Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 67 of 187
Found at i:19826299 original size:17 final size:18
Alignment explanation
Indices: 19826249--19826291 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
19826239 CATAATAAGT
* *
19826249 AATAATAATATATAATTAA
1 AATAATACT-TATAATCAA
19826268 AATAATACTTATAATCAA
1 AATAATACTTATAATCAA
19826286 AATAAT
1 AATAAT
19826292 TTTATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATACTTATAATCAA
Found at i:19828000 original size:83 final size:83
Alignment explanation
Indices: 19827781--19828050 Score: 360
Period size: 83 Copynumber: 3.2 Consensus size: 83
19827771 TTCGATTTGT
* * * * *
19827781 AAGGATGTCAAATCATCTTGAGTCTGTCTGAAAACATTTGAGAGTCATATCTGCAAGGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
19827846 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* * * * *
19827864 GAGGGTACTTAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTTATATCTGCAATGTCCTCG
1 AAGGATGC-CAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
19827929 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* * * *
19827948 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATCTGAGAATCAAATCTGCTATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
**
19828013 TTTGTTCCTTGTAAATAC
66 TTTGTTCCTTGTAAGCAC
* *
19828031 AAGAATGCCAAATCATCTTG
1 AAGGATGCCAAACCATCTTG
19828051 GATCTGCTTC
Statistics
Matches: 162, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 89 0.55
84 73 0.45
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:19828186 original size:119 final size:119
Alignment explanation
Indices: 19827974--19828451 Score: 762
Period size: 119 Copynumber: 4.0 Consensus size: 119
19827964 CTTGAGTCTG
* * *
19827974 TTTGAGAACATCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAATACAAGAATGC
1 TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
*
19828039 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATC
* *
19828093 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCC-TATAAACACAAGAATA
1 TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTG-TTCCTTGTAAACACAAGAATA
* *
19828157 CCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGGTCTGCTATC
65 CCAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATC
*
19828212 TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTGCTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
* * *
19828277 CAAATCATCCTGGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATC
* *
19828331 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
* ** *
19828396 CAAATCATCTTGGATCTGCTTCAACATAAATGTCTGAA-GTCTAGATCTGCTGTC
66 CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGT-TAGATCTGCTATC
19828450 TT
1 TT
19828452 CAATTTATTT
Statistics
Matches: 332, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
118 5 0.02
119 323 0.97
120 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAATCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAATATAAACATCTGAAGGTTAGATCTGCTATC
Found at i:19837180 original size:30 final size:30
Alignment explanation
Indices: 19837146--19837247 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 30
19837136 AAAAAAATAA
19837146 AAATTGTATTTTGACCCCTAAACTTTTC-CT
1 AAATT-TATTTTGACCCCTAAACTTTTCTCT
* * * *
19837176 AAATTCCATTTTGACACTTAAAC-TTTCTTT
1 AAATT-TATTTTGACCCCTAAACTTTTCTCT
* *
19837206 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTT-ATTTTGACCCCTAAACTTTTC-TCT
19837236 AAATTTCATTTT
1 AAATTT-ATTTT
19837248 AATCCTAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 4 0.07
30 52 0.91
31 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTATTTTGACCCCTAAACTTTTCTCT
Found at i:19837512 original size:20 final size:20
Alignment explanation
Indices: 19837489--19837546 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
19837479 AAAACTTGCA
19837489 AAAAAGAGAAAAAGAAGAGG
1 AAAAAGAGAAAAAGAAGAGG
* *
19837509 AAAAGGAGAGAAAG-AGAGG
1 AAAAAGAGAAAAAGAAGAGG
* *
19837528 AGAAAG-G-AGAAGAAGAGG
1 AAAAAGAGAAAAAGAAGAGG
19837546 A
1 A
19837547 GAGCCTCCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 3 0.10
18 7 0.23
19 9 0.29
20 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAAAAGAAGAGG
Found at i:19837518 original size:22 final size:20
Alignment explanation
Indices: 19837494--19837537 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19837484 TTGCAAAAAA
*
19837494 GAGAAAAAGAAGAGGA-AAAG
1 GAGAGAAAG-AGAGGAGAAAG
19837514 GAGAGAAAGAGAGGAGAAAG
1 GAGAGAAAGAGAGGAGAAAG
19837534 GAGA
1 GAGA
19837538 AGAAGAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (20 bp):
GAGAGAAAGAGAGGAGAAAG
Found at i:19837588 original size:18 final size:17
Alignment explanation
Indices: 19837565--19837607 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
19837555 GACAGCGGCT
19837565 CGACGGCGAAGACGACGG
1 CGACGGCGAAG-CGACGG
*
19837583 CGACGGCACAAGCGACGG
1 CGACGGC-GAAGCGACGG
19837601 CG-CGGCG
1 CGACGGCG
19837608 CGGCGGCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.23, C:0.33, G:0.44, T:0.00
Consensus pattern (17 bp):
CGACGGCGAAGCGACGG
Found at i:19837642 original size:3 final size:3
Alignment explanation
Indices: 19837634--19837717 Score: 111
Period size: 3 Copynumber: 29.0 Consensus size: 3
19837624 TGAAGCTCGT
*
19837634 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
19837682 GGA GAA GAA GAA -AA -AA GAA AAA GAA AAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
19837718 AAAGGAAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
2 6 0.08
3 65 0.92
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19837720 original size:6 final size:6
Alignment explanation
Indices: 19837638--19837727 Score: 74
Period size: 6 Copynumber: 14.3 Consensus size: 6
19837628 GCTCGTGAAG
* * * * * *
19837638 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAA AAGGAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA-GA-AA
19837688 GAAGAAAA AAGAAA AAGAAA AAG-AA AAGAAA AAGGAAA AA
1 -AAG-AAA AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AA
19837728 AATAAAAAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
5 5 0.06
6 53 0.69
7 11 0.14
8 5 0.06
9 3 0.04
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:19837725 original size:12 final size:12
Alignment explanation
Indices: 19837674--19837726 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 12
19837664 GAAGAAGAAG
19837674 AAGAAAAAGGAGAA
1 AAGAAAAA-G-GAA
*
19837688 GAAGAAAAAAGAAA
1 -AAG-AAAAAGGAA
19837702 AAGAAAAA-GAA
1 AAGAAAAAGGAA
19837713 AAGAAAAAGGAA
1 AAGAAAAAGGAA
19837725 AA
1 AA
19837727 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 10 0.29
12 10 0.29
13 3 0.09
14 2 0.06
15 4 0.12
16 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGGAA
Found at i:19838429 original size:37 final size:37
Alignment explanation
Indices: 19838368--19838513 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
19838358 TACGTATGAT
* *
19838368 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
19838403 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
19838440 CACTTATCACTTTGTTTTTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
19838477 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
19838514 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:19838530 original size:46 final size:46
Alignment explanation
Indices: 19838477--19838745 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
19838467 TAAGTGTAGC
* **
19838477 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
19838523 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
19838569 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
19838621 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
19838667 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
19838719 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
19838746 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:19838596 original size:52 final size:52
Alignment explanation
Indices: 19838520--19838739 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
19838510 TAGCTAAAGC
* *
19838520 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19838573 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
19838625 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
19838671 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
19838723 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
19838740 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:19838642 original size:98 final size:98
Alignment explanation
Indices: 19838477--19838745 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
19838467 TAAGTGTAGC
