Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 55 of 345
Found at i:16787152 original size:40 final size:41
Alignment explanation
Indices: 16787006--16787151 Score: 161
Period size: 40 Copynumber: 3.5 Consensus size: 41
16786996 GGCCTCGGGT
*
16787006 CTAGCAGGCTATAATGCCGGTGAAATG-ATATCGGGCTTCAAGC
1 CTAGCAGGCTA-AATGCCGGTG-AATGAAT-TCGGGCTTAAAGC
* * * *
16787049 CTAGCAGGCGAAATGCCGGTGAATGAATTCAGACTTAAAGT
1 CTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAAGC
*** * *
16787090 CTAGCAGGCTTCGTGCCGGTG-ATGAATTCGGGTTTAAAAC
1 CTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAAGC
16787130 CTAGCAGGCTAAATGCCGGTGA
1 CTAGCAGGCTAAATGCCGGTGA
16787152 TTTGATAAAA
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
40 32 0.38
41 30 0.36
42 12 0.14
43 10 0.12
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAAGC
Found at i:16794942 original size:14 final size:15
Alignment explanation
Indices: 16794920--16794949 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16794910 GAATATCAAA
16794920 ACATGAATTAAGAAC
1 ACATGAATTAAGAAC
16794935 ACAT-AATTAAGAAC
1 ACATGAATTAAGAAC
16794949 A
1 A
16794950 AGTCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (15 bp):
ACATGAATTAAGAAC
Found at i:16808940 original size:14 final size:14
Alignment explanation
Indices: 16808921--16808952 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16808911 AGTTACCTTA
16808921 TTTATAGTCTAAGG
1 TTTATAGTCTAAGG
16808935 TTTATAGTCTAAGG
1 TTTATAGTCTAAGG
16808949 TTTA
1 TTTA
16808953 AGACGAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (14 bp):
TTTATAGTCTAAGG
Found at i:16811260 original size:102 final size:103
Alignment explanation
Indices: 16811075--16811281 Score: 407
Period size: 102 Copynumber: 2.0 Consensus size: 103
16811065 GAAAGGGAAA
16811075 CAATCGAAGGCGGATGGCGTCATTAGAAGCGCCATAATTTTAAAGGTATCGCAAAATTCTAGGAA
1 CAATCGAAGGCGGATGGCGTCATTAGAAGCGCCATAATTTTAAAGGTATCGCAAAATTCTAGGAA
16811140 ATTTTCCAAGTGAGCATTGGGATCCATATCCTGCAAAC
66 ATTTTCCAAGTGAGCATTGGGATCCATATCCTGCAAAC
16811178 CAATCGAA-GCGGATGGCGTCATTAGAAGCGCCATAATTTTAAAGGTATCGCAAAATTCTAGGAA
1 CAATCGAAGGCGGATGGCGTCATTAGAAGCGCCATAATTTTAAAGGTATCGCAAAATTCTAGGAA
16811242 ATTTTCCAAGTGAGCATTGGGATCCATATCCTGCAAAC
66 ATTTTCCAAGTGAGCATTGGGATCCATATCCTGCAAAC
16811280 CA
1 CA
16811282 TCAAACTGAA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 96 0.92
103 8 0.08
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (103 bp):
CAATCGAAGGCGGATGGCGTCATTAGAAGCGCCATAATTTTAAAGGTATCGCAAAATTCTAGGAA
ATTTTCCAAGTGAGCATTGGGATCCATATCCTGCAAAC
Found at i:16839321 original size:55 final size:55
Alignment explanation
Indices: 16839236--16839364 Score: 150
Period size: 55 Copynumber: 2.3 Consensus size: 55
16839226 AAATCACCAC
* * **
16839236 GAACCTGCCAAAACAACACAGGCGTGCGACACGCCCATGCCTTGAAACCGTGGCT
1 GAACCTGCCAAAACAACACAGGCATACGACACGCCCATGCCAAGAAACCGTGGCT
* ** * * * *
16839291 GAACCTGTCAAATTAACACAGGCATACGACACGCTCGTGCCAAGCAACCGTGGGT
1 GAACCTGCCAAAACAACACAGGCATACGACACGCCCATGCCAAGAAACCGTGGCT
*
16839346 GAACCTACCAAAACAACAC
1 GAACCTGCCAAAACAACAC
16839365 GGGCGTGGAC
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.13
Consensus pattern (55 bp):
GAACCTGCCAAAACAACACAGGCATACGACACGCCCATGCCAAGAAACCGTGGCT
Found at i:16843830 original size:14 final size:13
Alignment explanation
Indices: 16843811--16843840 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
16843801 ATATTTGACT
16843811 TGTTCTTAATTATG
1 TGTTCTTAATTA-G
16843825 TGTTCTTAATTAG
1 TGTTCTTAATTAG
16843838 TGT
1 TGT
16843841 CTTGATATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.57
Consensus pattern (13 bp):
TGTTCTTAATTAG
Found at i:16889587 original size:43 final size:43
Alignment explanation
Indices: 16889442--16889585 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
16889432 ATAAAGCTCG
* * * *
16889442 TACAATGCC-ATATCCCAGATATGGCCTTACATGTTATCAC-A
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAA
** * * **
16889483 TATTGATGCCACTGCCCCAGACATGGTCTTACATAAAATCA-AA
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAA
* *
16889526 TAACGATGCCAATGTCCTAGACATGGTCTTACATGTAATCACAA
1 T-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAA
16889570 TACAATGCCAATGTCC
1 TACAATGCCAATGTCC
16889586 TATACATTTA
Statistics
Matches: 81, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 5 0.06
43 70 0.86
44 4 0.05
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAA
Found at i:16890331 original size:8 final size:9
Alignment explanation
Indices: 16890309--16890333 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16890299 GTAACAATCA
16890309 CAAAAACAT
1 CAAAAACAT
16890318 CAAAAACAT
1 CAAAAACAT
16890327 CAAAAAC
1 CAAAAAC
16890334 TGAGCAAAGA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (9 bp):
CAAAAACAT
Found at i:16891862 original size:13 final size:14
Alignment explanation
Indices: 16891818--16891865 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
16891808 CAAAGTTTGA
*
16891818 ATAATTATTTACTAA
1 ATAATTATTTA-TAT
* *
16891833 ATGATTATTTATTT
1 ATAATTATTTATAT
16891847 ATAATTATTATATAT
1 ATAATTATT-TATAT
16891862 ATAA
1 ATAA
16891866 CATGATTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
ATAATTATTTATAT
Found at i:16892292 original size:21 final size:21
Alignment explanation
Indices: 16892268--16892307 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16892258 TAATGATCAG
*
16892268 CACATTTTGGTGGTATATCCA
1 CACATTTTGGTAGTATATCCA
16892289 CACATTTTGGTAGTATATC
1 CACATTTTGGTAGTATATC
16892308 TGCAATTCTG
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:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (21 bp):
CACATTTTGGTAGTATATCCA
Found at i:16894370 original size:144 final size:144
Alignment explanation
Indices: 16894136--16894419 Score: 543
Period size: 144 Copynumber: 2.0 Consensus size: 144
16894126 AACTCTATAC
16894136 GTTACAACTATCAAATAGCAAGGATGTCAAAGGATGTAAGAACAGTAGGGCATGAGTGAAAAGCC
1 GTTACAACTATCAAATAGCAAGGATGTCAAAGGATGTAAGAACAGTAGGGCATGAGTGAAAAGCC
16894201 CTGCTTGGGGGGTCACATATGATTGAATAATAGTAAGCTATCTGTAATGGGGATTCTAATAGGAA
66 CTGCTTGGGGGGTCACATATGATTGAATAATAGTAAGCTATCTGTAATGGGGATTCTAATAGGAA
16894266 TTTTATGGTCATGA
131 TTTTATGGTCATGA
*
16894280 GTTACAACTATCAAATAGCAAGGATGTCAAAGGATGTGAGAACAGTAGGGCATGAGTGAAAAGCC
1 GTTACAACTATCAAATAGCAAGGATGTCAAAGGATGTAAGAACAGTAGGGCATGAGTGAAAAGCC
16894345 CT-CATTGGGGGGTCACATATGATTGAATAATAGTAAGCTATCTGTAATGGGGATTCTAATAGGA
66 CTGC-TTGGGGGGTCACATATGATTGAATAATAGTAAGCTATCTGTAATGGGGATTCTAATAGGA
16894409 ATTTTATGGTC
130 ATTTTATGGTC
16894420 TTTTAAGCAA
Statistics
Matches: 138, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
143 1 0.01
144 137 0.99
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (144 bp):
GTTACAACTATCAAATAGCAAGGATGTCAAAGGATGTAAGAACAGTAGGGCATGAGTGAAAAGCC
CTGCTTGGGGGGTCACATATGATTGAATAATAGTAAGCTATCTGTAATGGGGATTCTAATAGGAA
TTTTATGGTCATGA
Found at i:16897719 original size:30 final size:30
Alignment explanation
Indices: 16897685--16897770 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
16897675 TTTTTGAGCA
*
16897685 TAGGGGTAAAATGGTCATTTTGCCAAGGTC
1 TAGGGGCAAAATGGTCATTTTGCCAAGGTC
16897715 TAGGGGCAAAATGGTCATTTTGCCAAGGTC
1 TAGGGGCAAAATGGTCATTTTGCCAAGGTC
*
16897745 TAGGGGCAAAATGGTCATTTTACCAA
1 TAGGGGCAAAATGGTCATTTTGCCAA
16897771 AGATGTGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTGCCAAGGTC
Found at i:16898185 original size:47 final size:47
Alignment explanation
Indices: 16898110--16898421 Score: 239
Period size: 47 Copynumber: 6.6 Consensus size: 47
16898100 AATTTCTTGT
* * *
16898110 GTGCCAATGTAAGATATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGA
* * * *
16898156 GTGCCAGTATAAGACCATGTCTGGAACATGGCATCGACGTA-GA-GATGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACGATGATGA
* *
16898204 GTGCCAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGATGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGA
* * * * * * *
16898251 -TAGCCAGTGTAAGACGTGTCTGGGACACGCATAGGCTA-AAAG-T-T
1 GT-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGA
* *
16898295 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CACGTAT-ATACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACG-ATGAT--GA
* * * * *
16898343 GAGCTAGTATAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATG-
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGATGATGA
*
16898391 CTAGCCAGTGTAAGACCATGTCTGGGACATG
1 GT-GCCAGTGTAAGA-CATGTCTGGGACATG
16898422 GCATTGACAA
Statistics
Matches: 210, Mismatches: 37, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
43 1 0.00
44 28 0.13
45 4 0.02
46 23 0.11
47 61 0.29
48 37 0.18
49 42 0.20
50 9 0.04
51 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (47 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGA
Found at i:16898383 original size:141 final size:140
Alignment explanation
Indices: 16898156--16898419 Score: 354
Period size: 139 Copynumber: 1.9 Consensus size: 140
16898146 CACATTATGA
* * *
16898156 GTGCCAGTATAAGACCATGTCTGGAACATGGCATCGACGTAGAGATGAGTGCCAGTGTAAGACAT
1 GTGCCAGTATAAGACCATGTCTGGAACATGGCATCGACGTAGAGACGAGAGCCAGTATAAGACAT
** *
16898221 GTCTGGGACATGCATTGGCCTCGATGATGATAGCCAGTGTAAGA-CGTGTCTGGGACACGCATAG
66 GTCTGGGACATGCATCAGCCTCGATGATGATAGCCAGTGTAAGACCATGTCTGGGACACGCATAG
16898285 GCTAAAAGTT
131 GCTAAAAGTT
* * * * * *
16898295 GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCACGTATATACGAGAGCTAGTATAAGAC
1 GTGCCAGTATAAGACCATGTCTGGAACATGGCATC-G-ACGTAGAGACGAGAGCCAGTATAAGA-
*
16898358 CATGTCTGGGACATGGCATCAGCCTCGATGATGCTAGCCAGTGTAAGACCATGTCTGGGACA
63 CATGTCTGGGACAT-GCATCAGCCTCGATGATGATAGCCAGTGTAAGACCATGTCTGGGACA
16898420 TGGCATTGAC
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
137 5 0.05
138 14 0.13
