Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 52 of 203
Found at i:17022017 original size:30 final size:29
Alignment explanation
Indices: 17021969--17022032 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
17021959 AAATTTTATA
*
17021969 ATTT-AAATTTAACATTTAAT-TGTTCAAT
1 ATTTAAAATTTAACATTTAATATG-TCAAC
*
17021997 ATTTAAAATTTTAGCATTTAATATGTCAAC
1 ATTTAAAA-TTTAACATTTAATATGTCAAC
17022027 ATTTAA
1 ATTTAA
17022033 TTTTTCAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.13
29 3 0.10
30 22 0.71
31 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (29 bp):
ATTTAAAATTTAACATTTAATATGTCAAC
Found at i:17025104 original size:51 final size:52
Alignment explanation
Indices: 17025024--17025126 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 52
17025014 GAAATCATCA
* *
17025024 TATAAGGTATTATATCTTTTTTATACATCGAAACAAAGGCATGATATTGCAC
1 TATAAGGTATAATATCTTTTTCATACATCGAAACAAAGGCATGATATTGCAC
* * * *
17025076 TATAAGGT-TAATGTCTTTTTCATGCATCGAGACAAAGGCGTGATATTGCAC
1 TATAAGGTATAATATCTTTTTCATACATCGAAACAAAGGCATGATATTGCAC
17025127 GTGGTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
51 37 0.82
52 8 0.18
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (52 bp):
TATAAGGTATAATATCTTTTTCATACATCGAAACAAAGGCATGATATTGCAC
Found at i:17027195 original size:3 final size:3
Alignment explanation
Indices: 17027187--17027227 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17027177 GTGGGGAGAG
17027187 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
17027228 GCAAGGACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:17027943 original size:24 final size:23
Alignment explanation
Indices: 17027887--17027946 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
17027877 TGTGCTGTCC
*
17027887 CATCAATTTTTTTTTTGTTTTTT
1 CATCAATTTTTTTATTGTTTTTT
* *
17027910 CATTAGTTTTATTTATTGTTTTTT
1 CATCAATTTT-TTTATTGTTTTTT
17027934 CATCAATTTTTTT
1 CATCAATTTTTTT
17027947 TTTATGTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (23 bp):
CATCAATTTTTTTATTGTTTTTT
Found at i:17033333 original size:3 final size:3
Alignment explanation
Indices: 17033325--17033350 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17033315 AACAAATAGG
17033325 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
17033351 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17039625 original size:110 final size:109
Alignment explanation
Indices: 17039400--17039730 Score: 608
Period size: 110 Copynumber: 3.0 Consensus size: 109
17039390 ACAAGGTGAA
17039400 TCACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
1 TCACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
* *
17039465 ATTACAAAAGTCCTCCCCTCCTTTTTTTTGTTTCTCTTTTTTTT
66 GTTACAAAAGTCCCCCCCTCCTTTTTTTTGTTTCTCTTTTTTTT
*
17039509 TTACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
1 TCACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
17039574 GTTACAAAAGTCCCCCCCTCCTTTTTTTTTGTTTCTCTTTTTTTT
66 GTTACAAAAGTCCCCCCCTCC-TTTTTTTTGTTTCTCTTTTTTTT
*
17039619 TCACCTTCTAAAGCCCCTTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
1 TCACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTC-TTTTT
17039684 TGTTACAAAAGTCCCCCCCTCCTTTTTTTTGTTTCTCTTTTTTTT
65 TGTTACAAAAGTCCCCCCCTCCTTTTTTTTGTTTCTCTTTTTTTT
17039729 TC
1 TC
17039731 CCCTGGTGCG
Statistics
Matches: 215, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
109 83 0.39
110 105 0.49
111 27 0.13
ACGTcount: A:0.17, C:0.26, G:0.05, T:0.53
Consensus pattern (109 bp):
TCACCTTCTAAAGCCCCCTTTTTTATTTCTTTCAATTTTTTCAAAAGCCGAATCTTCTCTTTTTT
GTTACAAAAGTCCCCCCCTCCTTTTTTTTGTTTCTCTTTTTTTT
Found at i:17044438 original size:166 final size:164
Alignment explanation
Indices: 17044034--17044472 Score: 567
Period size: 166 Copynumber: 2.6 Consensus size: 164
17044024 CATGACAGCA
* *
17044034 TCTCTCTACGTAATGCATACATGATGGAATCACATGATTACTAAACCTTAAA-CTTCCGCGGGTT
1 TCTCTCTACGTAATGCATGCATGATGGAATCACATGATTGCTAAACCTTAAATCTT--GCGGG-T
* * *
17044098 GTA-TTCAAAGAAGTAATTCGTTGATCATGAAATATGTTTCAGTTTTATAGGTGGAGATTGAACC
63 G-ACTTCAAAGAAGTAATTCGTTGATCATGAAATATGTTTCAGTCTCATAGGTGGAAATTGAACC
* *
17044162 CTCAACCACGTGAATAAAGGATAAAGTGAGTAATTATC
127 CTCAACCACGTAAATAAAGGATAAAGTGAGTAAGTATC
* * * *
17044200 TCTCTCTACGTAATGTATGCATGATGGAATCACATGATTGCTAAACCTTAAATTCTCGTGGATGG
1 TCTCTCTACGTAATGCATGCATGATGGAATCACATGATTGCTAAACCTTAAA-TCTTGCGGGT-G
* * * * *
17044265 TCTTCAAAGAAGTAATTCGTTAATCATAAAATATGTTTTAGTCTCATAGGTGGAAATTTAACCCT
64 ACTTCAAAGAAGTAATTCGTTGATCATGAAATATGTTTCAGTCTCATAGGTGGAAATTGAACCCT
* * *
17044330 CAACCATGTAAATGAAGGATGAAGTGAGTAAGTATC
129 CAACCACGTAAATAAAGGATAAAGTGAGTAAGTATC
* *
17044366 TCTCTCTCCTTAATGCATGCATGATGGAATCACATGATTGCTAAACCTTAAATCCTTGCGGGTGA
1 TCTCTCTACGTAATGCATGCATGATGGAATCACATGATTGCTAAACCTTAAAT-CTTGCGGGTGA
* * * *
17044431 CCTTCAAAAAAATAACTCGTTGATCATGAAATATATTTCAGT
65 -CTTCAAAGAAGTAATTCGTTGATCATGAAATATGTTTCAGT
17044473 GAAATTTAAC
Statistics
Matches: 234, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
165 3 0.01
166 229 0.98
168 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (164 bp):
TCTCTCTACGTAATGCATGCATGATGGAATCACATGATTGCTAAACCTTAAATCTTGCGGGTGAC
TTCAAAGAAGTAATTCGTTGATCATGAAATATGTTTCAGTCTCATAGGTGGAAATTGAACCCTCA
ACCACGTAAATAAAGGATAAAGTGAGTAAGTATC
Found at i:17057917 original size:31 final size:31
Alignment explanation
Indices: 17057863--17057957 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
17057853 CATACTATTC
* *
17057863 GGCACTTGAGTTTGG-TTCAATGTTCAATTT
1 GGCACCTGAATTTGGCTTCAATGTTCAATTT
* *
17057893 GGCCCCTGAATTTGGCTTCCATGTTCAATTT
1 GGCACCTGAATTTGGCTTCAATGTTCAATTT
* * *
17057924 GGTACCTGAATTTAGCTTTAATGTTCAATTT
1 GGCACCTGAATTTGGCTTCAATGTTCAATTT
17057955 GGC
1 GGC
17057958 TTCAATTTGG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 12 0.22
31 42 0.78
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (31 bp):
GGCACCTGAATTTGGCTTCAATGTTCAATTT
Found at i:17058241 original size:31 final size:30
Alignment explanation
Indices: 17058204--17058282 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
17058194 GGGGGGAAAA
*
17058204 AAACTCAGCTGCCAAATTAAACATGGAAGCC
1 AAACTCAG-TACCAAATTAAACATGGAAGCC
* * *
17058235 AAACTCAAGTACCAAATTGAACATTGAAGCT
1 AAACTC-AGTACCAAATTAAACATGGAAGCC
*
17058266 AAACTCAGGTATCAAAT
1 AAACTCA-GTACCAAAT
17058283 GGTATATGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 38 0.93
32 2 0.05
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (30 bp):
AAACTCAGTACCAAATTAAACATGGAAGCC
Found at i:17061370 original size:30 final size:30
Alignment explanation
Indices: 17061331--17061387 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17061321 TTTTATAAAT
17061331 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
17061361 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
17061388 AACAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:17061983 original size:25 final size:25
Alignment explanation
Indices: 17061914--17061983 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
17061904 TCTTGCCCAC
17061914 ATTATTTTAAATTT-TTTTTAAAAATA
1 ATTATTTT--ATTTATTTTTAAAAATA
* * ** **
17061940 TTTATATTATTTAAATTTAAATTTA
1 ATTATTTTATTTATTTTTAAAAATA
17061965 ATTATTTTATTTATTTTTA
1 ATTATTTTATTTATTTTTA
17061984 TATAGTCATC
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
24 4 0.12
25 23 0.70
26 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTATTTTATTTATTTTTAAAAATA
Found at i:17065038 original size:19 final size:20
Alignment explanation
Indices: 17065014--17065055 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17065004 ACGGATAGAA
17065014 TTTTGTTCTCGA-GTTAGGG
1 TTTTGTTCTCGAGGTTAGGG
* *
17065033 TTTTGTTTTCGAGGTTTGGG
1 TTTTGTTCTCGAGGTTAGGG
17065053 TTT
1 TTT
17065056 GTACGTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.07, C:0.07, G:0.31, T:0.55
Consensus pattern (20 bp):
TTTTGTTCTCGAGGTTAGGG
Found at i:17075890 original size:13 final size:13
Alignment explanation
Indices: 17075853--17075890 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17075843 AAGAAACAAA
17075853 TTTGATTGATTCTT
1 TTTGATTGATT-TT
*
17075867 TTT-ATTTATTTT
1 TTTGATTGATTTT
17075879 TTTGATTGATTT
1 TTTGATTGATTT
17075891 GAATTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 13 0.62
14 3 0.14
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.71
Consensus pattern (13 bp):
TTTGATTGATTTT
Found at i:17076208 original size:28 final size:30
Alignment explanation
Indices: 17076163--17076225 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 30
17076153 CAAAGTTTTA
* *
17076163 ATTTTAATTTTTATAAT-A-TAAAAATAAAT
1 ATTTTAATATTTAAAATAACTAAAAAT-AAT
17076192 ATTTT-ATATTTAAAATAACTTAAAAATAAT
1 ATTTTAATATTTAAAATAAC-TAAAAATAAT
