Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 70 of 82
Found at i:25408220 original size:23 final size:23
Alignment explanation
Indices: 25408190--25408233 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
25408180 ACTGACTTTG
*
25408190 GACATTGCGTGACTGGTTGATAT
1 GACATTGCGTGACTAGTTGATAT
25408213 GACATTGCGTGACTAGTTGAT
1 GACATTGCGTGACTAGTTGAT
25408234 GGGCATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.34
Consensus pattern (23 bp):
GACATTGCGTGACTAGTTGATAT
Found at i:25408246 original size:22 final size:23
Alignment explanation
Indices: 25408189--25408248 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
25408179 GACTGACTTT
*
25408189 GGACATTGCGTGACTGGTTGATA
1 GGACATTGCGTGACTAGTTGATA
*
25408212 TGACATTGCGTGACTAGTTGAT-
1 GGACATTGCGTGACTAGTTGATA
* *
25408234 GGGCATTGTGTGACT
1 GGACATTGCGTGACT
25408249 TGCTAGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (23 bp):
GGACATTGCGTGACTAGTTGATA
Found at i:25408610 original size:19 final size:19
Alignment explanation
Indices: 25408586--25408622 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
25408576 CCATTTGACT
25408586 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25408605 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
25408623 AGTTTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:25412334 original size:22 final size:22
Alignment explanation
Indices: 25412306--25412386 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
25412296 AGGCATTGCT
25412306 TAAAAATCAATCACGCAATGCC
1 TAAAAATCAATCACGCAATGCC
25412328 TAAAAATCAATCACGCAATGCC
1 TAAAAATCAATCACGCAATGCC
* * *
25412350 T-AAAATCAATAACGTAATGCT
1 TAAAAATCAATCACGCAATGCC
25412371 TAAAAA-CAAGTCACGC
1 TAAAAATCAA-TCACGC
25412387 GGTGATTAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 21 0.40
22 31 0.60
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (22 bp):
TAAAAATCAATCACGCAATGCC
Found at i:25412356 original size:21 final size:21
Alignment explanation
Indices: 25412308--25412386 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
25412298 GCATTGCTTA
25412308 AAAATCAATCACGCAATGCCT
1 AAAATCAATCACGCAATGCCT
25412329 AAAAATCAATCACGCAATGCCT
1 -AAAATCAATCACGCAATGCCT
* * *
25412351 AAAATCAATAACGTAATGCTT
1 AAAATCAATCACGCAATGCCT
*
25412372 AAAAACAAGTCACGC
1 AAAATCAA-TCACGC
25412387 GGTGATTAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
21 25 0.50
22 25 0.50
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAATCAATCACGCAATGCCT
Found at i:25414292 original size:19 final size:19
Alignment explanation
Indices: 25414250--25414292 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
25414240 AGGAAATGAA
25414250 AATAT-TTAACTATTATTT
1 AATATATTAACTATTATTT
25414268 AATATATTAA-TATTATTT
1 AATATATTAACTATTATTT
25414286 AACTATA
1 AA-TATA
25414293 ATAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATATTAACTATTATTT
Found at i:25414300 original size:21 final size:18
Alignment explanation
Indices: 25414250--25414304 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
25414240 AGGAAATGAA
* *
25414250 AATATTTAACTATTATTT
1 AATATATAAATATTATTT
*
25414268 AATATATTAATATTATTT
1 AATATATAAATATTATTT
25414286 AACTATAATAAAATATTAT
1 AA-TAT-AT-AAATATTAT
25414305 AAAGAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 17 0.57
19 3 0.10
20 2 0.07
21 8 0.27
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATATAAATATTATTT
Found at i:25414370 original size:45 final size:46
Alignment explanation
Indices: 25414278--25414372 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
25414268 AATATATTAA
*
25414278 TATTATTTAACTATAATAAAATATTATAAAGAATATTACTTAATAT
1 TATTATTTAACTATAATAAAATATAATAAAGAATATTACTTAATAT
* * *
25414324 TATTATTTGAAC-ATAAT-AAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTT-AACTATAATAAAATATAATAAAGAATATTACTTAATAT
25414369 TATT
1 TATT
25414373 TAAATTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 28 0.64
46 13 0.30
47 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (46 bp):
TATTATTTAACTATAATAAAATATAATAAAGAATATTACTTAATAT
Found at i:25415070 original size:22 final size:22
Alignment explanation
Indices: 25415049--25415095 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
25415039 ATTTATTATT
25415049 TTAAT-AAT-TTATTAAAAATA
1 TTAATAAATATTATTAAAAATA
*
25415069 TTAATAAATATTATT-AAAATG
1 TTAATAAATATTATTAAAAATA
25415090 TTAATA
1 TTAATA
25415096 TGATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAATAAATATTATTAAAAATA
Found at i:25415905 original size:113 final size:112
Alignment explanation
Indices: 25415773--25416153 Score: 311
Period size: 113 Copynumber: 3.4 Consensus size: 112
25415763 TATTAATATT
* * * *
25415773 TTAAAAATATTAATA-TTAAATTATAAATAAAATATTAATATTTATATGATCAATTATTAATA-A
1 TTAAACATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATCATCAATTATTAATATA
* * ** *
25415836 AATAAATTATAAATTATTCCTA-TTTAAAAACAAAATAAATTAAAAA
66 AATAAATTACAAATTAATAATATTTTAAAAACAAAATAAAATAAAAA
* * *
25415882 TAAATAAACATAAT-ATCATTTAAATTATATAA-ACAATATTAATAATTAAATCATCAATTCTTA
1 T---TAAACATAATAAT-ATTTAAATTATA-AATAAAATATTAATATTTAAATCATCAATTATTA
* *
25415945 ATATTTTAAATAAATTACCAATTAATAATATTTTAAAAATAAAATAAAATAAAAA
61 ATA---TAAATAAATTACAAATTAATAATATTTTAAAAACAAAATAAAATAAAAA
* * * * * *
25416000 TTAATCATAATAATATTTAAA-T-TAATTAATATATTAATATTTGAA-CTATCTATTAGTAATAT
1 TTAAACATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATC-ATCAATTATTAATA-
* * * *
25416062 TTTAAATAAATAATC-AGTTATTAAT-TTTTAAAAATAAAATAAAA-AAATAA
64 --TAAATAAATTA-CAAATTAATAATATTTTAAAAACAAAATAAAATAAA-AA
* *
25416112 TTGATCATAATAATATTTAAA-T-TAAATAAAATATTAATATTT
1 TTAAACATAATAATATTTAAATTATAAATAAAATATTAATATTT
25416154 TAAAATATAA
Statistics
Matches: 227, Mismatches: 29, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
109 1 0.00
111 5 0.02
112 71 0.31
113 87 0.38
114 4 0.02
115 16 0.07
116 2 0.01
117 18 0.08
118 23 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (112 bp):
TTAAACATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATCATCAATTATTAATATA
AATAAATTACAAATTAATAATATTTTAAAAACAAAATAAAATAAAAA
Found at i:25416121 original size:112 final size:113
Alignment explanation
Indices: 25415858--25416153 Score: 348
Period size: 112 Copynumber: 2.6 Consensus size: 113
25415848 ATTATTCCTA
* * * *
25415858 TTTAAAAACAAAATAAATTAAAAATAAATAAACATAAT-ATCATTTAAATTATATAAACAATATT
1 TTTAAAAATAAAATAAAATAAAAAT---TAATCATAATAAT-ATTTAAATTAAAT-AA-AATATT
* * * ** *
25415922 AATAATT-AAATCATCAATTCTTAATATTTTAAATAAATTACCAATTAATAATAT
60 AATATTTGAACT-ATCTATTAGTAATATTTTAAATAAATAACCAATTAATAATAT
* *
25415976 TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAATTAATATATTAATATT
1 TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATATTAATATT
* * *
25416041 TGAACTATCTATTAGTAATATTTTAAATAAATAATCAGTTATTAAT-T
66 TGAACTATCTATTAGTAATATTTTAAATAAATAACCAATTAATAATAT
*
25416088 TTTAAAAATAAAATAAAA-AAATAATTGATCATAATAATATTTAAATTAAATAAAATATTAATAT
1 TTTAAAAATAAAATAAAATAAA-AATTAATCATAATAATATTTAAATTAAATAAAATATTAATAT
25416152 TT
65 TT
25416154 TAAAATATAA
Statistics
Matches: 157, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
111 3 0.02
112 60 0.38
113 44 0.28
114 5 0.03
115 20 0.13
116 2 0.01
118 23 0.15
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (113 bp):
TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATATTAATATT
TGAACTATCTATTAGTAATATTTTAAATAAATAACCAATTAATAATAT
Found at i:25416128 original size:66 final size:65
Alignment explanation
Indices: 25416056--25416281 Score: 217
Period size: 64 Copynumber: 3.5 Consensus size: 65
25416046 TATCTATTAG
25416056 TAATATTTTAAA-TAAATAATCAGTTATTAAT-TTTTAAAAATAAAATAAAAAAATAATTGATCA
1 TAATA-TTTAAATTAAATAATCAG-TATTAATATTTTAAAAATAAAATAAAAAAATAATT-ATCA
25416119 TAA
63 TAA
* * *
25416122 TAATATTTAAATTAAATAA--AATATTAATATTTT-AAAAT---ATAAAACATTAAATTAT-A-A
1 TAATATTTAAATTAAATAATCAGTATTAATATTTTAAAAATAAAATAAAAAAAT-AATTATCATA
25416179 A
65 A
* *
25416180 TAAAATATTAATATTTAAATTATCAAGTATTAATATTTTAAAAATAAAATAAAATAAA-AATTAA
1 TAATAT-TTAA-A-TTAAATAATC-AGTATTAATATTTTAAAAATAAAATAAAA-AAATAATT-A
25416244 TCATAA
60 TCATAA
*
25416250 TAATATTTAAATTAAATAA--AATATTAATATTT
1 TAATATTTAAATTAAATAATCAGTATTAATATTT
25416282 AAATTATCAA
Statistics
Matches: 132, Mismatches: 11, Indels: 36
0.74 0.06 0.20
Matches are distributed among these distances:
58 7 0.05
59 5 0.04
60 11 0.08
61 11 0.08
63 12 0.09
64 30 0.23
65 11 0.08
66 12 0.09
67 11 0.08
68 9 0.07
69 6 0.05
70 7 0.05
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (65 bp):
TAATATTTAAATTAAATAATCAGTATTAATATTTTAAAAATAAAATAAAAAAATAATTATCATAA
Found at i:25416140 original size:42 final size:42
Alignment explanation
Indices: 25416093--25416272 Score: 115
Period size: 42 Copynumber: 4.2 Consensus size: 42
25416083 TAATTTTTAA
*
25416093 AAATAAAATAAAAAAATAATTGATCATAATAATATTTAAATT
1 AAATAAAATAAAAAAATAATTAATCATAATAATATTTAAATT
** * * *
25416135 AAATAAAATATTAATAT-TTTAAAAT-ATAA-AACA-TTAAATTAT
1 AAATAAAATAAAAAAATAATT--AATCATAATAATATTTAAA-T-T
* ** * *
25416177 AAATAAAATATTAATATTTAAATT-ATCAAGTATTAATATTTTAA--
1 AAATAAAATA--AAAAAAT-AATTAATC-A-TAATAATATTTAAATT
25416221 AAATAAAATAAAATAAA-AATTAATCATAATAATATTTAAATT
1 AAATAAAATAAAA-AAATAATTAATCATAATAATATTTAAATT
25416263 AAATAAAATA
1 AAATAAAATA
25416273 TTAATATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
40 17 0.17
41 11 0.11
42 44 0.43
43 5 0.05
44 13 0.13
45 1 0.01
46 4 0.04
47 3 0.03
48 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (42 bp):
AAATAAAATAAAAAAATAATTAATCATAATAATATTTAAATT
Found at i:25416180 original size:112 final size:113
Alignment explanation
Indices: 25415858--25416312 Score: 328
Period size: 112 Copynumber: 3.9 Consensus size: 113
25415848 ATTATTCCTA