139 32 0.30
140 14 0.13
141 30 0.28
142 12 0.11
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (140 bp):
GTGCCAGTATAAGACCATGTCTGGAACATGGCATCGACGTAGAGACGAGAGCCAGTATAAGACAT
GTCTGGGACATGCATCAGCCTCGATGATGATAGCCAGTGTAAGACCATGTCTGGGACACGCATAG
GCTAAAAGTT
Found at i:16909939 original size:11 final size:11
Alignment explanation
Indices: 16909923--16909964 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
16909913 TGTTCCACAG
16909923 TTATTTCTTTT
1 TTATTTCTTTT
** *
16909934 TTATTTCACTA
1 TTATTTCTTTT
16909945 TTATTTCTTTT
1 TTATTTCTTTT
16909956 TTA-TTCTTT
1 TTATTTCTTT
16909965 CATATTTTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTCTTTT
Found at i:16911615 original size:62 final size:59
Alignment explanation
Indices: 16911547--16911663 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
16911537 AGTGATTATC
* * *
16911547 TTAATATTAAAGTTAATTTAATGTTTATCTTATAGATAAATATTCTATTAATTTAATAATAT
1 TTAATATTAAAGTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAATAT
*
16911609 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAAGTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
16911664 CTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 23 0.45
60 1 0.02
61 1 0.02
62 26 0.51
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAAGTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAATAT
Found at i:16915062 original size:52 final size:52
Alignment explanation
Indices: 16915006--16915330 Score: 278
Period size: 53 Copynumber: 6.2 Consensus size: 52
16914996 CCTTTTAAAA
* * * * *
16915006 TTAAAAAAAATGGATGCTGGGACACTGATGGTCGACACTCTTGCACCAGATT
1 TTAAAAAAAATGGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
* * * * *
16915058 TTAAAAAAAATAGATGTTGAGACACTGATGGTCGACACCCTAGTACCAGATT
1 TTAAAAAAAATGGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
* * * *
16915110 TTAAAAAAAATTAGGGTGCTGGGACACTTATGG-CTGGCGCTCC-AATACCAAATT
1 TTAAAAAAAA-T-GGGTGCTGGGACACTGATGGTC-GACAC-CCTAGTACCAAATT
* ** *
16915164 TAAAAAAAAATTGGGTGCTGGGACACTGATGAACGACACCCTAGTACCAAAAT
1 TTAAAAAAAA-TGGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
* * * * *
16915217 TTAAAAAAATAAGGGTGTTGGGACACTAATGGTCGACACCTTAGTACTAAA-T
1 TTAAAAAAA-ATGGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
* * * ** * * *
16915269 TTAAAAAAGATTGGGGTGTTGGAACACTGATGGTCGGTACCCCAGTACTATATT
1 TTAAAAAA-AAT-GGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
16915323 TTAAAAAA
1 TTAAAAAA
16915331 TAAATATTTT
Statistics
Matches: 224, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
52 67 0.30
53 106 0.47
54 49 0.22
55 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (52 bp):
TTAAAAAAAATGGGTGCTGGGACACTGATGGTCGACACCCTAGTACCAAATT
Found at i:16928285 original size:34 final size:34
Alignment explanation
Indices: 16928247--16928312 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
16928237 TGTTTGTATT
* *
16928247 TTTTTTTC-AAGATTTATCAGTTTTTAATTTTTAA
1 TTTTTTTCTAA-ATTTATAACTTTTTAATTTTTAA
16928281 TTTTTTTCTAAATTTATAACTTTTTAATTTTT
1 TTTTTTTCTAAATTTATAACTTTTTAATTTTT
16928313 TAAAATATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (34 bp):
TTTTTTTCTAAATTTATAACTTTTTAATTTTTAA
Found at i:16932040 original size:22 final size:21
Alignment explanation
Indices: 16932007--16932047 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16931997 TTAAAAATTG
16932007 AAAAATAAAAATAAATATATA
1 AAAAATAAAAATAAATATATA
* *
16932028 AAAAATCATAAATATATATA
1 AAAAAT-AAAAATAAATATA
16932048 ATCTAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATAAATATATA
Found at i:16932064 original size:20 final size:18
Alignment explanation
Indices: 16932043--16932077 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16932033 TCATAAATAT
*
16932043 ATATAATCTAGAAAAAGA
1 ATATAAACTAGAAAAAGA
*
16932061 ATATAAACTATAAAAAG
1 ATATAAACTAGAAAAAG
16932078 TTTATAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (18 bp):
ATATAAACTAGAAAAAGA
Found at i:16932173 original size:21 final size:21
Alignment explanation
Indices: 16932148--16932192 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16932138 ATATTATTAC
16932148 AAAAATGTAAAAAAAAAGTTGT
1 AAAAAT-TAAAAAAAAAGTTGT
* *
16932170 AAAAATTATAAAAAAATTTGT
1 AAAAATTAAAAAAAAAGTTGT
16932191 AA
1 AA
16932193 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAATTAAAAAAAAAGTTGT
Found at i:16932234 original size:23 final size:22
Alignment explanation
Indices: 16932208--16932266 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
16932198 TTGAAGTTTA
*
16932208 AAAATATTTTTTTATAAAATTCT
1 AAAA-ATTTATTTATAAAATTCT
* * *
16932231 AAAACATATAATTCTAAAATTCT
1 AAAA-ATTTATTTATAAAATTCT
16932254 AAAAATTTATTTA
1 AAAAATTTATTTA
16932267 AATTTGATTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATTTATTTATAAAATTCT
Found at i:16932365 original size:7 final size:7
Alignment explanation
Indices: 16932355--16932398 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
16932345 ATTTTGATTT
*
16932355 TTTAAAA
1 TTTATAA
*
16932362 TTTAAAA
1 TTTATAA
16932369 TTATATAA
1 TT-TATAA
16932377 TTTATAA
1 TTTATAA
16932384 TTTATAA
1 TTTATAA
16932391 TTTTATAA
1 -TTTATAA
16932399 AAATTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 21 0.62
8 13 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TTTATAA
Found at i:16932380 original size:15 final size:14
Alignment explanation
Indices: 16932355--16932393 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
16932345 ATTTTGATTT
*
16932355 TTTAAAATTTAAAA
1 TTTATAATTTAAAA
*
16932369 TTATATAATTTATAA
1 TT-TATAATTTAAAA
16932384 TTTATAATTT
1 TTTATAATTT
16932394 TATAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATAATTTAAAA
Found at i:16932385 original size:22 final size:22
Alignment explanation
Indices: 16932355--16932398 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16932345 ATTTTGATTT
16932355 TTTAAAATTTAAAATTATATAA
1 TTTAAAATTTAAAATTATATAA
* * *
16932377 TTTATAATTTATAATTTTATAA
1 TTTAAAATTTAAAATTATATAA
16932399 AAATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAAATTTAAAATTATATAA
Found at i:16932395 original size:15 final size:15
Alignment explanation
Indices: 16932360--16932398 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
16932350 GATTTTTTAA
*
16932360 AATTTAAAATTATAT
1 AATTTATAATTATAT
16932375 AATTTATAATT-TAT
1 AATTTATAATTATAT
16932389 AATTTTATAA
1 AA-TTTATAA
16932399 AAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTATAATTATAT
Found at i:16932728 original size:30 final size:30
Alignment explanation
Indices: 16932694--16932766 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
16932684 AATATTTTTA
*
16932694 TAAAATTATAAAATATATAAT-TTTAAATTT
1 TAAAATTATAAAATA-ATAATATATAAATTT
*
16932724 TAAAA-AAGTAAAA-AATAATATATAAATTT
1 TAAAATTA-TAAAATAATAATATATAAATTT
16932753 TAAAAATTA-AAAAT
1 T-AAAATTATAAAAT
16932767 GTTTACAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
28 5 0.14
29 15 0.43
30 14 0.40
31 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
TAAAATTATAAAATAATAATATATAAATTT
Found at i:16932878 original size:25 final size:25
Alignment explanation
Indices: 16932822--16932885 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
16932812 TTTGTAAATT
* * * *
16932822 TATTTCTATAAATTTTATTTTTCTA
1 TATTTATATATATTTGATTTTTATA
*
16932847 GATTTTATATATATTTGATTTTTATA
1 TA-TTTATATATATTTGATTTTTATA
*
16932873 TATTTATTTATAT
1 TATTTATATATAT
16932886 ATTATAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (25 bp):
TATTTATATATATTTGATTTTTATA
Found at i:16947982 original size:12 final size:11
Alignment explanation
Indices: 16947959--16947992 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
16947949 GTCAAATTTG
*
16947959 ATTAAGTTTAA
1 ATTATGTTTAA
16947970 ATTATGATTTAA
1 ATTATG-TTTAA
16947982 ATTATGTTTAA
1 ATTATGTTTAA
16947993 TAATAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (11 bp):
ATTATGTTTAA
Found at i:16949230 original size:28 final size:28
Alignment explanation
Indices: 16949179--16949233 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
16949169 GCAGGGGTTT
16949179 TCACACAGCCTGACACACGTCCATGTCCC
1 TCACACAGCCTGACACACG-CCATGTCCC
*
16949208 TCACACGGCCATGACACAC-CCATGTC
1 TCACACAGCC-TGACACACGCCATGTC
16949234 TTAGCCCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.25, C:0.44, G:0.15, T:0.16
Consensus pattern (28 bp):
TCACACAGCCTGACACACGCCATGTCCC
Found at i:16951939 original size:38 final size:36
Alignment explanation
Indices: 16951871--16951941 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
16951861 AAGCTTAATC
* * *
16951871 CAAAATATATATATTTAAAATCATTTAATTCATATA
1 CAAAATATATATATATAAAATCAATAAATTCATATA
16951907 CAAAATATATATATATAACATATCAATAAATTCAT
1 CAAAATATATATATATAA-A-ATCAATAAATTCAT
16951942 TATTGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 17 0.57
37 1 0.03
38 12 0.40
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (36 bp):
CAAAATATATATATATAAAATCAATAAATTCATATA
Found at i:16954056 original size:46 final size:46
Alignment explanation
Indices: 16953890--16954063 Score: 251
Period size: 46 Copynumber: 3.8 Consensus size: 46
16953880 GATGCCATAA
* * * *
16953890 TATCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGG
** * * *
16953936 TATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
16953982 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
16954028 TATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TATCTTTCAACCATGGTCTTACACATTTCATATCAG
16954064 AGAGCACACT
Statistics
Matches: 118, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.03
46 114 0.97
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
Found at i:16956188 original size:11 final size:11
Alignment explanation
Indices: 16956172--16956232 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 11