17076222 ATTT
1 ATTT
17076226 AAAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 9 0.31
29 6 0.21
30 7 0.24
31 7 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTTAATATTTAAAATAACTAAAAATAAT
Found at i:17076398 original size:20 final size:20
Alignment explanation
Indices: 17076373--17076412 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17076363 CAACAAAGAT
17076373 GTTTAACTTTATTCATCAAA
1 GTTTAACTTTATTCATCAAA
17076393 GTTTAACTTTATTCATCAAA
1 GTTTAACTTTATTCATCAAA
17076413 TGACTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
GTTTAACTTTATTCATCAAA
Found at i:17076673 original size:21 final size:21
Alignment explanation
Indices: 17076631--17076675 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17076621 TCTTTTGAAA
**
17076631 TTTTATAAAATTTTTATATAT
1 TTTTATAAAATTTGAATATAT
* *
17076652 TTTTTTAAAATTTGAATTTAT
1 TTTTATAAAATTTGAATATAT
17076673 TTT
1 TTT
17076676 ATTTTTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATAAAATTTGAATATAT
Found at i:17082694 original size:28 final size:27
Alignment explanation
Indices: 17082653--17082705 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17082643 GAGGGGTTGA
* *
17082653 GGATTAGGGGTTTTAGATTGGAATTTGG
1 GGATTAGGGCTTTTAAATT-GAATTTGG
*
17082681 GGATTTGGGCTTTTAAATTGAATTT
1 GGATTAGGGCTTTTAAATTGAATTT
17082706 TAGGGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (27 bp):
GGATTAGGGCTTTTAAATTGAATTTGG
Found at i:17084995 original size:6 final size:6
Alignment explanation
Indices: 17084984--17085010 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17084974 CAAGTAATAT
17084984 CCTAAG CCTAAG CCTAAG CCTAAG CCT
1 CCTAAG CCTAAG CCTAAG CCTAAG CCT
17085011 TGTCAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.19
Consensus pattern (6 bp):
CCTAAG
Found at i:17093141 original size:12 final size:11
Alignment explanation
Indices: 17093124--17093153 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17093114 TTTTATTTTT
17093124 TATTTTTAAAA
1 TATTTTTAAAA
*
17093135 TACTTTTAAAA
1 TATTTTTAAAA
17093146 TATTTTTA
1 TATTTTTA
17093154 TTTTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:17093190 original size:29 final size:26
Alignment explanation
Indices: 17093138--17093191 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
17093128 TTTAAAATAC
*
17093138 TTTTAAAATATTTTTATTTTTATTAT
1 TTTTAAAATATTTTTATGTTTATTAT
17093164 TTTTAAAATAATTTTTTAATGTTTATTA
1 TTTTAAAAT-A-TTTTT-ATGTTTATTA
17093192 AAAAATAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
28 5 0.21
29 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAAAATATTTTTATGTTTATTAT
Found at i:17093260 original size:13 final size:13
Alignment explanation
Indices: 17093242--17093269 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17093232 TTTCCTGGGC
17093242 TGGTGAATCCGGT
1 TGGTGAATCCGGT
17093255 TGGTGAATCCGGT
1 TGGTGAATCCGGT
17093268 TG
1 TG
17093270 AAGACTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.32
Consensus pattern (13 bp):
TGGTGAATCCGGT
Found at i:17097119 original size:144 final size:140
Alignment explanation
Indices: 17096860--17097330 Score: 592
Period size: 144 Copynumber: 3.4 Consensus size: 140
17096850 AGAAAAAACC
* * *
17096860 CTTTCAAATGCAAAACAATATAAGGGTTCTAGCCCGGCTTTGCGCCCTTAACAACACTAGTTGTG
1 CTTTCGAATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCGCCCTTAACAACACTAGTTGTG
* * * *
17096925 ACATTGCCTAATGAATTTAGCTTTAGTACAAAAATGTCCCGAACCCTTTCAAGTGAGAAACACTC
66 ACATTGCCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAA-TGAGAGACACTC
17096990 ACAAGAAAGAAAT
130 ACAA-AAA-AAAT
* * *
17097003 CCTTTCGAATGCAAGACAATATTAGGGTTCTAGCTCGGCTTTGCTCCCTTAACAACACCAGTTGT
1 -CTTTCGAATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCGCCCTTAACAACACTAGTTGT
* * *
17097068 GACATTGCCTAGTGAATTTAGCTCTAGTACAAAAATATCTCGAACCCTTTCAAATGAGAGAGACA
65 GACATTGCCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTC-AATGAGAGACACT
17097133 CAC-AAAAAAA-
129 CACAAAAAAAAT
* * * * *
17097143 --TTCGAATGCAAGACAATATAAGGGTTCTAGCTTGGTTTTGCACCTTTAACAACACTAGTTTTG
1 CTTTCGAATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCGCCCTTAACAACACTAGTTGTG
* * * *
17097206 CCATTGCCTAGTGAATTTAGCTCTACTACAAAAATGTCTTGAACCCTTTCGAATAAGAGACACAT
66 ACATTGCCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTC-AATGAGAGACAC-T
**
17097271 -ACAAAAAACCT
129 CACAAAAAAAAT
* * * *
17097282 CTTTCGAATGCAAGATAATTTAAGGGTTTTAGCTTGGCTTTGCGCCCTT
1 CTTTCGAATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCGCCCTT
17097331 TCTGCTAGAG
Statistics
Matches: 285, Mismatches: 36, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
137 114 0.40
138 5 0.02
141 44 0.15
142 3 0.01
143 1 0.00
144 116 0.41
145 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (140 bp):
CTTTCGAATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCGCCCTTAACAACACTAGTTGTG
ACATTGCCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAATGAGAGACACTCA
CAAAAAAAAT
Found at i:17097222 original size:137 final size:137
Alignment explanation
Indices: 17096866--17097330 Score: 561
Period size: 137 Copynumber: 3.3 Consensus size: 137
17096856 AACCCTTTCA
* * *
17096866 AATGCAAAACAATATAAGGGTTCTAGCCCGGCTTTGCGCCCTTAACAACACTAGTTGTGACATTG
1 AATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCACCCTTAACAACACTAGTTGTGACATTG
* * * * * *
17096931 CCTAATGAATTTAGCTTTAGTACAAAAATGTCCCGAACCCTTTCAAGTGAGAAACACTCACAAGA
66 CCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAAATGAGAGACACACAC-A-A
17096996 AAGAAATCCTTTCG
129 AA-AAA----TTCG
* * *
17097010 AATGCAAGACAATATTAGGGTTCTAGCTCGGCTTTGCTCCCTTAACAACACCAGTTGTGACATTG
1 AATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCACCCTTAACAACACTAGTTGTGACATTG
* *
17097075 CCTAGTGAATTTAGCTCTAGTACAAAAATATCTCGAACCCTTTCAAATGAGAGAGACACACAAAA
66 CCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAAATGAGAGACACACACAAAA
17097140 AAATTCG
131 AAATTCG
* * * * *
17097147 AATGCAAGACAATATAAGGGTTCTAGCTTGGTTTTGCACCTTTAACAACACTAGTTTTGCCATTG
1 AATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCACCCTTAACAACACTAGTTGTGACATTG
* * * * *
17097212 CCTAGTGAATTTAGCTCTACTACAAAAATGTCTTGAACCCTTTCGAATAAGAGACACATACAAAA
66 CCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAAATGAGAGACACACACAAAA
*
17097277 AACCTCTTTCG
131 AA----ATTCG
* * * * *
17097288 AATGCAAGATAATTTAAGGGTTTTAGCTTGGCTTTGCGCCCTT
1 AATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCACCCTT
17097331 TCTGCTAGAG
Statistics
Matches: 282, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
137 121 0.43
141 44 0.16
142 3 0.01
143 1 0.00
144 113 0.40
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (137 bp):
AATGCAAGACAATATAAGGGTTCTAGCTCGGCTTTGCACCCTTAACAACACTAGTTGTGACATTG
CCTAGTGAATTTAGCTCTAGTACAAAAATGTCTCGAACCCTTTCAAATGAGAGACACACACAAAA
AAATTCG
Found at i:17113022 original size:7 final size:7
Alignment explanation
Indices: 17113010--17113034 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17113000 AAAAACTTTC
17113010 AAAAAAT
1 AAAAAAT
17113017 AAAAAAT
1 AAAAAAT
17113024 AAAAAAT
1 AAAAAAT
17113031 AAAA
1 AAAA
17113035 TAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:17116291 original size:22 final size:21
Alignment explanation
Indices: 17116266--17116307 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
17116256 ATAATTAATT
*
17116266 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
17116288 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
17116308 TAGAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:17136467 original size:231 final size:232
Alignment explanation
Indices: 17136059--17136529 Score: 649
Period size: 231 Copynumber: 2.0 Consensus size: 232
17136049 CAGGTTCTTC
* * *
17136059 TTCTTCGACCTTTTGCAACAGAGTCTTGACTTGACTCCTTAGTAATGCCTCACCAGAACCAGGGG
1 TTCTTCGACCTTTTGCAACAGAGTCTTGACCTGACCCCTTAGTAATGCCTCACCAGAACCAGGAG
*
17136124 TCATCATCTTCATCATTTTATTGGCTCTCCATTGCTTAGATGTTTCAGACAATGGTGTCCCCATC
66 TCATCA--TTCATCATTTTATTGGCTCTCCATTGCTTAGATGTTTCAGACAATGGCGTCCCCATC
* ** * * * * *
17136189 GCAAGCCCGATGATAGGCGAATCGTTCCTTACATCGATAAGGGCAGACCTTTCTTGTTGCTGCTG
129 GCAAGCCCAACAATAGGAGAATCATTCCTTACATCAATAAGGGCAGACCTTTCTTCTTGCTGCTC
* * * * *
17136254 CTTTTCATTTCTTGTTTTCAAGATACTCTTCTTCTCCGA
194 CTTTCCATTTCTTGTTTGCAACACACTCTTCTTCTCAGA
* * *
17136293 TTCTTCGTCTTTTTGGAACAGAGTCTTGACCTGACCCCTTAGTAATGCCTCACCAGAACCAGGAG
1 TTCTTCGACCTTTTGCAACAGAGTCTTGACCTGACCCCTTAGTAATGCCTCACCAGAACCAGGAG
* * * *
17136358 TCATCA-TCATCATTTTCTTGGGTCTCCATTGCTTAGATGTATT-TGACGATGGCGTCCCCATCG
66 TCATCATTCATCATTTTATTGGCTCTCCATTGCTTAGATGT-TTCAGACAATGGCGTCCCCATCG
* * * *
17136421 CAAGCCCAACAATAGGAGAATCATTCGTTATATCAATAAGGGCAGACCTTTCTTCTTGTTTCTCC