* * * *
25415858 TTTAAAAACAAAATAAATTAAAAATAAATAAACATAAT-ATCATTTAAATTATATAAACAATATT
1 TTTAAAAATAAAATAAAATAAAAAT---TAATCATAATAAT-ATTTAAATTAAAT-AA-AATATT
* ** *
25415922 AATAATT-AAATCATCAATTC-TTAATATTTTAAATAAATTACCAATTAATAATAT
60 AATATTTAAAAT-AT-AAAACATTAATATTTTAAATAAATAACCAATTAATAATAT
* *
25415976 TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAATTAATATATTAATATT
1 TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATATTAATATT
* * ** ** * * * *
25416041 TGAACTATCTATTAGTAATATTTTAAATAAATAATCAGTTATTAAT-T
66 TAAAATATAAAACATTAATATTTTAAATAAATAACCAATTAATAATAT
*
25416088 TTTAAAAATAAAATAAAA-AAATAATTGATCATAATAATATTTAAATTAAATAAAATATTAATAT
1 TTTAAAAATAAAATAAAATAAA-AATTAATCATAATAATATTTAAATTAAATAAAATATTAATA-
* ** * *
25416152 TTTAAAATATAAAACATTAA-ATTATAAATAAAATATTAATATTTAAATTATCAAGT
64 TTTAAAATATAAAACATTAATATTTTAAAT-AAATA--ACCAATT-AATAAT--A-T
* * *
25416208 ATTAATATTTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATA
1 TTTAA-A----AATAA-AATA-A-AATAAAAATTAATCATAATAATATTTAAATTAAATAAAATA
* * ** * *
25416273 TTAATATTTAAATTATCAATTATTAATGTTTTAATTAAAT
58 TTAATATTTAAAATATAAAACATTAATATTTTAAATAAAT
25416313 TCTAGATTAT
Statistics
Matches: 270, Mismatches: 44, Indels: 37
0.77 0.13 0.11
Matches are distributed among these distances:
111 3 0.01
112 66 0.24
113 58 0.21
114 5 0.02
115 24 0.09
116 6 0.02
118 23 0.09
120 5 0.02
121 1 0.00
125 4 0.01
126 3 0.01
127 21 0.08
128 48 0.18
129 3 0.01
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (113 bp):
TTTAAAAATAAAATAAAATAAAAATTAATCATAATAATATTTAAATTAAATAAAATATTAATATT
TAAAATATAAAACATTAATATTTTAAATAAATAACCAATTAATAATAT
Found at i:25416184 original size:19 final size:19
Alignment explanation
Indices: 25416133--25416199 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
25416123 AATATTTAAA
*
25416133 TTAAATAAAATATTAATATT
1 TTAAATAAAACATTAATA-T
25416153 TTAAAATATAAAACATTAA-AT
1 TT--AA-ATAAAACATTAATAT
*
25416174 TATAAATAAAATATTAATAT
1 T-TAAATAAAACATTAATAT
25416194 TTAAAT
1 TTAAAT
25416200 TATCAAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 16 0.40
20 7 0.17
21 2 0.05
22 4 0.10
23 11 0.28
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATAAAACATTAATAT
Found at i:25416211 original size:22 final size:21
Alignment explanation
Indices: 25416122--25416309 Score: 84
Period size: 22 Copynumber: 8.7 Consensus size: 21
25416112 TTGATCATAA
*
25416122 TAATATTTAAATTAAATAAAATAT
1 TAATATTTAAATT--AT-CAATAT
* * *
25416146 TAATATTTTAAAATATAAAACAT
1 TAATA-TTTAAATTAT-CAATAT
*
25416169 TAA-ATTATAAA-TA-AAATAT
1 TAATATT-TAAATTATCAATAT
25416188 TAATATTTAAATTATCAAGTAT
1 TAATATTTAAATTATCAA-TAT
* *
25416210 TAATATTTTAAA-AAT-AA-AA
1 TAATA-TTTAAATTATCAATAT
* ** *
25416229 TAAAATAAAAATTAATC-ATAA
1 TAATATTTAAATT-ATCAATAT
*
25416250 TAATATTTAAATTAAATAAAATAT
1 TAATATTTAAATT--AT-CAATAT
25416274 TAATATTTAAATTATCAATTAT
1 TAATATTTAAATTATCAA-TAT
* *
25416296 TAATGTTTTAATTA
1 TAATATTTAAATTA
25416310 AATTCTAGAT
Statistics
Matches: 131, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.03
19 17 0.13
20 8 0.06
21 22 0.17
22 35 0.27
23 17 0.13
24 21 0.16
25 7 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (21 bp):
TAATATTTAAATTATCAATAT
Found at i:25418015 original size:20 final size:21
Alignment explanation
Indices: 25417970--25418016 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
25417960 AGATGTCTAA
*
25417970 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
25417991 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
25418011 AATAAT
1 AATAAT
25418017 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:25419907 original size:22 final size:22
Alignment explanation
Indices: 25419865--25419907 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
25419855 TAACTTTTGT
* *
25419865 CACTTGTTTTCTTGAATTTCCA
1 CACTTGTTTTCTTCAAATTCCA
25419887 CACTT-TTTCTCTTCAAATTCC
1 CACTTGTTT-TCTTCAAATTCC
25419908 CCACCTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.19, C:0.28, G:0.05, T:0.49
Consensus pattern (22 bp):
CACTTGTTTTCTTCAAATTCCA
Found at i:25420993 original size:18 final size:18
Alignment explanation
Indices: 25420970--25421006 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25420960 ACAACTAAAC
*
25420970 ATGAAGATGTATTACACA
1 ATGAAGATATATTACACA
25420988 ATGAAGATATATTACACA
1 ATGAAGATATATTACACA
25421006 A
1 A
25421007 AGTACACACC
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:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (18 bp):
ATGAAGATATATTACACA
Found at i:25425492 original size:39 final size:39
Alignment explanation
Indices: 25425438--25425518 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
25425428 AATAAGCGTT
25425438 TTTCTCTTATTTTTATTTTT-AAGATAAAATTACATTTGG
1 TTTCTCTTATTTTTATTTTTAAAG-TAAAATTACATTTGG
25425477 TTTCTCTTATTTTTATTTTTAAAGTAAAATTACATTTGG
1 TTTCTCTTATTTTTATTTTTAAAGTAAAATTACATTTGG
25425516 TTT
1 TTT
25425519 AATATAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 38 0.93
40 3 0.07
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.58
Consensus pattern (39 bp):
TTTCTCTTATTTTTATTTTTAAAGTAAAATTACATTTGG
Found at i:25426407 original size:18 final size:20
Alignment explanation
Indices: 25426384--25426431 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
25426374 TGAAAATATT
25426384 TAAATATTATTTAA-TAT-A
1 TAAATATTATTTAACTATAA
*
25426402 TTAATATTATTTAACTATAA
1 TAAATATTATTTAACTATAA
25426422 TAAATATTAT
1 TAAATATTAT
25426432 AAAGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATATTATTTAACTATAA
Found at i:25426415 original size:10 final size:10
Alignment explanation
Indices: 25426380--25426454 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
25426370 GTAATGAAAA
25426380 TATTTAAATAT
1 TATTT-AATAT
25426391 TATTTAATA-
1 TATTTAATAT
25426400 TA-TTAATAT
1 TATTTAATAT
25426409 TATTTAACTA-
1 TATTTAA-TAT
* *
25426419 TAATAAATAT
1 TATTTAATAT
**
25426429 TATAAAGAATAT
1 TAT--TTAATAT
25426441 TATTTAATAT
1 TATTTAATAT
25426451 TATT
1 TATT
25426455 ATTTGAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 24 0.47
11 7 0.14
12 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (10 bp):
TATTTAATAT
Found at i:25426466 original size:45 final size:45
Alignment explanation
Indices: 25426406--25426499 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
25426396 AATATATTAA
*
25426406 TATTATTTAACTATAATAAATATTATAAAGAATATTATTTAATAT
1 TATTATTTAACTATAATAAATATAATAAAGAATATTATTTAATAT
* *
25426451 TATTATTTGAA-TATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTT-AACTATAATAAATATAATAAAGAATATTATTTAATAT
25426496 TATT
1 TATT
25426500 TAAATTTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (45 bp):
TATTATTTAACTATAATAAATATAATAAAGAATATTATTTAATAT
Found at i:25427254 original size:34 final size:36
Alignment explanation
Indices: 25427182--25427252 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
25427172 ATTATTTTAA
*
25427182 TAATTTATTAAAATATTAATAAATTATTATTTATTT
1 TAATTTATCAAAATATTAATAAATTATTATTTATTT
*
25427218 TAATTTA-CAAAATATTAAT-AATTTTTATTTCATTT
1 TAATTTATCAAAATATTAATAAATTATTATTT-ATTT
25427253 AAATAGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 10 0.31
35 15 0.47
36 7 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (36 bp):
TAATTTATCAAAATATTAATAAATTATTATTTATTT
Found at i:25427291 original size:22 final size:22
Alignment explanation
Indices: 25427241--25427291 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
25427231 ATTAATAATT
*
25427241 TTTATT-TCATTTAAATAGTAA
1 TTTATTATAATTTAAATAGTAA
* *
25427262 -TAATTTATAATTTAAATATTAA
1 TTTA-TTATAATTTAAATAGTAA
25427284 TTTATTAT
1 TTTATTAT
25427292 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
20 2 0.09
21 2 0.09
22 17 0.74
23 2 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTATTATAATTTAAATAGTAA
Found at i:25434116 original size:2 final size:2
Alignment explanation
Indices: 25434111--25434168 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
25434101 TGTGTGTGTG
25434111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25434153 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
25434169 ATAGAAAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25440690 original size:28 final size:28
Alignment explanation
Indices: 25440658--25440726 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
25440648 GAATTAAATC
* *
25440658 AAACTTTAAAAATGATGGAAAGAGGAAT
1 AAACTTTAAAAATGACGGAAAGAAGAAT
*
25440686 AAACTTAAAAAATGACGGAAAGAAGAAT
1 AAACTTTAAAAATGACGGAAAGAAGAAT
25440714 AAACTTTAAAAAT
1 AAACTTTAAAAAT
25440727 AATGAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.20
Consensus pattern (28 bp):
AAACTTTAAAAATGACGGAAAGAAGAAT
Found at i:25442637 original size:27 final size:28
Alignment explanation
Indices: 25442581--25442639 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
25442571 CAATTGAATC
* *
25442581 AAATTTTAAAAATGACGAAAAGAATGAT
1 AAATTTTAAAAAAGACGAAAAAAATGAT
*
25442609 AAATTTTAAAAAAGATGAAAAAAAT-AT
1 AAATTTTAAAAAAGACGAAAAAAATGAT
25442636 AAAT
1 AAAT
25442640 ACATGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (28 bp):
AAATTTTAAAAAAGACGAAAAAAATGAT
Found at i:25445655 original size:15 final size:15
Alignment explanation
Indices: 25445635--25445663 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25445625 CTGGTCCTAT
25445635 CAAATCAAAACAAAA
1 CAAATCAAAACAAAA
25445650 CAAATCAAAACAAA
1 CAAATCAAAACAAA
25445664 TCATAAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.07
Consensus pattern (15 bp):
CAAATCAAAACAAAA
Found at i:25445664 original size:10 final size:10
Alignment explanation
Indices: 25445633--25445666 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
25445623 CACTGGTCCT
*
25445633 ATCAAATCAA
1 ATCAAAACAA