16956162 CTTTATATAC
16956172 TAATAAAATAA
1 TAATAAAATAA
16956183 TAATAAAATATA
1 TAATAAAATA-A
*
16956195 TTATTAAAATATA
1 -TAATAAAATA-A
* *
16956208 TTATTAAAATAT
1 -TAATAAAATAA
16956220 TAATAAAATAA
1 TAATAAAATAA
16956231 TA
1 TA
16956233 TTTATCTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
11 21 0.48
12 1 0.02
13 22 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:16956204 original size:13 final size:13
Alignment explanation
Indices: 16956186--16956219 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
16956176 AAAATAATAA
16956186 TAAAATATATTAT
1 TAAAATATATTAT
16956199 TAAAATATATTAT
1 TAAAATATATTAT
16956212 TAAAATAT
1 TAAAATAT
16956220 TAATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATATATTAT
Found at i:16957709 original size:16 final size:16
Alignment explanation
Indices: 16957688--16957718 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16957678 TTTAATCCAA
16957688 AAACACATAAATGGGC
1 AAACACATAAATGGGC
16957704 AAACACATAAATGGG
1 AAACACATAAATGGG
16957719 AAAATTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (16 bp):
AAACACATAAATGGGC
Found at i:16958176 original size:17 final size:16
Alignment explanation
Indices: 16958154--16958187 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16958144 TCGAACCTAG
16958154 CTTTTGTTGTTTCTTTT
1 CTTTTGTT-TTTCTTTT
*
16958171 CTTTTGTTTTTGTTTT
1 CTTTTGTTTTTCTTTT
16958187 C
1 C
16958188 GGTGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (16 bp):
CTTTTGTTTTTCTTTT
Found at i:16958736 original size:49 final size:48
Alignment explanation
Indices: 16958650--16958767 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 48
16958640 CAATGCCATG
*
16958650 TCCCAGACAGGTCTTACACTGACTTTCATATAACGAGGCGGATGACATA
1 TCCCAGACAGGTCTTACACTGACTTTCATATAACGAGGCCGATG-CATA
** *
16958699 TCCCAGACAGGTCTTACACT-AGCTTGT-ATATCTCGAGGCCGATGCATG
1 TCCCAGACAGGTCTTACACTGA-CTT-TCATATAACGAGGCCGATGCATA
* * *
16958747 TCCTAAACATGTCTTACACTG
1 TCCCAGACAGGTCTTACACTG
16958768 GCTCTCATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 21 0.36
49 37 0.63
50 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (48 bp):
TCCCAGACAGGTCTTACACTGACTTTCATATAACGAGGCCGATGCATA
Found at i:16959886 original size:21 final size:21
Alignment explanation
Indices: 16959848--16959887 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16959838 AGTCCTTTTT
*
16959848 TAAAATTAAGCTCACAAATGC
1 TAAAATTAACCTCACAAATGC
16959869 TAAAATT-ACCTCACCAAAT
1 TAAAATTAACCTCA-CAAAT
16959888 TTTTCATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAAATTAACCTCACAAATGC
Found at i:16964313 original size:19 final size:19
Alignment explanation
Indices: 16964289--16964326 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16964279 TTGCAGAATG
16964289 ATAGTTTAATATAGTCAAT
1 ATAGTTTAATATAGTCAAT
16964308 ATAGTTTAATATAGTCAAT
1 ATAGTTTAATATAGTCAAT
16964327 GTTAGGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
ATAGTTTAATATAGTCAAT
Found at i:16964318 original size:10 final size:10
Alignment explanation
Indices: 16964289--16964322 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
16964279 TTGCAGAATG
16964289 ATAGTTTAAT
1 ATAGTTTAAT
*
16964299 ATAG-TCAAT
1 ATAGTTTAAT
16964308 ATAGTTTAAT
1 ATAGTTTAAT
16964318 ATAGT
1 ATAGT
16964323 CAATGTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (10 bp):
ATAGTTTAAT
Found at i:16973731 original size:3 final size:3
Alignment explanation
Indices: 16973723--16973760 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16973713 ATCACATGTT
16973723 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16973761 TGGATGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16973842 original size:73 final size:73
Alignment explanation
Indices: 16973761--16973946 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
16973751 TATTATTATT
*
16973761 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
16973826 ATTTTAAG
66 ATTTTAAG
16973834 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
16973899 ATTTTAAG
66 ATTTTAAG
16973907 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
16973947 GTCAAGTTGT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:16978264 original size:73 final size:73
Alignment explanation
Indices: 16978182--16978367 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
16978172 TATTATTATT
* *
16978182 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
16978247 ATTTTAAG
66 ATTTTAAG
16978255 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
16978320 ATTTTAAG
66 ATTTTAAG
16978328 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
16978368 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAAGTGGTGATTT
ATTTTAAG
Found at i:16982766 original size:23 final size:23
Alignment explanation
Indices: 16982740--16982784 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
16982730 TTTTGATTTT
16982740 TTTTATAT-TTCATAAAATTTAGC
1 TTTTATATCTTCA-AAAATTTAGC
*
16982763 TTTTATATCTTCAAAATTTTAG
1 TTTTATATCTTCAAAAATTTAG
16982785 AATTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTATATCTTCAAAAATTTAGC
Found at i:16984186 original size:23 final size:23
Alignment explanation
Indices: 16984160--16984203 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16984150 TCTATCGGAA
*
16984160 ATAAATTTCTTAAACTAAATTAC
1 ATAAATATCTTAAACTAAATTAC
* *
16984183 ATAAATATCTTTAATTAAATT
1 ATAAATATCTTAAACTAAATT
16984204 TATCTTTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATATCTTAAACTAAATTAC
Found at i:16990709 original size:18 final size:18
Alignment explanation
Indices: 16990688--16990724 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16990678 TTGGTAGATT
*
16990688 TATATTAATAAGTTTATA
1 TATATTAATAAATTTATA
16990706 TATATTAATAAATTTATA
1 TATATTAATAAATTTATA
16990724 T
1 T
16990725 TTTAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTAATAAATTTATA
Found at i:16990723 original size:16 final size:18
Alignment explanation
Indices: 16990688--16990729 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16990678 TTGGTAGATT
*
16990688 TATATTAATAAGTTTATA
1 TATATTAATAAGATTATA
16990706 TATATTAATAA-ATT-TA
1 TATATTAATAAGATTATA
*
16990722 TATTTTAA
1 TATATTAA
16990730 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 2 0.09
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATATTAATAAGATTATA
Found at i:16991082 original size:23 final size:23
Alignment explanation
Indices: 16991056--16991100 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
16991046 CAACCTTGAG
16991056 AAAATTTTTGAAGTCAAATTATT
1 AAAATTTTTGAAGTCAAATTATT
16991079 AAAATTTTTGAAGTCAAATTAT
1 AAAATTTTTGAAGTCAAATTAT
16991101 ACTTAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (23 bp):
AAAATTTTTGAAGTCAAATTATT
Found at i:16993795 original size:21 final size:21
Alignment explanation
Indices: 16993771--16993813 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16993761 AAGAGTAAGC
16993771 GTACCTTGAGAATAAAATGAG
1 GTACCTTGAGAATAAAATGAG
*
16993792 GTACCTTGAGAATAAGATGAG
1 GTACCTTGAGAATAAAATGAG
16993813 G
1 G
16993814 ATTGAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.28, T:0.23
Consensus pattern (21 bp):
GTACCTTGAGAATAAAATGAG
Found at i:16994203 original size:18 final size:18
Alignment explanation
Indices: 16994180--16994230 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
16994170 GCAACCCAAG
*
16994180 GGGAAGAGAAAAGGGAAA
1 GGGAAGAGGAAAGGGAAA
* * *
16994198 GGGAAGGGGAAGGGGAAG
1 GGGAAGAGGAAAGGGAAA
16994216 GGGAAGAGGAAAGGG
1 GGGAAGAGGAAAGGG
16994231 GAGAAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
GGGAAGAGGAAAGGGAAA
Found at i:16994207 original size:12 final size:12
Alignment explanation
Indices: 16994192--16994232 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
16994182 GAAGAGAAAA
16994192 GGGAAAGGGAAG
1 GGGAAAGGGAAG
*
16994204 GGGAAGGGGAAG
1 GGGAAAGGGAAG
*
16994216 GGGAAGAGGAAAG
1 GGGAA-AGGGAAG
16994229 GGGA
1 GGGA
16994233 GAAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (12 bp):
GGGAAAGGGAAG
Found at i:16999790 original size:46 final size:46
Alignment explanation
Indices: 16999703--16999791 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
16999693 ATCTTGACTT
**
16999703 ACACCTACAAAGTACGAGTCAAAGTTACATTATTAGGAAAAACGAG
1 ACACCTACAAAGTACGAGTCAAAGTTACATTATTAACAAAAACGAG
* *
16999749 ACACCTGCAAAGTACGAGTCAAAGTTACGTTATTAACAAAAAC
1 ACACCTACAAAGTACGAGTCAAAGTTACATTATTAACAAAAAC
16999792 AAAGACCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (46 bp):
ACACCTACAAAGTACGAGTCAAAGTTACATTATTAACAAAAACGAG
Found at i:17002579 original size:22 final size:22
Alignment explanation
Indices: 17002553--17002603 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
17002543 AAATTTTAGT
17002553 GCGCTTATCGTCTTGCGCTTTA
1 GCGCTTATCGTCTTGCGCTTTA
17002575 GCGCTTATCGTCTTGCGCTTTA
1 GCGCTTATCGTCTTGCGCTTTA
*
17002597 GTGCTTA
1 GCGCTTA
17002604 CTGTTTCGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.41
Consensus pattern (22 bp):
GCGCTTATCGTCTTGCGCTTTA
Found at i:17002622 original size:22 final size:22
Alignment explanation
Indices: 17002598--17002674 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
17002588 TGCGCTTTAG
*
17002598 TGCTTACTGTTTCGCACTTCGG
1 TGCTTACTGTTTCGCACTTCGA
* *
17002620 TGCTTA-TCGTTCCGCACTTCAA
1 TGCTTACT-GTTTCGCACTTCGA
*
17002642 TGCTTACTGTTTTGCACTTCGA
1 TGCTTACTGTTTCGCACTTCGA
*
17002664 TGCCTACTGTT
1 TGCTTACTGTT
17002675 ATATTAGTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.96
23 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.18, T:0.42
Consensus pattern (22 bp):
TGCTTACTGTTTCGCACTTCGA
Found at i:17003295 original size:16 final size:16
Alignment explanation