* * *
19838477 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
19838542 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
19838576 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
19838641 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
19838674 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
19838739 GATCAGA
66 GATCAGA
19838746 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:19840787 original size:18 final size:18
Alignment explanation
Indices: 19840764--19840806 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
19840754 CAGGTCAAAC
19840764 CGACCCGATCCGGCGACA
1 CGACCCGATCCGGCGACA
* *
19840782 CGACCCGATCCGGTGACC
1 CGACCCGATCCGGCGACA
19840800 CGACCCG
1 CGACCCG
19840807 CAACCCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.47, G:0.28, T:0.07
Consensus pattern (18 bp):
CGACCCGATCCGGCGACA
Found at i:19841094 original size:7 final size:7
Alignment explanation
Indices: 19841084--19841163 Score: 81
Period size: 7 Copynumber: 11.1 Consensus size: 7
19841074 GAAAAAGAAG
19841084 GAAAAAA
1 GAAAAAA
*
19841091 GAAAACA
1 GAAAAAA
*
19841098 GAAAACA
1 GAAAAAA
19841105 GAAAAAA
1 GAAAAAA
19841112 GAAAAAA
1 GAAAAAA
19841119 GAAAAGAGA
1 GAAAA-A-A
*
19841128 AAAAAAA
1 GAAAAAA
*
19841135 GGGAAAAA
1 -GAAAAAA
*
19841143 G-GAAAA
1 GAAAAAA
19841149 GAAAAAA
1 GAAAAAA
19841156 GAAAAAA
1 GAAAAAA
19841163 G
1 G
19841164 GAAGGCTCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
6 5 0.08
7 45 0.73
8 7 0.11
9 5 0.08
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:19841110 original size:21 final size:21
Alignment explanation
Indices: 19841084--19841163 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
19841074 GAAAAAGAAG
*
19841084 GAAAAAAGAAAACAGAAAACA
1 GAAAAAAGAAAAAAGAAAACA
*
19841105 GAAAAAAGAAAAAAGAAAAGA
1 GAAAAAAGAAAAAAGAAAACA
* *
19841126 GAAAAAAAAGGGAAAAAGGAAA-A
1 G--AAAAAA-GAAAAAAGAAAACA
19841149 GAAAAAAGAAAAAAG
1 GAAAAAAGAAAAAAG
19841164 GAAGGCTCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.14
21 26 0.51
23 8 0.16
24 10 0.20
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (21 bp):
GAAAAAAGAAAAAAGAAAACA
Found at i:19841152 original size:12 final size:12
Alignment explanation
Indices: 19841070--19841160 Score: 69
Period size: 12 Copynumber: 7.2 Consensus size: 12
19841060 GAAGCAGGCC
*
19841070 AAAGGAAAAAG-
1 AAAGAAAAAAGA
*
19841081 AAGGAAAAAAGAA
1 AAAGAAAAAAG-A
*
19841094 AACAGAAAACAGAAA
1 AA-AGAAAA-A-AGA
19841109 AAAGAAAAAAGA
1 AAAGAAAAAAGA
19841121 AAAGAGAAAAA-A
1 AAAGA-AAAAAGA
* *
19841133 AAGGGAAAAAGGA
1 AA-AGAAAAAAGA
19841146 AAAGAAAAAAGA
1 AAAGAAAAAAGA
19841158 AAA
1 AAA
19841161 AAGGAAGGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
11 9 0.14
12 25 0.40
13 13 0.21
14 11 0.17
15 4 0.06
16 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:19841212 original size:21 final size:21
Alignment explanation
Indices: 19841188--19841227 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19841178 TGTAACCCTC
19841188 TCGGTCAAGCTCGTATTTTGA
1 TCGGTCAAGCTCGTATTTTGA
*
19841209 TCGGTCAATCTCGTATTTT
1 TCGGTCAAGCTCGTATTTT
19841228 TGAGCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (21 bp):
TCGGTCAAGCTCGTATTTTGA
Found at i:19841529 original size:17 final size:17
Alignment explanation
Indices: 19841504--19841674 Score: 73
Period size: 17 Copynumber: 9.6 Consensus size: 17
19841494 ATTTTTGTTT
*
19841504 TTTTTAAAAATTTCGTG
1 TTTTCAAAAATTTCGTG
*
19841521 TTTTC-AAAATTCCAGTG
1 TTTTCAAAAATTTC-GTG
*
19841538 -TTTCAAAAATTTTCATG
1 TTTTCAAAAA-TTTCGTG
***
19841555 TTTT-AAAAA-AAAGTG
1 TTTTCAAAAATTTCGTG
* *
19841570 TTTTCAAAAATTCCCGTA
1 TTTTCAAAAATT-TCGTG
* * *
19841588 TTTTGAAAATTTTCTTG
1 TTTTCAAAAATTTCGTG
19841605 TTTTCAAAAAAAATTTCTGTG
1 TTTTC---AAAAATTTC-GTG
19841626 TTTTACAAAAAAAATTCTCGT-
1 TTTT-C---AAAAATT-TCGTG
* *
19841647 CTTTCAAAAATTTTCATG
1 TTTTCAAAAA-TTTCGTG
19841665 TTTTCAAAAA
1 TTTTCAAAAA
19841675 AATTGACCGT
Statistics
Matches: 116, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
15 6 0.05
16 16 0.14
17 32 0.28
18 29 0.25
20 9 0.08
21 9 0.08
22 13 0.11
23 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTTCAAAAATTTCGTG
Found at i:19841637 original size:22 final size:20
Alignment explanation
Indices: 19841593--19841676 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
19841583 CCGTATTTTG
*
19841593 AAAATTTTCTTGTTTTCAAA
1 AAAAATTTCTTGTTTTCAAA
19841613 AAAAATTTCTGTGTTTTACAAA
1 AAAAATTTCT-TGTTTT-CAAA
*
19841635 AAAAA-TTCTCGTCTTTC--A
1 AAAAATTTCTTGT-TTTCAAA
* *
19841653 AAAATTTTCATGTTTTCAAA
1 AAAAATTTCTTGTTTTCAAA
19841673 AAAA
1 AAAA
19841677 TTGACCGTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
18 9 0.17
19 5 0.09
20 17 0.32
21 13 0.25
22 9 0.17
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (20 bp):
AAAAATTTCTTGTTTTCAAA
Found at i:19841655 original size:19 final size:18
Alignment explanation
Indices: 19841603--19841678 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 18
19841593 AAAATTTTCT
*
19841603 TGTTTTCAAAAAAAATTTCTG
1 TGTTTTC-AAAAAAA-TTC-A
19841624 TGTTTTACAAAAAAAATTC-
1 TGTTTT-C-AAAAAAATTCA
**
19841643 TCGTCTTTCAAAAATTTTCA
1 T-GT-TTTCAAAAAAATTCA
19841663 TGTTTTCAAAAAAATT
1 TGTTTTCAAAAAAATT
19841679 GACCGTGTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
18 11 0.23
19 11 0.23
20 4 0.09
21 12 0.26
22 9 0.19
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (18 bp):
TGTTTTCAAAAAAATTCA
Found at i:19841687 original size:60 final size:54
Alignment explanation
Indices: 19841509--19841687 Score: 170
Period size: 60 Copynumber: 3.3 Consensus size: 54
19841499 TGTTTTTTTT
* * *
19841509 AAAAATTTCGTGTTTTC-AAAATTCCAGTGTTTCAAAAATTTTCATGTTTT-AA
1 AAAAATTACGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTTCATGTTTTCAA
** *
19841561 AAAAA--A-GTGTTTTCAAAAATTCCCGTATTTTGAAAATTTTCTTGTTTTCAAA
1 AAAAATTACGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTTCATGTTTTC-AA
* * *
19841613 AAAAATTTCTGTGTTTTACAAAAAAAATTCTCGTCTTTCAAAAATTTTCATGTTTTCAA
1 AAAAATTAC-GTGTTTT-C---AAAAATTCCCGTATTTCAAAAATTTTCATGTTTTCAA
19841672 AAAAATTGACCGTGTT
1 AAAAATT-A-CGTGTT
19841688 CATAAATTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
49 8 0.08
50 28 0.28
52 12 0.12
56 7 0.07
57 1 0.01
59 9 0.09
60 35 0.35
61 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (54 bp):
AAAAATTACGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTTCATGTTTTCAA
Found at i:19841727 original size:37 final size:38
Alignment explanation
Indices: 19841618--19841727 Score: 118
Period size: 37 Copynumber: 2.9 Consensus size: 38
19841608 TCAAAAAAAA
* * *
19841618 TTTCTGTGTTTTACAAAAAAAATTCTCGTCTTTCAAAAAT
1 TTTC-GTGTTTT-CAAAAAAAATACTCGTGTTTCATAAAT
* *
19841658 TTTCATGTTTTCAAAAAAATTGAC-CGTG-TTCATAAAT
1 TTTCGTGTTTTCAAAAAAAAT-ACTCGTGTTTCATAAAT
*
19841695 TTTCGTGTTTT-AAAAAAAATCCTCGTGTTTCAT
1 TTTCGTGTTTTCAAAAAAAATACTCGTGTTTCAT
19841728 TTTTTATCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
35 1 0.02
36 12 0.20
37 23 0.39
38 12 0.20
39 7 0.12
40 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (38 bp):
TTTCGTGTTTTCAAAAAAAATACTCGTGTTTCATAAAT
Found at i:19841780 original size:16 final size:16
Alignment explanation
Indices: 19841759--19841793 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19841749 TTTCAAAAAC
19841759 AAATTTT-GTGTTTTAA
1 AAATTTTCGTG-TTTAA
19841775 AAATTTTCGTGTTTAA
1 AAATTTTCGTGTTTAA
19841791 AAA
1 AAA
19841794 AGAAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (16 bp):
AAATTTTCGTGTTTAA
Found at i:19841788 original size:38 final size:37
Alignment explanation
Indices: 19841736--19841814 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
19841726 ATTTTTTATC
* * * * *
19841736 AAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTA
1 AAAATTTTCATG-TTTAAAAAACAAAATTCGTGTTTCA
* *
19841774 AAAATTTTCGTGTTTAAAAAAGAAAATTCGTGTTTCA
1 AAAATTTTCATGTTTAAAAAACAAAATTCGTGTTTCA
19841811 AAAA
1 AAAA
19841815 AAATCTCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 24 0.71
38 10 0.29
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (37 bp):
AAAATTTTCATGTTTAAAAAACAAAATTCGTGTTTCA
Found at i:19841794 original size:17 final size:16
Alignment explanation
Indices: 19841759--19841794 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19841749 TTTCAAAAAC
*
19841759 AAATTTTGTGTTTTAA
1 AAATTTTGTGTTTAAA
19841775 AAATTTTCGTGTTTAAA
1 AAATTTT-GTGTTTAAA
19841792 AAA
1 AAA
19841795 GAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (16 bp):
AAATTTTGTGTTTAAA
Found at i:19841826 original size:19 final size:19
Alignment explanation