*
25445643 AACAAAACAA
1 ATCAAAACAA
25445653 ATCAAAACAA
1 ATCAAAACAA
25445663 ATCA
1 ATCA
25445667 TAAGCTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.68, C:0.21, G:0.00, T:0.12
Consensus pattern (10 bp):
ATCAAAACAA
Found at i:25448427 original size:145 final size:146
Alignment explanation
Indices: 25448258--25448541 Score: 525
Period size: 145 Copynumber: 2.0 Consensus size: 146
25448248 CTATGGCAAC
*
25448258 TTTTCATTGTAGGCCTTCTCTGGTTCAAACATCTTTTTGCTAACTTAGCAACTGCTATAATATCT
1 TTTTCATTGCAGGCCTTCTCTGGTTCAAACATCTTTTTGCTAACTTAGCAACTGCTATAATATCT
25448323 TCTTGTGGACCATCATTCTTCAAGAAAATCAAATAAGGAACTCTGTTTCATAGAAAGCAAGAAAA
66 TCTTGTGGACCATCATTCTTCAAGAAAATCAAATAAGGAACTCTGTTTCATAGAAAGCAAGAAAA
25448388 A-GATACCAGCAACTT
131 AGGATACCAGCAACTT
*
25448403 TTTTCATTGCAGGCCTTCTCTGGTTCAAACATCTTTTTGCTAACTTAGCAACTGCTATAATCTCT
1 TTTTCATTGCAGGCCTTCTCTGGTTCAAACATCTTTTTGCTAACTTAGCAACTGCTATAATATCT
* *
25448468 TCTTGTGGACCATCATTCTTCAAGAATATCAAATAAGGAACTTTGTTTCATAGAAAGCAAGAAAA
66 TCTTGTGGACCATCATTCTTCAAGAAAATCAAATAAGGAACTCTGTTTCATAGAAAGCAAGAAAA
25448533 AGGATACCA
131 AGGATACCA
25448542 AGCTTCTCAC
Statistics
Matches: 134, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
145 127 0.95
146 7 0.05
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (146 bp):
TTTTCATTGCAGGCCTTCTCTGGTTCAAACATCTTTTTGCTAACTTAGCAACTGCTATAATATCT
TCTTGTGGACCATCATTCTTCAAGAAAATCAAATAAGGAACTCTGTTTCATAGAAAGCAAGAAAA
AGGATACCAGCAACTT
Found at i:25449287 original size:53 final size:53
Alignment explanation
Indices: 25449223--25449326 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
25449213 TTTCAATATT
*
25449223 ATCTTCATTGCTGGACAATTACTGTTGCAGTAGCAAACCTCCATTCATTTTAA
1 ATCTTCATTGCTGGACAATTACGGTTGCAGTAGCAAACCTCCATTCATTTTAA
* * * *
25449276 ATCTTCGTTGCTGGACAATTGCGGTTGTAGTAGTAAACCTCCATTCATTTT
1 ATCTTCATTGCTGGACAATTACGGTTGCAGTAGCAAACCTCCATTCATTTT
25449327 GTTTGAGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (53 bp):
ATCTTCATTGCTGGACAATTACGGTTGCAGTAGCAAACCTCCATTCATTTTAA
Found at i:25454656 original size:26 final size:26
Alignment explanation
Indices: 25454627--25454680 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
25454617 CATCTTCTCG
25454627 TATAAATAATTTTCCAATTAAAATTT
1 TATAAATAATTTTCCAATTAAAATTT
*
25454653 TATAAATAATTTTTCAATTAAAATTT
1 TATAAATAATTTTCCAATTAAAATTT
25454679 TA
1 TA
25454681 ATGAATTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TATAAATAATTTTCCAATTAAAATTT
Found at i:25457797 original size:2 final size:2
Alignment explanation
Indices: 25457790--25457826 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25457780 CAAGTAAATC
25457790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25457827 ATGTCTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25460793 original size:8 final size:8
Alignment explanation
Indices: 25460748--25460799 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 8
25460738 CAACTATTTC
25460748 AAAAAAAT
1 AAAAAAAT
25460756 CAAAAAAAT
1 -AAAAAAAT
25460765 AAATAATAAT
1 AAA-AA-AAT
*
25460775 GAAATATAAT
1 -AAA-AAAAT
25460785 AAAAAAAT
1 AAAAAAAT
25460793 AAAAAAA
1 AAAAAAA
25460800 ATAAGAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 14 0.37
9 13 0.34
10 6 0.16
11 5 0.13
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAAAT
Found at i:25462110 original size:16 final size:16
Alignment explanation
Indices: 25462078--25462126 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
25462068 AATAATCATT
*
25462078 ATAAAAAAATAACATAC
1 ATAAAAAAAT-ATATAC
*
25462095 ATCAAAAAATATATAC
1 ATAAAAAAATATATAC
25462111 ATAATAATAAATATAT
1 ATAA-AA-AAATATAT
25462127 GAACAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAAAATATATAC
Found at i:25462112 original size:20 final size:18
Alignment explanation
Indices: 25462078--25462126 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
25462068 AATAATCATT
25462078 ATAAAAAA-ATA-ACATA
1 ATAAAAAATATATACATA
25462094 CATCAAAAAATATATACATA
1 -AT-AAAAAATATATACATA
*
25462114 ATAATAAATATAT
1 ATAAAAAATATAT
25462127 GAACAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 16 0.57
19 5 0.18
20 5 0.18
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAAAAATATATACATA
Found at i:25466383 original size:30 final size:30
Alignment explanation
Indices: 25466347--25466409 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
25466337 TCGGAGTAAG
25466347 CTATATAAGAAGATTTTGAACTGTTTTACT
1 CTATATAAGAAGATTTTGAACTGTTTTACT
25466377 CTATATAAGAAGATTTTGAACTGTTTTACT
1 CTATATAAGAAGATTTTGAACTGTTTTACT
25466407 CTA
1 CTA
25466410 CTATTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (30 bp):
CTATATAAGAAGATTTTGAACTGTTTTACT
Found at i:25471859 original size:2 final size:2
Alignment explanation
Indices: 25471852--25471884 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25471842 TCAGTGTAAA
25471852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25471885 AGTCTTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25478812 original size:39 final size:37
Alignment explanation
Indices: 25478758--25478832 Score: 132
Period size: 39 Copynumber: 2.0 Consensus size: 37
25478748 TTTTTTCCGT
25478758 CGTGTGTGTGTGTGTATATATATATATATATAATAAAG
1 CGTGTGTGTGTGTGTATATATATATATATAT-ATAAAG
25478796 NCGTGTGTGTGTGTGTATATATATATATATATATAAA
1 -CGTGTGTGTGTGTGTATATATATATATATATATAAA
25478833 AGATAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 5 0.14
39 31 0.86
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (37 bp):
CGTGTGTGTGTGTGTATATATATATATATATATAAAG
Found at i:25484605 original size:111 final size:110
Alignment explanation
Indices: 25484449--25484672 Score: 310
Period size: 112 Copynumber: 2.0 Consensus size: 110
25484439 AAGAGTTATG
*
25484449 TCTCTGCACATATATTTTTATTCTTCTTAAGTCTTACTTGCTGAAACTTT-CCTTTTTCTCAATT
1 TCTCCGCACATATATTTTTATTCTTCTTAAGTCTTACTTGCTGAAACTTTACCTTTTTCTCAATT
* *
25484513 CTCATGGAAGGTTGAGTCAAACCCACATGGTTTTATTTCCAAATGT
66 CTCACGGAAGGTTGAGTCAAACCCACATGGTTTTA-TTCCAAATAT
* * * *
25484559 TCTCCGCACCTATCTTTTTCTTCTTCTCT-AGTTCTTACTAT-CTGAAACTTTACTTTTTTCTCA
1 TCTCCGCACATATATTTTTATTCTTCT-TAAG-TCTTACT-TGCTGAAACTTTACCTTTTTCTCA
**
25484622 ATTCTCACGGAAGGTTGAGTCAAACTTACATGGTTTTATTCCAAATAT
63 ATTCTCACGGAAGGTTGAGTCAAACCCACATGGTTTTATTCCAAATAT
25484670 TCT
1 TCT
25484673 TTGGACTTGA
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
110 25 0.25
111 30 0.30
112 46 0.46
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (110 bp):
TCTCCGCACATATATTTTTATTCTTCTTAAGTCTTACTTGCTGAAACTTTACCTTTTTCTCAATT
CTCACGGAAGGTTGAGTCAAACCCACATGGTTTTATTCCAAATAT
Found at i:25494189 original size:6 final size:6
Alignment explanation
Indices: 25494178--25494205 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25494168 CCTCTACGTG
25494178 TTCCTC TTCCTC TTCCTC TTCCTC TTCC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCC
25494206 ACCCAAGCCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCCTC
Found at i:25502077 original size:34 final size:34
Alignment explanation
Indices: 25502038--25502105 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
25502028 AGTAGAACAT
* * *
25502038 ATATAAAAAAAACTTAATAATGAAGAATGCATCA
1 ATATAAAAAAAACTTAATAAGGAAAAATCCATCA
*
25502072 ATATAAAAATAACTTAATAAGGAAAAATCCATCA
1 ATATAAAAAAAACTTAATAAGGAAAAATCCATCA
25502106 GCATTATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (34 bp):
ATATAAAAAAAACTTAATAAGGAAAAATCCATCA
Found at i:25503388 original size:2 final size:2
Alignment explanation
Indices: 25503376--25503405 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25503366 AATATAAGGG
*
25503376 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25503406 TCGAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:25507060 original size:84 final size:83
Alignment explanation
Indices: 25506919--25507086 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 83
25506909 GTTTGTTCTC
*
25506919 TACCCTTCTCTCTTTCTGTTCAAGTGTTTGACATTTATGGATTTTGTTGCAAGACTTACATATGA
1 TACCCTTCTCTCTTTCTGTTCAAGTGTTCGACATTTATGGATTTTGTTGCAAGACTTACATATGA
*
25506984 ACCCCAAGTATGACATCTT
66 A-CCCAAATATGACATCTT
* *
25507003 TACCCTTTTCTCTTTCTTTTCAAGTGTTCGACATTTATGGATTTTGTTGCAAGACTTACATATGA
1 TACCCTTCTCTCTTTCTGTTCAAGTGTTCGACATTTATGGATTTTGTTGCAAGACTTACATATGA
*
25507068 ACCCAAATGTGACATCTT
66 ACCCAAATATGACATCTT
25507086 T
1 T
25507087 TCCTGAAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 16 0.20
84 63 0.80
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (83 bp):
TACCCTTCTCTCTTTCTGTTCAAGTGTTCGACATTTATGGATTTTGTTGCAAGACTTACATATGA
ACCCAAATATGACATCTT
Found at i:25510351 original size:2 final size:2
Alignment explanation
Indices: 25510346--25510421 Score: 70
Period size: 2 Copynumber: 39.5 Consensus size: 2
25510336 TAAAAAATTA
* * *
25510346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T ANN NT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
25510387 AA AA AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25510422 ATGTTAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
1 4 0.06
2 58 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:25510681 original size:3 final size:3
Alignment explanation
Indices: 25510673--25510698 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25510663 TAAACTTAAC
25510673 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
25510699 ATTCATGAAC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25511629 original size:25 final size:25
Alignment explanation
Indices: 25511584--25511631 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25511574 AAGAGACTTT
**
25511584 TAATTAAAATAATTGTATAAATAAA
1 TAATTAAAATAAACGTATAAATAAA
*
25511609 TAATTAAAATAAACGTTTAAATA
1 TAATTAAAATAAACGTATAAATA