Indices: 17003271--17003303 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17003261 CGAAACAGGG
17003271 AGAAAAAGAAA-GAAA
1 AGAAAAAGAAAGGAAA
17003286 AGAAAGAAGAAAGGAAA
1 AGAAA-AAGAAAGGAAA
17003303 A
1 A
17003304 ATTAAGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGGAAA
Found at i:17004313 original size:40 final size:39
Alignment explanation
Indices: 17004192--17004326 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 39
17004182 GACTTCGAGT
*
17004192 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATATATT
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGAAT-TATC
* ** *
17004233 CGATGAGGCACTGGGTGTCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
17004270 CGATGAGACACTGGGTGTCAACTTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGAATTATC
**
17004310 CGATGAGGTACTGGGTG
1 CGATGAGACACTGGGTG
17004327 CCAAACTGGT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
37 22 0.28
38 9 0.11
39 2 0.03
40 27 0.34
41 20 0.25
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
Found at i:17008745 original size:31 final size:30
Alignment explanation
Indices: 17008710--17008812 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
17008700 AACCAGTCTG
*
17008710 TTTGGGTGTGTGTATAACGGGTCTGGGCTAT
1 TTTGGGT-TGTGTGTAACGGGTCTGGGCTAT
*
17008741 TTTGGGTT-TGCTGTAACGGGTCTGAGCTAT
1 TTTGGGTTGTG-TGTAACGGGTCTGGGCTAT
17008771 TTTGGGTT-TGTTGTAACGGGTCTGAGG-TA-
1 TTTGGGTTGTG-TGTAACGGGTCTG-GGCTAT
17008800 TTTGGGCTTGTGT
1 TTTGGG-TTGTGT
17008813 TTGGGCTCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
29 8 0.12
30 46 0.72
31 10 0.16
ACGTcount: A:0.12, C:0.10, G:0.37, T:0.42
Consensus pattern (30 bp):
TTTGGGTTGTGTGTAACGGGTCTGGGCTAT
Found at i:17008760 original size:30 final size:30
Alignment explanation
Indices: 17008724--17008802 Score: 124
Period size: 30 Copynumber: 2.6 Consensus size: 30
17008714 GGTGTGTGTA
17008724 TAACGGGTCTGGGCTATTTTGGGTTTGCTG
1 TAACGGGTCTGGGCTATTTTGGGTTTGCTG
* *
17008754 TAACGGGTCTGAGCTATTTTGGGTTTGTTG
1 TAACGGGTCTGGGCTATTTTGGGTTTGCTG
17008784 TAACGGGTCTGAGG-TATTT
1 TAACGGGTCTG-GGCTATTT
17008803 GGGCTTGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 44 0.98
31 1 0.02
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.41
Consensus pattern (30 bp):
TAACGGGTCTGGGCTATTTTGGGTTTGCTG
Found at i:17009024 original size:21 final size:20
Alignment explanation
Indices: 17008998--17009059 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
17008988 TATTTTATAG
*
17008998 ACTCTAAATCTTGAACCTCAA
1 ACTCTAAA-CTCGAACCTCAA
17009019 ACTCTAAACCTCGAACC-CTAA
1 ACTCTAAA-CTCGAACCTC-AA
*
17009040 ACACTAAACTCGAA-CTCAA
1 ACTCTAAACTCGAACCTCAA
17009059 A
1 A
17009060 TCTCAAACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.11
20 8 0.22
21 24 0.67
ACGTcount: A:0.42, C:0.32, G:0.05, T:0.21
Consensus pattern (20 bp):
ACTCTAAACTCGAACCTCAA
Found at i:17009056 original size:34 final size:34
Alignment explanation
Indices: 17009018--17009103 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
17009008 TTGAACCTCA
*
17009018 AACTCTAAACCTCGAACCCT-AAACACTAAACTCG
1 AACTC-AAACCTCAAACCCTCAAACACTAAACTCG
* * *
17009052 AACTCAAATCTCAAACCCTCAAACCCTAAACTATG
1 AACTCAAACCTCAAACCCTCAAACACTAAACT-CG
* *
17009087 ATCTCAAACCTTAAACC
1 AACTCAAACCTCAAACC
17009104 TTAAAGTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 12 0.28
34 16 0.37
35 15 0.35
ACGTcount: A:0.42, C:0.35, G:0.03, T:0.20
Consensus pattern (34 bp):
AACTCAAACCTCAAACCCTCAAACACTAAACTCG
Found at i:17009118 original size:28 final size:29
Alignment explanation
Indices: 17009058--17009118 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
17009048 CTCGAACTCA
17009058 AATCTCAAACCCTCAAACCCTAAACTATG
1 AATCTCAAACCCTCAAACCCTAAACTATG
* * * *
17009087 -ATCTCAAA-CCTTAAACCTTAAAGTTTG
1 AATCTCAAACCCTCAAACCCTAAACTATG
17009114 AATCT
1 AATCT
17009119 TGAACTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (29 bp):
AATCTCAAACCCTCAAACCCTAAACTATG
Found at i:17009250 original size:13 final size:13
Alignment explanation
Indices: 17009175--17009251 Score: 57
Period size: 14 Copynumber: 5.8 Consensus size: 13
17009165 TAGGGTTCAG
17009175 TTTGGGTTTGAGA
1 TTTGGGTTTGAGA
* *
17009188 TTTAGGGTTTAAAA
1 TTT-GGGTTTGAGA
**
17009202 TTTGGGTTCAAG-
1 TTTGGGTTTGAGA
* * *
17009214 GTTAGGTTCGAGA
1 TTTGGGTTTGAGA
*
17009227 TTTAGGATTTGAGA
1 TTT-GGGTTTGAGA
17009241 TTTGGGTTTGA
1 TTTGGGTTTGA
17009252 ATTCGAAGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
12 9 0.18
13 19 0.39
14 21 0.43
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (13 bp):
TTTGGGTTTGAGA
Found at i:17017885 original size:17 final size:17
Alignment explanation
Indices: 17017863--17017901 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17017853 ATTTTGCCAT
*
17017863 TTTTTTTAAGGTTAGGA
1 TTTTTTAAAGGTTAGGA
*
17017880 TTTTTTAAAGGTTAGGG
1 TTTTTTAAAGGTTAGGA
17017897 TTTTT
1 TTTTT
17017902 GGTAGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (17 bp):
TTTTTTAAAGGTTAGGA
Found at i:17018220 original size:115 final size:113
Alignment explanation
Indices: 17018078--17018302 Score: 364
Period size: 115 Copynumber: 2.0 Consensus size: 113
17018068 GGTTAGGATT
* *
17018078 TTAGTGGTTTAAGGGTTTTAGTGTTTTTTAAGGGAAAAATTAATAAACACTTAGAGTTGAGGGTT
1 TTAGTGGCTTAAGGGTTTTAGTGTTTTTTAAGAGAAAAATTAATAAACACTTAGAGTTGAGGGTT
*
17018143 AGTTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGC
66 AATTAATTAAATTAACTATGAAAAT-A-AAAAAATCAATTAAATTAGGGC
*
17018193 TTAGTGGCTT-AGGGTTTTTAAG-GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGG
1 TTAGTGGCTTAAGGG-TTTT-AGTGTTTTTTAAGAGAAAAATTAATAAACACTTAGAGTTGAGGG
17018256 TTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
64 TTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
17018303 TGTTTAGGGT
Statistics
Matches: 104, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
113 19 0.18
114 5 0.05
115 78 0.75
116 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (113 bp):
TTAGTGGCTTAAGGGTTTTAGTGTTTTTTAAGAGAAAAATTAATAAACACTTAGAGTTGAGGGTT
AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGC
Found at i:17018370 original size:161 final size:163
Alignment explanation
Indices: 17018193--17018634 Score: 685
Period size: 161 Copynumber: 2.7 Consensus size: 163
17018183 AAATTAGGGC
* *
17018193 TTAGTGGCTTAGGGTTTTTAAG-GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGT
1 TTAGTGGTTTAGGGTTTTT-AGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGT
* *
17018257 TAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGTGTTTAGGGTTTTTT-AGA
65 TAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGA
*
17018321 GTTAAGTTTTTTGATTG-TT-TTAGGGTTAGGGTT
130 -TTAAGGTTTTTGATTGTTTGTTAGGGTTAGGGTT
*
17018354 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGATGGTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
17018419 AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGAT
66 AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGAT
*
17018484 TAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTT
131 TAAGGTTTTTGATTG-TTT---GTTAGGGTTAGGGTT
* * * *
17018521 TTAGTGGTTTAGGGTTTTTAGTGTTTTTAAAGGGAAAAATTAACGACCACTTGGAGTTGAGGGTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
17018586 AATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGG
66 AATTAATTAAATTAACTATGAAAAT-A-AAAAAATCAATTAAATTAGGG
17018635 CTTAGTGGTT
Statistics
Matches: 259, Mismatches: 12, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
160 2 0.01
161 131 0.51
162 3 0.01
163 2 0.01
167 99 0.38
168 1 0.00
169 21 0.08
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (163 bp):
TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGAT
TAAGGTTTTTGATTGTTTGTTAGGGTTAGGGTT
Found at i:17018379 original size:16 final size:16
Alignment explanation
Indices: 17018337--17018376 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
17018327 TTTTTTGATT
17018337 GTTTTAG-GG-TTAGG
1 GTTTTAGTGGTTTAGG
17018351 GTTTTAGTGGTTTAGG
1 GTTTTAGTGGTTTAGG
17018367 GTTTTTAGTG
1 G-TTTTAGTG
17018377 TTTTTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 6 0.26
17 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (16 bp):
GTTTTAGTGGTTTAGG
Found at i:17018431 original size:276 final size:274
Alignment explanation
Indices: 17017931--17018465 Score: 887
Period size: 276 Copynumber: 1.9 Consensus size: 274
17017921 TGGTTTAAGA
* *
17017931 TTTTTAGGGTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTTAGGGTTAATTAATTAAATTAA
1 TTTTTAGGGTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAA
*
17017996 CTATAAAAATAAAAAAAACTAATTAAATTAGGGTTTAGGGATTTTTAAGATTAGGGTTTTTGATT
66 CTATAAAAATAAAAAAAACTAATTAAATTAGGGTTTAGGGATTTTTAAGATTAAGGTTTTTGATT
17018061 GTTTTAGGGTTAGGATTTTAGTGGTTTAAGGGTTTTAGTGTTTTTTAAGGGAAAAATTAATAAAC
131 GTTTTAGGGTTAGGATTTTAGTGGTTTAAGGGTTTTAGTGTTTTTTAAGGGAAAAATTAATAAAC
*
17018126 ACTTAGAGTTGAGGGTTAGTTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGG
196 ACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAAT-A-AAAAAATCAATTAAATTAGG
17018191 GCTTAGTGGCTTAGGG
259 GCTTAGTGGCTTAGGG
*
17018207 TTTTTAAGGTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTA
1 TTTTT-AGGGTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTA
* * * * *
17018272 ACTATGAAAATAAAAAAATC-AATTAAATTAGTGTTTAGGG-TTTTTTAGAGTTAAGTTTTTTGA
65 ACTATAAAAATAAAAAAAACTAATTAAATTAGGGTTTAGGGATTTTTAAGA-TTAAGGTTTTTGA
* *
17018335 TTGTTTTAGGGTTAGGGTTTTAGTGGTTT-AGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATG
129 TTGTTTTAGGGTTAGGATTTTAGTGGTTTAAGGG-TTTTAGTGTTTTTTAAGGGAAAAATTAATA
*
17018399 AACACTTAGAGTTGATGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
193 AACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
17018464 GG
258 GG
17018466 TTTAAGGTTT