Indices: 19841791--19841832 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
19841781 TCGTGTTTAA
*
19841791 AAAAGAAAATTCGTGTTTC
1 AAAAGAAAATTCATGTTTC
19841810 AAAA-AAAATCTCATGTTTC
1 AAAAGAAAAT-TCATGTTTC
19841829 AAAA
1 AAAA
19841833 TTTTCATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAAGAAAATTCATGTTTC
Found at i:19841980 original size:16 final size:16
Alignment explanation
Indices: 19841959--19841993 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19841949 TTTCAAAAAC
19841959 AAATTTT-GTGTTTTAA
1 AAATTTTCGTG-TTTAA
19841975 AAATTTTCGTGTTTAA
1 AAATTTTCGTGTTTAA
19841991 AAA
1 AAA
19841994 AGAAAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (16 bp):
AAATTTTCGTGTTTAA
Found at i:19841988 original size:38 final size:38
Alignment explanation
Indices: 19841949--19842031 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
19841939 ATTTTTATGT
* * *
19841949 TTTCAAAAACAAATTTTGTGTTT-TAAAAATTTTCGTG
1 TTTCAAAAACAAAATTCGTGTTTCAAAAAATTTTCGTG
* * * *
19841986 TTTAAAAAAGAAAATTCGTGTTTCAAAAAAATCTCGTG
1 TTTCAAAAACAAAATTCGTGTTTCAAAAAATTTTCGTG
19842024 TTTCAAAA
1 TTTCAAAA
19842032 TTTTCGTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
37 19 0.51
38 18 0.49
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (38 bp):
TTTCAAAAACAAAATTCGTGTTTCAAAAAATTTTCGTG
Found at i:19842024 original size:18 final size:17
Alignment explanation
Indices: 19841996--19842031 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19841986 TTTAAAAAAG
19841996 AAAATTCGTGTTTCAAA
1 AAAATTCGTGTTTCAAA
19842013 AAAATCTCGTGTTTCAAA
1 AAAAT-TCGTGTTTCAAA
19842031 A
1 A
19842032 TTTTCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (17 bp):
AAAATTCGTGTTTCAAA
Found at i:19842031 original size:16 final size:16
Alignment explanation
Indices: 19841996--19842042 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
19841986 TTTAAAAAAG
19841996 AAAATTCGTGTTTCAAA
1 AAAATTCGTGTTTC-AA
19842013 AAAATCTCGTGTTTCAA
1 AAAAT-TCGTGTTTCAA
**
19842030 AATTTTCGTGTTT
1 AAAATTCGTGTTT
19842043 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (16 bp):
AAAATTCGTGTTTCAA
Found at i:19842054 original size:199 final size:201
Alignment explanation
Indices: 19841670--19842069 Score: 768
Period size: 200 Copynumber: 2.0 Consensus size: 201
19841660 TCATGTTTTC
19841670 AAAAAAATTGACCGTGTTCATAAATTTTCGTGTTTTAAAAAAAATCCTCGTGTTTCATTTTTTAT
1 AAAAAAATTGACCGTGTTCATAAATTTTCGTGTTTTAAAAAAAATCCTCGTGTTTCATTTTTTAT
19841735 CAAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTAAAAAAGAAAA
66 CAAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTAAAAAAGAAAA
19841800 TTCGTGTTTCAAAAAAAATCTCATGTTTCAAAATTTTCATGTTTTTTTTT-AAAAAATCGGGTTT
131 TTCGTGTTTCAAAAAAAATCTCATGTTTCAAAATTTTCATGTTTTTTTTTAAAAAAATCGGGTTT
19841864 CTGAAA
196 CTGAAA
19841870 AAAAAAATTGACCGTGTTCATAAATTTTCGTGTTTTAAAAAAAATCCTCGTGTTTCATTTTTTAT
1 AAAAAAATTGACCGTGTTCATAAATTTTCGTGTTTTAAAAAAAATCCTCGTGTTTCATTTTTTAT
19841935 CAAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTAAAAAAGAAAA
66 CAAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTAAAAAAGAAAA
* *
19842000 TTCGTGTTTC-AAAAAAATCTCGTGTTTCAAAATTTTCGTGTTTTTTTTTAAAAAAATCGGGTTT
131 TTCGTGTTTCAAAAAAAATCTCATGTTTCAAAATTTTCATGTTTTTTTTTAAAAAAATCGGGTTT
19842064 CTGAAA
196 CTGAAA
19842070 TTCTTGTATT
Statistics
Matches: 197, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
199 37 0.19
200 160 0.81
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (201 bp):
AAAAAAATTGACCGTGTTCATAAATTTTCGTGTTTTAAAAAAAATCCTCGTGTTTCATTTTTTAT
CAAAATTTTTATGTTTTCAAAAACAAATTTTGTGTTTTAAAAATTTTCGTGTTTAAAAAAGAAAA
TTCGTGTTTCAAAAAAAATCTCATGTTTCAAAATTTTCATGTTTTTTTTTAAAAAAATCGGGTTT
CTGAAA
Found at i:19842311 original size:81 final size:81
Alignment explanation
Indices: 19842171--19842332 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
19842161 TTAAATGGAA
19842171 CTCGTATTTTTGAAAATTAAGACAACATGCGTTTAACGAGATACCAATTTTGGGAGTCGCGAGGG
1 CTCGTATTTTTGAAAATTAAGACAACATGCGTTTAACGAGATACCAATTTTGGGAGTCGCGAGGG
19842236 TGCTAATACCTTCCTC
66 TGCTAATACCTTCCTC
*
19842252 CTCGTATTTTTGAAAATTAAGACAACATGCGTTTAACGAGATACCAATTTTGGGCGTCGCGAGGG
1 CTCGTATTTTTGAAAATTAAGACAACATGCGTTTAACGAGATACCAATTTTGGGAGTCGCGAGGG
19842317 TGCTAATACCTTCCTC
66 TGCTAATACCTTCCTC
19842333 GCGCGTAACC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (81 bp):
CTCGTATTTTTGAAAATTAAGACAACATGCGTTTAACGAGATACCAATTTTGGGAGTCGCGAGGG
TGCTAATACCTTCCTC
Found at i:19855421 original size:16 final size:18
Alignment explanation
Indices: 19855388--19855423 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
19855378 TGAATTTGGG
19855388 TATTATTTAAATATTAAA
1 TATTATTTAAATATTAAA
19855406 TATT-TTTAAA-ATTAAA
1 TATTATTTAAATATTAAA
19855422 TA
1 TA
19855424 ACATAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATTTAAATATTAAA
Found at i:19856023 original size:16 final size:16
Alignment explanation
Indices: 19856002--19856050 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
19855992 TTCGTTGTAT
19856002 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
19856018 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
19856034 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
19856050 T
1 T
19856051 AGCAATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:19856304 original size:18 final size:17
Alignment explanation
Indices: 19856283--19856317 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19856273 TTATTATTAA
*
19856283 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19856301 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19856318 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19856476 original size:120 final size:120
Alignment explanation
Indices: 19856263--19856587 Score: 586
Period size: 120 Copynumber: 2.7 Consensus size: 120
19856253 TTAATCATAT
19856263 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
19856328 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
19856383 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAAATTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
19856448 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* *
19856503 TTT-A-A-AATTATTATTAAATATA-ATTAGATAAAAATATATAATTTAATAAAATTCTTAATAA
1 TTTAACATAATTATTATTAAATATATTTTA-ATTAAAATATATAATTTAATAAAATTCTTAATAA
19856564 TCAATATTCTTATATGAATTTACT
65 TCAATATTCTTATATGAATTTACT
19856588 NAAGTATATC
Statistics
Matches: 200, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
116 3 0.01
117 73 0.37
118 1 0.00
119 1 0.00
120 122 0.61
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:19860855 original size:17 final size:17
Alignment explanation
Indices: 19860833--19860868 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
19860823 ATTATTTTTT
19860833 TGAAATT-TTAAAAATAA
1 TGAAATTATTAAAAA-AA
19860850 TGAAATTATTAAAAAAA
1 TGAAATTATTAAAAAAA
19860867 TG
1 TG
19860869 CACGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (17 bp):
TGAAATTATTAAAAAAA
Found at i:19861032 original size:16 final size:17
Alignment explanation
Indices: 19861008--19861040 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19860998 CTATCTATCT
*
19861008 ATACGAAATTA-TAAAA
1 ATACAAAATTACTAAAA
19861024 ATACAAAATTACTAAAA
1 ATACAAAATTACTAAAA
19861041 TTCACAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (17 bp):
ATACAAAATTACTAAAA
Found at i:19871535 original size:20 final size:21
Alignment explanation
Indices: 19871497--19871536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19871487 CAATTTGTTA
**
19871497 TGAACTAAGAGAATTATAAAT
1 TGAACTAAGAGAAGAATAAAT
19871518 TGAAC-AAGAGAAGAATAAA
1 TGAACTAAGAGAAGAATAAA
19871537 AAAAATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (21 bp):
TGAACTAAGAGAAGAATAAAT
Found at i:19874363 original size:13 final size:14
Alignment explanation
Indices: 19874345--19874375 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
19874335 GTTAGTGAAA
19874345 AAAATTCAATA-TT
1 AAAATTCAATATTT
19874358 AAAATTCAATATTT
1 AAAATTCAATATTT
19874372 AAAA
1 AAAA
19874376 GAGATCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTCAATATTT
Found at i:19879719 original size:16 final size:16
Alignment explanation
Indices: 19879686--19879719 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19879676 ACAAATTGTT
* *
19879686 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
19879702 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
19879718 AA
1 AA
19879720 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:19882547 original size:21 final size:21
Alignment explanation
Indices: 19882521--19882561 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19882511 AGACGAGCAA