25511632 CCTGCAACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TAATTAAAATAAACGTATAAATAAA
Found at i:25520930 original size:84 final size:85
Alignment explanation
Indices: 25520837--25521005 Score: 261
Period size: 85 Copynumber: 2.0 Consensus size: 85
25520827 TTCACATGTA
* *
25520837 TTTCAAGATTCAAACTCGAAACACATTTTTTT-AATGAAAATTTCAGTTTTCAACGGTTAAGATA
1 TTTCAAGATTCAAACTCGAAACACATTTTTTTAAATGAAAATTTCAATTTTCAACGGTCAAGATA
25520901 TTCCA-TCAGAAATATTTTTT
66 TTCCATTC-GAAATATTTTTT
* *
25520921 TTTCAAGATTCTAACTTGAAACACATTTTTTTAAATGAAAATTTCAATTTTCAACGGTCAAGATA
1 TTTCAAGATTCAAACTCGAAACACATTTTTTTAAATGAAAATTTCAATTTTCAACGGTCAAGATA
* *
25520986 TTCTATTCGAATTATTTTTT
66 TTCCATTCGAAATATTTTTT
25521006 CGATTTTCGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
84 30 0.39
85 45 0.58
86 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (85 bp):
TTTCAAGATTCAAACTCGAAACACATTTTTTTAAATGAAAATTTCAATTTTCAACGGTCAAGATA
TTCCATTCGAAATATTTTTT
Found at i:25525968 original size:39 final size:39
Alignment explanation
Indices: 25525925--25526002 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
25525915 CTTGCTTCTT
*
25525925 GGTTTTCTCAGCAGACTC-CACCTCATCAGCAGGAACTAA
1 GGTTTTCTCAGCAGACTCTCA-CTCATCAACAGGAACTAA
** *
25525964 GGTTTTCTCATTAGACTCTGACTCATCAACAGGAACTAA
1 GGTTTTCTCAGCAGACTCTCACTCATCAACAGGAACTAA
25526003 CTGCAGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.97
40 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (39 bp):
GGTTTTCTCAGCAGACTCTCACTCATCAACAGGAACTAA
Found at i:25540688 original size:2 final size:2
Alignment explanation
Indices: 25540681--25540711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25540671 TTTTATGTCT
25540681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25540712 TTCTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25540720 original size:2 final size:2
Alignment explanation
Indices: 25540715--25540753 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25540705 TCTCTCTTTC
25540715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25540754 TATTTTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25553507 original size:24 final size:25
Alignment explanation
Indices: 25553470--25553516 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
25553460 AATTTTTTTA
*
25553470 ATTTAAAATAAAAATATAAAAATTT
1 ATTTAAAATAAAAATAAAAAAATTT
*
25553495 ATTT-AAATTAAAATAAAAAAAT
1 ATTTAAAATAAAAATAAAAAAAT
25553517 ATTTGATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
ATTTAAAATAAAAATAAAAAAATTT
Found at i:25553514 original size:31 final size:31
Alignment explanation
Indices: 25553454--25553513 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
25553444 ATCATTAGTG
* *
25553454 ATAAAGAATTTTTTTAATTTAAAATAAAAAT
1 ATAAAGAATTTATTTAAATTAAAATAAAAAT
25553485 ATAAA-AATTTATTTAAATTAAAATAAAAA
1 ATAAAGAATTTATTTAAATTAAAATAAAAA
25553514 AATATTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATAAAGAATTTATTTAAATTAAAATAAAAAT
Found at i:25553520 original size:26 final size:26
Alignment explanation
Indices: 25553470--25553537 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 26
25553460 AATTTTTTTA
* *
25553470 ATTTAAAATAAAA-ATATAAAAATTT-
1 ATTTAAATTAAAATA-AAAAAAATTTG
25553495 ATTTAAATTAAAATAAAAAAATATTTG
1 ATTTAAATTAAAATAAAAAAA-ATTTG
*
25553522 A-TTAAATT-TAATAAAA
1 ATTTAAATTAAAATAAAA
25553538 GTATAAAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 24 0.65
26 12 0.32
27 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (26 bp):
ATTTAAATTAAAATAAAAAAAATTTG
Found at i:25554539 original size:30 final size:29
Alignment explanation
Indices: 25554472--25554539 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
25554462 ACATTTAAAC
* *
25554472 AAATTTTTATTTTTTTATTGTTTTCAATT
1 AAATTTTTATATTTTTATTGTTTTCAAAT
*
25554501 AAAATTTTATATTTTTATT-TTTAATCAAAT
1 AAATTTTTATATTTTTATTGTTT--TCAAAT
25554531 AAATTTTTA
1 AAATTTTTA
25554540 ATTGATTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 3 0.09
29 17 0.52
30 13 0.39
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (29 bp):
AAATTTTTATATTTTTATTGTTTTCAAAT
Found at i:25554718 original size:19 final size:20
Alignment explanation
Indices: 25554682--25554720 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25554672 ATAATAAATT
* *
25554682 ATAAAAATTTATTTAATTTA
1 ATAAAAATATATTGAATTTA
25554702 ATAAAAATATA-TGAATTTA
1 ATAAAAATATATTGAATTTA
25554721 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAAAAATATATTGAATTTA
Found at i:25554718 original size:28 final size:29
Alignment explanation
Indices: 25554687--25554742 Score: 96
Period size: 28 Copynumber: 1.9 Consensus size: 29
25554677 AAATTATAAA
25554687 AATTTATTTAATTT-AATAAAAATATATG
1 AATTTATTTAATTTAAATAAAAATATATG
25554715 AATTTATTTAATTTAAAATAAAAATATA
1 AATTTATTTAATTT-AAATAAAAATATA
25554743 AAATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 14 0.54
30 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
AATTTATTTAATTTAAATAAAAATATATG
Found at i:25554737 original size:30 final size:30
Alignment explanation
Indices: 25554668--25554754 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
25554658 GCACGAAATA
25554668 TAAAATAATAAATTATAAAAATTTATTTAATT
1 TAAAATAA-AAA-TATAAAAATTTATTTAATT
**
25554700 T--AATAAAAATATATGAATTTATTTAATT
1 TAAAATAAAAATATAAAAATTTATTTAATT
*
25554728 TAAAATAAAAATATAAAATTTTATTTA
1 TAAAATAAAAATATAAAAATTTATTTA
25554755 TTATTTGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 18 0.38
29 3 0.06
30 26 0.54
32 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
TAAAATAAAAATATAAAAATTTATTTAATT
Found at i:25565312 original size:2 final size:2
Alignment explanation
Indices: 25565305--25565346 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
25565295 GAATTTTAGA
*
25565305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25565347 GAAAAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25565612 original size:21 final size:21
Alignment explanation
Indices: 25565587--25565628 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
25565577 ACCCTCCACG
*
25565587 TCTCCTACGCTCTCTCCCAAC
1 TCTCCCACGCTCTCTCCCAAC
25565608 TCTCCCACGCTCTCTCCCAAC
1 TCTCCCACGCTCTCTCCCAAC
25565629 CTCTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.55, G:0.05, T:0.26
Consensus pattern (21 bp):
TCTCCCACGCTCTCTCCCAAC
Found at i:25575882 original size:66 final size:66
Alignment explanation
Indices: 25575808--25575939 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
25575798 AAATTAGGAA
*
25575808 ACTAAATTAGTTAATTTTTTAATAAAAAGGCTAAATTAAAGAAAACGATTGGATATAGGAACCAA
1 ACTAAATTAGTTAATTTTTTAATAAAAAGGCTAAATTAAAGAAAACGATTGGATATAAGAACCAA
25575873 T
66 T
* *
25575874 ACTAAATTAGTTAATTTTTTAATAAAGAGGCTAAATTAACGAAAACGATTGGATATAAGAACCAA
1 ACTAAATTAGTTAATTTTTTAATAAAAAGGCTAAATTAAAGAAAACGATTGGATATAAGAACCAA
25575939 T
66 T
25575940 TGGGTACTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (66 bp):
ACTAAATTAGTTAATTTTTTAATAAAAAGGCTAAATTAAAGAAAACGATTGGATATAAGAACCAA
T
Found at i:25580378 original size:18 final size:18
Alignment explanation
Indices: 25580351--25580386 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25580341 ATCACTTTCT
25580351 TAACAAAGTTTTATTGTC
1 TAACAAAGTTTTATTGTC
*
25580369 TAACAGAGTTTTATTGTC
1 TAACAAAGTTTTATTGTC
25580387 AAGATACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (18 bp):
TAACAAAGTTTTATTGTC
Found at i:25591917 original size:114 final size:114
Alignment explanation
Indices: 25591733--25591947 Score: 349
Period size: 114 Copynumber: 1.9 Consensus size: 114
25591723 GCGGTAGTGC
* * *
25591733 CAATGGTGGTGCTAAGGGTGGAGGAGAACTTGGTGTTGCTGATGGAGTTAATGAAGGAGTCAGAG
1 CAATGGTGGTGCTAAGGGTGGAGGAGAACTTGGTGTTGCTGATGGAGTCAATAAAGGAATCAGAG
25591798 CTAATGGTGGATTTGCCAAAGGAGAAGGAGTAGGTGGTGGAGGTGGTGT
66 CTAATGGTGGATTTGCCAAAGGAGAAGGAGTAGGTGGTGGAGGTGGTGT
* * *
25591847 CAATGGTGGTGTTAAGGGTGGAGGAGAATTTGGTGTTGCTGATGGAGTCAATAAAGGAATCAGTG
1 CAATGGTGGTGCTAAGGGTGGAGGAGAACTTGGTGTTGCTGATGGAGTCAATAAAGGAATCAGAG
* * *
25591912 TTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTG
66 CTAATGGTGGATTTGCCAAAGGAGAAGGAGTAGGTG
25591948 CAGGGCTAGG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 92 1.00
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.27
Consensus pattern (114 bp):
CAATGGTGGTGCTAAGGGTGGAGGAGAACTTGGTGTTGCTGATGGAGTCAATAAAGGAATCAGAG
CTAATGGTGGATTTGCCAAAGGAGAAGGAGTAGGTGGTGGAGGTGGTGT
Found at i:25592034 original size:141 final size:141
Alignment explanation
Indices: 25591843--25592508 Score: 806
Period size: 141 Copynumber: 4.7 Consensus size: 141
25591833 GGTGGAGGTG
* *
25591843 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAATTTGGTGTTGCTGATGGAGTCAATAAAGGAATC
1 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAAGTTGGTGTTGCTGGTGGAGTCAATAAAGGAATC
* *
25591908 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGCAGGGCTAGGGGCTAGTGGAGGAGG
66 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGAGGGCTAGGGGGTAGTGGAGGAGG
*
25591973 CTTCGTG-GGCA
131 CTTAG-GAGGCA
* *
25591984 GTGTTAATGGTGGT-TCTAAGGGTGGAGGAGAAGTTGGTGTTGTTGGTGGAGTCAATAAAGGAAT
1 GTGTCAATGGTGGTGT-TAAGGGTGGAGGAGAAGTTGGTGTTGCTGGTGGAGTCAATAAAGGAAT
* * * * *
25592048 CAATGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTCGGT-GATGGGC-ATTGGGTTGGTGGAGG
65 CAGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGA-GGGCTA-GGGGGTAGTGGAGG
*
25592111 AGGCTTAGGAGGTA
128 AGGCTTAGGAGGCA
* * * * *
25592125 GTTTTAATGGTGGTGTTAATGGTGGAGGAGAAGTTGGTGTTGCTAGTGGAGTCAATAAAGGAATT
1 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAAGTTGGTGTTGCTGGTGGAGTCAATAAAGGAATC
* * * * *
25592190 AGTGTTAATGGTGGATTTGCCAAAGGTGTCGGAATAGGTGGTGGGCTTGGGGGTGGTGGAGGCGG
66 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGAGGGC-T-AGGG-GGT--A-GTGG