Statistics
Matches: 243, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
274 21 0.09
275 13 0.05
276 135 0.56
277 74 0.30
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (274 bp):
TTTTTAGGGTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAA
CTATAAAAATAAAAAAAACTAATTAAATTAGGGTTTAGGGATTTTTAAGATTAAGGTTTTTGATT
GTTTTAGGGTTAGGATTTTAGTGGTTTAAGGGTTTTAGTGTTTTTTAAGGGAAAAATTAATAAAC
ACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGC
TTAGTGGCTTAGGG
Found at i:17018675 original size:282 final size:275
Alignment explanation
Indices: 17018354--17018909 Score: 902
Period size: 282 Copynumber: 2.0 Consensus size: 275
17018344 GGTTAGGGTT
* *
17018354 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGATGGTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTT
17018419 AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTA-AGA
66 AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAG-
* * *
17018483 TTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGTTTAGGGTTTTTAGTGTTTT
130 TTAGGATTTTTGATTG--TT----TTAGGGTTAGGGTTTTAGTGGTTTAGAGTTTTTAGTATTTT
* * * *
17018548 TAAAGG-GAAAAATTAACGACCACTTGGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAATA
189 T-AAGGAAAAAAATTAACGAACACTTAGAGTTGAGGGCTAATTAATTAAATTAACTATGAAAATA
17018612 AGAAAAAATCAATTAAATTAGGGC
253 A-AAAAAATCAATTAAATTAGGGC
17018636 TTAGTGGTTTAGGGTTTTTAAG-GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGT
1 TTAGTGGTTTAGGGTTTTT-AGTGTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGT
17018700 TAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAG
65 TAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAG
17018765 TTAGGATTTTTGATTGTTTTAGGGTTAGGGTTTTAGTGGTTTAGAGTTTTTAGTATTTTTAAGGA
130 TTAGGATTTTTGATTGTTTTAGGGTTAGGGTTTTAGTGGTTTAGAGTTTTTAGTATTTTTAAGGA
* *
17018830 AAAAAATTAATGAACACTTAGAGTTGATGGCTAATTAATTAAATTAACTATGAAAATAAAAAAAA
195 AAAAAATTAACGAACACTTAGAGTTGAGGGCTAATTAATTAAATTAACTATGAAAATAAAAAAAA
17018895 TCAATTAAATTAGGG
260 TCAATTAAATTAGGG
17018910 TTTAAAGTTT
Statistics
Matches: 260, Mismatches: 11, Indels: 13
0.92 0.04 0.05
Matches are distributed among these distances:
275 25 0.10
276 93 0.36
280 2 0.01
282 136 0.52
283 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.39
Consensus pattern (275 bp):
TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTT
AATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAGT
TAGGATTTTTGATTGTTTTAGGGTTAGGGTTTTAGTGGTTTAGAGTTTTTAGTATTTTTAAGGAA
AAAAATTAACGAACACTTAGAGTTGAGGGCTAATTAATTAAATTAACTATGAAAATAAAAAAAAT
CAATTAAATTAGGGC
Found at i:17018732 original size:443 final size:443
Alignment explanation
Indices: 17018027--17019092 Score: 1827
Period size: 443 Copynumber: 2.4 Consensus size: 443
17018017 ATTAAATTAG
* *
17018027 GGTTTAGGGATTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTA-GG--A---TTTTAGTGGT
1 GGTTTAAGGTTTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGT
* * *
17018086 TTAAGGG-TTTTAGTGTTTTTTAAGGGAAAAATTAATAAACACTTAGAGTTGAGGGTTAGTTAAT
66 TT-AGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTGGAGTTGAGGGTTAATTAAT
*
17018150 TAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGCTTAGGGTTTTTAAG
130 TAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAAG
17018215 GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAA
195 GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAA
* * *
17018280 AATAAAAAAATCAATTAAATTAGTGTTTAGGGTTTTTTAGAGTTAAGTTTTTTGATTGTTTTAGG
260 AATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAGTTAAGATTTTTGATTGTTTTAGG
*
17018345 GTTAGGGTTTTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAG
325 GTTAGGGTTTTAGTGGTTTAGGGTTTTTAGTGATTTTTAAGGGAAAAATTAATGAACACTTAGAG
17018410 TTGATGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
390 TTGATGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
17018464 GGTTTAAGGTTTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGT
1 GGTTTAAGGTTTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGT
* * *
17018529 TTAGGGTTTTTAGTGTTTTTAAAGGGAAAAATTAACGACCACTTGGAGTTGAGGGTTAATTAATT
66 TTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTGGAGTTGAGGGTTAATTAATT
17018594 AAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAAGG
131 AAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAAGG
17018659 TTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAA
196 TTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAA
*
17018724 ATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAGTTAGGATTTTTGATTGTTTTAGGG
261 ATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAGTTAAGATTTTTGATTGTTTTAGGG
* *
17018789 TTAGGGTTTTAGTGGTTTAGAGTTTTTAGT-ATTTTTAAGGAAAAAAATTAATGAACACTTAGAG
326 TTAGGGTTTTAGTGGTTTAGGGTTTTTAGTGATTTTTAAGG-GAAAAATTAATGAACACTTAGAG
*
17018853 TTGATGGCTAATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAG
390 TTGATGGTTAATTAATTAAATTAACTATGAAAAT-AAAAAAATCAATTAAATTAG
* *
17018908 GGTTTAAAGTTTTTTAAGATTAGGGTTTTTTATTG--TT----TTAGGGTTAGGGTTTTAGTGGT
1 GGTTTAAGGTTTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGT
*
17018967 TTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGATCACTTGGAGTTGAGGGTTAATTAATT
66 TTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTGGAGTTGAGGGTTAATTAATT
17019032 AAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTT
131 AAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTT
17019093 TGGTGGTTTA
Statistics
Matches: 598, Mismatches: 22, Indels: 17
0.94 0.03 0.03
Matches are distributed among these distances:
437 44 0.07
438 147 0.25
440 1 0.00
442 15 0.03
443 338 0.57
444 53 0.09
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (443 bp):
GGTTTAAGGTTTTTTAAGATTAGGGTTTTTGATTGTTTTAGGGTTAGGGTTAGGGTTTTAGTGGT
TTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTGGAGTTGAGGGTTAATTAATT
AAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAAGG
TTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAA
ATAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGAGTTAAGATTTTTGATTGTTTTAGGG
TTAGGGTTTTAGTGGTTTAGGGTTTTTAGTGATTTTTAAGGGAAAAATTAATGAACACTTAGAGT
TGATGGTTAATTAATTAAATTAACTATGAAAATAAAAAAATCAATTAAATTAG
Found at i:17018762 original size:115 final size:115
Alignment explanation
Indices: 17018521--17018747 Score: 379
Period size: 115 Copynumber: 2.0 Consensus size: 115
17018511 GGTTAGGGTT
* * *
17018521 TTAGTGGTTTAGGGTTTTTAGTGTTTTTAAAGGGAAAAATTAACGACCACTTGGAGTTGAGGGTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTAAAGAGAAAAATTAACGAACACTTAGAGTTGAGGGTT
17018586 AATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGC
66 AATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGC
* *
17018636 TTAGTGGTTTAGGGTTTTTAAG-GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGT
1 TTAGTGGTTTAGGGTTTTT-AGTGTTTTTAAAGAGAAAAATTAACGAACACTTAGAGTTGAGGGT
17018700 TAATTAATTAAATTAACTATGAAAAT-A-AAAAAATCAATTAAATTAGGG
65 TAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGG
17018748 TTTAAGGTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
113 21 0.20
114 1 0.01
115 82 0.77
116 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.35
Consensus pattern (115 bp):
TTAGTGGTTTAGGGTTTTTAGTGTTTTTAAAGAGAAAAATTAACGAACACTTAGAGTTGAGGGTT
AATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGC
Found at i:17018969 original size:162 final size:161
Alignment explanation
Indices: 17018636--17019233 Score: 800
Period size: 162 Copynumber: 3.8 Consensus size: 161
17018626 AAATTAGGGC
*
17018636 TTAGTGGTTTAGGGTTTTTAAG-GTTTTTTAAGAGAAAAATTAATGAACACTTAGAGTTGAGGGT
1 TTAGTGGTTTAGGGTTTTT-AGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGT
*
17018700 TAATTAATTAAATTAACTATGAAAAT-AAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAGA
65 TAATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTTTTAGA
* *
17018764 GTTAGGATTTTTGATTGTTTTAGGGTTAGGGTT
130 -TTAGGGTTTTTTATTGTTTTAGGGTTAGGGTT
* * * * *
17018797 TTAGTGGTTTAGAGTTTTTAGT-ATTTTTAAGGAAAAAAATTAATGAACACTTAGAGTTGATGGC
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGG-GAAAAATTAATGAACACTTAGAGTTGAGGGT
17018861 TAATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTTTTAAG
65 TAATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTTTT-AG
17018926 ATTAGGGTTTTTTATTGTTTTAGGGTTAGGGTT
129 ATTAGGGTTTTTTATTGTTTTAGGGTTAGGGTT
* *
17018959 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGATCACTTGGAGTTGAGGGTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
* * *
17019024 AATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTT--AG-----TGGT
66 AATTAATTAAATTAACTATGAAAATAA-AAAAAATCAATTAAATTAGGGTTTAAAGTTTTTTAGA
** * *
17019082 TTAGGGTTTTTTGGTGGTTTA-----AGGTTT
130 TTAGGGTTTTTTATTGTTTTAGGGTTAGGGTT
* ** * *
17019109 TTAATGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATTTA-A-TTAGAGTTCAGGTTT
1 TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
**
17019172 AATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTA-GGTTTAGGGTTTTTTAG
66 AATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTTTTAG
17019234 TGTTTATTAA
Statistics
Matches: 391, Mismatches: 33, Indels: 34
0.85 0.07 0.07
Matches are distributed among these distances:
146 4 0.01
147 18 0.05
148 40 0.10
149 1 0.00
150 48 0.12
153 2 0.01
155 19 0.05
156 1 0.00
160 10 0.03
161 74 0.19
162 139 0.36
163 35 0.09
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.41
Consensus pattern (161 bp):
TTAGTGGTTTAGGGTTTTTAGTGTTTTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTT
AATTAATTAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTTTTAGAT
TAGGGTTTTTTATTGTTTTAGGGTTAGGGTT
Found at i:17018984 original size:16 final size:16
Alignment explanation
Indices: 17018942--17018981 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