* *
19882521 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
19882542 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
19882562 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:19884500 original size:16 final size:16
Alignment explanation
Indices: 19884467--19884500 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19884457 GGAGATTGTT
* *
19884467 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
19884483 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
19884499 AA
1 AA
19884501 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:19885700 original size:41 final size:40
Alignment explanation
Indices: 19885668--19885777 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 40
19885658 ATGTCCTGGT
19885668 CTTTAGCAGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGAG
1 CTTTAGCAGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG-G
* * * * *
19885709 ATTTAGCGGTGTTTTTGGAAAAGCGCCGCTAATGCTCAGAA
1 CTTTAGCAGCGTTTTTGGAGAAGCGCCGCTAATGCTCAG-G
19885750 CTTTAG-AGTCGTTTTTGGAGAAGCGCCG
1 CTTTAGCAG-CGTTTTTGGAGAAGCGCCG
19885778 TTAAAACATT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 1 0.02
41 58 0.98
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
CTTTAGCAGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGG
Found at i:19886202 original size:14 final size:15
Alignment explanation
Indices: 19886174--19886206 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
19886164 AACGTTTATA
19886174 GATTATGGAATTAGG
1 GATTATGGAATTAGG
19886189 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
19886203 GATT
1 GATT
19886207 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:19886354 original size:7 final size:7
Alignment explanation
Indices: 19886341--19886393 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
19886331 TTAAATAAGA
19886341 TTTAGGG
1 TTTAGGG
*
19886348 GTTAGGG
1 TTTAGGG
*
19886355 GTTAGGG
1 TTTAGGG
* *
19886362 ATT-CGG
1 TTTAGGG
19886368 TTTAGGG
1 TTTAGGG
19886375 TTTAGGG
1 TTTAGGG
19886382 TTTAGGG
1 TTTAGGG
19886389 TTTAG
1 TTTAG
19886394 ATAAATTAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 4 0.10
7 36 0.90
ACGTcount: A:0.15, C:0.02, G:0.43, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:19886462 original size:14 final size:14
Alignment explanation
Indices: 19886432--19886475 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19886422 TAAATAAGGT
*
19886432 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
19886446 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
* *
19886460 TTAGTGGTTAAGAG
1 TTAGGGGTTAGGAG
19886474 TT
1 TT
19886476 GTGATTTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.36
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:19886593 original size:7 final size:7
Alignment explanation
Indices: 19886581--19886623 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
19886571 ATTGTAAAAG
19886581 AGGGGTT
1 AGGGGTT
19886588 AGGGGTT
1 AGGGGTT
*
19886595 AGAGGTT
1 AGGGGTT
* *
19886602 AAGGATT
1 AGGGGTT
19886609 AGGGGTT
1 AGGGGTT
19886616 AGGGGTT
1 AGGGGTT
19886623 A
1 A
19886624 TGGATAGGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.49, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:19886612 original size:21 final size:21
Alignment explanation
Indices: 19886586--19886628 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19886576 AAAAGAGGGG
19886586 TTAGGGGTTAGAGGTTAAGGA
1 TTAGGGGTTAGAGGTTAAGGA
* *
19886607 TTAGGGGTTAGGGGTTATGGA
1 TTAGGGGTTAGAGGTTAAGGA
19886628 T
1 T
19886629 AGGTAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAAGGA
Found at i:19890844 original size:26 final size:27
Alignment explanation
Indices: 19890794--19890863 Score: 108
Period size: 26 Copynumber: 2.6 Consensus size: 27
19890784 AAAAATAAAA
*
19890794 ATTTACCAAAATGT-TATAACTTTTTTT
1 ATTTACCAAAATATATATAAC-TTTTTT
19890821 ATTTACCAAAATATATATAA-TTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
19890847 ATTTACCAAAATATATA
1 ATTTACCAAAATATATA
19890864 AAAAAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 23 0.56
27 13 0.32
28 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTTACCAAAATATATATAACTTTTTT
Found at i:19890888 original size:10 final size:9
Alignment explanation
Indices: 19890863--19890887 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19890853 CAAAATATAT
19890863 AAAAAAACA
1 AAAAAAACA
19890872 AAAAAAACA
1 AAAAAAACA
19890881 AAAAAAA
1 AAAAAAA
19890888 AAACCTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:19890973 original size:27 final size:27
Alignment explanation
Indices: 19890943--19891010 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
19890933 ACGCCAATGG
19890943 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* * *
19890970 CATTGGCGGCATCAATGGTGCCAATAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
19890997 CATTGGCGGCACCA
1 CATTGGCGGCACCA
19891011 GTTAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:19891064 original size:4 final size:4
Alignment explanation
Indices: 19891050--19891180 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
19891040 GAGCAGAAGG
* *
19891050 AGAA GGAA AGAA AGAA AGAA AGGAGA GGAA AGAA AG-A A-AA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA AGAA
* * * *
19891098 AGGAGA GGAA AG-G AGAA GAGAA AAAA AGAA AG-A AG-A AGAA AAAA AGGAAA
1 A-GA-A AGAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-G-AA
*
19891148 AGAGA AGAA A-AA AGAA AGAA AGAA GGAA AGAA A
1 AGA-A AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
19891181 AGGAAAGGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
3 15 0.15
4 63 0.63
5 17 0.17
6 5 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:19891078 original size:22 final size:23
Alignment explanation
Indices: 19891046--19891213 Score: 91
Period size: 24 Copynumber: 7.0 Consensus size: 23
19891036 GTGGGAGCAG
19891046 AAGGAGAAGGAAAGAAAGAAAGA
1 AAGGAGAAGGAAAGAAAGAAAGA
19891069 AAGGAG-AGGAAAGAAAGAAAAAGA
1 AAGGAGAAGGAAAGAAAG--AAAGA
*
19891093 AA-GA-AAGGAGAGGAAAGGAGAAGA
1 AAGGAGAAGGA-AAGAAA-GA-AAGA
* * *
19891117 GAA--AAAAAGAAAGAAGAAGAAAAA
1 -AAGGAGAAGGAAAG-A-AAGAAAGA
*
19891141 AAGGA-AAAGAGAAGAAA-AAAGA
1 AAGGAGAAGGA-AAGAAAGAAAGA
*
19891163 AAGAAAGAAGGAAAGAAAAGGAAAGGA
1 AAG-GAGAAGGAAAG-AAA-GAAA-GA
*
19891190 AAGGAGAAGAGAAA-AAAAAAAGA
1 AAGGAGAAG-GAAAGAAAGAAAGA
19891213 A
1 A
19891214 GAAGAAGAGG
Statistics
Matches: 116, Mismatches: 9, Indels: 40
0.70 0.05 0.24
Matches are distributed among these distances:
22 18 0.16
23 24 0.21
24 38 0.33
25 17 0.15
26 10 0.09
27 9 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AAGGAGAAGGAAAGAAAGAAAGA
Found at i:19891080 original size:14 final size:14
Alignment explanation
Indices: 19891063--19891109 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
19891053 AGGAAAGAAA
19891063 GAAAGAAAGGAGAG
1 GAAAGAAAGGAGAG
* * *
19891077 GAAAGAAAGAAAAA
1 GAAAGAAAGGAGAG
19891091 GAAAGAAAGGAGAG
1 GAAAGAAAGGAGAG
19891105 GAAAG
1 GAAAG
19891110 GAGAAGAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGGAGAG
Found at i:19891091 original size:10 final size:10
Alignment explanation
Indices: 19891078--19891219 Score: 69
Period size: 10 Copynumber: 13.6 Consensus size: 10
19891068 AAAGGAGAGG
19891078 AAAGAAAGAA
1 AAAGAAAGAA
19891088 AAAGAAAG-A
1 AAAGAAAGAA
* * *
19891097 AAGGAGAGGA
1 AAAGAAAGAA
*
19891107 AAGGAGAAGAGA
1 AAAGA-AAGA-A
19891119 AAA-AAAGAA
1 AAAGAAAGAA
19891128 AGAAG-AAG-A
1 A-AAGAAAGAA
*
19891137 AAA-AAAGGA
1 AAAGAAAGAA
19891146 AAAGAGAAGAAA
1 AAAGA-AAG-AA
19891158 AAAGAAAGAA
1 AAAGAAAGAA
19891168 AGAAGGAAAGAA
1 A-AA-GAAAGAA
*
19891180 AAGGAAAGGAA
1 AAAGAAA-GAA
*
19891191 AGGAGAAGAGAAA
1 A-AAGAA-AG-AA
*
19891204 AAAAAAAGAA
1 AAAGAAAGAA
*
19891214 GAAGAA
1 AAAGAA
19891220 GAGGGAAGGA
Statistics
Matches: 103, Mismatches: 13, Indels: 32
0.70 0.09 0.22
Matches are distributed among these distances:
8 5 0.05
9 15 0.15
10 37 0.36
11 18 0.17
12 24 0.23
13 4 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:19891111 original size:5 final size:5
Alignment explanation
Indices: 19891046--19891194 Score: 61
Period size: 5 Copynumber: 31.0 Consensus size: 5
19891036 GTGGGAGCAG
* * *
19891046 AAGGA GAAGGA AA-GA AA-GA AA-GA AAGGA GAGGA AA-GA AAGAA AAAGA
1 AAGGA -AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA
* * *
19891093 AA-GA AAGGA GAGGA AAGGA GAAGAGA AA--A AAAGA AA-GA AGAAGA
1 AAGGA AAGGA AAGGA AAGGA -AAG-GA AAGGA AAGGA AAGGA A-AGGA
* * * * *
19891137 AA-AA AAGGA AAAGA GAAGAAA AAAGA AA-GA AA-G- AAGGA AAGAA AAGGA