130 CAAGCCCAACAATAGGAGAATCATTCCTTACATCAATAAGGGCAGACCTTTCTTCTTGCTGCTCC
17136486 TTTCCATTTCTTGTTTGCAACACACTCTTCTTCTCAGA
195 TTTCCATTTCTTGTTTGCAACACACTCTTCTTCTCAGA
17136524 TTCTTC
1 TTCTTC
17136530 TAAAAAAAAT
Statistics
Matches: 208, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
231 141 0.68
232 2 0.01
234 65 0.31
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (232 bp):
TTCTTCGACCTTTTGCAACAGAGTCTTGACCTGACCCCTTAGTAATGCCTCACCAGAACCAGGAG
TCATCATTCATCATTTTATTGGCTCTCCATTGCTTAGATGTTTCAGACAATGGCGTCCCCATCGC
AAGCCCAACAATAGGAGAATCATTCCTTACATCAATAAGGGCAGACCTTTCTTCTTGCTGCTCCT
TTCCATTTCTTGTTTGCAACACACTCTTCTTCTCAGA
Found at i:17142272 original size:21 final size:21
Alignment explanation
Indices: 17142248--17142304 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
17142238 AGGTTTGGGA
* *
17142248 TTCAGGGTTTGGGGTTCGAGG
1 TTCAGGGTCTAGGGTTCGAGG
17142269 TTCAGGGTCTAGGGTTCGA-G
1 TTCAGGGTCTAGGGTTCGAGG
17142289 TTCTA-GGT-TAGGGTTC
1 TTC-AGGGTCTAGGGTTC
17142305 AGGATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 18 0.55
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.35
Consensus pattern (21 bp):
TTCAGGGTCTAGGGTTCGAGG
Found at i:17157142 original size:4 final size:4
Alignment explanation
Indices: 17157133--17157191 Score: 91
Period size: 4 Copynumber: 14.8 Consensus size: 4
17157123 TCTAATTCTA
* * *
17157133 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
17157181 ATAC ATAC ATA
1 ATAC ATAC ATA
17157192 TGACATGACA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:17162090 original size:5 final size:5
Alignment explanation
Indices: 17162080--17162108 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
17162070 TTATTAAGTA
17162080 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
17162109 ATAAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:17163115 original size:37 final size:40
Alignment explanation
Indices: 17163020--17163154 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
17163010 AACTTCGAGT
*
17163020 CGATGAGACACTGGGTGTCAATTTACTACTTCGAATTAATT
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCGAATTAATC
* * **
17163061 CGATGACACATTGGGTGTCAA-TT-TACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTATACTTCGAATTAATC
* *
17163098 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCGAATTAATC
* *
17163138 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
17163155 CCAAACTGGT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 18 0.23
38 13 0.17
39 1 0.01
40 26 0.34
41 19 0.25
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATACTTCGAATTAATC
Found at i:17164262 original size:11 final size:11
Alignment explanation
Indices: 17164248--17164277 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17164238 TTTTTTATTG
17164248 TTATTTTGCTA
1 TTATTTTGCTA
*
17164259 TTATATTGCTA
1 TTATTTTGCTA
17164270 TTATTTTG
1 TTATTTTG
17164278 TTGCTGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (11 bp):
TTATTTTGCTA
Found at i:17165192 original size:5 final size:5
Alignment explanation
Indices: 17165182--17165217 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
17165172 AAAAGGTAGA
17165182 AAAAT AAAAT AAAAT --AAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
17165218 TTTTTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
5 26 0.90
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17165202 original size:13 final size:13
Alignment explanation
Indices: 17165184--17165211 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17165174 AAGGTAGAAA
17165184 AATAAAATAAAAT
1 AATAAAATAAAAT
17165197 AATAAAATAAAAT
1 AATAAAATAAAAT
17165210 AA
1 AA
17165212 AATAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:17165205 original size:18 final size:18
Alignment explanation
Indices: 17165182--17165216 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17165172 AAAAGGTAGA
17165182 AAAATAAAATAAAATAAT
1 AAAATAAAATAAAATAAT
17165200 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
17165217 ATTTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAATAAAATAAT
Found at i:17173098 original size:16 final size:15
Alignment explanation
Indices: 17173054--17173105 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
17173044 ATTTTAAAAA
17173054 AATATATTT-ATATTAT
1 AATAT-TTTAATATT-T
*
17173070 ATTATTTTAATATTT
1 AATATTTTAATATTT
*
17173085 AATATTTAATATATTT
1 AATATTTTA-ATATTT
17173101 AATAT
1 AATAT
17173106 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATATTTTAATATTT
Found at i:17177874 original size:198 final size:198
Alignment explanation
Indices: 17177536--17177936 Score: 730
Period size: 198 Copynumber: 2.0 Consensus size: 198
17177526 AGTTGACATT
* * *
17177536 TAAAACCCATTTAGACTGCCACGTAGGATTGCCGCTAGGGAGGTAACGGAGTTTAATGGTAGAGT
1 TAAAACCCATTTAGACTGACACGTAGGATTGCAGCTAGGAAGGTAACGGAGTTTAATGGTAGAGT
**
17177601 GATTACTTCGTAACAAAACGATAACGTAAGTGACTAAAATGTAATCTGAGACAAACAAAAGTAAC
66 GACCACTTCGTAACAAAACGATAACGTAAGTGACTAAAATGTAATCTGAGACAAACAAAAGTAAC
17177666 TTTTTGTAGCTTACCCATTTTTATATTTATCAAGTTTAGGGATCAAAATGGATTTAATCGTTTAA
131 TTTTTGTAGCTTACCCATTTTTATATTTATCAAGTTTAGGGATCAAAATGGATTTAATCGTTTAA
*
17177731 GTA
196 ATA
17177734 TAAAACCCATTTAGACTGACACGTAGGATTGCAGCTAGGAAGGTAACGGAGTTTAATGGTAGAGT
1 TAAAACCCATTTAGACTGACACGTAGGATTGCAGCTAGGAAGGTAACGGAGTTTAATGGTAGAGT
* *
17177799 GACCACTTCGTAACAAAACGATAACGTAAGTGACTAAAATGTAATCTGAGGCAAATAAAAGTAAC
66 GACCACTTCGTAACAAAACGATAACGTAAGTGACTAAAATGTAATCTGAGACAAACAAAAGTAAC
17177864 TTTTTGTAGCTTACCCATTTTTATATTTATCAAGTTTAGGGATCAAAATGGATTTAATCGTTTAA
131 TTTTTGTAGCTTACCCATTTTTATATTTATCAAGTTTAGGGATCAAAATGGATTTAATCGTTTAA
17177929 ATA
196 ATA
17177932 TAAAA
1 TAAAA
17177937 AAAAAGTGTA
Statistics
Matches: 195, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 195 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (198 bp):
TAAAACCCATTTAGACTGACACGTAGGATTGCAGCTAGGAAGGTAACGGAGTTTAATGGTAGAGT
GACCACTTCGTAACAAAACGATAACGTAAGTGACTAAAATGTAATCTGAGACAAACAAAAGTAAC
TTTTTGTAGCTTACCCATTTTTATATTTATCAAGTTTAGGGATCAAAATGGATTTAATCGTTTAA
ATA
Found at i:17178273 original size:17 final size:18
Alignment explanation
Indices: 17178237--17178271 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17178227 TACACATTGA
17178237 GTAATTTGGTTTTTTTTT
1 GTAATTTGGTTTTTTTTT
17178255 GTAATTTGGTTTTTTTT
1 GTAATTTGGTTTTTTTT
17178272 GTGAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.17, T:0.71
Consensus pattern (18 bp):
GTAATTTGGTTTTTTTTT
Found at i:17178279 original size:19 final size:18
Alignment explanation
Indices: 17178239--17178279 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
17178229 CACATTGAGT
*
17178239 AATTTGGTTTTTTTTTGT
1 AATTTGGTTTTTTTTTGA
17178257 AATTTGGTTTTTTTTGTGA
1 AATTTGGTTTTTTTT-TGA
17178276 AATT
1 AATT
17178280 AAGGGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (18 bp):
AATTTGGTTTTTTTTTGA
Found at i:17178644 original size:47 final size:46
Alignment explanation
Indices: 17178564--17178657 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 46
17178554 ACGTGACTAG
**
17178564 AAAAGACAAAATTAAATAGTTGGGTGATCATTTTGTAACCTTTTCAT
1 AAAAGACAAAATTAAATAGTTGAATGATCATTTTGTAA-CTTTTCAT
17178611 AAAAGACAAAATTAAATAGTTGAATGA-CTATTTTGTAACTTTTCAT
1 AAAAGACAAAATTAAATAGTTGAATGATC-ATTTTGTAACTTTTCAT
17178657 A
1 A
17178658 GTTTGGTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 10 0.23
47 34 0.77
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (46 bp):
AAAAGACAAAATTAAATAGTTGAATGATCATTTTGTAACTTTTCAT
Found at i:17184593 original size:34 final size:34
Alignment explanation
Indices: 17184555--17184649 Score: 90
Period size: 33 Copynumber: 2.8 Consensus size: 34
17184545 AAAAATATTT
17184555 ATAAAATTAAAATATATAATAAGTTTTT-ATAGAA
1 ATAAAATTAAAATATATAATAAGTTTTTAAT-GAA
* * *
17184589 ATAAAA-AAATAAT-TATAATAATTTTTTAATTAA
1 ATAAAATTAA-AATATATAATAAGTTTTTAATGAA
17184622 A-AAAATTAAAAAATTATATAATAAGTTT
1 ATAAAATT--AAAA-TATATAATAAGTTT
17184650 AATTTTGCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
32 4 0.08
33 18 0.37
34 13 0.27
35 3 0.06
36 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (34 bp):
ATAAAATTAAAATATATAATAAGTTTTTAATGAA
Found at i:17184651 original size:34 final size:34
Alignment explanation
Indices: 17184563--17184653 Score: 89
Period size: 37 Copynumber: 2.7 Consensus size: 34
17184553 TTATAAAATT
* *
17184563 AAAA-TATATAATAAGTTT--TTATAGAAATAAA
1 AAAATTATATAATAAGTTTAATTAAAAAAATAAA
* * *
17184594 AAAATAATTATAATAATTTTTTAATTAAAAAAATTAA
1 AAAATTA-TATAATAA--GTTTAATTAAAAAAATAAA
17184631 AAAATTATATAATAAGTTTAATT
1 AAAATTATATAATAAGTTTAATT
17184654 TTGCCAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 4 0.09
32 1 0.02
33 8 0.17
34 7 0.15
35 3 0.06