17018932 GTTTTTTATT
17018942 GTTTTAG-GG-TTAGG
1 GTTTTAGTGGTTTAGG
17018956 GTTTTAGTGGTTTAGG
1 GTTTTAGTGGTTTAGG
17018972 GTTTTTAGTG
1 G-TTTTAGTG
17018982 TTTTTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 6 0.26
17 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (16 bp):
GTTTTAGTGGTTTAGG
Found at i:17019100 original size:18 final size:18
Alignment explanation
Indices: 17019074--17019131 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 18
17019064 AAATTAGGGC
17019074 TTAGTGGTTTAGGGTTTT
1 TTAGTGGTTTAGGGTTTT
* *
17019092 TTGGTGGTTTAAGG-TTT
1 TTAGTGGTTTAGGGTTTT
*
17019109 TTAATGGTTTAGGG-TTT
1 TTAGTGGTTTAGGGTTTT
17019126 TTAGTG
1 TTAGTG
17019132 TTTTTTAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (18 bp):
TTAGTGGTTTAGGGTTTT
Found at i:17019487 original size:126 final size:126
Alignment explanation
Indices: 17019258--17019692 Score: 649
Period size: 126 Copynumber: 3.5 Consensus size: 126
17019248 TTTAACTATT
* *
17019258 AATTACGGAAAAAAGCTCCCACGTGGATGCTCTTTTGCTATAGTAGTATCTGATAAAATAATTTT
1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT
* * *
17019323 GAGAAGATGTTT-TTAACAAAATAGGGTAAAAAACGCTTTAAGAAGGATACACTTTCAGCAA
66 GAGAAGATGTTTCTGAAC-AAATAGTGTCAAAAACGCTTTAAGAAGGATACACTTTCAGCAA
* * *
17019384 AATTACGGAAAAAACCTCCTACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAACTTT
1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT
* * *
17019449 GAGAAGATGTTTCTGAACAAATAGTATCAAAAATGCTTTAAGAAGGATGCACTTTCAGCAA
66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATACACTTTCAGCAA
* *
17019510 AATTACGGAAAAGAGCTCCCACGTGGACGCTTTTTTGCTACAGTAGTATCTGATAAAATAATTTT
1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT
* * * *
17019575 GAGAAAATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATCCACTTTCAGGAA
66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATACACTTTCAGCAA
* * * * *
17019636 AATTATGGGAAAAATCTCTCACGTGGACGCTCTTTTACTACAGTAGTATCTGA-AAAA
1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAA
17019693 GCCTTAGATT
Statistics
Matches: 279, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
125 4 0.01
126 271 0.97
127 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (126 bp):
AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT
GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATACACTTTCAGCAA
Found at i:17023450 original size:30 final size:30
Alignment explanation
Indices: 17023404--17023470 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
17023394 TTGAAGTGTT
* *
17023404 GACCCAGGTGGTTGTGTAGGCGCTGTTGATG
1 GACCC-GGTGATTGTGTAGGCGCTGCTGATG
* *
17023435 GGCCCGGTGATTGTGTGGGCGCTGCTGATG
1 GACCCGGTGATTGTGTAGGCGCTGCTGATG
17023465 GACCCG
1 GACCCG
17023471 TGTCGTCATC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.10, C:0.21, G:0.43, T:0.25
Consensus pattern (30 bp):
GACCCGGTGATTGTGTAGGCGCTGCTGATG
Found at i:17023979 original size:7 final size:7
Alignment explanation
Indices: 17023967--17023992 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17023957 TTATATAGGT
17023967 AATACTA
1 AATACTA
17023974 AATACTA
1 AATACTA
17023981 AATACTA
1 AATACTA
17023988 AATAC
1 AATAC
17023993 GAAACGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:17025401 original size:40 final size:38
Alignment explanation
Indices: 17025357--17025437 Score: 92
Period size: 40 Copynumber: 2.1 Consensus size: 38
17025347 CCACGTCAGC
*
17025357 ACAAAGCGCGCCCTCAAG-GAAGCGCTTTGTGCTGACATGG
1 ACAAAACGCGCCC-CAAGAGAAGCG-TTT-TGCTGACATGG
* * *
17025397 ACAAAACGCTCCCCTAGAGACGCGTTTTGCTGACATGG
1 ACAAAACGCGCCCCAAGAGAAGCGTTTTGCTGACATGG
17025435 ACA
1 ACA
17025438 CTGACTTCGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 14 0.39
39 6 0.17
40 16 0.44
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (38 bp):
ACAAAACGCGCCCCAAGAGAAGCGTTTTGCTGACATGG
Found at i:17025813 original size:42 final size:41
Alignment explanation
Indices: 17025715--17025813 Score: 92
Period size: 42 Copynumber: 2.4 Consensus size: 41
17025705 CGCTTTTCAC
* * *
17025715 AAACGCCGCTAAAAACATGACCTTTAGTGACATTTTTCCTA
1 AAACGCCGCTAAAAACATGACCTTTAGAGACACTTTCCCTA
* * * * *
17025756 TAATGTCGTTAAAAAACATGACCTTTAGCAG-CGCTTTCCCTAA
1 AAACGCCGCT-AAAAACATGACCTTTAG-AGACACTTTCCCT-A
17025799 AAACGCCGCTAAAAA
1 AAACGCCGCTAAAAA
17025814 TCATATCAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
41 6 0.14
42 29 0.67
43 8 0.19
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (41 bp):
AAACGCCGCTAAAAACATGACCTTTAGAGACACTTTCCCTA
Found at i:17026013 original size:31 final size:31
Alignment explanation
Indices: 17025970--17026031 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
17025960 TAATAACTAC
17025970 AGTACATACTTTCTTCTAAAACTAAAATCTT
1 AGTACATACTTTCTTCTAAAACTAAAATCTT
*
17026001 AGTATATACTTTCTTCTAAAACTAAAATCTT
1 AGTACATACTTTCTTCTAAAACTAAAATCTT
17026032 TGAAACTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (31 bp):
AGTACATACTTTCTTCTAAAACTAAAATCTT
Found at i:17026486 original size:25 final size:26
Alignment explanation
Indices: 17026452--17026503 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
17026442 ATTACAAAAG
17026452 AAACAAAAG-AAATATACTGAATTTA
1 AAACAAAAGAAAATATACTGAATTTA
17026477 AAACAAAAGAAAAAATATACTGAATTT
1 AAACAAAAG--AAAATATACTGAATTT
17026504 CCATCATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 9 0.38
28 15 0.62
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (26 bp):
AAACAAAAGAAAATATACTGAATTTA
Found at i:17035034 original size:24 final size:24
Alignment explanation
Indices: 17034991--17035036 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17034981 CTAAAATGAG
*
17034991 TATCTTTTCCTAGTTAAACTCTGT
1 TATCTTTTCCTAGTCAAACTCTGT
*
17035015 TATCTTTTCCTAGTCGAACTCT
1 TATCTTTTCCTAGTCAAACTCT
17035037 AATAACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.48
Consensus pattern (24 bp):
TATCTTTTCCTAGTCAAACTCTGT
Found at i:17035045 original size:24 final size:24
Alignment explanation
Indices: 17034994--17035045 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
17034984 AAATGAGTAT
* ** *
17034994 CTTTTCCTAGTTAAACTCTGTTAT
1 CTTTTCCTAGTCAAACTCTAATAA
*
17035018 CTTTTCCTAGTCGAACTCTAATAA
1 CTTTTCCTAGTCAAACTCTAATAA
17035042 CTTT
1 CTTT
17035046 AGGGATATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (24 bp):
CTTTTCCTAGTCAAACTCTAATAA
Found at i:17036417 original size:13 final size:13
Alignment explanation
Indices: 17036386--17036411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17036376 ATTTATGATT
17036386 AGTATTATGCATA
1 AGTATTATGCATA
17036399 AGTATTATGCATA
1 AGTATTATGCATA
17036412 TATATTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AGTATTATGCATA
Found at i:17040982 original size:15 final size:15
Alignment explanation
Indices: 17040964--17041003 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
17040954 TTATATTGTC
*
17040964 TATTTTTAATATCAT
1 TATTTTTAATAACAT
*
17040979 TATTTTTTATAACAT
1 TATTTTTAATAACAT
*
17040994 TTTTTTTAAT
1 TATTTTTAAT
17041004 TTGTAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTAATAACAT
Found at i:17047101 original size:15 final size:16
Alignment explanation
Indices: 17047081--17047120 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
17047071 TTTGTGAAAT
17047081 TTTGATATGTTA-GTA-
1 TTTGATAT-TTATGTAC
17047096 TTTGAT-TTTATGTAC
1 TTTGATATTTATGTAC
17047111 TTTGATATTT
1 TTTGATATTT
17047121 GTGCAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 4 0.18
15 12 0.55
16 3 0.14
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (16 bp):
TTTGATATTTATGTAC
Found at i:17047251 original size:20 final size:20
Alignment explanation
Indices: 17047227--17047273 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
17047217 AAATAATCTT
*
17047227 TTATA-ATTTTTAATAAAT-
1 TTATATATTTTTAAAAAATA
17047245 TTATATATTTTTAAAAAATA
1 TTATATATTTTTAAAAAATA
*
17047265 TTATTTATT
1 TTATATATT
17047274 AACATTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATATTTTTAAAAAATA
Found at i:17047631 original size:26 final size:27
Alignment explanation
Indices: 17047582--17047632 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
17047572 AGTTAAAATG
17047582 GATAAATGAATATTTTATTAATTTATC
1 GATAAATGAATATTTTATTAATTTATC
*
17047609 GATAAATTAATA-TTTATTAATTTA
1 GATAAATGAATATTTTATTAATTTA
17047633 CAGAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (27 bp):
GATAAATGAATATTTTATTAATTTATC
Found at i:17064921 original size:13 final size:13
Alignment explanation
Indices: 17064903--17064928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17064893 TAATATTGGC
17064903 TTGAAAAATAGGA
1 TTGAAAAATAGGA
17064916 TTGAAAAATAGGA
1 TTGAAAAATAGGA
17064929 ATGGACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TTGAAAAATAGGA
Found at i:17065064 original size:3 final size:3
Alignment explanation
Indices: 17065054--17065149 Score: 62
Period size: 3 Copynumber: 33.3 Consensus size: 3
17065044 ATTTTTTCTC
* * *
17065054 TAT T-T TAT TAT TAT T-T TAA TAT TA- TAT TAC TAC TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
17065098 TAT TAT T-T AAA TAT TAT ATAT AAAT TAT T-T TAT TAT TAAT T-T TAT
1 TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT T-AT TAT TAT
17065143 TAT TAT T
1 TAT TAT T
17065150 TTAAAAGACA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
2 13 0.18
3 52 0.70
4 9 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:17065105 original size:36 final size:36
Alignment explanation
Indices: 17065058--17065148 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
17065048 TTTCTCTATT
*
17065058 TTATTATTATTTTAATATTATAT-TACTACTATTTTA
1 TTATTATTATTTTAATATTATATATA-AACTATTTTA
* *
17065094 TTATTATTATTTAAATATTATATATAAATTATTTTA
1 TTATTATTATTTTAATATTATATATAAACTATTTTA
*