*
25592255 TCAAGGAGGCTTAGGAGGCG
125 ---AGGAGGCTTAGGAGGCA
* * *
25592275 GTGTCAATGGTGGTGTTAAGAGTGGAGGAGAATTTGGTGTTGCTAGTGGAGTCAATAAAGGAATC
1 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAAGTTGGTGTTGCTGGTGGAGTCAATAAAGGAATC
* * * *
25592340 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGTGGGTTTGGGGGTGGTGGAGGAGG
66 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGAGGGCTAGGGGGTAGTGGAGGAGG
*
25592405 CCTAGGAGGCA
131 CTTAGGAGGCA
* * * *
25592416 GTGTCAATGGTGGTGCTT-AGGGTGGAGGAGAA-TTAAGTGTTGCTGGTGGAGTTAATAAAAGAG
1 GTGTCAATGGTGGTG-TTAAGGGTGGAGGAGAAGTT-GGTGTTGCTGGTGGAGTCAATAAAGGAA
*
25592479 TCAGAT-TTAATGGTGTATTTGCCAAAGGTG
64 TCAG-TGTTAATGGTGGATTTGCCAAAGGTG
25592509 GATTCGTTGC
Statistics
Matches: 456, Mismatches: 50, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
140 6 0.01
141 311 0.68
142 5 0.01
143 2 0.00
144 5 0.01
147 6 0.01
148 3 0.01
149 1 0.00
150 117 0.26
ACGTcount: A:0.24, C:0.07, G:0.42, T:0.28
Consensus pattern (141 bp):
GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAAGTTGGTGTTGCTGGTGGAGTCAATAAAGGAATC
AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGAGGGCTAGGGGGTAGTGGAGGAGG
CTTAGGAGGCA
Found at i:25592366 original size:291 final size:280
Alignment explanation
Indices: 25591843--25592508 Score: 847
Period size: 291 Copynumber: 2.3 Consensus size: 280
25591833 GGTGGAGGTG
25591843 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAATTTGGTGTTGCTGATGGAGTCAATAAAGGAATC
1 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAA-TTGGTGTTGCTG-TGGAGTCAATAAAGGAATC
* *
25591908 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGCAGGGCTAGGGGCTAGTGGAGGAGG
64 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAATAGGTGCAGGGCTAGGGGCTAGCGGAGGAGG
* * * * *
25591973 CTTCGTGGGCAGTGTTAATGGTGGTTCTAAGGGTGGAGGAGAAGTTGGTGTTGTTGGTGGAGTCA
129 CTTAGTGGGCAGTGTCAATGGTGGTTCTAAGAGTGGAGGAGAAGTTGGTGTTGCTAGTGGAGTCA
* *
25592038 ATAAAGGAATCAATGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTCGGTGATGGGCATT-GGGT
194 ATAAAGGAATCAATGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGATGGG-ATTGGGGG
* *
25592102 TGGTGGAGGAGGCTTAGGAGGTA
258 TGGTGGAGGAGGCCTAGGAGGCA
* * * *
25592125 GTTTTAATGGTGGTGTTAATGGTGGAGGAGAAGTTGGTGTTGCTAGTGGAGTCAATAAAGGAATT
1 GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAA-TTGGTGTTGCT-GTGGAGTCAATAAAGGAATC
* ** * *
25592190 AGTGTTAATGGTGGATTTGCCAAAGGTGTCGGAATAGGTGGTGGGCTTGGGGGTGGTGGAGGCGG
64 AGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAATAGGTGCAGGGC-T-AGGG-GCT--A-GCGG
* *
25592255 TCAAGGAGGCTTAG-GAGGCGGTGTCAATGGTGGTGT-TAAGAGTGGAGGAGAATTTGGTGTTGC
123 ---AGGAGGCTTAGTG-GGCAGTGTCAATGGTGGT-TCTAAGAGTGGAGGAGAAGTTGGTGTTGC
* *
25592318 TAGTGGAGTCAATAAAGGAATCAGTGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGGTG
183 TAGTGGAGTCAATAAAGGAATCAATGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGATG
*
25592383 GGTTTGGGGGTGGTGGAGGAGGCCTAGGAGGCA
248 GGATTGGGGGTGGTGGAGGAGGCCTAGGAGGCA
* * * *
25592416 GTGTCAATGGTGGTGCTT-AGGGTGGAGGAGAATTAAGTGTTGCTGGTGGAGTTAATAAAAGAGT
1 GTGTCAATGGTGGTG-TTAAGGGTGGAGGAGAATT-GGTGTTGCT-GTGGAGTCAATAAAGGAAT
*
25592480 CAGAT-TTAATGGTGTATTTGCCAAAGGTG
63 CAG-TGTTAATGGTGGATTTGCCAAAGGTG
25592509 GATTCGTTGC
Statistics
Matches: 332, Mismatches: 36, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
282 100 0.30
283 2 0.01
284 3 0.01
285 2 0.01
287 1 0.00
288 3 0.01
290 5 0.02
291 212 0.64
292 4 0.01
ACGTcount: A:0.24, C:0.07, G:0.42, T:0.28
Consensus pattern (280 bp):
GTGTCAATGGTGGTGTTAAGGGTGGAGGAGAATTGGTGTTGCTGTGGAGTCAATAAAGGAATCAG
TGTTAATGGTGGATTTGCCAAAGGTGTAGGAATAGGTGCAGGGCTAGGGGCTAGCGGAGGAGGCT
TAGTGGGCAGTGTCAATGGTGGTTCTAAGAGTGGAGGAGAAGTTGGTGTTGCTAGTGGAGTCAAT
AAAGGAATCAATGTTAATGGTGGATTTGCCAAAGGTGTAGGAGTAGGTGATGGGATTGGGGGTGG
TGGAGGAGGCCTAGGAGGCA
Found at i:25604998 original size:34 final size:34
Alignment explanation
Indices: 25604955--25605037 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
25604945 ATGTTACACA
* *
25604955 CTAAAACTTCAACAGCAAATGTTACACGTTAAGG
1 CTAAAACTTCAACACCAAATGTTACACGTCAAGG
* *
25604989 CTAAAACTTCAATACCAAATGTTACATGTCAAGG
1 CTAAAACTTCAACACCAAATGTTACACGTCAAGG
* **
25605023 CCAAAGTTTCAACAC
1 CTAAAACTTCAACAC
25605038 TAGATATTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (34 bp):
CTAAAACTTCAACACCAAATGTTACACGTCAAGG
Found at i:25620646 original size:6 final size:6
Alignment explanation
Indices: 25620637--25620665 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25620627 AAGAAAAAGC
25620637 CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
25620666 GTGCAGGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:25657191 original size:13 final size:13
Alignment explanation
Indices: 25657154--25657191 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
25657144 AAAGAAGAAA
*
25657154 AAGCTCTTCTTTT
1 AAGCTCTTTTTTT
*
25657167 GAGCT-TTTTTTT
1 AAGCTCTTTTTTT
25657179 AAGCTCTTTTTTT
1 AAGCTCTTTTTTT
25657192 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (13 bp):
AAGCTCTTTTTTT
Found at i:25662069 original size:24 final size:24
Alignment explanation
Indices: 25662023--25662070 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
25662013 AGTGTTTTAA
* *
25662023 TTTATTTAGTTTTTTATATTAATT
1 TTTATTTAGTTTTTTAAAATAATT
25662047 TTTATTTA-TTATTTTAAAATAATT
1 TTTATTTAGTT-TTTTAAAATAATT
25662071 AAATTGTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATTTAGTTTTTTAAAATAATT
Found at i:25666315 original size:26 final size:27
Alignment explanation
Indices: 25666286--25666350 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
25666276 TTATTCATAA
* *
25666286 TTTAAACATTATTATG-ATTATTTATT
1 TTTAAACATTATAATGTATAATTTATT
25666312 TTTAAACATTAATAATGTATAATTTATT
1 TTTAAACATT-ATAATGTATAATTTATT
* *
25666340 TTAAAATATTA
1 TTTAAACATTA
25666351 AAAATTGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.30
27 6 0.18
28 17 0.52
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
TTTAAACATTATAATGTATAATTTATT
Found at i:25666880 original size:41 final size:41
Alignment explanation
Indices: 25666837--25666915 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
25666827 TTGATTTCAA
25666837 TTTCACTTAATAATTTAAAAAATAATATT-TTAAAATATTAAT
1 TTTCA-TTAATAATTT-AAAAATAATATTATTAAAATATTAAT
* * * *
25666879 TTTTATTTATAATTTAAATATATTATTATTAAAATAT
1 TTTCATTAATAATTTAAAAATAATATTATTAAAATAT
25666916 AAAAAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 10 0.31
41 18 0.56
42 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (41 bp):
TTTCATTAATAATTTAAAAATAATATTATTAAAATATTAAT
Found at i:25666958 original size:26 final size:26
Alignment explanation
Indices: 25666866--25666968 Score: 63
Period size: 26 Copynumber: 4.0 Consensus size: 26
25666856 AAATAATATT
25666866 TTAAAATATTAA-TTTTT-ATTTATAA
1 TTAAAATATTAATTTTTTAATTT-TAA
* * * *
25666891 TTTAAATATATT-ATTATTAAAATATAA
1 -TTAAA-ATATTAATTTTTTAATTTTAA
* *
25666918 --AAAATTAATATTTTTTTAATTTTAA
1 TTAAAA-TATTAATTTTTTAATTTTAA
* *
25666943 TTAAAATATTAATTTTATAAGTTTAA
1 TTAAAATATTAATTTTTTAATTTTAA
25666969 GTTTTTAATT
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
23 1 0.02
24 6 0.11
25 10 0.18
26 22 0.39
27 15 0.27
28 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TTAAAATATTAATTTTTTAATTTTAA
Found at i:25669849 original size:24 final size:24
Alignment explanation
Indices: 25669822--25669868 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
25669812 CGCCATAATG
25669822 TTACACGCCATATACAAAAACATA
1 TTACACGCCATATACAAAAACATA
*
25669846 TTACACGCCATGTACAAAAACAT
1 TTACACGCCATATACAAAAACAT
25669869 GTGATATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.06, T:0.21
Consensus pattern (24 bp):
TTACACGCCATATACAAAAACATA
Found at i:25670009 original size:45 final size:45
Alignment explanation
Indices: 25669900--25670012 Score: 154
Period size: 45 Copynumber: 2.5 Consensus size: 45
25669890 GTTACACACA
* * *
25669900 ATGGTTAAATTGTTACTCGCCATGTACAAAAACATGTGACACATC
1 ATGGTTAAGTTGTTACACGTCATGTACAAAAACATGTGACACATC
* * **
25669945 ATGGTTACGTTGTTACACGTCATGTACAAAAACATGTGATATGTC
1 ATGGTTAAGTTGTTACACGTCATGTACAAAAACATGTGACACATC
*
25669990 ATGGTTAGGTTGTTACACGTCAT
1 ATGGTTAAGTTGTTACACGTCAT
25670013 ATTGAAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (45 bp):
ATGGTTAAGTTGTTACACGTCATGTACAAAAACATGTGACACATC
Found at i:25670052 original size:29 final size:28
Alignment explanation
Indices: 25670020--25670094 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 28
25670010 CATATTGAAA
* *
25670020 AAAAAATATTGTTGTTATACGCCATGTT
1 AAAAAATATTGTTGTTACACGCCATATT
* * *
25670048 GAAAAAATATCGTTCTTACACGCTATATT
1 -AAAAAATATTGTTGTTACACGCCATATT
*
25670077 CAAAAATATT-TTGTTACA
1 AAAAAATATTGTTGTTACA
25670095 TTTTAATGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 7 0.18
28 8 0.21
29 23 0.61
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAAAATATTGTTGTTACACGCCATATT
Found at i:25670093 original size:27 final size:28
Alignment explanation
Indices: 25669999--25670094 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 28
25669989 CATGGTTAGG
*
25669999 TTGTTACACGTCATATTGAAAAAAAAATATT
1 TTGTTACACGCCATATTG---AAAAAATATT
* * *
25670030 GTTGTTATACGCCATGTTGAAAAAATATCG
1 -TTGTTACACGCCATATTGAAAAAATAT-T
* * *
25670060 TTCTTACACGCTATATT-CAAAAATATT
1 TTGTTACACGCCATATTGAAAAAATATT
25670087 TTGTTACA
1 TTGTTACA
25670095 TTTTAATGCC
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
27 7 0.13
28 8 0.15
29 22 0.42
32 15 0.29
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (28 bp):
TTGTTACACGCCATATTGAAAAAATATT
Found at i:25670977 original size:118 final size:118
Alignment explanation
Indices: 25670768--25670984 Score: 312
Period size: 118 Copynumber: 1.8 Consensus size: 118