1 AAGGA AAGGA AAGGA -AAG-GA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA
19891185 AAGGA AAGGA
1 AAGGA AAGGA
19891195 GAAGAGAAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
3 5 0.04
4 32 0.28
5 56 0.50
6 17 0.15
7 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:19891144 original size:44 final size:44
Alignment explanation
Indices: 19891078--19891219 Score: 174
Period size: 44 Copynumber: 3.4 Consensus size: 44
19891068 AAAGGAGAGG
* *
19891078 AAAGAAAGAAAAAGAAAGAAAGGAGAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAGAAGAAAAAAAGGAGAGGAAAGGAGAAGAGAAAA
*
19891122 AAAGAAAGAAGAAGAAAAAAA-G-GA--AAA-GAGAAGAAAAAA
1 AAAGAAAGAAGAAGAAAAAAAGGAGAGGAAAGGAGAAGAGAAAA
*
19891161 GAAAGAAAGAAG--GAAAGAAAAGGAAAGGAAAGGAGAAGAGAAAA
1 -AAAGAAAGAAGAAGAAA-AAAAGGAGAGGAAAGGAGAAGAGAAAA
19891205 AAA-AAAGAAGAAGAA
1 AAAGAAAGAAGAAGAA
19891220 GAGGGAAGGA
Statistics
Matches: 84, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
38 4 0.05
39 15 0.18
40 15 0.18
41 1 0.01
42 9 0.11
43 7 0.08
44 33 0.39
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (44 bp):
AAAGAAAGAAGAAGAAAAAAAGGAGAGGAAAGGAGAAGAGAAAA
Found at i:19891222 original size:22 final size:22
Alignment explanation
Indices: 19891118--19891222 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
19891108 AGGAGAAGAG
19891118 AAAAAAAGAAAGAAGAAGA-AAA
1 AAAAAAAG-AAGAAGAAGAGAAA
19891140 AAAGGAAAAG-AGAAGAA-A-AAA
1 AAA--AAAAGAAGAAGAAGAGAAA
*
19891161 GAAAGAAAGAAG--GAA-AGAAA
1 -AAAAAAAGAAGAAGAAGAGAAA
** * *
19891181 AGGAAAGGAAAGGAGAAGAGAAA
1 AAAAAAAG-AAGAAGAAGAGAAA
19891204 AAAAAAAGAAGAAGAAGAG
1 AAAAAAAGAAGAAGAAGAG
19891223 GGAAGGAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
19 8 0.12
20 10 0.15
21 6 0.09
22 26 0.40
23 10 0.15
24 5 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAGAAGAAGAGAAA
Found at i:19897420 original size:105 final size:104
Alignment explanation
Indices: 19897249--19897609 Score: 519
Period size: 104 Copynumber: 3.5 Consensus size: 104
19897239 GGTGGATCCC
* * ** *
19897249 GCACTTAGC-ACCACCACTGAATTGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
** * *
19897313 TAGCAACCCCCTTTTTCATTTCAAAGATATGGTGGAATCA
66 TAGCAACCCCCTTTCACATTT-AAAAATACGGTGGAATCA
* ** *
19897353 GCACTTAGCAACCACCAGTGGGTAGGGGAATCAGCATTTAGCAACCCCTCGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
*
19897418 TAGCAACCCCCTTTCACATTTAAAAATACGGTGGACTCA
66 TAGCAACCCCCTTTCACATTTAAAAATACGGTGGAATCA
* *
19897457 GCACATAGCAACCACCAAT-AAGTAGGGGAATCAGCACTTAGAAACCCCTCGGGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGAA-TAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
19897521 TTAGCAACCCCCTTTCACATTTAAAAATACGGTGGAATCA
65 TTAGCAACCCCCTTTCACATTTAAAAATACGGTGGAATCA
* **
19897561 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCT
19897610 TTATATGTAA
Statistics
Matches: 229, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
104 161 0.70
105 68 0.30
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (104 bp):
GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACT
TAGCAACCCCCTTTCACATTTAAAAATACGGTGGAATCA
Found at i:19897971 original size:30 final size:29
Alignment explanation
Indices: 19897937--19898001 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
19897927 TAATCCACCA
19897937 CCCAACTATTTGAAAAATTACAATTTTGCC
1 CCCAACT-TTTGAAAAATTACAATTTTGCC
* * * *
19897967 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
19897997 CCCAA
1 CCCAA
19898002 GCTTGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 24 0.80
31 4 0.13
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:19900792 original size:62 final size:62
Alignment explanation
Indices: 19900668--19900785 Score: 236
Period size: 62 Copynumber: 1.9 Consensus size: 62
19900658 CCCTCTTGCA
19900668 TTAACACACACCCAAGGCCATTCAACGATGCATCACTGTAAATTACAAACTCCTTCTCGGAC
1 TTAACACACACCCAAGGCCATTCAACGATGCATCACTGTAAATTACAAACTCCTTCTCGGAC
19900730 TTAACACACACCCAAGGCCATTCAACGATGCATCACTGTAAATTACAAACTCCTTC
1 TTAACACACACCCAAGGCCATTCAACGATGCATCACTGTAAATTACAAACTCCTTC
19900786 CTGGACTCAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (62 bp):
TTAACACACACCCAAGGCCATTCAACGATGCATCACTGTAAATTACAAACTCCTTCTCGGAC
Found at i:19901256 original size:61 final size:61
Alignment explanation
Indices: 19901181--19901301 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
19901171 CCGATTCATC
19901181 CCGAGAATAGATTAAAATATCATCTATGAACACTACCACGAACTTGTCTAAGTACAGCCGG
1 CCGAGAATAGATTAAAATATCATCTATGAACACTACCACGAACTTGTCTAAGTACAGCCGG
*
19901242 CCGAGAATAGATTAAAATATCATCTATGAACACTACCACGAACTTGTCTAAGTACGGCCG
1 CCGAGAATAGATTAAAATATCATCTATGAACACTACCACGAACTTGTCTAAGTACAGCCG
19901302 AAAAATTCGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
CCGAGAATAGATTAAAATATCATCTATGAACACTACCACGAACTTGTCTAAGTACAGCCGG
Found at i:19905133 original size:105 final size:104
Alignment explanation
Indices: 19904951--19905216 Score: 356
Period size: 105 Copynumber: 2.5 Consensus size: 104
19904941 ACCGTTATCA
* * *
19904951 GTGGATCCCGCACTTAGCACCACCACTGAATTGGGGAATCAGCACACAGCAACCCCTTGAGGGAA
1 GTGGATCACGCACTTAGCACCACCACTGAATAGGGGAATCAGCACACAGCAACCCCTCGAGGGAA
* **
19905016 TCAGCACTTAGCAACCCCCTTTTTCATTTCAAAGATATG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
* ** ** *
19905055 GTGGAATCA-GCACTTAGCAACCACCAGTGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GTGG-ATCACGCACTTAGC-ACCACCACTGAATAGGGGAATCAGCACACAGCAACCCCTCGAGGG
19905119 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
64 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
* * *
19905160 GTGGATCACGCACATAGCACCACC-CATAAATCGGGGAATCAGCACACAGCAACCCCT
1 GTGGATCACGCACTTAGCACCACCAC-TGAATAGGGGAATCAGCACACAGCAACCCCT
19905217 TTTATATACA
Statistics
Matches: 138, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
104 48 0.35
105 90 0.65
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GTGGATCACGCACTTAGCACCACCACTGAATAGGGGAATCAGCACACAGCAACCCCTCGAGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATG
Found at i:19905578 original size:29 final size:29
Alignment explanation
Indices: 19905545--19905608 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
19905535 TAATCCACCA
19905545 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
19905574 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
19905604 CCCAA
1 CCCAA
19905609 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:19905582 original size:30 final size:30
Alignment explanation
Indices: 19905552--19905608 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19905542 CCACCCAACT
19905552 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
19905581 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
19905609 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:19907149 original size:18 final size:18
Alignment explanation
Indices: 19907126--19907170 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
19907116 ATCCCAATGA
19907126 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
19907144 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
19907162 TCACCACCA
1 TCGCCACCA
19907171 ACCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:19910065 original size:3 final size:3
Alignment explanation
Indices: 19910057--19910094 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
19910047 TCTTAATACT
*
19910057 AAC AAC AAC AAC AAC AAC GAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
19910095 TAATAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:19910185 original size:19 final size:21
Alignment explanation
Indices: 19910161--19910199 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
19910151 ACTAAAACAA
*
19910161 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
19910180 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
19910200 ATCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:19910370 original size:27 final size:27
Alignment explanation
Indices: 19910340--19910421 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
19910330 ATCAATATGA
19910340 CACCATTGGTGCCGCCAATGGCATTGG
1 CACCATTGGTGCCGCCAATGGCATTGG
**
19910367 CACCATTGGTGCCGCCAATGGTTTTGG
1 CACCATTGGTGCCGCCAATGGCATTGG
* *
19910394 CACCTTTGGTGCCGCCAATGCCATTGG
1 CACCATTGGTGCCGCCAATGGCATTGG
19910421 C
1 C
19910422 GTGACCAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (27 bp):
CACCATTGGTGCCGCCAATGGCATTGG
Found at i:19910539 original size:26 final size:26
Alignment explanation
Indices: 19910478--19910548 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 26
19910468 TTTTGTTTTT
19910478 TTAT-ATATTTTGGTAAATAAAAAAA
1 TTATAATATTTTGGTAAATAAAAAAA
* *
19910503 TTATATGTATTTTGGTAAATAAAAAAG