17065130 TTATTA--ATTTTATTATTAT
1 TTATTATTATTTTAATATTAT
17065149 TTTAAAAGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 11 0.22
36 36 0.73
37 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (36 bp):
TTATTATTATTTTAATATTATATATAAACTATTTTA
Found at i:17065141 original size:12 final size:11
Alignment explanation
Indices: 17065031--17065152 Score: 95
Period size: 11 Copynumber: 10.7 Consensus size: 11
17065021 TTTTTTAATG
*
17065031 TTATTTTTTTA
1 TTATTTTATTA
*
17065042 TTATTTT-TTC
1 TTATTTTATTA
17065052 TCTATTTTATTA
1 T-TATTTTATTA
*
17065064 TTATTTTAATA
1 TTATTTTATTA
* *
17065075 TTATATTACTA
1 TTATTTTATTA
*
17065086 CTATTTTATTA
1 TTATTTTATTA
*
17065097 TTATTATTTAAATA
1 TTA-T-TTT-ATTA
* *
17065111 TTA-TATATAAA
1 TTATTTTAT-TA
17065122 TTATTTTATTA
1 TTATTTTATTA
17065133 TTAATTTTATTA
1 TT-ATTTTATTA
17065145 TTATTTTA
1 TTATTTTA
17065153 AAAGACATTT
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
10 4 0.05
11 56 0.64
12 19 0.22
13 3 0.03
14 6 0.07
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:17071017 original size:19 final size:19
Alignment explanation
Indices: 17070993--17071033 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17070983 GTTATAATAT
*
17070993 TAATATTCCTTTAATATTA
1 TAATATTCATTTAATATTA
*
17071012 TAATATTCATTTCATATTA
1 TAATATTCATTTAATATTA
17071031 TAA
1 TAA
17071034 AACAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTCATTTAATATTA
Found at i:17071564 original size:47 final size:47
Alignment explanation
Indices: 17071490--17071614 Score: 153
Period size: 47 Copynumber: 2.6 Consensus size: 47
17071480 GATGAGTACT
* ** *
17071490 TATACCATGGCCCGTAGCCAAAGCAAGGTAACT-TATCCTGGAGCACC
1 TATACCATGGCCCGTAGCCAAATCAAGGTAACTCTATCC-AAAACACC
* *
17071537 TATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCCAAAATACC
1 TATACCATGGCCCGTAGCCAAATCAAGGTAACT-CTATCCAAAACACC
**
17071585 TATACCATGGCCCAAAGCCAAATCAAGGTA
1 TATACCATGGCCCGTAGCCAAATCAAGGTA
17071615 TAACTCGCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 32 0.47
48 32 0.47
49 4 0.06
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (47 bp):
TATACCATGGCCCGTAGCCAAATCAAGGTAACTCTATCCAAAACACC
Found at i:17071653 original size:50 final size:48
Alignment explanation
Indices: 17071538--17071655 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 48
17071528 TGGAGCACCT
* * *
17071538 ATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCCAAAATACCT
1 ATACCATGGCCCGAAGCCAAATCAAGGTAACTCCACTCCAAAATACCG
* * * *
17071586 ATACCATGGCCCAAAGCCAAATCAAGGTATAACTCGCAC-CCGAAGTGCCG
1 ATACCATGGCCCGAAGCCAAATCAAGG--TAACTC-CACTCCAAAATACCG
*
17071636 ATATCATGGCCCGAAGCCAA
1 ATACCATGGCCCGAAGCCAA
17071656 CTTATTACCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
48 25 0.43
50 31 0.53
51 2 0.03
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (48 bp):
ATACCATGGCCCGAAGCCAAATCAAGGTAACTCCACTCCAAAATACCG
Found at i:17073664 original size:11 final size:11
Alignment explanation
Indices: 17073648--17073672 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17073638 TTCAGCTGAT
17073648 GAAAATGAAGA
1 GAAAATGAAGA
17073659 GAAAATGAAGA
1 GAAAATGAAGA
17073670 GAA
1 GAA
17073673 TTCTAAATAT
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:17080518 original size:46 final size:46
Alignment explanation
Indices: 17080468--17080643 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
17080458 TGGTTGAGCA
*
17080468 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
17080514 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
** *
17080561 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCGTGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
17080607 CCCGAGCTCATTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17080644 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 29 0.28
48 2 0.02
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:17080624 original size:93 final size:93
Alignment explanation
Indices: 17080465--17080636 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
17080455 GGATGGTTGA
* * * *
17080465 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAGT
17080530 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
17080558 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCGTGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAGT
*
17080623 TGAGTTCGAGTTCG
66 TGAGTCCGAGTTCG
17080637 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17083574 original size:15 final size:15
Alignment explanation
Indices: 17083554--17083622 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
17083544 GTATCTTGGG
17083554 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
17083569 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
17083584 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
17083599 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
17083614 TTTCTTTAT
1 TTTCTTTAT
17083623 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:17083623 original size:30 final size:30
Alignment explanation
Indices: 17083545--17083632 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
17083535 CATAGTATCG
* * * *
17083545 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
17083575 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
17083605 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
17083633 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:17086044 original size:46 final size:45
Alignment explanation
Indices: 17085994--17086157 Score: 171
Period size: 46 Copynumber: 3.6 Consensus size: 45
17085984 ATGTTGAGCA
17085994 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
* *
17086040 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATG-GATGCGAA-T--G
*
17086085 CATCCG-ACTCGTTGAGTTGAGTCCGAGTTCAC--TGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
* *
17086129 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
17086158 TTATGGGCGG
Statistics
Matches: 102, Mismatches: 6, Indels: 23
0.78 0.05 0.18
Matches are distributed among these distances:
42 7 0.07
43 28 0.27
44 2 0.02
45 1 0.01
46 55 0.54
47 8 0.08
48 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
Found at i:17086153 original size:89 final size:91
Alignment explanation
Indices: 17085991--17086157 Score: 275
Period size: 89 Copynumber: 1.8 Consensus size: 91
17085981 AGGATGTTGA
* *
17085991 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-T-TGGATGCGAACGCCCGAACTCGTTGAGT
17086056 TGAGTCCGAGTTCGTGAGATGTAACTAG
64 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
17086084 GCATCCG-ACTCGTTGAGTTGAGTCCGAGTTCAC-TGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAACGCCCGAACTCGTTGAGTTG
17086147 AGTCCGAGTTC
66 AGTCCGAGTTC
17086158 TTATGGGCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
89 38 0.54
92 26 0.37
93 7 0.10
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17089836 original size:40 final size:40
Alignment explanation
Indices: 17089753--17089973 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
17089743 ACCCAAGTAT
** * *
17089753 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
17089791 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
17089831 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
17089871 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
17089911 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
*
17089952 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
17089974 CATTCGAATA
Statistics
Matches: 153, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 15 0.10
40 97 0.63
41 29 0.19
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17097872 original size:40 final size:40
Alignment explanation
Indices: 17097789--17098009 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
17097779 ACCCAAGTAT
** * *
17097789 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
17097827 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
17097867 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
17097907 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
17097947 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
*
17097988 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
17098010 CATTCGAATA
Statistics
Matches: 153, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 15 0.10
40 97 0.63
41 29 0.19
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17101036 original size:55 final size:55
Alignment explanation
Indices: 17100975--17101088 Score: 210
Period size: 55 Copynumber: 2.1 Consensus size: 55
17100965 CAAGCTGCTG
17100975 ATGTCTTCACTAAACCTTTCCTGAACAAGGCATTCCAAGAATCACGAGAGAAGCT
1 ATGTCTTCACTAAACCTTTCCTGAACAAGGCATTCCAAGAATCACGAGAGAAGCT
* *
17101030 ATGTCTTCACTAAACCTTTCCTGACCAAGGTATTCCAAGAATCACGAGAGAAGCT
1 ATGTCTTCACTAAACCTTTCCTGAACAAGGCATTCCAAGAATCACGAGAGAAGCT
17101085 ATGT
1 ATGT
17101089 GTCATCCCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (55 bp):
ATGTCTTCACTAAACCTTTCCTGAACAAGGCATTCCAAGAATCACGAGAGAAGCT
Found at i:17116636 original size:25 final size:25
Alignment explanation
Indices: 17116602--17116662 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
17116592 CCTTAGCGCT
* *
17116602 CTCTCTGATTATTAGCATGTTAGTG
1 CTCTCTGATTATTAGCACGCTAGTG
*
17116627 CTCTCCGATTATTAGCACGCTAGTG
1 CTCTCTGATTATTAGCACGCTAGTG
*
17116652 CTATCTGATTA
1 CTCTCTGATTA
17116663 GCACATTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACGCTAGTG
Found at i:17121312 original size:7 final size:7
Alignment explanation
Indices: 17121300--17121325 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17121290 AATTAAGGTA
17121300 AAATTTT
1 AAATTTT
17121307 AAATTTT
1 AAATTTT
17121314 AAATTTT
1 AAATTTT
17121321 AAATT
1 AAATT