36 8 0.17
37 16 0.34
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (34 bp):
AAAATTATATAATAAGTTTAATTAAAAAAATAAA
Found at i:17189442 original size:163 final size:164
Alignment explanation
Indices: 17188958--17189573 Score: 810
Period size: 164 Copynumber: 3.7 Consensus size: 164
17188948 AACGTTGACG
* * * * * ** * *
17188958 ACTTAGACGTATGTTGATGTAAGGACGTAAGTTTTGAGTCT-AGGACGGCAAGATGCCGGAGCTA
1 ACTTAGACATACGTTGACGTAAGGACGGAAGTTTTGAGCCTAAGG-CCACATGATACCGGAGCTA
* * * * * *
17189022 AAGTCTCT-TCCATTCTCATGCAACGGACGGGCAAGTTTCGAGTACTCTTTAATAAAGGTAGGAA
65 AAGTCTCTGT-CATGCTCATGTAACGGA----CAAGTTTCGAGTACTCATCAATAAATGTAAGAA
* *
17189086 AATCAGCGTTACACATTAGAAAAAGTTGCATATACATATA
125 AATCAACTTTACACATTAGAAAAAGTTGCATATACATATA
* * *
17189126 ACTTAGACATACCTTAACGTAAGGACGGAAGTTTTGAGCCTAAGGCCACATGATACCGGAACTAA
1 ACTTAGACATACGTTGACGTAAGGACGGAAGTTTTGAGCCTAAGGCCACATGATACCGGAGCTAA
*
17189191 AGTCTCTGTCATGCTCATGTAACGGACAAGTTTCGAGTACTCGTCAATAAATGTAAGAAAATC-A
66 AGTCTCTGTCATGCTCATGTAACGGACAAGTTTCGAGTACTCATCAATAAATGTAAGAAAATCAA
* * *
17189255 GTGTTACACATTAGAACAAGTTGCATATACATAAA
131 CT-TTACACATTAGAAAAAGTTGCATATACATATA
*
17189290 ACTTAGACATACGTTGACGTAAGGACGGGAGTTTTGAGCCTAAGGCCACATGATACCGGAGCTAA
1 ACTTAGACATACGTTGACGTAAGGACGGAAGTTTTGAGCCTAAGGCCACATGATACCGGAGCTAA
* * *
17189355 AG-CTCTGTCATGCTCATGTAACCGACATGTTTCGAGTATTCATCAATAAATGTAAGAAAATCAA
66 AGTCTCTGTCATGCTCATGTAACGGACAAGTTTCGAGTACTCATCAATAAATGTAAGAAAATCAA
17189419 CTTTACACATTAGAAAAAGTTGCATATACATATA
131 CTTTACACATTAGAAAAAGTTGCATATACATATA
* * *
17189453 ACTTAGACATAAGTTGACGTAAGGACAGAAGTTTTGAGCCTAAGGCCACATGATACTGGAGCTAA
1 ACTTAGACATACGTTGACGTAAGGACGGAAGTTTTGAGCCTAAGGCCACATGATACCGGAGCTAA
* * * *
17189518 AGTCTCTGTCATACTCATTTGATGGACAAGTTTCGAGTACTCA-CTAATAAATGTAA
66 AGTCTCTGTCATGCTCATGTAACGGACAAGTTTCGAGTACTCATC-AATAAATGTAA
17189574 AGAATTGCAT
Statistics
Matches: 397, Mismatches: 45, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
163 150 0.38
164 172 0.43
168 71 0.18
169 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (164 bp):
ACTTAGACATACGTTGACGTAAGGACGGAAGTTTTGAGCCTAAGGCCACATGATACCGGAGCTAA
AGTCTCTGTCATGCTCATGTAACGGACAAGTTTCGAGTACTCATCAATAAATGTAAGAAAATCAA
CTTTACACATTAGAAAAAGTTGCATATACATATA
Found at i:17191804 original size:19 final size:19
Alignment explanation
Indices: 17191766--17191815 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
17191756 TCAATTCCAT
17191766 AAATCTGAAACACCAAAAATG
1 AAATC-GAAACA-CAAAAATG
17191787 CAAATCGAAACA-AAAAATG
1 -AAATCGAAACACAAAAATG
17191806 AATATCGAAA
1 AA-ATCGAAA
17191816 GATATGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.07
19 14 0.52
21 6 0.22
22 5 0.19
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.14
Consensus pattern (19 bp):
AAATCGAAACACAAAAATG
Found at i:17207769 original size:20 final size:20
Alignment explanation
Indices: 17207744--17207783 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17207734 ATTTACATTA
17207744 TTATTTATTTA-AATATTTTT
1 TTATTTATTTAGAA-ATTTTT
*
17207764 TTATTTCTTTAGAAATTTTT
1 TTATTTATTTAGAAATTTTT
17207784 GGAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTATTTAGAAATTTTT
Found at i:17208105 original size:29 final size:29
Alignment explanation
Indices: 17208068--17208123 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17208058 TTGAATTTCT
*
17208068 TTTAATAGTATAAGGATTAAATTGACACA
1 TTTAATAGTATAAGGACTAAATTGACACA
*
17208097 TTTATTAGTATAAGGACTAAATTGACA
1 TTTAATAGTATAAGGACTAAATTGACA
17208124 AAATCTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (29 bp):
TTTAATAGTATAAGGACTAAATTGACACA
Found at i:17211300 original size:66 final size:65
Alignment explanation
Indices: 17211194--17211364 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 65
17211184 CGGACTATCC
* *** * **
17211194 TCAATATTCCGTTAGACACCGTAACGACCACTCAGCTCCGTCTTTTGCACCAACGGCTGAGTCTT
1 TCAATATTCCGTTAG-CACCATAACGGTTACTCAGATCCGTCTTTTGCACCAACGGCACAGTCTT
17211259 T
65 T
* * *
17211260 TCAATATTCCGTCAGTCACCATAACGGTTACTCAGATCCGTCTTTTGCGCCAACGGCACCGTCTT
1 TCAATATTCCGTTAG-CACCATAACGGTTACTCAGATCCGTCTTTTGCACCAACGGCACAGTCTT
17211325 T
65 T
* *
17211326 TGAATATTCCGTTAGCGGCCATAACGGTTACTCAGATCC
1 TCAATATTCCGTTAGC-ACCATAACGGTTACTCAGATCC
17211365 TTCTCCTCCT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 1 0.01
66 89 0.99
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (65 bp):
TCAATATTCCGTTAGCACCATAACGGTTACTCAGATCCGTCTTTTGCACCAACGGCACAGTCTTT
Found at i:17212217 original size:18 final size:18
Alignment explanation
Indices: 17212164--17212223 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
17212154 TATGATGTTA
* *
17212164 CTTTTTTATGTTTTCATTT
1 CTTTTTT-TCTTTTCTTTT
17212183 CTTTTTTTCTTTTCTTTT
1 CTTTTTTTCTTTTCTTTT
17212201 CTTTTTTT-TTTTCCTTTT
1 CTTTTTTTCTTTT-CTTTT
*
17212219 GTTTT
1 CTTTT
17212224 GGATAATGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.11
18 26 0.70
19 7 0.19
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.80
Consensus pattern (18 bp):
CTTTTTTTCTTTTCTTTT
Found at i:17215420 original size:29 final size:29
Alignment explanation
Indices: 17215387--17215445 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17215377 TTTTACATGT
17215387 ACCATGGAGACCATATATGTATAGTTTTC
1 ACCATGGAGACCATATATGTATAGTTTTC
17215416 ACCATGGAGACCATATATGTATAGTTTTC
1 ACCATGGAGACCATATATGTATAGTTTTC
17215445 A
1 A
17215446 ATTTTAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (29 bp):
ACCATGGAGACCATATATGTATAGTTTTC
Found at i:17215626 original size:16 final size:16
Alignment explanation
Indices: 17215607--17215650 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 16
17215597 TTTAGAAAAA
17215607 ACTTGAACTTGAAATG
1 ACTTGAACTTGAAATG
17215623 ACTTGAACAAACTTGAAATG
1 ACTTG----AACTTGAAATG
17215643 ACTTGAAC
1 ACTTGAAC
17215651 AAGTAACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 8 0.33
20 16 0.67
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (16 bp):
ACTTGAACTTGAAATG
Found at i:17215637 original size:20 final size:20
Alignment explanation
Indices: 17215612--17215652 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17215602 AAAAAACTTG
17215612 AACTTGAAATGACTTGAACA
1 AACTTGAAATGACTTGAACA
17215632 AACTTGAAATGACTTGAACA
1 AACTTGAAATGACTTGAACA
17215652 A
1 A
17215653 GTAACACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (20 bp):
AACTTGAAATGACTTGAACA
Found at i:17215817 original size:7 final size:7
Alignment explanation
Indices: 17215807--17215832 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17215797 ACAATTATAG
17215807 TCTCAAC
1 TCTCAAC
17215814 TCTCAAC
1 TCTCAAC
17215821 TCTCAAC
1 TCTCAAC
17215828 TCTCA
1 TCTCA
17215833 TCTCCCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.42, G:0.00, T:0.31
Consensus pattern (7 bp):
TCTCAAC
Found at i:17222797 original size:146 final size:145
Alignment explanation
Indices: 17222533--17222889 Score: 522
Period size: 146 Copynumber: 2.4 Consensus size: 145
17222523 TTTTTCTCAG
* * *
17222533 CTCATCCATGGCTGAAACTAGAGGGTCAAATTCTGGTTTTGGTCCCTCTGTTATGCTCAAATTTG
1 CTCATCCATGGCTGAAACTAGCGGGTCAAATTCTGATTTT-GTCCCTCTGTTATGCTTAAATTTG
*
17222598 GGGTTGTGCTTAAAATTTGGCATGATTCTTTTCCTTTAGTTGATCAAAATATCGTTAGAATTCCA
65 GGGTTGTGCTTAAAATTTGGCATGATTCTTTTCCTTTAGTTAATCAAAATATCGTTAGAATTCCA
* *
17222663 ATGAAATAGTATTTTA
130 ATCAAATAGTAGTTTA
17222679 CTCATCCATGGCTGAAACTAGCGGGTCAAATTCTGATTTTGTTCCCTCTGTTATGCTTAAATTTG
1 CTCATCCATGGCTGAAACTAGCGGGTCAAATTCTGATTTTG-TCCCTCTGTTATGCTTAAATTTG
* *
17222744 GGGTTGTGTTTATAATTTGGCATGATTCTTTTCCTTTAGTTAATCAAAATATCGTTAGAATTCCA
65 GGGTTGTGCTTAAAATTTGGCATGATTCTTTTCCTTTAGTTAATCAAAATATCGTTAGAATTCCA
*
17222809 ATCAAATAGTAGTTTG
130 ATCAAATAGTAGTTTA
* * * * *
17222825 CTCATCCATGG-TTAAA--ATCAGGGTCAAATTCTGATTTTGGCCCTTCTATTATGCTCTAATTT
1 CTCATCCATGGCTGAAACTAGC-GGGTCAAATTCTGATTTTGTCCC-TCTGTTATGCT-TAAATT
17222887 TGG
63 TGG
17222890 AATTAGTCCC
Statistics
Matches: 193, Mismatches: 14, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
143 5 0.03
144 29 0.15
145 13 0.07
146 146 0.76
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (145 bp):
CTCATCCATGGCTGAAACTAGCGGGTCAAATTCTGATTTTGTCCCTCTGTTATGCTTAAATTTGG
GGTTGTGCTTAAAATTTGGCATGATTCTTTTCCTTTAGTTAATCAAAATATCGTTAGAATTCCAA
TCAAATAGTAGTTTA
Found at i:17234595 original size:4 final size:4
Alignment explanation
Indices: 17234586--17234639 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
17234576 AGCCATGACC
17234586 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
17234634 ACAT AC
1 ACAT AC
17234640 CTTCCTGCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:17236497 original size:31 final size:32
Alignment explanation
Indices: 17236444--17236513 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