25670758 TTTCTTCTAG
** **
25670768 TTTTATAACATATTGTTTATAATTAGTTATTATTTATACAAACTTTGTTATAAAACATTTTAACA
1 TTTTATAACATATTGTTTATAATTAGTTATTATTTATACAAACTTTAATATAAAACATTACAACA
* *
25670833 TATAATTTGTATCATTAATTATATATATA-ATAAAGTAATATTATATATATANA
66 TATAAGTTATATCATTAATTATATATATATATAAAGTAATATTATATATATA-A
* * * *
25670886 TTTTATAATATATTTTTTATAATTAGTTATTATTTATTCAAACTTTAATATAAAACATTACATCA
1 TTTTATAACATATTGTTTATAATTAGTTATTATTTATACAAACTTTAATATAAAACATTACAACA
25670951 TATAAGTTATATCATTAATT-TCATATATATATAA
66 TATAAGTTATATCATTAATTAT-ATATATATATAA
25670985 TTAATATATA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
117 1 0.01
118 82 0.94
119 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (118 bp):
TTTTATAACATATTGTTTATAATTAGTTATTATTTATACAAACTTTAATATAAAACATTACAACA
TATAAGTTATATCATTAATTATATATATATATAAAGTAATATTATATATATAA
Found at i:25672682 original size:15 final size:15
Alignment explanation
Indices: 25672662--25672691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25672652 TTTTAAAATA
25672662 CTTTTATAAATTAAT
1 CTTTTATAAATTAAT
*
25672677 CTTTTATTAATTAAT
1 CTTTTATAAATTAAT
25672692 ATATAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTTTATAAATTAAT
Found at i:25672970 original size:59 final size:59
Alignment explanation
Indices: 25672904--25673021 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
25672894 ATGTCTTAAA
*
25672904 CATATCAATATAATTAATATACAAAACACAATTAATTTAAACTTAAACATATTTAAATT
1 CATATCAATATAATTAATATACAAAACACAATTAATTTAAACTCAAACATATTTAAATT
* * *
25672963 CATATCAATATAATTAATATACGAAACATAGTTAATTTAAACTCAAACATATTTAAATT
1 CATATCAATATAATTAATATACAAAACACAATTAATTTAAACTCAAACATATTTAAATT
25673022 AATTGATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.36
Consensus pattern (59 bp):
CATATCAATATAATTAATATACAAAACACAATTAATTTAAACTCAAACATATTTAAATT
Found at i:25673258 original size:100 final size:100
Alignment explanation
Indices: 25673085--25673285 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
25673075 TTTGCTCACC
*
25673085 CCTACCTAAAGCACAAGTAAGCATGTGATGTGAGTTAAAAATCTATTTTGTGATTAATGGGAGGT
1 CCTACCTAAAGCACAAGTAAGCATGTGATGTGAGTTAAAAATCTATTTTGTAATTAATGGGAGGT
25673150 GACCCTAAAATTGAAACAAAACCATAACTGAATGT
66 GACCCTAAAATTGAAACAAAACCATAACTGAATGT
25673185 CCTACCTAAAGCACAAGTAAGCATGTGATGTGAGTTAAAAATCTATTTTGTAATTAATGGGAGGT
1 CCTACCTAAAGCACAAGTAAGCATGTGATGTGAGTTAAAAATCTATTTTGTAATTAATGGGAGGT
25673250 GACCCTAAAATTGAAACAAAACCATAACTGAATGT
66 GACCCTAAAATTGAAACAAAACCATAACTGAATGT
25673285 C
1 C
25673286 TCATCTGTAA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (100 bp):
CCTACCTAAAGCACAAGTAAGCATGTGATGTGAGTTAAAAATCTATTTTGTAATTAATGGGAGGT
GACCCTAAAATTGAAACAAAACCATAACTGAATGT
Found at i:25674287 original size:2 final size:2
Alignment explanation
Indices: 25674280--25674309 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25674270 ATGTACCCAT
25674280 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
25674310 CGACNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25674352 original size:2 final size:2
Alignment explanation
Indices: 25674345--25674380 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25674335 NNNNNNNNNN
25674345 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
25674381 CCTATGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25678700 original size:16 final size:17
Alignment explanation
Indices: 25678666--25678700 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25678656 ACTCATTCAT
*
25678666 TTAAAATATATTTACTA
1 TTAAAATATATTTAATA
25678683 TTAAAATAT-TTTAATA
1 TTAAAATATATTTAATA
25678699 TT
1 TT
25678701 TTTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATATATTTAATA
Found at i:25680023 original size:286 final size:291
Alignment explanation
Indices: 25679554--25680130 Score: 853
Period size: 286 Copynumber: 2.0 Consensus size: 291
25679544 TTTCTTGTTN
* * **
25679554 CTATGTTCTTTTTTTTTTTTGGTTATGTGAATTTTATTTTACATGATTTTAGTTTTTAAAAATTA
1 CTATGTTCTTTCTTTTTTTTGGTTATATGAATTTTATTTTACATGATTTTAGCCTTTAAAAATTA
* *
25679619 AAAAATTATTATGTAATTCTCAAATATAAGTTGTAGTATTATACTACTGTTTAAAATTTCATCAA
66 AAAAATTATTATGTAATTCTCAAAAATAAGTTGTAGTATTATACTACTGCTTAAAATTTCATCAA
* *** *
25679684 TGTATTATTTTTTTATTAATCTTGATTAGATAAGAGGGGATTATCTTTTTTATTTGCTTTATGTT
131 TGTATCATTTTTTTATTAATCTTGATTAGATAAGAGAAAATTATCTTTTTTATTTGCTTCATGTT
* * * *
25679749 TTATATTTAGTTGAAAGAATATTAGTATATATGAGAAAATTATCTTAAGTATTTAATCTTTAAAT
196 TTATATTTAGTTGAAAGAAAATTAGTATATATAAGAAAATTATCTTAAATATTTAATCTTTAAAC
25679814 AATTCTGATTATATAAGAGAAAATTATTAAT
261 AATTCTGATTATATAAGAGAAAATTATTAAT
* *
25679845 CTATGTTC-TTCTTTTTTTT-GTTATATGGATTTTATTTT-CTATGA-TTTAGCCTTTAAAAGTT
1 CTATGTTCTTTCTTTTTTTTGGTTATATGAATTTTATTTTAC-ATGATTTTAGCCTTTAAAAATT
* *
25679906 AAAAAATTATTATGTAATTTTCAAAAATAAGTTGTAGTA-T-TGC-ACTGCTTAAAATTTCATCA
65 AAAAAATTATTATGTAATTCTCAAAAATAAGTTGTAGTATTATACTACTGCTTAAAATTTCATCA
*
25679968 ATGTATCATTTTTTTTATTAATCTTGATTATATAAGAGAAAATTATCTTTTTTATTTGCTTCATG
130 ATGTATCA-TTTTTTTATTAATCTTGATTAGATAAGAGAAAATTATCTTTTTTATTTGCTTCATG
* * *
25680033 TTTTGTATTTAGTTGAAAGAAAATTAGTATATATAAGGAAATTATCTTAAATATTTAGTCTTTAA
194 TTTTATATTTAGTTGAAAGAAAATTAGTATATATAAGAAAATTATCTTAAATATTTAATCTTTAA
* * *
25680098 ACCATTTTGATTATATAAGAGGAAATTATTAAT
259 ACAATTCTGATTATATAAGAGAAAATTATTAAT
25680131 ATTTTATATC
Statistics
Matches: 258, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
285 25 0.10
286 141 0.55
287 1 0.00
288 52 0.20
289 21 0.08
290 10 0.04
291 8 0.03
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (291 bp):
CTATGTTCTTTCTTTTTTTTGGTTATATGAATTTTATTTTACATGATTTTAGCCTTTAAAAATTA
AAAAATTATTATGTAATTCTCAAAAATAAGTTGTAGTATTATACTACTGCTTAAAATTTCATCAA
TGTATCATTTTTTTATTAATCTTGATTAGATAAGAGAAAATTATCTTTTTTATTTGCTTCATGTT
TTATATTTAGTTGAAAGAAAATTAGTATATATAAGAAAATTATCTTAAATATTTAATCTTTAAAC
AATTCTGATTATATAAGAGAAAATTATTAAT
Found at i:25680589 original size:9 final size:9
Alignment explanation
Indices: 25680564--25680598 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
25680554 ACATGTTATC
25680564 TAAA-ATTA
1 TAAATATTA
25680572 TAGAATATTA
1 TA-AATATTA
25680582 TAAATATTA
1 TAAATATTA
25680591 TAAATATT
1 TAAATATT
25680599 TTAATTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 2 0.08
9 17 0.68
10 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
TAAATATTA
Found at i:25684175 original size:19 final size:19
Alignment explanation
Indices: 25684151--25684204 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
25684141 AAATATAAAA
25684151 TAATTTTATATATTTAATT
1 TAATTTTATATATTTAATT
* *
25684170 TAATTTTAAAATTTTTAATT
1 TAATTTT-ATATATTTAATT
25684190 TATATTATTAT-TATT
1 TA-ATT-TTATATATT
25684205 ATTTATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 4 0.14
22 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAATTTTATATATTTAATT
Found at i:25688674 original size:4 final size:4
Alignment explanation
Indices: 25688665--25688699 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
25688655 TCTTTAAACA
25688665 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
25688700 CCTCAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:25703114 original size:13 final size:13
Alignment explanation
Indices: 25703096--25703126 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
25703086 CAGATATTAA
25703096 AATAAAAAAAATC
1 AATAAAAAAAATC
*
25703109 AATAAAAAAAATG
1 AATAAAAAAAATC
25703122 AATAA
1 AATAA
25703127 CTTTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
AATAAAAAAAATC
Found at i:25722045 original size:79 final size:76
Alignment explanation
Indices: 25721933--25722093 Score: 200
Period size: 75 Copynumber: 2.1 Consensus size: 76
25721923 CAAGGCTCCC
* *
25721933 TAATTGAGATTGGCATTATCCTTTTCTTTTTCTTTTTATTTTCAAGACATTTGACATATGAT-TT
1 TAATTGAGATTGGCATTATCCTTTTC---TTCTTCTT-TTTGCAAGACATTTGACATATGATGTT
25721997 TTTTTCTTAATTATT
62 TTTTTCTTAATTATT
* * * *
25722012 TAATTGGGATTGGGATTGTCCATTTT-TTCTTCTTTTTGGAAGACATTTGACATATGATGGTTTT
1 TAATTGAGATTGGCATTATCC-TTTTCTTCTTCTTTTTGCAAGACATTTGACATATGAT-GTTTT
25722076 TTTCTTAATTATT
64 TTTCTTAATTATT
25722089 TAATT
1 TAATT
25722094 TTTTGAAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
75 22 0.30
76 7 0.10
77 22 0.30
79 18 0.25
80 4 0.05
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (76 bp):
TAATTGAGATTGGCATTATCCTTTTCTTCTTCTTTTTGCAAGACATTTGACATATGATGTTTTTT
TCTTAATTATT
Found at i:25741790 original size:2 final size:2
Alignment explanation
Indices: 25741783--25741829 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
25741773 TTGGCCTTGC
25741783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
25741825 GT AT A
1 AT AT A
25741830 CAAGGACGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25759623 original size:18 final size:18
Alignment explanation
Indices: 25759596--25759632 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25759586 TAAAAAATAA
* *
25759596 AAAGATAAAAAAGAAGAG
1 AAAGAGAAAAAAAAAGAG
25759614 AAAGAGAAAAAAAAAGAG
1 AAAGAGAAAAAAAAAGAG
25759632 A
1 A
25759633 GAGAAAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (18 bp):
AAAGAGAAAAAAAAAGAG
Found at i:25759709 original size:8 final size:8
Alignment explanation
Indices: 25759696--25759738 Score: 68
Period size: 8 Copynumber: 5.2 Consensus size: 8
25759686 TGGTGTCATA
25759696 TATTTTAT
1 TATTTTAT
*
25759704 TATTTTAA
1 TATTTTAT
25759712 TATTTTAT
1 TATTTTAT
25759720 TATTTTAT
1 TATTTTAT
25759728 TATTTATAT
1 TATTT-TAT
25759737 TA
1 TA
25759739 ATTATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 27 0.84
9 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAT
Found at i:25760599 original size:29 final size:28
Alignment explanation
Indices: 25760557--25760690 Score: 110
Period size: 29 Copynumber: 4.6 Consensus size: 28