17121326 CGATTTAGTC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:17127175 original size:23 final size:22
Alignment explanation
Indices: 17127123--17127175 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17127113 TCCACGTCTT
*
17127123 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17127145 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17127168 TTTCTTTT
1 TTTCTTTT
17127176 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:17152166 original size:23 final size:23
Alignment explanation
Indices: 17152129--17152175 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17152119 TCCATTTTCT
* *
17152129 ATTTAGTTTTATTTTTACTTGTA
1 ATTTAGGTTTATTTTCACTTGTA
* *
17152152 ATTTAGGTTTCTTTTCAGTTGTA
1 ATTTAGGTTTATTTTCACTTGTA
17152175 A
1 A
17152176 GCGTAGTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (23 bp):
ATTTAGGTTTATTTTCACTTGTA
Found at i:17173411 original size:12 final size:12
Alignment explanation
Indices: 17173396--17173420 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17173386 AAAACTTTTC
17173396 TTTTATTATATA
1 TTTTATTATATA
17173408 TTTTATTATATA
1 TTTTATTATATA
17173420 T
1 T
17173421 ATATTTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:17173443 original size:6 final size:6
Alignment explanation
Indices: 17173434--17173466 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17173424 TTTATTCTGT
*
17173434 TTTTTA TTTTTA TTTCT- TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
17173467 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:17173474 original size:16 final size:16
Alignment explanation
Indices: 17173391--17173476 Score: 68
Period size: 17 Copynumber: 5.2 Consensus size: 16
17173381 TTTTAAAAAC
*
17173391 TTTTCTTTTATTATAT
1 TTTTATTTTATTATAT
*
17173407 ATTTTATTATATATATAT
1 -TTTTATTTTAT-TATAT
*
17173425 TTATTCTGTTT-TT-TAT
1 TT-TTAT-TTTATTATAT
* *
17173441 TTTTATTTCTTTTTTAT
1 TTTTATTT-TATTATAT
17173458 TTTTATTTTATTATAT
1 TTTTATTTTATTATAT
17173474 TTT
1 TTT
17173477 ATATGTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.04
15 4 0.07
16 16 0.29
17 23 0.41
18 9 0.16
19 2 0.04
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATTATAT
Found at i:17173756 original size:3 final size:3
Alignment explanation
Indices: 17173748--17173793 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
17173738 ATATTACTAC
*
17173748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
17173794 GGCACATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17185822 original size:175 final size:175
Alignment explanation
Indices: 17185531--17186085 Score: 952
Period size: 175 Copynumber: 3.2 Consensus size: 175
17185521 CGATGATGAG
*
17185531 CAAATCGAAGACATAGCAGATCTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
1 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
* * *
17185596 GATCTGGCATTTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTCAC
66 GATCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTAC
17185661 TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
131 TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
*
17185706 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTTTCACACCAAAGCAGATCCAAGATAACA
1 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
17185771 GATCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTAACCTTCAGATG-TTTATA
66 GATCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTT-TA
*
17185835 CTGAAGTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
130 CTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
*
17185881 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAAGCAGATCCAAGATAACA
1 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
* * *
17185946 GATCTAGCATCTCCATTTCAACAGAGAGTAGATACATAGCAGATCTAACCTTCAGATGATTTTAC
66 GATCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTAC
* *
17186011 TGAAGCAGATCCAAGATGATTTGGCA-TCTTTGTGTTCACAAGGAG
131 TGAAGCAGATCCAAGATGATTTGGCATTC-TTGTGTTTACAAGGAA
* *
17186056 CAAATCGAAGACACAGCAGATTTGGCTTTC
1 CAAATCGAAGACATAGCAGATTTGACTTTC
17186086 ATGTGTTACG
Statistics
Matches: 361, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
174 5 0.01
175 353 0.98
176 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (175 bp):
CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
GATCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTAACCTTCAGATGATTTTAC
TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
Found at i:17185829 original size:88 final size:87
Alignment explanation
Indices: 17185541--17186027 Score: 328
Period size: 88 Copynumber: 5.6 Consensus size: 87
17185531 CAAATCGAAG
* * * * *
17185541 ACATAGCAGATCTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCA-
*
17185606 TTCCATTTCGACGGAGAGCAGAT
65 TTCCATTTCGACAGAGAGCAGAT
* * *
17185629 ACATAGCAGATCTAACCTTCAGATGATTT--CACTGAAGCAGATCCAAGAT----GATTTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
* ** * *
17185688 T-CTTGTGTTTACA-AGGAACAAATCGAAG
66 TCCAT-T-TCGACAGA-GAGC--A--G-AT
* * * * *
17185716 ACATAGCAGATTTGACTTTCGGATGTTTTCACACCAAAGCAGATCCAAGATAACAGATCTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
17185781 CTCCATTTCGACAGAGAGCAGAT
66 -TCCATTTCGACAGAGAGCAGAT
* * * *
17185804 ACATAGCAGATCTAACCTTCAGATG-TTT-ATACTGAAGTAGATCCAAGAT----GATTTGGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
* ** * *
17185863 T-CTTGTGTTTACA-AGGAACAAATCGAAG
66 TCCAT-T-TCGACAGA-GAGC--A--G-AT
* * * * * *
17185891 ACATAGCAGATTTGACTTTCGGATGTTCTCACACCGAAGCAGATCCAAGATAACAGATCTAGCAT
1 ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
* *
17185956 CTCCATTTCAACAGAGAGTAGAT
66 -TCCATTTCGACAGAGAGCAGAT
*
17185979 ACATAGCAGATCTAACCTTCAGATGATTTT---ACTGAAGCAGATCCAAGAT
1 ACATAGCAGATCTAACCTTCAGATG-TTTTCACACCGAAGCAGATCCAAGAT
17186028 GATTTGGCAT
Statistics
Matches: 301, Mismatches: 63, Indels: 72
0.69 0.14 0.17
Matches are distributed among these distances:
80 4 0.01
81 7 0.02
82 30 0.10
84 2 0.01
86 55 0.18
87 50 0.17
88 70 0.23
89 41 0.14
91 2 0.01
93 30 0.10
94 6 0.02
95 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (87 bp):
ACATAGCAGATCTAACCTTCAGATGTTTTCACACCGAAGCAGATCCAAGATAACAGATCTGGCAT
TCCATTTCGACAGAGAGCAGAT
Found at i:17186380 original size:15 final size:15
Alignment explanation
Indices: 17186360--17186390 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17186350 GCCTTAAACT
*
17186360 AAAATAAAAAAGTAA
1 AAAATAAAAAAATAA
17186375 AAAATAAAAAAATAA
1 AAAATAAAAAAATAA
17186390 A
1 A
17186391 GTTCATTTAT
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:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAATAAAAAAATAA
Found at i:17187875 original size:12 final size:12
Alignment explanation
Indices: 17187860--17187916 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
17187850 AAAAATTTTC
17187860 TTTTATTATATA
1 TTTTATTATATA
17187872 TTTTATTATATA
1 TTTTATTATATA
* * *
17187884 TATTTATTCTGTT
1 T-TTTATTATATA
*
17187897 TTTTATT-TTTA
1 TTTTATTATATA
17187908 TTTTATTAT
1 TTTTATTAT
17187917 TTTTTATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 9 0.24
12 20 0.53
13 9 0.24
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:17189863 original size:41 final size:41
Alignment explanation
Indices: 17189817--17190076 Score: 344
Period size: 41 Copynumber: 6.4 Consensus size: 41
17189807 GCGTTTGAAA
* *
17189817 CAAAACGCGGCAAAAAACTGAGCAATAGTGGCGTTTTTATG
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
* * *
17189858 CAAAACGCTGCAAAAAATTGAGCAGTAGTGGCGTTTTTATC
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
* * *
17189899 CAAAACGTCGCGAAAAACTGAGCAATAGTGGAGTTTTTATC
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
17189940 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
* ** *
17189981 CAAAACACCGTGAAAAACTGAGCAATAGTGGCG-TTTTGTC
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
* * * *
17190021 CAAAACTCCGCGAAAAACTGAGAAATAGTGGCGTTTTTGGTC
1 CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTT-ATC
*
17190063 C-AAACGCCACAAAA
1 CAAAACGCCGCAAAA
17190077 GGTTGAGCTA
Statistics
Matches: 194, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 36 0.19
41 154 0.79
42 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (41 bp):
CAAAACGCCGCAAAAAACTGAGCAATAGTGGCGTTTTTATC
Found at i:17190620 original size:7 final size:7
Alignment explanation
Indices: 17190608--17190663 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
17190598 GAATTTTAGC
17190608 CCCTAAA
1 CCCTAAA
17190615 CCCTAAA
1 CCCTAAA
*
17190622 CTCTAAA
1 CCCTAAA
* *
17190629 GCCTAAT
1 CCCTAAA
*
17190636 CCCAAAA
1 CCCTAAA
*
17190643 CCTTAAA
1 CCCTAAA
17190650 CCCTAAA
1 CCCTAAA
17190657 CCCTAAA
1 CCCTAAA
17190664 ATATAAAGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.43, C:0.38, G:0.02, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:17190633 original size:21 final size:21
Alignment explanation
Indices: 17190609--17190684 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
17190599 AATTTTAGCC
17190609 CCTAAACCCTAAACTCTAAAG
1 CCTAAACCCTAAACTCTAAAG
* * *
17190630 CCTAATCCCAAAAC-CTTAAAC
1 CCTAAACCCTAAACTC-TAAAG
* *
17190651 CCTAAACCCTAAAATATAAAG
1 CCTAAACCCTAAACTCTAAAG
*
17190672 CCTAACCCCTAAA
1 CCTAAACCCTAAA
17190685 TCATAACTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.45, C:0.34, G:0.03, T:0.18
Consensus pattern (21 bp):
CCTAAACCCTAAACTCTAAAG
Found at i:17191915 original size:20 final size:20
Alignment explanation
Indices: 17191870--17191915 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
17191860 CCCCACCCAA
*
17191870 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
17191890 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
17191909 ATTTCCC
1 ATTTCCC
17191916 AGAATCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Done.