17236434 AAAACAACCT
17236444 AGTGACTTAAAAATAAAAACTTTCAAATAGTTC
1 AGTGACTT-AAAATAAAAACTTTCAAATAGTTC
* * *
17236477 AGTGACTT-AAATGAAAACTTTCAAATATTTT
1 AGTGACTTAAAATAAAAACTTTCAAATAGTTC
17236508 AGTGAC
1 AGTGAC
17236514 AATTTTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 26 0.76
33 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (32 bp):
AGTGACTTAAAATAAAAACTTTCAAATAGTTC
Found at i:17238119 original size:10 final size:10
Alignment explanation
Indices: 17238106--17238131 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17238096 TTCATTATTT
17238106 AATTATAAAA
1 AATTATAAAA
17238116 AATTATAAAA
1 AATTATAAAA
17238126 AATTAT
1 AATTAT
17238132 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATTATAAAA
Found at i:17238724 original size:18 final size:18
Alignment explanation
Indices: 17238701--17238737 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17238691 TAAAATGTAA
17238701 ATGAAATCAAGTCAAGTT
1 ATGAAATCAAGTCAAGTT
17238719 ATGAAATCAAGTCAAGTT
1 ATGAAATCAAGTCAAGTT
17238737 A
1 A
17238738 AGCCCGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (18 bp):
ATGAAATCAAGTCAAGTT
Found at i:17240116 original size:30 final size:31
Alignment explanation
Indices: 17240075--17240151 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
17240065 TAATAAAAGT
17240075 AAAATTGTAATTTAATTCATTTAAAAAAT-TA
1 AAAATT-TAATTTAATTCATTTAAAAAATATA
* *
17240106 AAAATTTAATTTAA-TCTTTTAAAAATTATA
1 AAAATTTAATTTAATTCATTTAAAAAATATA
17240136 AAAATTTAATTTAATT
1 AAAATTTAATTTAATT
17240152 TATACGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 11 0.26
30 24 0.57
31 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAATTTAATTTAATTCATTTAAAAAATATA
Found at i:17246061 original size:102 final size:103
Alignment explanation
Indices: 17245882--17246076 Score: 302
Period size: 102 Copynumber: 1.9 Consensus size: 103
17245872 TAGGAGTGGA
** *
17245882 GAAAATACCGGTAGGAGAGCTTGCTTTCTTAAGGGTCTAATTCGGCTAAACTCCGGGTTTAGTTA
1 GAAAATACCACTAGGAGAGCTTGCTTTCGTAAGGGTCTAATTCGGCTAAACTCCGGGTTTAGTTA
*
17245947 AGTTCAACGTAGCTACCAGATAG-GGGGAGTCTGGATT
66 AGTCCAACGTAGCTACCAGATAGAGGGGAGTCTGGATT
* * *
17245984 GAAAATACCACTAGGAGAGCTTGCTTTCGTAAGGGTCTAATTTGGCTAAACTTCGGGTTTATTTA
1 GAAAATACCACTAGGAGAGCTTGCTTTCGTAAGGGTCTAATTCGGCTAAACTCCGGGTTTAGTTA
* *
17246049 AGTCCAATGTAGCTACCGGATAGAGGGG
66 AGTCCAACGTAGCTACCAGATAGAGGGG
17246077 TCTTAGGCTA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 79 0.95
103 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (103 bp):
GAAAATACCACTAGGAGAGCTTGCTTTCGTAAGGGTCTAATTCGGCTAAACTCCGGGTTTAGTTA
AGTCCAACGTAGCTACCAGATAGAGGGGAGTCTGGATT
Found at i:17248910 original size:11 final size:11
Alignment explanation
Indices: 17248878--17248927 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
17248868 CCTCTTTCAT
17248878 ATTTCCTCTCA
1 ATTTCCTCTCA
17248889 A-TTCCTCTCA
1 ATTTCCTCTCA
*
17248899 ATTTCCTTTCAA
1 ATTTCCTCTC-A
*
17248911 AATT-CTCTCA
1 ATTTCCTCTCA
17248921 ATTTCCT
1 ATTTCCT
17248928 TCCAAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 14 0.44
11 14 0.44
12 4 0.12
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTCCTCTCA
Found at i:17248921 original size:22 final size:22
Alignment explanation
Indices: 17248888--17248943 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
17248878 ATTTCCTCTC
*
17248888 AATTCCTCTCAATTTCCTTTCAA
1 AATT-CTCTCAATTTCCTTCCAA
17248911 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
*
17248933 AATTCTTTCAA
1 AATTCTCTCAA
17248944 ATCTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:17248979 original size:51 final size:51
Alignment explanation
Indices: 17248915--17249030 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
17248905 TTTCAAAATT
* * * *
17248915 CTCTCAATTTCCTTCCAAAATTCTTTCAAATCTATATTTAATTTTAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
17248966 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
17249017 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
17249031 TTTTAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.47
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:17250183 original size:7 final size:7
Alignment explanation
Indices: 17250173--17250197 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17250163 ATTCGATTGA
17250173 TATTTAG
1 TATTTAG
17250180 TATTTAG
1 TATTTAG
17250187 TATTTAG
1 TATTTAG
17250194 TATT
1 TATT
17250198 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:17250876 original size:18 final size:18
Alignment explanation
Indices: 17250850--17250884 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17250840 AGGTGCGTTT
*
17250850 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
17250868 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
17250885 TCATTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:17251305 original size:43 final size:44
Alignment explanation
Indices: 17251248--17251390 Score: 119
Period size: 53 Copynumber: 3.0 Consensus size: 44
17251238 CTAATTTATT
17251248 TATACAAATATTTTGAATATTTTGATATTATTTTATGTAAAAAAA
1 TATA-AAATATTTTGAATATTTTGATATTATTTTATGTAAAAAAA
*
17251293 TATAAAATTTTTGAGTTATTTTGAATATTTTAATATTATTTTATGT-AAAAAA
1 TAT-AAA------A--TATTTTGAATATTTTGATATTATTTTATGTAAAAAAA
* * * * *
17251345 TAT-AAATTTTTTTAGTTATTTTGATATTATTTAATGTAATAAAA
1 TATAAAATATTTTGA-ATATTTTGATATTATTTTATGTAAAAAAA
17251389 TA
1 TA
17251391 AAAGTTTATG
Statistics
Matches: 80, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
42 6 0.08
43 19 0.24
44 8 0.10
45 5 0.06
46 1 0.01
50 2 0.03
51 1 0.01
52 9 0.11
53 29 0.36
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (44 bp):
TATAAAATATTTTGAATATTTTGATATTATTTTATGTAAAAAAA
Found at i:17251379 original size:53 final size:53
Alignment explanation
Indices: 17251256--17251372 Score: 193
Period size: 53 Copynumber: 2.2 Consensus size: 53
17251246 TTTATACAAA
*
17251256 TATTTTGAATATTTTGATATTATTTTATGTAAAAAAATATAAAATTTTTGAGT
1 TATTTTGAATATTTTAATATTATTTTATGTAAAAAAATATAAAATTTTTGAGT
* *
17251309 TATTTTGAATATTTTAATATTATTTTATGT-AAAAAATATAAATTTTTTTAGT
1 TATTTTGAATATTTTAATATTATTTTATGTAAAAAAATATAAAATTTTTGAGT
17251361 TATTTTG-ATATT
1 TATTTTGAATATT
17251373 ATTTAATGTA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 5 0.08
52 27 0.44
53 29 0.48
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (53 bp):
TATTTTGAATATTTTAATATTATTTTATGTAAAAAAATATAAAATTTTTGAGT
Found at i:17251506 original size:29 final size:29
Alignment explanation
Indices: 17251473--17251528 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17251463 CGAAACCCTT
17251473 AATTAAAAACCCTAACCCTAACCTAATTC
1 AATTAAAAACCCTAACCCTAACCTAATTC
* *
17251502 AATTAAAAACCCTAACCTTAACGTAAT
1 AATTAAAAACCCTAACCCTAACCTAAT
17251529 ATTTGATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (29 bp):
AATTAAAAACCCTAACCCTAACCTAATTC
Found at i:17251643 original size:17 final size:18
Alignment explanation
Indices: 17251602--17251643 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
17251592 TTTACTAACC
* *
17251602 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
17251620 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
17251637 ATTAATA
1 ATTAATA
17251644 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:17254986 original size:126 final size:124
Alignment explanation
Indices: 17254595--17254946 Score: 472
Period size: 126 Copynumber: 2.8 Consensus size: 124
17254585 CCCAAACATG
* * * * * *
17254595 CTACTATAACAAAATCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
* * * *
17254660 TATAAGCGATTTTATATTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTAGATGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTTAAAAAAAATTATTTCTTATATGAC
* * * * *
17254719 CTACTGTAGCAAAAGCGC-ACTGACGAGGCCACAATTTCACAAATTCTTCTCAAATAACATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTG
* * * *
17254783 CTAGAAACGATTTTATACTATTTGCTTAGAAACGTTTAAAAAATAATTATTTCTTCTATGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACG-TTAAAAAA-AATTATTTCTTATATGAC
*
17254845 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
**
17254910 TAGAAGCGATTTTATATTATTTTATCAGAAACGTTAA
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTTAA
17254947 CTCGAAATTA
Statistics
Matches: 194, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
123 1 0.01
124 80 0.41
125 11 0.06
126 101 0.52
127 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTTAAAAAAAATTATTTCTTATATGAC
Found at i:17256774 original size:18 final size:20
Alignment explanation
Indices: 17256730--17256779 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
17256720 GACTTATCTC
*
17256730 TTTCTTTCTTCTCCCGTTTT
1 TTTCTTTCTTCTCCCGTTCT