25760547 CGTTTTTGGC
*
25760557 ATATGTGGAAACTAATATTATACTTGTGT
1 ATAT-TGGAAACTAATATCATACTTGTGT
* * * *
25760586 ATATATGGCAACTAATGTCACACTTGTAT
1 ATAT-TGGAAACTAATATCATACTTGTGT
*
25760615 ATATTAGGAAACTAATATCATATTTGTGT
1 ATATT-GGAAACTAATATCATACTTGTGT
* **
25760644 TTATGTAAAAACTAATA-CGATA-TGTGTGT
1 ATAT-TGGAAACTAATATC-ATACT-TGTGT
25760673 ATATTTGGAAACTAATAT
1 ATA-TTGGAAACTAATAT
25760691 ATTGTGTGTA
Statistics
Matches: 82, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.04
29 77 0.94
30 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (28 bp):
ATATTGGAAACTAATATCATACTTGTGT
Found at i:25761450 original size:29 final size:29
Alignment explanation
Indices: 25761382--25761661 Score: 196
Period size: 29 Copynumber: 9.8 Consensus size: 29
25761372 TATAATTGTG
** * *
25761382 TGTGTATATTCAGAAACGAATATGAT--A
1 TGTGTATATTTGGAAACTAATATCATACA
* *
25761409 TGTGAATATTTGGAAACTAATATGATACA
1 TGTGTATATTTGGAAACTAATATCATACA
*
25761438 TGTGTATATTTGGAAACTAATAT-ATTATA
1 TGTGTATATTTGGAAACTAATATCA-TACA
* * * *
25761467 TGTGTATGTTCT-GACACTGATAT-ACACA
1 TGTGTATATT-TGGAAACTAATATCATACA
* * *
25761495 GGTGTATATTCGGAAACTAATGTCATACA
1 TGTGTATATTTGGAAACTAATATCATACA
* * * * *
25761524 TGTGTACATTT-GAAATTGATATCAAACG
1 TGTGTATATTTGGAAACTAATATCATACA
**
25761552 TGTGTATATTCAGAAACTAATATCATACCA
1 TGTGTATATTTGGAAACTAATATCATA-CA
* * * *
25761582 -GTGAATATGTGGAAACTAATATAATACT
1 TGTGTATATTTGGAAACTAATATCATACA
*** * *
25761610 TGTGTATATTCAAAAACTAATATTATACC
1 TGTGTATATTTGGAAACTAATATCATACA
* *
25761639 TGTGTTTATGTGGAAACTAATAT
1 TGTGTATATTTGGAAACTAATAT
25761662 AAGACTTATG
Statistics
Matches: 194, Mismatches: 50, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
27 22 0.11
28 41 0.21
29 129 0.66
30 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (29 bp):
TGTGTATATTTGGAAACTAATATCATACA
Found at i:25761527 original size:57 final size:57
Alignment explanation
Indices: 25761381--25761643 Score: 171
Period size: 57 Copynumber: 4.6 Consensus size: 57
25761371 GTATAATTGT
* * * * * * * *
25761381 GTGTGTATATTCAGAAACGAATATGAT--ATGTGAATATTTGGAAACTAATATGATAC
1 GTGTGTATATTCGGAAACTAATATCATACATGTGTACATTT-GAAACTGATATCAAAC
* * * ** * *
25761437 ATGTGTATATTTGGAAACTAATAT-ATTATATGTGTATGTTCTGACACTGATAT-ACAC
1 GTGTGTATATTCGGAAACTAATATCA-TACATGTGTACATT-TGAAACTGATATCAAAC
* *
25761494 AG-GTGTATATTCGGAAACTAATGTCATACATGTGTACATTTGAAATTGATATCAAAC
1 -GTGTGTATATTCGGAAACTAATATCATACATGTGTACATTTGAAACTGATATCAAAC
* * * * *
25761551 GTGTGTATATTCAGAAACTAATATCATACCA-GTGAATATGTGGAAACTAATAT-AATAC
1 GTGTGTATATTCGGAAACTAATATCATA-CATGTGTACAT-TTGAAACTGATATCAA-AC
* ** * *
25761609 TTGTGTATATTCAAAAACTAATATTATACCTGTGT
1 GTGTGTATATTCGGAAACTAATATCATACATGTGT
25761644 TTATGTGGAA
Statistics
Matches: 165, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
55 1 0.01
56 32 0.19
57 70 0.42
58 61 0.37
59 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (57 bp):
GTGTGTATATTCGGAAACTAATATCATACATGTGTACATTTGAAACTGATATCAAAC
Found at i:25761596 original size:86 final size:84
Alignment explanation
Indices: 25761381--25761615 Score: 215
Period size: 86 Copynumber: 2.7 Consensus size: 84
25761371 GTATAATTGT
* * * *
25761381 GTGTGTATATTCAGAAACGAATATGATA-TGTGAATATTTGGAAACTAATATGATACATGTGTAT
1 GTGTGTATATTCAGAAACTAATAT-ATACAGTGAATA-TTGGAAACTAATATAATACATGTGTAC
* *
25761445 ATTTGGAAACTAATATATTAT
64 ATTTGGAAACTAATATATAAC
* * * * * * * * *
25761466 ATGTGTATGTTCTGACACTGATATACACAGGTGTATATTCGGAAACTAATGTCATACATGTGTAC
1 GTGTGTATATTCAGAAACTAATATATACA-GTGAATATT-GGAAACTAATATAATACATGTGTAC
* *
25761531 ATTT-GAAATTGATATCA-AAC
64 ATTTGGAAACTAATAT-ATAAC
*
25761551 GTGTGTATATTCAGAAACTAATATCATACCAGTGAATATGTGGAAACTAATATAATACTTGTGTA
1 GTGTGTATATTCAGAAACTAATAT-ATA-CAGTGAATAT-TGGAAACTAATATAATACATGTGTA
25761616 TATTCAAAAA
Statistics
Matches: 117, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
84 2 0.02
85 49 0.42
86 63 0.54
87 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (84 bp):
GTGTGTATATTCAGAAACTAATATATACAGTGAATATTGGAAACTAATATAATACATGTGTACAT
TTGGAAACTAATATATAAC
Found at i:25761627 original size:58 final size:58
Alignment explanation
Indices: 25761552--25761674 Score: 183
Period size: 58 Copynumber: 2.1 Consensus size: 58
25761542 ATATCAAACG
* *
25761552 TGTGTATATTCAGAAACTAATATCATACCAGTGAATATGTGGAAACTAATATAATACT
1 TGTGTATATTCAAAAACTAATATCATACCAGTGAATATGTGGAAACTAATATAAGACT
* * **
25761610 TGTGTATATTCAAAAACTAATATTATACCTGTGTTTATGTGGAAACTAATATAAGACT
1 TGTGTATATTCAAAAACTAATATCATACCAGTGAATATGTGGAAACTAATATAAGACT
*
25761668 TATGTAT
1 TGTGTAT
25761675 TCAAGATCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (58 bp):
TGTGTATATTCAAAAACTAATATCATACCAGTGAATATGTGGAAACTAATATAAGACT
Found at i:25766870 original size:6 final size:6
Alignment explanation
Indices: 25766859--25766890 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
25766849 GAGAGGGTTT
25766859 GCATAG GCATAG GCATAG GCATAG GCAT-G GCA
1 GCATAG GCATAG GCATAG GCATAG GCATAG GCA
25766891 AAGTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.19, G:0.34, T:0.16
Consensus pattern (6 bp):
GCATAG
Found at i:25778615 original size:7 final size:7
Alignment explanation
Indices: 25778603--25778640 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
25778593 CCTCACTTGC
25778603 TTTTTTA
1 TTTTTTA
25778610 TTTTTTA
1 TTTTTTA
25778617 TTTTTTA
1 TTTTTTA
25778624 -TTTTTA
1 TTTTTTA
25778630 -TTTTTA
1 TTTTTTA
25778636 TTTTT
1 TTTTT
25778641 GTAATAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:25778620 original size:6 final size:6
Alignment explanation
Indices: 25778604--25778640 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
25778594 CTCACTTGCT
25778604 TTTTTA TTTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
25778641 GTAATAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:25800784 original size:25 final size:25
Alignment explanation
Indices: 25800728--25800784 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 25
25800718 CACGAAAAGA
*
25800728 TCAATCATCATTACACTTATCACTC
1 TCAATCATCATCACACTTATCACTC
*
25800753 TCGATCATCA-C-C-CTTATCACTC
1 TCAATCATCATCACACTTATCACTC
25800775 TCAATCATCA
1 TCAATCATCA
25800785 CCAATACCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 19 0.66
23 1 0.03
25 9 0.31
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (25 bp):
TCAATCATCATCACACTTATCACTC
Found at i:25800786 original size:22 final size:22
Alignment explanation
Indices: 25800734--25800786 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
25800724 AAGATCAATC
* * *
25800734 ATCATTACACTTATCACTCTCG
1 ATCATCACCCTTATCACTCTCA
25800756 ATCATCACCCTTATCACTCTCA
1 ATCATCACCCTTATCACTCTCA
25800778 ATCATCACC
1 ATCATCACC
25800787 AATACCAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.38, G:0.02, T:0.32
Consensus pattern (22 bp):
ATCATCACCCTTATCACTCTCA
Found at i:25803041 original size:271 final size:272
Alignment explanation
Indices: 25802557--25803103 Score: 1017
Period size: 271 Copynumber: 2.0 Consensus size: 272
25802547 TCTGGTCCTC
*
25802557 TAGCTTTCGTAGATCTTTCAATGTTGCTTCAGCATTATGAATCTTAGCATCCAGGTTATCAATGT
1 TAGCTTTCGCAGATCTTTCAATGTTGCTTCAGCATTATGAATCTTAGCATCCAGGTTATCAATGT
*
25802622 TTTTTTCCAAGTCCTGTATTTGGCTTTTCAAAGATTCTGTTTTTTCTTGATCTTGAGCAATGCTT
66 TTTTTTCCAAGTCCTGTATTTGGCTTTTCAAAGATTCAGTTTTTTCTTGATCTTGAGCAATGCTT
*
25802687 TCTCGAAGCTGTATAACAAACCATATCAAGAAAAATCCTTTAAGTTAAGGTTCATAAGATGTTCA
131 TCTCAAAGCTGTATAACAAACCATATCAAGAAAAATCCTTTAAGTTAAGGTTCATAAGATGTTCA
* *
25802752 ATGTTAGGGTAATTATAAACCCAAACCCTACTGTAAACAGATGGGTTAGATCCTTGTAAACATAT
196 ATATTAGGGTAATTATAAACCCAAACCCTACTGTAAACAGATGGGTTAGATCCCTGTAAACATAT
25802817 CAAATATCAGAT
261 CAAATATCAGAT
*
25802829 TAGCTTTCGCAGATCTTTCAATGTTGCTTCAGCATTATGAATCTTAGCATCGAGGTTATCAAT-T
1 TAGCTTTCGCAGATCTTTCAATGTTGCTTCAGCATTATGAATCTTAGCATCCAGGTTATCAATGT
25802893 TTTTTTCCAAGTCCTGTATTTGGCTTTTCAAAGATTCAGTTTTTTCTTGATCTTGAGCAATGCTT
66 TTTTTTCCAAGTCCTGTATTTGGCTTTTCAAAGATTCAGTTTTTTCTTGATCTTGAGCAATGCTT
25802958 TCTCAAAGCTGTATAA-AGAACCATATCAAGAAAAATCCTTTAAGTTAAGGTTCATAAGATGTTC
131 TCTCAAAGCTGTATAACA-AACCATATCAAGAAAAATCCTTTAAGTTAAGGTTCATAAGATGTTC
25803022 AATATTAGGGTAATTATAAACCCAAACCCTACTGTAAACAGATGGGTTAGATCCCTGTAAACATA
195 AATATTAGGGTAATTATAAACCCAAACCCTACTGTAAACAGATGGGTTAGATCCCTGTAAACATA
25803087 TCAAATATCAGAT
260 TCAAATATCAGAT
25803100 TAGC
1 TAGC
25803104 GCCATATTTC
Statistics
Matches: 268, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
270 1 0.00
271 206 0.77
272 61 0.23
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (272 bp):
TAGCTTTCGCAGATCTTTCAATGTTGCTTCAGCATTATGAATCTTAGCATCCAGGTTATCAATGT
TTTTTTCCAAGTCCTGTATTTGGCTTTTCAAAGATTCAGTTTTTTCTTGATCTTGAGCAATGCTT
TCTCAAAGCTGTATAACAAACCATATCAAGAAAAATCCTTTAAGTTAAGGTTCATAAGATGTTCA
ATATTAGGGTAATTATAAACCCAAACCCTACTGTAAACAGATGGGTTAGATCCCTGTAAACATAT
CAAATATCAGAT
Found at i:25804468 original size:25 final size:25
Alignment explanation
Indices: 25804434--25804483 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
25804424 GATGCTTGAA
25804434 TGATTTGATACATTTAAAGTTTGTT
1 TGATTTGATACATTTAAAGTTTGTT
25804459 TGATTTGATACATTTAAAGTTTGTT
1 TGATTTGATACATTTAAAGTTTGTT
25804484 GTCCCTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (25 bp):
TGATTTGATACATTTAAAGTTTGTT
Found at i:25804884 original size:6 final size:6
Alignment explanation
Indices: 25804873--25804899 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25804863 GGAAAAGAGT
25804873 GAAGGA GAAGGA GAAGGA GAAGGA GAA
1 GAAGGA GAAGGA GAAGGA GAAGGA GAA
25804900 AGATAACAGC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:25808608 original size:1 final size:1
Alignment explanation
Indices: 25808602--25808679 Score: 93
Period size: 1 Copynumber: 78.0 Consensus size: 1