1 TTATA-ATATTTTGGTAAATAAAAAAA
*
19910530 TTATAATATTTTGATAAAT
1 TTATAATATTTTGGTAAAT
19910549 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.10
26 12 0.30
27 24 0.60
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (26 bp):
TTATAATATTTTGGTAAATAAAAAAA
Found at i:19910564 original size:18 final size:19
Alignment explanation
Indices: 19910538--19910573 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19910528 AGTTATAATA
19910538 TTTTGATAA-ATTTTTATT
1 TTTTGATAATATTTTTATT
*
19910556 TTTTTATAATATTTTTAT
1 TTTTGATAATATTTTTAT
19910574 AAAAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTGATAATATTTTTATT
Found at i:19910570 original size:11 final size:11
Alignment explanation
Indices: 19910530--19910575 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
19910520 AATAAAAAAG
19910530 TTATAATATTT
1 TTATAATATTT
*
19910541 TGATAA-ATTT
1 TTATAATATTT
19910551 TTAT--T-TTT
1 TTATAATATTT
19910559 TTATAATATTT
1 TTATAATATTT
19910570 TTATAA
1 TTATAA
19910576 AAAACCCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 7 0.24
10 8 0.28
11 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATAATATTT
Found at i:19911678 original size:15 final size:14
Alignment explanation
Indices: 19911652--19911694 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
19911642 TCATAGAAAT
*
19911652 AAATATTATTTAAA
1 AAATATTTTTTAAA
19911666 AAATTATTTTTTAAA
1 AAA-TATTTTTTAAA
*
19911681 AGATATGTTTTTAA
1 AAATAT-TTTTTAA
19911695 CGGCGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
AAATATTTTTTAAA
Found at i:19911849 original size:86 final size:86
Alignment explanation
Indices: 19911697--19911918 Score: 279
Period size: 86 Copynumber: 2.6 Consensus size: 86
19911687 GTTTTTAACG
*
19911697 GCGTTTGTGTGAAAAGCGCCGCTAAAGGT-CTGTTCTATAGCGGCGTTTGTGGGAAAAAGCGCCG
1 GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT-TGGGAAAAAGCGCCG
* *
19911761 CTAAAGGTCTTTATCTATAGCA
65 CTAAAGGTCCTAATCTATAGCA
* * * * *
19911783 GTGTTTGTG-GAACAAGCGCCGCTAAAAGTCCTGATCTATAGCGGCGTTTTGTGAAGAAGCGTCG
1 GCGTTTGTGTGAA-AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTGGGAAAAAGCGCCG
*
19911847 CTAAAGGTCCTAATCTATAGCG
65 CTAAAGGTCCTAATCTATAGCA
*** *
19911869 GCGTTTTGTGTGGTTA-CGCCGCTAAAGGTCCTAATCTATAGCGGCGTTTT
1 GCG-TTTGTGTGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTT
19911919 TTGCGGCGCT
Statistics
Matches: 117, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
85 3 0.03
86 88 0.75
87 25 0.21
88 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (86 bp):
GCGTTTGTGTGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTGGGAAAAAGCGCCGC
TAAAGGTCCTAATCTATAGCA
Found at i:19911918 original size:43 final size:43
Alignment explanation
Indices: 19911695--19911918 Score: 249
Period size: 43 Copynumber: 5.2 Consensus size: 43
19911685 ATGTTTTTAA
**
19911695 CGGCGTTTGTGTGAA-AAGCGCCGCTAAAGGT-CTGTTCTATAG
1 CGGCGTTT-TGTGAAGAAGCGCCGCTAAAGGTCCTAATCTATAG
* * * *
19911737 CGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTTATCTATAG
1 CGGCGTTT-TGTGAAGAAGCGCCGCTAAAGGTCCTAATCTATAG
* * * * *
19911781 CAGTG-TTTGTGGAACAAGCGCCGCTAAAAGTCCTGATCTATAG
1 CGGCGTTTTGT-GAAGAAGCGCCGCTAAAGGTCCTAATCTATAG
*
19911824 CGGCGTTTTGTGAAGAAGCGTCGCTAAAGGTCCTAATCTATAG
1 CGGCGTTTTGTGAAGAAGCGCCGCTAAAGGTCCTAATCTATAG
** *
19911867 CGGCGTTTTGTGTGGTTA-CGCCGCTAAAGGTCCTAATCTATAG
1 CGGCGTTTTGTGAAG-AAGCGCCGCTAAAGGTCCTAATCTATAG
19911910 CGGCGTTTT
1 CGGCGTTTT
19911919 TTGCGGCGCT
Statistics
Matches: 156, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
42 16 0.10
43 123 0.79
44 17 0.11
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (43 bp):
CGGCGTTTTGTGAAGAAGCGCCGCTAAAGGTCCTAATCTATAG
Found at i:19912021 original size:34 final size:35
Alignment explanation
Indices: 19911973--19912039 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
19911963 CATTTCTCCC
*
19911973 TCAAATCTTCTTTTCTTTCAAAACC-CCAAAAAAT
1 TCAAATCTTCTTTTCCTTCAAAACCACCAAAAAAT
*
19912007 TCAAAT-TTCTTTTTCCTTGAAAACCACCAAAAA
1 TCAAATCTTC-TTTTCCTTCAAAACCACCAAAAA
19912040 GAGGTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 3 0.10
34 19 0.66
35 7 0.24
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAAATCTTCTTTTCCTTCAAAACCACCAAAAAAT
Found at i:19913827 original size:33 final size:33
Alignment explanation
Indices: 19913787--19913853 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
19913777 GAGTTCAATG
19913787 ATGGCATGTGTGTTGTCTAATAAAATTGGTTCA
1 ATGGCATGTGTGTTGTCTAATAAAATTGGTTCA
19913820 ATGGCATGTGTGTTGTCTAATAAAATTGGTTCA
1 ATGGCATGTGTGTTGTCTAATAAAATTGGTTCA
19913853 A
1 A
19913854 CGTTAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (33 bp):
ATGGCATGTGTGTTGTCTAATAAAATTGGTTCA
Found at i:19935390 original size:17 final size:18
Alignment explanation
Indices: 19935360--19935393 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19935350 ATTTTGCCGA
*
19935360 GGCATTATTGTTAGTAAG
1 GGCATTATTCTTAGTAAG
19935378 GGCA-TATTCTTAGTAA
1 GGCATTATTCTTAGTAA
19935394 TCCCGACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (18 bp):
GGCATTATTCTTAGTAAG
Found at i:19937278 original size:28 final size:25
Alignment explanation
Indices: 19937246--19937310 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 25
19937236 GTCACTTACT
19937246 TTAAAGAATGTTAAATGTACAATTTTGA
1 TTAAAGAATGTT--AT-TACAATTTTGA
*
19937274 TTAAA-TAT-TTATTACAATTTTGA
1 TTAAAGAATGTTATTACAATTTTGA
19937297 TTAAATGAAATGTT
1 TTAAA-G-AATGTT
19937311 CATCCTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 16 0.52
24 2 0.06
26 4 0.13
27 4 0.13
28 5 0.16
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (25 bp):
TTAAAGAATGTTATTACAATTTTGA
Found at i:19937956 original size:20 final size:19
Alignment explanation
Indices: 19937926--19937994 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
19937916 GCTTTGTGAA
19937926 CCAAGATGCACATTC-TGTG
1 CCAAGATGCAC-TTCGTGTG
19937945 CCAAGAATGCACTTCGTGTG
1 CCAAG-ATGCACTTCGTGTG
* * *
19937965 -CTAGTATGCACTTTGTGCG
1 CCAAG-ATGCACTTCGTGTG
*
19937984 CCAATATGCAC
1 CCAAGATGCAC
19937995 AATACGTGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (19 bp):
CCAAGATGCACTTCGTGTG
Found at i:19940056 original size:9 final size:9
Alignment explanation
Indices: 19940039--19940069 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19940029 GAGATTAAAT
*
19940039 TAATATTAA
1 TAATTTTAA
19940048 TAATTTTAA
1 TAATTTTAA
19940057 TAATTTTAA
1 TAATTTTAA
19940066 TAAT
1 TAAT
19940070 ACGATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATTTTAA
Found at i:19948312 original size:29 final size:28
Alignment explanation
Indices: 19948263--19948318 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
19948253 TTTACGTACA
19948263 TAATAAAAAAAAGAGTCATTTTTATAAT
1 TAATAAAAAAAAGAGTCATTTTTATAAT
*
19948291 TAATAAAAAAATCAG-GTTATTTTTATAA
1 TAATAAAAAAA--AGAGTCATTTTTATAA
19948319 AATAATCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 11 0.44
29 12 0.48
30 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
TAATAAAAAAAAGAGTCATTTTTATAAT
Found at i:19958145 original size:30 final size:31
Alignment explanation
Indices: 19958103--19958169 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
19958093 ATTTTTTAGC
*
19958103 AAATTTTAATT-AACCTCCT-AAAATTTTTAA
1 AAATTTTAATTAAACCT-CTGAAAAATTTTAA
*
19958133 AAATTATT-ATTAAACCTTTGAAAAATTTTAA
1 AAATT-TTAATTAAACCTCTGAAAAATTTTAA
19958164 AAATTT
1 AAATTT
19958170 CTATTAGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATTTTAATTAAACCTCTGAAAAATTTTAA
Found at i:19958470 original size:21 final size:22
Alignment explanation
Indices: 19958441--19958481 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19958431 TCTATTTAAA
* *
19958441 AATATAAATAT-TTATATATCT
1 AATAAAAATATATAATATATCT
19958462 AATAAAAATATATAATATAT
1 AATAAAAATATATAATATAT
19958482 TGTATGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAAAATATATAATATATCT
Found at i:19969574 original size:5 final size:5
Alignment explanation
Indices: 19969428--19969556 Score: 242
Period size: 5 Copynumber: 26.0 Consensus size: 5
19969418 ATAATAACTT
19969428 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
19969478 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
19969528 TATAA TATAA TATAA TAT-A TATAT TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA
19969557 GCTTTATAAA
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
4 4 0.03
5 117 0.97
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:19999101 original size:35 final size:35
Alignment explanation
Indices: 19999062--19999129 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
19999052 GCTATATCCT