17256750 TTCTCTTTCTTCT-CC-TTCT
1 TT-TCTTTCTTCTCCCGTTCT
17256769 TTTCTTTCTTC
1 TTTCTTTCTTC
17256780 CTTTCCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 5 0.18
20 4 0.14
21 10 0.36
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCTTTCTTCTCCCGTTCT
Found at i:17257676 original size:291 final size:291
Alignment explanation
Indices: 17257147--17257720 Score: 769
Period size: 291 Copynumber: 2.0 Consensus size: 291
17257137 AAACCAATAC
*
17257147 AAAGAAGCTAACCACTAGTGAAAGAACACAAGCAGACCTAGAACCAATGTGCAGCAAGAACAAAT
1 AAAGAAGCTAAACACTAGTGAAAGAACACAAGCAGACCTAGAACCAATGTGCAGCAAGAACAAAT
* * * * * * * * *
17257212 TGAAGTTAAAGTGTCCCTCCTCCAATGTTACTAATTAAAAAGAAAGTCAGAAGATGTAAGCTTCA
66 CGAAGTGAAAGAGGCACTCCTCCAATGTAACTAATGAAAAAGAAACTCAGAAGATATAAGCTTCA
* * * *
17257277 CGATCCATTAGATGATATTTCCCATTATATAACTTGCATGATTCTTTGCTCCATTCTCCAGAGTA
131 CAATCCATTAAATGA-ATTTCCCACTATATAACTTGCATGATTCTTTGCTCCAGTCTCCAGAGTA
* * *
17257342 AATTTACATGCAGCTTTGGTACAAGTTAGGTTTCATGTTCAAGCAACATTTCACCATGGGCAAAA
195 AATTTACATGCAGCTTTAGTACAAGCTAGGTTTCATGTTCAAGCAACATTCCACCATGGGCAAAA
** *
17257407 TGCAATTTCACTAGATTCTAGCTAATACAAAG
260 CACAATTTCACTAAATTCTAGCTAATACAAAG
** *
17257439 AAAGAAGCTAAACTGTAGTGAAAGAACACAAGCAGGCCTAGAACCAATGTGCAGCAAGAACAAAT
1 AAAGAAGCTAAACACTAGTGAAAGAACACAAGCAGACCTAGAACCAATGTGCAGCAAGAACAAAT
* * * *
17257504 CGAAGTGAAAGAGGGACTCTTTCACTGTAACTAATGAATAAA-AAACTCATTGAAGATATAAGCT
66 CGAAGTGAAAGAGGCACTCCTCCAATGTAACTAATGAA-AAAGAAACTCA--GAAGATATAAGCT
* ** * * *
17257568 TCATAATCTGTTAAATG-A-TTCCCACTATATAACTTGCATGATTTTTTGTTCCAGTCTCCAG-T
128 TCACAATCCATTAAATGAATTTCCCACTATATAACTTGCATGATTCTTTGCTCCAGTCTCCAGAG
*
17257630 TCAAATTTACATGCAGCTTTAGTACAAGCTAGGTTTCATTTTCAAGCAACATTCCACCATGGGCA
193 T-AAATTTACATGCAGCTTTAGTACAAGCTAGGTTTCATGTTCAAGCAACATTCCACCATGGGCA
17257695 AAACACAATTTCACTAAATTCTAGCT
257 AAACACAATTTCACTAAATTCTAGCT
17257721 TATATCTTCA
Statistics
Matches: 244, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
290 1 0.00
291 121 0.50
292 95 0.39
293 3 0.01
294 24 0.10
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (291 bp):
AAAGAAGCTAAACACTAGTGAAAGAACACAAGCAGACCTAGAACCAATGTGCAGCAAGAACAAAT
CGAAGTGAAAGAGGCACTCCTCCAATGTAACTAATGAAAAAGAAACTCAGAAGATATAAGCTTCA
CAATCCATTAAATGAATTTCCCACTATATAACTTGCATGATTCTTTGCTCCAGTCTCCAGAGTAA
ATTTACATGCAGCTTTAGTACAAGCTAGGTTTCATGTTCAAGCAACATTCCACCATGGGCAAAAC
ACAATTTCACTAAATTCTAGCTAATACAAAG
Found at i:17263526 original size:6 final size:7
Alignment explanation
Indices: 17263507--17263534 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
17263497 TACAACTCTC
17263507 TCTTTTT
1 TCTTTTT
17263514 TCTTTTT
1 TCTTTTT
17263521 TCTTTTT
1 TCTTTTT
17263528 TCTTTTT
1 TCTTTTT
17263535 AATATCCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TCTTTTT
Found at i:17266726 original size:4 final size:4
Alignment explanation
Indices: 17266717--17266777 Score: 122
Period size: 4 Copynumber: 15.2 Consensus size: 4
17266707 TTCTTGCAGG
17266717 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
17266765 TACA TACA TACA T
1 TACA TACA TACA T
17266778 GAAGTTTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:17270982 original size:21 final size:21
Alignment explanation
Indices: 17270956--17270996 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17270946 AGACGAGCAA
* *
17270956 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17270977 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17270997 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:17276860 original size:29 final size:30
Alignment explanation
Indices: 17276828--17276888 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
17276818 TTAAATTAGT
*
17276828 AAAA-TTGTATTTTATCC-CTAAAAATAATA
1 AAAATTTG-ATTTAATCCTCTAAAAATAATA
* *
17276857 AAAATTTGATTTAATCCTTTAAAAATTATA
1 AAAATTTGATTTAATCCTCTAAAAATAATA
17276887 AA
1 AA
17276889 GATAGAGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTTGATTTAATCCTCTAAAAATAATA
Found at i:17277963 original size:15 final size:16
Alignment explanation
Indices: 17277943--17277975 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17277933 ATTAAAATTT
*
17277943 TAAATTT-TTTCTAAC
1 TAAATTTATGTCTAAC
17277958 TAAATTTATGTCTAAC
1 TAAATTTATGTCTAAC
17277974 TA
1 TA
17277976 GTTGATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (16 bp):
TAAATTTATGTCTAAC
Found at i:17278020 original size:3 final size:3
Alignment explanation
Indices: 17278012--17278036 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17278002 ATATAGATTT
17278012 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
17278037 ACCAGACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17282128 original size:58 final size:58
Alignment explanation
Indices: 17282059--17282211 Score: 225
Period size: 58 Copynumber: 2.6 Consensus size: 58
17282049 AGATATTGGA
* *
17282059 AAATTCAAGTTGATTGGCATTAAGTTCAGAGTTTAATCGAGTCAATCATATTGATGGT
1 AAATTCAAGTTGATTGGCGTTAAGTTCAGAGTTTAATCGAGTCAATCATATTGATAGT
* * * *
17282117 AAATTCAAGTTGATTGGCGTTAAATTCAAAGTTTAATCGAGTCAATGATATTGCTAGT
1 AAATTCAAGTTGATTGGCGTTAAGTTCAGAGTTTAATCGAGTCAATCATATTGATAGT
* * *
17282175 AAGTTCAAGTTAATTGGCGTTAAGTTTAGAGTTTAAT
1 AAATTCAAGTTGATTGGCGTTAAGTTCAGAGTTTAAT
17282212 TCCGATGAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 84 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (58 bp):
AAATTCAAGTTGATTGGCGTTAAGTTCAGAGTTTAATCGAGTCAATCATATTGATAGT
Found at i:17283087 original size:11 final size:12
Alignment explanation
Indices: 17283050--17283105 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
17283040 ATGTATTACT
*
17283050 TAATATTTAAGTA
1 TAATATATAA-TA
17283063 -AATATATAATA
1 TAATATATAATA
*
17283074 TAATA-ATAAAA
1 TAATATATAATA
17283085 TAA-ATATAATA
1 TAATATATAATA
*
17283096 TAATAAATAA
1 TAATATATAA
17283106 GTAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 1 0.03
11 18 0.50
12 17 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
TAATATATAATA
Found at i:17283110 original size:22 final size:22
Alignment explanation
Indices: 17283057--17283123 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
17283047 ACTTAATATT
17283057 TAAGTAAATATATAATATAAT-AA
1 TAAGT-AA-ATATAATATAATAAA
*
17283080 TAAAATAAATATAATATAATAAA
1 T-AAGTAAATATAATATAATAAA
17283103 TAAGTAAATGA-AATA-AATAAA
1 TAAGTAAAT-ATAATATAATAAA
17283124 GAAAGGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 6 0.15
22 23 0.59
23 7 0.18
24 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
TAAGTAAATATAATATAATAAA
Found at i:17284189 original size:40 final size:39
Alignment explanation
Indices: 17284077--17284191 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 39
17284067 GAGTCGAGAT
** * **
17284077 ACTGGGTGTCAATCTATTACTTCGGGTTAATTCGATGAGGC
1 ACTGGGTGTCAAT-TATTACTTCGAATT-ATCCGATGAAAC
* * *
17284118 ACTGGGTGCCAA-T-TTACTTC-AGTTTAGCCGATGAAAC
1 ACTGGGTGTCAATTATTACTTCGA-ATTATCCGATGAAAC
17284155 ACTGGGTGTCAAATTATTACTTCGAATTATCCGATGA
1 ACTGGGTGTC-AATTATTACTTCGAATTATCCGATGA
17284192 GGTACTCGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
37 17 0.29
38 11 0.19
39 2 0.03
40 17 0.29
41 12 0.20
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (39 bp):
ACTGGGTGTCAATTATTACTTCGAATTATCCGATGAAAC
Found at i:17286127 original size:39 final size:39
Alignment explanation
Indices: 17286080--17286155 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
17286070 TATTTTCTTG
* *
17286080 AACACCTTAAAACACAAGATTACTGGATTCGAATTTTTA
1 AACACCTTAAAACACAAGACTACTAGATTCGAATTTTTA
** *
17286119 AACACCTTAAAACTTAAGACTGCTAGATTCGAATTTT
1 AACACCTTAAAACACAAGACTACTAGATTCGAATTTT
17286156 AATATAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (39 bp):
AACACCTTAAAACACAAGACTACTAGATTCGAATTTTTA
Found at i:17286853 original size:23 final size:23
Alignment explanation
Indices: 17286823--17286868 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17286813 GTGTTTCATG
17286823 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
17286846 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
17286869 ACTAGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (23 bp):
TCTGCTGCCTGATTAAGTTACAT
Found at i:17287147 original size:25 final size:26
Alignment explanation
Indices: 17287112--17287160 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
17287102 TCTCCAATTC
*
17287112 TTAAACTTGATTTTGA-AATAAAAAA
1 TTAAACATGATTTTGATAATAAAAAA
*
17287137 TTAAACATGATTTTTATAATAAAA
1 TTAAACATGATTTTGATAATAAAA
17287161 CTTATTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (26 bp):
TTAAACATGATTTTGATAATAAAAAA
Found at i:17287224 original size:45 final size:46
Alignment explanation
Indices: 17287175--17287265 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
