ATAAAAATATTTTATATTATTTATAATAA-AATTTA
41711 TCTCGAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
ATAAAAATATTTTATATTATTTATAATAAAATTTAA
Found at i:42260 original size:13 final size:13
Alignment explanation
Indices: 42242--42284 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
42232 ATAAATAAAT
*
42242 TTAATTTTTTTAA
1 TTAATTTTTATAA
*
42255 TTAATTTATATAA
1 TTAATTTTTATAA
*
42268 TT-ATTTTTAAAA
1 TTAATTTTTATAA
42280 TTAAT
1 TTAAT
42285 AATGAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTTTTATAA
Found at i:45857 original size:2 final size:2
Alignment explanation
Indices: 45842--45876 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
45832 CAAGACAACC
* *
45842 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45877 GTTGTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50165 original size:11 final size:11
Alignment explanation
Indices: 50145--50179 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
50135 AAGAGTTAGG
*
50145 ATTATAGTAGC
1 ATTATCGTAGC
*
50156 ATTATCGTAGG
1 ATTATCGTAGC
50167 ATTATCGTAGC
1 ATTATCGTAGC
50178 AT
1 AT
50180 ATTTCCACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (11 bp):
ATTATCGTAGC
Found at i:54016 original size:22 final size:23
Alignment explanation
Indices: 53976--54021 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
53966 ATTAGTAATG
*
53976 TAAATATAAATTAATATAAATTAT
1 TAAATAT-AATTAAAATAAATTAT
*
54000 TAAATAT-ATTAAAATAATTTAT
1 TAAATATAATTAAAATAAATTAT
54022 GTATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATATAATTAAAATAAATTAT
Found at i:54306 original size:18 final size:18
Alignment explanation
Indices: 54279--54317 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
54269 ATGATTTTTT
54279 AAAATATT-AATTATATA
1 AAAATATTAAATTATATA
*
54296 AAAATTATTAAATTATGTA
1 AAAA-TATTAAATTATATA
54315 AAA
1 AAA
54318 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATATTAAATTATATA
Found at i:54318 original size:18 final size:17
Alignment explanation
Indices: 54278--54320 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54268 GATGATTTTT
54278 TAAAA-TATTAATTATA
1 TAAAATTATTAATTATA
*
54294 TAAAAATTATTAAATTATG
1 T-AAAATTATT-AATTATA
54313 TAAAATTA
1 TAAAATTA
54321 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 4 0.17
18 11 0.48
19 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:54328 original size:19 final size:19
Alignment explanation
Indices: 54285--54333 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
54275 TTTTAAAATA
54285 TTAATTATATAAAAATTAT
1 TTAATTATATAAAAATTAT
* *
54304 TAAATTATGT-AAAATTAAT
1 TTAATTATATAAAAATT-AT
*
54323 TTAATTTTATA
1 TTAATTATATA
54334 TTGATGTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATTATATAAAAATTAT
Found at i:55971 original size:2 final size:2
Alignment explanation
Indices: 55958--55992 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
55948 CTCCAACAAA
* *
55958 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55993 AAGCATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.43, T:0.03
Consensus pattern (2 bp):
AG
Found at i:56410 original size:23 final size:24
Alignment explanation
Indices: 56375--56419 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
56365 CGATTGAGAG
* *
56375 GAAAAATATGAAAAA-AAAAAAGA
1 GAAAAAAACGAAAAAGAAAAAAGA
56398 GAAAAAAACGAAAAAGAAAAAA
1 GAAAAAAACGAAAAAGAAAAAA
56420 AGTTAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (24 bp):
GAAAAAAACGAAAAAGAAAAAAGA
Found at i:56741 original size:28 final size:28
Alignment explanation
Indices: 56710--56772 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
56700 GACATATCCA
56710 TATATTTATTCGTATTCAT-ATTA-TTTTT
1 TATATTTA-TCGTATT-ATAATTATTTTTT
* *
56738 TATATCGTATCGTATTTTAATTATTTTTT
1 TATAT-TTATCGTATTATAATTATTTTTT
56767 TATATT
1 TATATT
56773 ATATATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 16 0.55
29 12 0.41
ACGTcount: A:0.25, C:0.06, G:0.05, T:0.63
Consensus pattern (28 bp):
TATATTTATCGTATTATAATTATTTTTT
Found at i:57433 original size:15 final size:15
Alignment explanation
Indices: 57413--57442 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57403 ACGCCTTAAG
57413 CCACCAAACCACAGC
1 CCACCAAACCACAGC
57428 CCACCAAACCACAGC
1 CCACCAAACCACAGC
57443 AACAAACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.53, G:0.07, T:0.00
Consensus pattern (15 bp):
CCACCAAACCACAGC
Found at i:58637 original size:7 final size:7
Alignment explanation
Indices: 58625--58659 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
58615 TGAAATTACT
58625 ATATACA
1 ATATACA
58632 ATATACA
1 ATATACA
*
58639 ATATGCA
1 ATATACA
58646 ATATACA
1 ATATACA
58653 ATATACA
1 ATATACA
58660 TGAATAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (7 bp):
ATATACA
Found at i:58647 original size:14 final size:14
Alignment explanation
Indices: 58612--58656 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
58602 AAATATATTC
* *
58612 ATATGAAAT-TACT
1 ATATGCAATATACA
*
58625 ATATACAATATACA
1 ATATGCAATATACA
58639 ATATGCAATATACA
1 ATATGCAATATACA
58653 ATAT
1 ATAT
58657 ACATGAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (14 bp):
ATATGCAATATACA
Found at i:59950 original size:19 final size:19
Alignment explanation
Indices: 59926--59993 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
59916 AATTCAACAA
59926 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
59945 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
59960 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
59977 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
59994 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:59965 original size:13 final size:13
Alignment explanation
Indices: 59947--59971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59937 ACATAAGTTT
59947 TGTATCGATACAA
1 TGTATCGATACAA
59960 TGTATCGATACA
1 TGTATCGATACA
59972 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:59969 original size:32 final size:32
Alignment explanation
Indices: 59928--59990 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
59918 TTCAACAATT
*
59928 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
59960 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
59991 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:60057 original size:33 final size:33
Alignment explanation
Indices: 60015--60079 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
60005 CAAGGAAATG
***
60015 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
60048 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
60080 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:65354 original size:29 final size:29
Alignment explanation
Indices: 65296--65367 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 29
65286 GAAAAAAAAT
* *
65296 CGGGATTGG-AGTAATCCCTCGGAAGTAA
1 CGGGATTGGAAGTAATCCCACGGAAATAA
*
65324 CGGGTTTGGAAGT-ATCCCACGTGAAATAA
1 CGGGATTGGAAGTAATCCCACG-GAAATAA
*
65353 CGAGGGTTGG-AGTAA
1 CG-GGATTGGAAGTAA
65368 GCCTCGCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 15 0.42
29 14 0.39
30 7 0.19
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.22
Consensus pattern (29 bp):
CGGGATTGGAAGTAATCCCACGGAAATAA
Done.