*
19999062 TTTGCTAGAGTAGTCTCACTATCACAACAGATACC
1 TTTGCTAGAGTAGCCTCACTATCACAACAGATACC
*
19999097 TTTGCTAGAGTAGCCTCACTATCACAACGGATA
1 TTTGCTAGAGTAGCCTCACTATCACAACAGATA
19999130 GAAATAGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (35 bp):
TTTGCTAGAGTAGCCTCACTATCACAACAGATACC
Found at i:20002619 original size:85 final size:85
Alignment explanation
Indices: 20002476--20002644 Score: 311
Period size: 85 Copynumber: 2.0 Consensus size: 85
20002466 GTAGGTGTCG
*
20002476 AACAAACCATCAGATAAACCATTCAATATATGGCCCATGCACATGTAGTCAGCATTGTCCCATTT
1 AACAAACCATCAGATAAACCATTCAATATATGGCCCATGCACATGTAATCAGCATTGTCCCATTT
20002541 TTGTCTTTCTCGAGTTGCAA
66 TTGTCTTTCTCGAGTTGCAA
*
20002561 AACAAACCATCAGATAAACCATTCAATATGTGGCCCATGCACATGTAATCAGCATTGTCCCATTT
1 AACAAACCATCAGATAAACCATTCAATATATGGCCCATGCACATGTAATCAGCATTGTCCCATTT
*
20002626 TTGTCTTTCTCGGGTTGCA
66 TTGTCTTTCTCGAGTTGCA
20002645 GCAACAGATT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (85 bp):
AACAAACCATCAGATAAACCATTCAATATATGGCCCATGCACATGTAATCAGCATTGTCCCATTT
TTGTCTTTCTCGAGTTGCAA
Found at i:20005496 original size:22 final size:22
Alignment explanation
Indices: 20005471--20005539 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
20005461 TCTTTAATTA
*
20005471 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCTGT
*
20005493 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
20005515 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
20005537 TTA
1 TTA
20005540 ATAGTGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:20007044 original size:26 final size:27
Alignment explanation
Indices: 20006987--20007044 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
20006977 AGTATCTATT
*
20006987 TTTTTTGTCACAAGTGGTACCTAAATC
1 TTTTTTGTCACAAGTGGCACCTAAATC
* *
20007014 ATTTTT-TCCCAAGTTGGCACCTAAA-C
1 TTTTTTGTCACAAG-TGGCACCTAAATC
20007040 TTTTT
1 TTTTT
20007045 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (27 bp):
TTTTTTGTCACAAGTGGCACCTAAATC
Found at i:20012842 original size:21 final size:21
Alignment explanation
Indices: 20012816--20012857 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20012806 GATACCTAGT
20012816 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
*
20012837 AAAAGGTATCGGTACTTTTTG
1 AAAAGGTATCGATACTTTTTG
20012858 TAATTGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:20014320 original size:31 final size:32
Alignment explanation
Indices: 20014265--20014335 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
20014255 AGTTTGATGA
*
20014265 TATTTTA-TAATTATTTAATTAGATA-AATAT
1 TATTTTATTAATTATTTAATGAGATATAATAT
**
20014295 TATTTTATTAA-TATTTTAATGAGATATTTTAT
1 TATTTTATTAATTA-TTTAATGAGATATAATAT
20014327 TATTTTATT
1 TATTTTATT
20014336 TAGTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.26
31 14 0.40
32 12 0.34
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (32 bp):
TATTTTATTAATTATTTAATGAGATATAATAT
Found at i:20016409 original size:21 final size:21
Alignment explanation
Indices: 20016385--20016499 Score: 72
Period size: 21 Copynumber: 5.5 Consensus size: 21
20016375 TATTAACTCA
20016385 TATGAGTTTCAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * * *
20016406 TATGGATTTTC-GTTCAGCTCT
1 TAT-GAGTTTCAGTTTAACCCT
* *
20016427 TTTGATTTTCAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
* * * *
20016448 AATGGGTTTTC-GTTTAGCTCT
1 TATGAG-TTTCAGTTTAACCCT
* * *
20016469 TTTAAGCTTCAGTTTAACCCT
1 TATGAGTTTCAGTTTAACCCT
*
20016490 TATGGGTTTC
1 TATGAGTTTC
20016500 CATTCCGCTC
Statistics
Matches: 65, Mismatches: 25, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
20 10 0.15
21 45 0.69
22 10 0.15
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (21 bp):
TATGAGTTTCAGTTTAACCCT
Found at i:20016458 original size:42 final size:42
Alignment explanation
Indices: 20016389--20016498 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
20016379 AACTCATATG
* *
20016389 AGTTTCAGTTTAACCCTTATGGATTTTCGTTCAGCTCTTTTG
1 AGTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTCTTTTA
* * *
20016431 ATTTTCAGTTTAACCCTAATGGGTTTTCGTTTAGCTCTTTTA
1 AGTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTCTTTTA
*
20016473 AGCTTCAGTTTAACCCTTATGGGTTT
1 AGTTTCAGTTTAACCCTTATGGGTTT
20016499 CCATTCCGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (42 bp):
AGTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGCTCTTTTA
Found at i:20016519 original size:42 final size:42
Alignment explanation
Indices: 20016387--20016541 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 42
20016377 TTAACTCATA
* * *
20016387 TGAGTTTCAGTTTAACCCTTATGGATTTTCGTTCAGCTCTTT
1 TGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTT
** * * *
20016429 TGATTTTCAGTTTAACCCTAATGGGTTTTCGTTTAGCTCTTT
1 TGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTT
* * * *
20016471 TAAGCTTCAGTTTAACCCTTATGGGTTTCCATTCCGCTCTTA
1 TGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTT
* * * * *
20016513 CGAGCTTCCGCTCAACCCTTATAGGTTTC
1 TGAGCTTCAGTTTAACCCTTATGGGTTTC
20016542 TGCTTAGCAG
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 94 1.00
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.43
Consensus pattern (42 bp):
TGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCTTT
Found at i:20028408 original size:21 final size:20
Alignment explanation
Indices: 20028367--20028403 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
20028357 TTTATTGATG
20028367 AATATTTTATATAATTAATT
1 AATATTTTATATAATTAATT
*
20028387 AATATTTT-TATATTTAA
1 AATATTTTATATAATTAA
20028404 AATTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTATATAATTAATT
Found at i:20028454 original size:16 final size:17
Alignment explanation
Indices: 20028367--20028459 Score: 70
Period size: 16 Copynumber: 5.5 Consensus size: 17
20028357 TTTATTGATG
*
20028367 AATATTTTATATAATTAATT
1 AATATTTTATAT-ATT--TA
20028387 AATATTTT-TATATTTA
1 AATATTTTATATATTTA
20028403 AA-ATTATT-TA-ATTTGA
1 AATATT-TTATATATTT-A
** *
20028419 TTTATTTAATATATTTA
1 AATATTTTATATATTTA
20028436 AATATTTTATATA-TTA
1 AATATTTTATATATTTA
20028452 AATATTTT
1 AATATTTT
20028460 TTAAAAACGT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.11
16 20 0.33
17 16 0.26
18 7 0.11
19 3 0.05
20 8 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
AATATTTTATATATTTA
Found at i:20029947 original size:6 final size:6
Alignment explanation
Indices: 20029936--20029971 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
20029926 GTTGAATATA
20029936 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG
20029972 GCAGGCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
TGGCAG
Found at i:20031984 original size:3 final size:3
Alignment explanation
Indices: 20031970--20032014 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
20031960 AATTGATGCG
*
20031970 TTA TTG TTA TTA TTA TTA TTA TTA TTA TT- TTA TATA TTA GTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TT
20032015 TTTCATGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20034552 original size:9 final size:9
Alignment explanation
Indices: 20034538--20034574 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20034528 TATAGTTTGA
20034538 TATTCGAAT
1 TATTCGAAT
20034547 TATTCGAAT
1 TATTCGAAT
*
20034556 TATTCGAGT
1 TATTCGAAT
20034565 TATTCGAAT
1 TATTCGAAT
20034574 T
1 T
20034575 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20034763 original size:5 final size:5
Alignment explanation
Indices: 20034748--20034783 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
20034738 ATTTTTCATC
20034748 TTTTCA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
20034784 ATACTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:20042621 original size:18 final size:18
Alignment explanation
Indices: 20042600--20042662 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
20042590 ATAATAATTA
20042600 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
20042618 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
20042633 --TT-TTAAATTATATAT
1 TTTTATTAAATTATATAT
20042648 TTTTATTAAATTATA
1 TTTTATTAAATTATA
20042663 CATATACCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.13
13 3 0.08
14 4 0.10
16 4 0.10
17 3 0.08
18 20 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:20042641 original size:30 final size:31
Alignment explanation
Indices: 20042595--20042662 Score: 120
Period size: 30 Copynumber: 2.2 Consensus size: 31
20042585 TTTTAATAAT
*
20042595 AATTATTTTATTAAATTATATATTTTTATTA
1 AATTATATTATTAAATTATATATTTTTATTA
20042626 AATTATATT-TTAAATTATATATTTTTATTA
1 AATTATATTATTAAATTATATATTTTTATTA
20042656 AATTATA