17287165 TTCTTCACAG
*
17287175 AATTAAA-TTCCTACTAT-AAATTTTTTAAAAAATACAACCACTATA
1 AATTAAATTTCCTACTATGAAA-TTTTCAAAAAATACAACCACTATA
* *
17287220 AATTAAATTTCCTACTTTGAAATTTTCAAAAAATACAATCACTATA
1 AATTAAATTTCCTACTATGAAATTTTCAAAAAATACAACCACTATA
17287266 GACATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 7 0.17
46 31 0.76
47 3 0.07
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.36
Consensus pattern (46 bp):
AATTAAATTTCCTACTATGAAATTTTCAAAAAATACAACCACTATA
Found at i:17292343 original size:18 final size:17
Alignment explanation
Indices: 17292315--17292349 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17292305 ATTATTAAGA
*
17292315 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17292332 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17292350 TTAATAATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17292564 original size:44 final size:45
Alignment explanation
Indices: 17292515--17292599 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
17292505 CCTCTATTCC
* *
17292515 ATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTAT
1 ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTAT
***
17292559 ATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCA
1 ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCA
17292600 ATACACCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.29
Consensus pattern (45 bp):
ATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTAT
Found at i:17292606 original size:16 final size:16
Alignment explanation
Indices: 17292585--17292653 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
17292575 GATTAGCTAT
17292585 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17292601 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
17292618 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
17292634 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
17292650 TACA
1 TACA
17292654 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17292627 original size:33 final size:32
Alignment explanation
Indices: 17292585--17292653 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
17292575 GATTAGCTAT
17292585 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
17292618 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
17292650 TACA
1 TACA
17292654 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:17298785 original size:9 final size:9
Alignment explanation
Indices: 17298771--17298813 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
17298761 TTTGGTTAAA
17298771 AATTACCCG
1 AATTACCCG
17298780 AATTACCCG
1 AATTACCCG
17298789 AATTACCCG
1 AATTACCCG
*
17298798 AATTAACCG
1 AATTACCCG
17298807 AATTACC
1 AATTACC
17298814 GAAAAATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:17299348 original size:19 final size:20
Alignment explanation
Indices: 17299321--17299362 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17299311 CCATACTTTC
17299321 AAATAATTATAAT-TAAAAT
1 AAATAATTATAATATAAAAT
* *
17299340 AAATTATTATAATATACAAT
1 AAATAATTATAATATAAAAT
17299360 AAA
1 AAA
17299363 ATTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAATTATAATATAAAAT
Found at i:17303106 original size:20 final size:20
Alignment explanation
Indices: 17303081--17303120 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17303071 TAAATATATT
17303081 TATTTTTT--AATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
17303099 TATTTTTTAAAATTTTAAAA
1 TATTTTTTAAAATTTTAAAA
17303119 TA
1 TA
17303121 CATTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTTAAAATTTTAAAA
Found at i:17305591 original size:13 final size:14
Alignment explanation
Indices: 17305557--17305596 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
17305547 CCCGAACCTA
*
17305557 AACTCTAAACCTCG
1 AACTCTAAACCTTG
17305571 AA-TCTAAACCTTG
1 AACTCTAAACCTTG
17305584 AACT-TAAA-CTTG
1 AACTCTAAACCTTG
17305596 A
1 A
17305597 GTTCTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.21
13 16 0.67
14 3 0.12
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (14 bp):
AACTCTAAACCTTG
Found at i:17306260 original size:24 final size:24
Alignment explanation
Indices: 17306210--17306261 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
17306200 TTTCTAGAAG
* * *
17306210 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCACAATAT
*
17306234 ATTTAGCATTTATTAGCACAATTT
1 ATTTAGCATTTATTAGCACAATAT
17306258 ATTT
1 ATTT
17306262 GACCTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCACAATAT
Found at i:17314320 original size:30 final size:30
Alignment explanation
Indices: 17314286--17314347 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
17314276 ACTTATTTTA
17314286 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
17314316 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
17314346 TT
1 TT
17314348 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:17314486 original size:11 final size:11
Alignment explanation
Indices: 17314470--17314500 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
17314460 TATATATATC
17314470 TAAAAATTATA
1 TAAAAATTATA
*
17314481 TAAAAATAATA
1 TAAAAATTATA
17314492 TAAAAATTA
1 TAAAAATTA
17314501 ATATGGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:17314497 original size:12 final size:11
Alignment explanation
Indices: 17314470--17314504 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
17314460 TATATATATC
*
17314470 TAAAAATTATA
1 TAAAAATAATA
17314481 TAAAAATAATA
1 TAAAAATAATA
17314492 TAAAAATTAATA
1 TAAAAA-TAATA
17314504 T
1 T
17314505 GGGTTGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:17315096 original size:29 final size:29
Alignment explanation
Indices: 17315054--17315111 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
17315044 AAATTGCATT
*
17315054 TTTCCCCTCTAAAAACTCTATCATCGCAC
1 TTTCCCCTCTAAAAACTCGATCATCGCAC
*
17315083 TTTCCCCTCTAAAAACTCGATCATTGCAC
1 TTTCCCCTCTAAAAACTCGATCATCGCAC
17315112 GATGCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (29 bp):
TTTCCCCTCTAAAAACTCGATCATCGCAC
Found at i:17319609 original size:72 final size:72
Alignment explanation
Indices: 17319528--17319673 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
17319518 GTGTTTCATA
* *
17319528 TGCATTCCTACTTGAGCTTGAGGCTGAGCTTGATTAAGCTTGTATGTATTCATGCTTGAGCTTGA
1 TGCATTCCTACTTGAGCTTGAGCCAGAGCTTGATTAAGCTTGTATGTATTCATGCTTGAGCTTGA
17319593 TAAGGCT
66 TAAGGCT
* *
17319600 TGCATTCCTACTTGAGCTTGAGCCAGAGTTTGGTTAAGCTTGTATGTATTCATGCTTGAGCTTGA
1 TGCATTCCTACTTGAGCTTGAGCCAGAGCTTGATTAAGCTTGTATGTATTCATGCTTGAGCTTGA
17319665 TAAGGCT
66 TAAGGCT
17319672 TG
1 TG
17319674 GAGCAGTTTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (72 bp):
TGCATTCCTACTTGAGCTTGAGCCAGAGCTTGATTAAGCTTGTATGTATTCATGCTTGAGCTTGA
TAAGGCT
Found at i:17323659 original size:29 final size:30
Alignment explanation
Indices: 17323594--17323660 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
17323584 TATATTTTTT
* *
17323594 ATTTTTTTTATTTTTAAATTTTTTTAAAATAC
1 ATTTTTTTTATTTTT--ATATTTTTAAAATAA
*
17323626 TTTTTTTTTATTTTT-TATTTTTAAAATAA
1 ATTTTTTTTATTTTTATATTTTTAAAATAA
17323655 ATTTTT
1 ATTTTT
17323661 GGTGTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 17 0.55
32 14 0.45
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTTTTTTTATTTTTATATTTTTAAAATAA
Found at i:17342688 original size:8 final size:8
Alignment explanation
Indices: 17342675--17342704 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
17342665 AGAAGAGCAG
17342675 CGATAATT
1 CGATAATT
17342683 CGATAATT
1 CGATAATT
17342691 CGATAATT
1 CGATAATT
17342699 CGATAA
1 CGATAA
17342705 CCTCTGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (8 bp):
CGATAATT
Found at i:17345014 original size:32 final size:32
Alignment explanation
Indices: 17344974--17345050 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
17344964 ATATTTCATT
* *
17344974 TCGCAACAAGTCACGAGAAA-AAGCATATTTCG
1 TCGCAACAAGTAACGA-AAAGAACCATATTTCG
*
17345006 TCGCAACAAGTAACGAAAAGAACCGTATTTCG
1 TCGCAACAAGTAACGAAAAGAACCATATTTCG
*
17345038 TCGCAACATGTAA
1 TCGCAACAAGTAA
17345051 AAAGCCAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 3 0.08
32 37 0.93
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (32 bp):
TCGCAACAAGTAACGAAAAGAACCATATTTCG
Found at i:17354970 original size:50 final size:50
Alignment explanation
Indices: 17354894--17355136 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
17354884 ATTTGGGTAA
*
17354894 AGAGGTCCCATGTAATACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
17354944 TGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
17354994 AGAGGTCCTATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