25808592 CACCACACAA
* * * * * *
25808602 CCCCCCCCCCCCNCCCTCCCCCACCCCCACCCCCCCCCCCCCCCTCCCCCCCCCCACCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
25808667 CCCCACCCCCCCC
1 CCCCCCCCCCCCC
25808680 GCCAAGAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.05, C:0.91, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:25808634 original size:28 final size:27
Alignment explanation
Indices: 25808601--25808679 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
25808591 ACACCACACA
25808601 ACCCCCCCCCCCCNCCCTCCCCCACCCCC
1 ACCCCCCCCCCCC-CCCTCCCCC-CCCCC
25808630 ACCCCCCCCCCCCCCCTCCCCCCCCCC
1 ACCCCCCCCCCCCCCCTCCCCCCCCCC
*
25808657 ACCCCCCCCCCCCCAC-CCCCCCC
1 ACCCCCCCCCCCCCCCTCCCCCCC
25808680 GCCAAGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 7 0.14
27 20 0.41
28 9 0.18
29 13 0.27
ACGTcount: A:0.06, C:0.90, G:0.00, T:0.03
Consensus pattern (27 bp):
ACCCCCCCCCCCCCCCTCCCCCCCCCC
Found at i:25808644 original size:33 final size:31
Alignment explanation
Indices: 25808602--25808679 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 31
25808592 CACCACACAA
* *
25808602 CCCCCCCCCCCCNCCCTCCCCCACCCCCACCC
1 CCCCCCCCCCCCCCCCCCCCCCACCCCC-CCC
25808634 CCCCCCCCCCCCTCCCCCCCCCCACCCCCCCC
1 CCCCCCCCCCCC-CCCCCCCCCCACCCCCCCC
*
25808666 CCCCCACCCCCCCC
1 CCCCCCCCCCCCCC
25808680 GCCAAGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 2 0.05
32 26 0.62
33 14 0.33
ACGTcount: A:0.05, C:0.91, G:0.00, T:0.03
Consensus pattern (31 bp):
CCCCCCCCCCCCCCCCCCCCCCACCCCCCCC
Found at i:25811634 original size:15 final size:14
Alignment explanation
Indices: 25811601--25811638 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
25811591 GAGCTTTTAT
*
25811601 GAAAAAAAGAAAAA
1 GAAAGAAAGAAAAA
25811615 GAAAGAAAGAAAAA
1 GAAAGAAAGAAAAA
25811629 GCAAAGAAAG
1 G-AAAGAAAG
25811639 CGTAAGAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGAAAAA
Found at i:25821470 original size:2 final size:2
Alignment explanation
Indices: 25821463--25821542 Score: 107
Period size: 2 Copynumber: 42.0 Consensus size: 2
25821453 TTAAAAATTA
25821463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- ANT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
25821503 AA AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25821543 TCAAATTATG
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
1 5 0.07
2 65 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25825843 original size:42 final size:41
Alignment explanation
Indices: 25825784--25825896 Score: 106
Period size: 41 Copynumber: 2.7 Consensus size: 41
25825774 TTTTTAAATA
*
25825784 TAAATATTTATAATTTATTTAAAATATTAAAAATTAATAGGT
1 TAAATATTAATAATTTATTTAAAAT-TTAAAAATTAATAGGT
* * **
25825826 TAAATATTAATATTTTATTTATAATTTAATCATTAATA--T
1 TAAATATTAATAATTTATTTAAAATTTAAAAATTAATAGGT
* *
25825865 TAAA-AATAATGATATTTGATTTATAATTTAAA
1 TAAATATTAAT-A-ATTT-ATTTAAAATTTAAA
25825897 TGTTATTATG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 5 0.08
39 6 0.10
40 3 0.05
41 24 0.40
42 22 0.37
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (41 bp):
TAAATATTAATAATTTATTTAAAATTTAAAAATTAATAGGT
Found at i:25825984 original size:27 final size:28
Alignment explanation
Indices: 25825924--25825985 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
25825914 ATTTCTATTT
* *
25825924 TATTTTATTTTTAAATATTAATCATTCA
1 TATTTTATTTATAAATATTAATAATTCA
*
25825952 TATTTTATTTAT-AATATTAATAATTTA
1 TATTTTATTTATAAATATTAATAATTCA
*
25825979 TCTTTTA
1 TATTTTA
25825986 AATACTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTTATTTATAAATATTAATAATTCA
Found at i:25825994 original size:22 final size:23
Alignment explanation
Indices: 25825959--25826001 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25825949 TCATATTTTA
*
25825959 TTTATAATATTAATAATTTATCT
1 TTTATAATACTAATAATTTATCT
*
25825982 TTTA-AATACTAATATTTTAT
1 TTTATAATACTAATAATTTAT
25826002 TTATAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTATAATACTAATAATTTATCT
Found at i:25825998 original size:117 final size:117
Alignment explanation
Indices: 25825835--25826131 Score: 377
Period size: 117 Copynumber: 2.5 Consensus size: 117
25825825 TTAAATATTA
* * ** *
25825835 ATATTTTATTTATAAT-TTAATCATTAATATTAAAAATAATGATATTTGATTTATAATTTAAATG
1 ATATTTTATTTATAATATTAATAATTAATCTTTTAAATAATAATATTT-ATTTATAATTTAAATG
*
25825899 TTATTA-TGATTATTTATTTCTATTT-TATTTTAT-TTTTAAATATTAATCATTC
65 TTATTACT-ATTATTTATTTCTATTTAT-TTTTATCTTTTAAATATTAATAATTC
* * *
25825951 ATATTTTATTTATAATATTAATAATTTATCTTTTAAATACTAATATTTTATTTATAATTTAAATT
1 ATATTTTATTTATAATATTAATAATTAATCTTTTAAATAATAATA-TTTATTTATAATTTAAATG
* *
25826016 TTATTACTATTATTTATTTTTATTTATTTTTATCTTTTAAATATTAATAATTT
65 TTATTACTATTATTTATTTCTATTTATTTTTATCTTTTAAATATTAATAATTC
* * * *
25826069 ATATTTTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATGTTATTTATAATTTAA
1 ATA-TTTTATTTATAATATTAATAATTAATCTTTTAAATAATAATAT-TTATTTATAATTTAA
25826132 TNNNNNNNNN
Statistics
Matches: 159, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
116 16 0.10
117 64 0.40
118 26 0.16
119 53 0.33
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (117 bp):
ATATTTTATTTATAATATTAATAATTAATCTTTTAAATAATAATATTTATTTATAATTTAAATGT
TATTACTATTATTTATTTCTATTTATTTTTATCTTTTAAATATTAATAATTC
Found at i:25826068 original size:28 final size:28
Alignment explanation
Indices: 25826040--25826095 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
25826030 TATTTTTATT
*
25826040 TATTTTTATCTTTTAAATATTAATAATTTA
1 TATTTTTA--TTTAAAATATTAATAATTTA
25826070 TATTTTTATTTAAAATATTAATAATT
1 TATTTTTATTTAAAATATTAATAATT
25826096 GATCATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.68
30 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTTTTATTTAAAATATTAATAATTTA
Found at i:25826069 original size:22 final size:23
Alignment explanation
Indices: 25826043--25826114 Score: 65
Period size: 28 Copynumber: 3.0 Consensus size: 23
25826033 TTTTATTTAT
25826043 TTTTATCTTTTAAATATTAATAA
1 TTTTATCTTTTAAATATTAATAA
*
25826066 TTTATATTTTTATTTAAAATATTAATAA
1 TTT-TA--TCT-TTT-AAATATTAATAA
* *
25826094 -TTGATCATTTAAATATTAATA
1 TTTTATCTTTTAAATATTAATA
25826115 TGTTATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 3 0.08
26 3 0.08
27 5 0.12
28 12 0.30
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTTATCTTTTAAATATTAATAA
Found at i:25826457 original size:16 final size:16
Alignment explanation
Indices: 25826422--25826466 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
25826412 ATAATTTAGA
*
25826422 AATTAATAATTTATTTAT
1 AATTAA-AATATA-TTAT
*
25826440 AATTTAAATATATTAT
1 AATTAAAATATATTAT
25826456 AATTAAAATAT
1 AATTAAAATAT
25826467 CAAAATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 5 0.21
18 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:25830433 original size:35 final size:36
Alignment explanation
Indices: 25830382--25830452 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
25830372 CCCCTCCCCC
*
25830382 CCCCTTCTCTCTCTCTCTCTCTTTTTTTC-ATTCTT
1 CCCCTTCTCTCTCTCTCTCTCCTTTTTTCTATTCTT
25830417 NCCCC-TCTCTCTCTCTCTCTCCTTTTTTCTATTCTT
1 -CCCCTTCTCTCTCTCTCTCTCCTTTTTTCTATTCTT
25830453 ACACCGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 23 0.70
36 10 0.30
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (36 bp):
CCCCTTCTCTCTCTCTCTCTCCTTTTTTCTATTCTT
Found at i:25836026 original size:346 final size:346
Alignment explanation
Indices: 25835393--25836089 Score: 1297
Period size: 347 Copynumber: 2.0 Consensus size: 346
25835383 GCAACCTATT
25835393 GTCTATACACGAGGGTTAATTGAAGCTCAATTTTTTCAAACTCTTCATTAATGTCCAAAAAGAAA
1 GTCTATACACGAGGGTTAATTGAAGCTCAATTTTTTCAAACTCTTCATTAATGTCCAAAAAGAAA
25835458 AAAAACAAAACATGAAAATAGTTATTTTCCTTCATAATATTTCAAAGAATAATAACATATAGTTC
66 AAAAACAAAACATGAAAATAGTTATTTTCCTTCATAATATTTCAAAGAATAATAACATATAGTTC
25835523 AGGAAAACGATGCTTTGTGCAAGTCAAAAAAACAGGGGAAAAAAAAAAGCAAGAATTCTGGAAAG
131 AGGAAAACGATGCTTTGTGCAAGTCAAAAAAACAGGGGAAAAAAAAAAGCAAGAATTCTGGAAAG
* *
25835588 AAAAGTTGACTGTTTGTTTGTATATGGCGTAGAGGCAGGGAATGTGTGGGCGTCAACACAAACAG
196 AAAAGTTGACTATTTGTTTGTAGATGGCGTAGAGGCAGGGAATGTGTGGGCGTCAACACAAACAG
25835653 GAGAACTTTCTGGGCATTGAACTTTAGTTATTCCCTGAGTTTTAGAAGAATCTATTTATCATACT
261 GAGAACTTTCTGGGCATTGAACTTTAGTTATTCCCTGAGTTTTAGAAGAATCTATTTATCATACT
25835718 TCAAGGAAATTTGAAGAACCC
326 TCAAGGAAATTTGAAGAACCC
* * *
25835739 GTCTATACACGGGGGTTGATTGAAGCTCATTTTTTTTCAAACTCTTCATTAATGTCCAAAAAGAA
1 GTCTATACACGAGGGTTAATTGAAGCTCA-ATTTTTTCAAACTCTTCATTAATGTCCAAAAAGAA
25835804 AAAAAACAAAACATGAAAATAGTTATTTTCCTTCATAATATTTCAAAGAATAATAACATATAGTT
65 AAAAAACAAAACATGAAAATAGTTATTTTCCTTCATAATATTTCAAAGAATAATAACATATAGTT
25835869 CAGGAAAACGATGCTTTGTGCAAGTCAAAAAAACAGGGGAAAAAAAAAAGCAAGAATTCTGGAAA
130 CAGGAAAACGATGCTTTGTGCAAGTCAAAAAAACAGGGGAAAAAAAAAAGCAAGAATTCTGGAAA
25835934 GAAAAGTTGAC-ATTTGTTTGTAGATGGCGTAGAGGCAGGGAATGTGTGGGCGTCAACACAAACA
195 GAAAAGTTGACTATTTGTTTGTAGATGGCGTAGAGGCAGGGAATGTGTGGGCGTCAACACAAACA
* * *
25835998 GGAGAACTTTCTGGGCGTTGAACTTTAGTTATTCGCTGAGTTTTGGAAGAATCTATTTATCATAC
260 GGAGAACTTTCTGGGCATTGAACTTTAGTTATTCCCTGAGTTTTAGAAGAATCTATTTATCATAC
*
25836063 TTCAAGGAAATTTGAAGTACCC
325 TTCAAGGAAATTTGAAGAACCC
25836085 GTCTA
1 GTCTA
25836090 CATTTTGGGG
Statistics
Matches: 341, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
346 166 0.49
347 175 0.51
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (346 bp):
GTCTATACACGAGGGTTAATTGAAGCTCAATTTTTTCAAACTCTTCATTAATGTCCAAAAAGAAA
AAAAACAAAACATGAAAATAGTTATTTTCCTTCATAATATTTCAAAGAATAATAACATATAGTTC
AGGAAAACGATGCTTTGTGCAAGTCAAAAAAACAGGGGAAAAAAAAAAGCAAGAATTCTGGAAAG
AAAAGTTGACTATTTGTTTGTAGATGGCGTAGAGGCAGGGAATGTGTGGGCGTCAACACAAACAG
GAGAACTTTCTGGGCATTGAACTTTAGTTATTCCCTGAGTTTTAGAAGAATCTATTTATCATACT
TCAAGGAAATTTGAAGAACCC
Done.