1 AATTATA
20042663 CATATACCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
AATTATATTATTAAATTATATATTTTTATTA
Found at i:20042651 original size:15 final size:15
Alignment explanation
Indices: 20042605--20042652 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
20042595 AATTATTTTA
20042605 TTAAATTATATATTT
1 TTAAATTATATATTT
*
20042620 TT--ATTAAATTATATT
1 TTAAATTATA-TAT-TT
20042635 TTAAATTATATATTT
1 TTAAATTATATATTT
20042650 TTA
1 TTA
20042653 TTAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 5 0.19
14 3 0.11
15 11 0.41
16 3 0.11
17 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAATTATATATTT
Found at i:20044511 original size:11 final size:11
Alignment explanation
Indices: 20044495--20044520 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20044485 TAGAAGAGAC
20044495 GAAACAGGGGA
1 GAAACAGGGGA
20044506 GAAACAGGGGA
1 GAAACAGGGGA
20044517 GAAA
1 GAAA
20044521 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:20046218 original size:21 final size:21
Alignment explanation
Indices: 20046177--20046219 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
20046167 AATAAAGTAG
*
20046177 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
20046198 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
20046219 A
1 A
20046220 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:20046270 original size:18 final size:18
Alignment explanation
Indices: 20046247--20046282 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20046237 TTATATTGAA
20046247 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
20046265 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
20046283 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:20046277 original size:38 final size:38
Alignment explanation
Indices: 20046235--20046398 Score: 101
Period size: 38 Copynumber: 4.2 Consensus size: 38
20046225 ATATAAGAAT
20046235 AATTATATTGAATTTTATTAAATTATATATTTTTATTA
1 AATTATATTGAATTTTATTAAATTATATATTTTTATTA
20046273 AATTATATAT-AATAATAATTATTTTAAATTATAT-TTTATAGTATTA
1 AATTATAT-TGAAT--T--TTA--TTAAATTATATATTT-T--TATTA
* * * ** *
20046319 TA-TATAATG-ATTTTAGTAAATTCATATA---AGAAT-
1 AATTATATTGAATTTTATTAAATT-ATATATTTTTATTA
*
20046352 AATTATATTGAATTTTATTAAATTATATATTTTAATTA
1 AATTATATTGAATTTTATTAAATTATATATTTTTATTA
*
20046390 AATGATATT
1 AATTATATT
20046399 TGATAACAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 38
0.65 0.09 0.26
Matches are distributed among these distances:
33 1 0.01
34 13 0.14
35 12 0.13
37 2 0.02
38 25 0.27
39 5 0.05
40 4 0.04
42 4 0.04
43 3 0.03
44 15 0.16
45 4 0.04
46 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (38 bp):
AATTATATTGAATTTTATTAAATTATATATTTTTATTA
Found at i:20046323 original size:117 final size:116
Alignment explanation
Indices: 20046184--20046397 Score: 392
Period size: 117 Copynumber: 1.8 Consensus size: 116
20046174 TAGATTATAT
*
20046184 ATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
1 ATTATTTTTATAGTATTATATATAATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
* *
20046249 TTATTAAATTATATATTTTTATTAAATTATATATAATAATAATTATTTTAA
66 TTATTAAATTATATATTTTAATTAAATGATATATAATAATAATTATTTTAA
20046300 ATTATATTTTATAGTATTATATATAATGATTTTAGTAAATTCATATAAGAATAATTATATTGAAT
1 ATTAT-TTTTATAGTATTATATATAATGATTTTAGTAAATTCATATAAGAATAATTATATTGAAT
20046365 TTTATTAAATTATATATTTTAATTAAATGATAT
65 TTTATTAAATTATATATTTTAATTAAATGATAT
20046398 TTGATAACAA
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 5 0.05
117 89 0.95
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (116 bp):
ATTATTTTTATAGTATTATATATAATGATTTTAGTAAATTCATATAAGAATAATTATATTGAATT
TTATTAAATTATATATTTTAATTAAATGATATATAATAATAATTATTTTAA
Found at i:20046391 original size:18 final size:17
Alignment explanation
Indices: 20046363--20046397 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20046353 ATTATATTGA
*
20046363 ATTTTATTAAATTATAT
1 ATTTTATTAAATGATAT
20046380 ATTTTAATTAAATGATAT
1 ATTTT-ATTAAATGATAT
20046398 TTGATAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAATGATAT
Found at i:20049125 original size:16 final size:16
Alignment explanation
Indices: 20049104--20049135 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20049094 GGTTGGGACG
*
20049104 TTAGTTCCGTGTTTAC
1 TTAGTTCCATGTTTAC
20049120 TTAGTTCCATGTTTAC
1 TTAGTTCCATGTTTAC
20049136 ATTCTAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (16 bp):
TTAGTTCCATGTTTAC
Found at i:20049983 original size:9 final size:9
Alignment explanation
Indices: 20049969--20050017 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
20049959 TTTAGTTAAA
20049969 AATTAACCG
1 AATTAACCG
20049978 AATTAACCG
1 AATTAACCG
*
20049987 AATTACCCG
1 AATTAACCG
*
20049996 AATTACCCG
1 AATTAACCG
*
20050005 GATTAACCG
1 AATTAACCG
20050014 AATT
1 AATT
20050018 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:20050162 original size:18 final size:18
Alignment explanation
Indices: 20050139--20050182 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20050129 AATTTTTATG
*
20050139 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
20050157 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
20050175 CTTGGGTT
1 ATTGGGTT
20050183 TGGATTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.02, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:20050561 original size:15 final size:15
Alignment explanation
Indices: 20050541--20050572 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20050531 CATTTCACTA
*
20050541 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
20050556 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
20050571 TT
1 TT
20050573 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:20052224 original size:11 final size:11
Alignment explanation
Indices: 20052184--20052259 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
20052174 ATTCCAAAAA
*
20052184 TAATATTATTT
1 TAATATTAATT
20052195 TAATAGTTTAATAT
1 TAATA--TTAAT-T
20052209 TAATATTAATT
1 TAATATTAATT
20052220 TAATACTT-ATCT
1 TAATA-TTAAT-T
* *
20052232 TAATAGT-AGT
1 TAATATTAATT
20052242 T--TATTAATT
1 TAATATTAATT
20052251 TAATATTAA
1 TAATATTAA
20052260 AATAATTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 2 0.04
11 21 0.40
12 13 0.25
13 4 0.08
14 6 0.12
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:20059555 original size:11 final size:11
Alignment explanation
Indices: 20059539--20059563 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20059529 AAAACCATAA
20059539 ATAAATCAATC
1 ATAAATCAATC
20059550 ATAAATCAATC
1 ATAAATCAATC
20059561 ATA
1 ATA
20059564 GTTAACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAATCAATC
Found at i:20059910 original size:42 final size:42
Alignment explanation
Indices: 20059851--20060044 Score: 232
Period size: 42 Copynumber: 4.6 Consensus size: 42
20059841 CAGCGTTTAC
*
20059851 GAAAATAAACGCC-CTAAAGGTCATGTTCTTTAGCGGCACTTA
1 GAAAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTA
* *
20059893 GAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTA
* * * *
20059935 AAAAAAAGACGTCGCTAAAGATCATGTTCTTTAGCGGCGC-TC
1 GAAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTA
*
20059977 GAAGAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCACTT-
1 GAA-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTA
* * *
20060019 GATAAAAAACTCCGCTATAGAACATG
1 GA-AAAAAACGCCGCTAAAGATCATG
20060045 ACTTTTAGCG
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
41 6 0.05
42 90 0.68
43 36 0.27
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTA
Found at i:20059955 original size:43 final size:42
Alignment explanation
Indices: 20059852--20060103 Score: 231
Period size: 42 Copynumber: 6.0 Consensus size: 42
20059842 AGCGTTTACG
* * *
20059852 AAAATAAACGCC-CTAAAGGTCATGTTCTTTAGCGGCACTTA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
* *
20059893 GAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
* **
20059935 AAAAAAAGACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTCG
1 AAAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
* * * *
20059978 AAGAAAAACGCCGCAAAAGATCATGTTCTTTAGCGGCACTTG
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
* * * * * * *
20060020 ATAAAAAACTCCGCTATAGAACATG-ACTTTTAGCGACGCTTTC
1 AAAAAAAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGC-TTA
*** * *
20060063 TTCACAAACGCCGCTAAAAGA-AATGTTCTTTAGCGGCGCTT
1 AAAAAAAACGCCGCT-AAAGATCATGTTCTTTAGCGGCGCTT
20060104 TCATCACAAA
Statistics
Matches: 172, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
41 10 0.06
42 94 0.55
43 63 0.37
44 5 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
Done.