17355044 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
17355094 AGTACATCCCATGTAAGACCACGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
17355137 TGTTATGATC
Statistics
Matches: 170, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 137 0.81
51 33 0.19
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:17357231 original size:15 final size:15
Alignment explanation
Indices: 17357213--17357243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17357203 TGTTACAGCT
17357213 GATTTGCAAATGTTA
1 GATTTGCAAATGTTA
*
17357228 GATTTGCAAATTTTA
1 GATTTGCAAATGTTA
17357243 G
1 G
17357244 GTCATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
GATTTGCAAATGTTA
Found at i:17360253 original size:21 final size:21
Alignment explanation
Indices: 17360212--17360254 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17360202 AATAAAGTAG
*
17360212 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
17360233 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
17360254 A
1 A
17360255 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:17360294 original size:37 final size:37
Alignment explanation
Indices: 17360237--17360334 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 37
17360227 TATAGTATTA
* *
17360237 TATATTATG-ATTTTAGTAAATTCATA-TAAGAATAAT
1 TATATTAAGAATTTTATTAAATT-ATATTAAGAATAAT
*
17360273 TATATTAAGAATTTTATTAAATTATATTTAATAATAAT
1 TATATTAAGAATTTTATTAAATTATA-TTAAGAATAAT
* * *
17360311 TATGTTAA-AATATGATTAAATTAT
1 TATATTAAGAATTTTATTAAATTAT
17360335 TTATTATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
36 11 0.21
37 26 0.49
38 16 0.30
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (37 bp):
TATATTAAGAATTTTATTAAATTATATTAAGAATAAT
Found at i:17360538 original size:45 final size:44
Alignment explanation
Indices: 17360456--17360548 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 44
17360446 ATTACAACAT
*
17360456 CATTCCATTCAACTAAACATAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACATAAGAATACTATTACAGTTCTATTC
* * *
17360500 CATTTCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTG
1 CATTCCATTCAACCAAACATA-AGAA-TACTATTACAGTTCTATTC
17360545 CATT
1 CATT
17360549 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 22 0.51
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (44 bp):
CATTCCATTCAACCAAACATAAGAATACTATTACAGTTCTATTC
Found at i:17360551 original size:16 final size:16
Alignment explanation
Indices: 17360530--17360569 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17360520 TTGAATTACT
* *
17360530 ATTACAGTTCTATTGC
1 ATTACAGCTCTATTCC
17360546 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
17360562 ATTACAGC
1 ATTACAGC
17360570 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17361057 original size:7 final size:7
Alignment explanation
Indices: 17361045--17361073 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
17361035 TTTACATTGT
17361045 AAATTTA
1 AAATTTA
17361052 AAATTTA
1 AAATTTA
17361059 AAATTTA
1 AAATTTA
17361066 AAATTTA
1 AAATTTA
17361073 A
1 A
17361074 TCACCGTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:17367204 original size:13 final size:13
Alignment explanation
Indices: 17367186--17367220 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
17367176 AGTAGAGGAA
17367186 GCAAAACCAGGGG
1 GCAAAACCAGGGG
17367199 GCAAAACCAGGGG
1 GCAAAACCAGGGG
17367212 GCAAAACCA
1 GCAAAACCA
17367221 TATAAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.31, T:0.00
Consensus pattern (13 bp):
GCAAAACCAGGGG
Found at i:17372609 original size:11 final size:11
Alignment explanation
Indices: 17372593--17372621 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17372583 AATAATCCAA
17372593 TTTTTTTTT-C
1 TTTTTTTTTCC
17372603 TTTTTTTTTCC
1 TTTTTTTTTCC
17372614 TTTTTTTT
1 TTTTTTTT
17372622 GTGTGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCC
Found at i:17377230 original size:6 final size:6
Alignment explanation
Indices: 17377219--17377246 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17377209 AATCATTAAG
17377219 AATTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
17377247 ACCGGGCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:17380746 original size:12 final size:12
Alignment explanation
Indices: 17380729--17380768 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
17380719 ATTTAAAAAT
17380729 ATAAAAATATTC
1 ATAAAAATATTC
17380741 A-AAAAATATT-
1 ATAAAAATATTC
17380751 ATAAAAA-ATTC
1 ATAAAAATATTC
17380762 ATAAAAA
1 ATAAAAA
17380769 CTTATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.15
11 21 0.81
12 1 0.04
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAAAAATATTC
Found at i:17382701 original size:18 final size:20
Alignment explanation
Indices: 17382643--17382704 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 20
17382633 ACAAAAATAA
17382643 ATTTA-AAAAA-TTCAAAAT
1 ATTTATAAAAATTTCAAAAT
*
17382661 GATTT-T-TAAATTTCAAAAT
1 -ATTTATAAAAATTTCAAAAT
17382680 ATTTATAAAAATTT-AAAA-
1 ATTTATAAAAATTTCAAAAT
17382698 ATTTATA
1 ATTTATA
17382705 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 14 0.38
19 17 0.46
20 6 0.16
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATAAAAATTTCAAAAT
Found at i:17388211 original size:17 final size:18
Alignment explanation
Indices: 17388178--17388211 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17388168 TTAACATAAT
*
17388178 TATATTTTAATTAAAATA
1 TATAATTTAATTAAAATA
17388196 TATAATTTAA-TAAAAT
1 TATAATTTAATTAAAAT
17388212 TCTTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATTTAATTAAAATA
Found at i:17388329 original size:59 final size:60
Alignment explanation
Indices: 17388173--17388354 Score: 158
Period size: 59 Copynumber: 3.0 Consensus size: 60
17388163 ATATTTTAAC
* * *
17388173 ATAATTATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTAT
1 ATAAATATATTTTAATTAAAATATATAATTTAATAAAATTATT-ATAATCAATATTATTAT
* * ** * * * *
17388234 ATAAATTTACTAAAATCATAATATATGATACT-ATAAAATATAATT-TAA-C-ATAATTATTAT
1 ATAAATATATTTTAATTAAAATATATAAT-TTAATAAAAT-T-ATTATAATCAAT-ATTATTAT
* *
17388294 -TAAATATATTTTAATTAAAATATATAATTTAATAAAATTTTTAATAATCAATATTCTTAT
1 ATAAATATATTTTAATTAAAATATATAATTTAATAAAATTATT-ATAATCAATATTATTAT
17388354 A
1 A
17388355 ACAAAAATTC
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 33 0.37
60 16 0.18
61 33 0.37
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (60 bp):
ATAAATATATTTTAATTAAAATATATAATTTAATAAAATTATTATAATCAATATTATTAT
Found at i:17388338 original size:17 final size:18
Alignment explanation
Indices: 17388297--17388331 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17388287 TTATTATTAA
*
17388297 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
17388315 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
17388332 TTTTAATAAT
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 (18 bp):
ATATAATTTAATTAAAAT
Found at i:17389705 original size:18 final size:18
Alignment explanation
Indices: 17389682--17389719 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17389672 ATATTGCTTG
17389682 AAGTTCAACAATCCTTCT
1 AAGTTCAACAATCCTTCT
* *
17389700 AAGTTCAGCAATCTTTCT
1 AAGTTCAACAATCCTTCT
17389718 AA
1 AA
17389720 CAAAAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (18 bp):
AAGTTCAACAATCCTTCT
Found at i:17392101 original size:15 final size:15
Alignment explanation
Indices: 17392077--17392107 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17392067 TAAAAAAAAT
*
17392077 ATTTTTATTTTTTTA
1 ATTTTAATTTTTTTA
17392092 ATTTTAATTTTTTTA
1 ATTTTAATTTTTTTA
17392107 A
1 A
17392108 AATATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTAATTTTTTTA
Found at i:17392128 original size:15 final size:14
Alignment explanation
Indices: 17392076--17392131 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
17392066 ATAAAAAAAA
17392076 TATTTTTATTTTTT
1 TATTTTTATTTTTT
*
17392090 TAATTTTAATTTTTT
1 T-ATTTTTATTTTTT
***
17392105 TA-AAATATTTTTT
1 TATTTTTATTTTTT
17392118 TATTTTTTATTTTT
1 TA-TTTTTATTTTT
17392132 AAAATATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
15 20 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTATTTTTT
Found at i:17392144 original size:26 final size:27
Alignment explanation
Indices: 17392082--17392144 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 27
17392072 AAAATATTTT
17392082 TATTTTTTTAATTTTAATTTTTTTAAAA
1 TATTTTTTTAATTTT-ATTTTTTTAAAA
17392110 TATTTTTTT-ATTTT-TTATTTTTAAAA
1 TATTTTTTTAATTTTATT-TTTTTAAAA
17392136 TATTTTTTT
1 TATTTTTTT
17392145 GGTGTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 2 0.06
26 18 0.53
27 5 0.15
28 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TATTTTTTTAATTTTATTTTTTTAAAA
Done.