Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 138 of 163
Found at i:45034179 original size:9 final size:9
Alignment explanation
Indices: 45034165--45034212 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
45034155 AATTCGGTCG
*
45034165 ATTAACTGA
1 ATTAACCGA
45034174 ATTAACCGA
1 ATTAACCGA
*
45034183 ATTACCCGA
1 ATTAACCGA
45034192 ATTAACCGA
1 ATTAACCGA
45034201 ATTAACCGA
1 ATTAACCGA
45034210 ATT
1 ATT
45034213 TAATTCCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (9 bp):
ATTAACCGA
Found at i:45036048 original size:26 final size:26
Alignment explanation
Indices: 45035937--45036049 Score: 78
Period size: 26 Copynumber: 4.5 Consensus size: 26
45035927 AGCTCCAGAT
* * * *
45035937 AGCCATATATCGGGAAGTTCAAG-CG
1 AGCCATATATCGGAAAGCTCACGAAG
45035962 AGCC--ATATCGGAAAGCTC-CGAAG
1 AGCCATATATCGGAAAGCTCACGAAG
* * *
45035985 AGCCAT-TAATC-AATAAGCTCACAAAA
1 AGCCATAT-ATCGGA-AAGCTCACGAAG
*
45036011 AGCC-TTTAATCGGAAAGCTCACGAAG
1 AGCCATAT-ATCGGAAAGCTCACGAAG
45036037 AGCCATATATCGG
1 AGCCATATATCGG
45036050 GACACTCAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
22 1 0.01
23 17 0.25
24 2 0.03
25 14 0.21
26 31 0.46
27 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (26 bp):
AGCCATATATCGGAAAGCTCACGAAG
Found at i:45039901 original size:77 final size:77
Alignment explanation
Indices: 45039789--45039959 Score: 229
Period size: 77 Copynumber: 2.2 Consensus size: 77
45039779 AAATAATCAA
* * * ** *
45039789 TGCATGCATATT-AAAAATAGTCAACAGCATATGACCATCTCCACTGACAATCATACACAGACAA
1 TGCATGCATATTAAAAAATAGTCAACAACATATGACCAGCCCCACCAACAATCATACACAAACAA
45039853 ATTA-AAAAACAC
66 ATTAGAAAAA-AC
* * * *
45039865 TGCATGCATGTTAAAAAATAGTCAATAACATGTGACCAGCCCCACCAACAATCATACATAAACAA
1 TGCATGCATATTAAAAAATAGTCAACAACATATGACCAGCCCCACCAACAATCATACACAAACAA
45039930 ATTAGAAAAAAC
66 ATTAGAAAAAAC
45039942 TGCATGCATATTAAAAAA
1 TGCATGCATATTAAAAAA
45039960 CACTCACTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
76 11 0.13
77 66 0.80
78 5 0.06
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (77 bp):
TGCATGCATATTAAAAAATAGTCAACAACATATGACCAGCCCCACCAACAATCATACACAAACAA
ATTAGAAAAAAC
Found at i:45043232 original size:17 final size:15
Alignment explanation
Indices: 45043196--45043235 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
45043186 ATTTATTTCA
45043196 TAATATAATAATAAT
1 TAATATAATAATAAT
*
45043211 TAATATAATTTATAATT
1 TAATATAA-TAATAA-T
45043228 TAATATAA
1 TAATATAA
45043236 AACCTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATAATAATAAT
Found at i:45045413 original size:23 final size:23
Alignment explanation
Indices: 45045386--45045454 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
45045376 AAAAATGAAA
45045386 CCAAAATTGAAATAACCCTAAAT
1 CCAAAATTGAAATAACCCTAAAT
45045409 CCAAAATTGAAATAACCCTAAAT
1 CCAAAATTGAAATAACCCTAAAT
* * *
45045432 TCAAAATTAAAATAACCCAAAAT
1 CCAAAATTGAAATAACCCTAAAT
45045455 AACCTTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.55, C:0.20, G:0.03, T:0.22
Consensus pattern (23 bp):
CCAAAATTGAAATAACCCTAAAT
Found at i:45046010 original size:31 final size:30
Alignment explanation
Indices: 45045975--45046035 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
45045965 CCAGTGATTA
* *
45045975 TTTTGACACTTTTTTATAATGTT-AGTGACTG
1 TTTTGACA-TTTTTCA-AAAGTTGAGTGACTG
*
45046006 TTTTGTCATTTTTCAAAAGTTGAGTGACTG
1 TTTTGACATTTTTCAAAAGTTGAGTGACTG
45046036 AAATAAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.54
31 7 0.27
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (30 bp):
TTTTGACATTTTTCAAAAGTTGAGTGACTG
Found at i:45055298 original size:3 final size:3
Alignment explanation
Indices: 45055290--45055347 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
45055280 TTTGTAGGCT
45055290 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45055338 TTA TTA TTA T
1 TTA TTA TTA T
45055348 ATATATATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45056739 original size:25 final size:26
Alignment explanation
Indices: 45056709--45056757 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
45056699 TACTTTTTTT
*
45056709 AATTTTT-GT-TTTAATTTTTAAAATA
1 AATTTTTAGTATTT-ATTTTAAAAATA
45056734 AATTTTTAGTATTTATTTTAAAAA
1 AATTTTTAGTATTTATTTTAAAAA
45056758 CGGGCCGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 11 0.52
27 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (26 bp):
AATTTTTAGTATTTATTTTAAAAATA
Found at i:45065319 original size:12 final size:12
Alignment explanation
Indices: 45065302--45065326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45065292 AAAAATGACG
45065302 AGAGGAATTTGT
1 AGAGGAATTTGT
45065314 AGAGGAATTTGT
1 AGAGGAATTTGT
45065326 A
1 A
45065327 CCTAGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AGAGGAATTTGT
Found at i:45066532 original size:13 final size:13
Alignment explanation
Indices: 45066490--45066532 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
45066480 TTGCTTTTGG
45066490 AAAGTGC-TGTGA
1 AAAGTGCTTGTGA
45066502 AAATGTGCTTGTGA
1 AAA-GTGCTTGTGA
* *
45066516 AAAGTGTTTTTGA
1 AAAGTGCTTGTGA
45066529 AAAG
1 AAAG
45066533 CTTGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 16 0.59
14 8 0.30
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (13 bp):
AAAGTGCTTGTGA
Found at i:45071134 original size:13 final size:13
Alignment explanation
Indices: 45071116--45071140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45071106 TTTAATGTAA
45071116 AAAAATAAAAAAT
1 AAAAATAAAAAAT
45071129 AAAAATAAAAAA
1 AAAAATAAAAAA
45071141 GGAACTACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:45077464 original size:32 final size:32
Alignment explanation
Indices: 45077423--45077517 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
45077413 TGTCCAGTAT
*
45077423 TGTTTTTAGCTTTTGAATTGAGATTCCATCAC
1 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
45077455 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
1 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
* *
45077487 TGTTTTTAGCTTCTGAATTGAGTTTCCATCA
1 TGTTTTTAGCTTATGAATTGAGATTCCATCA
45077518 ATCTATTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (32 bp):
TGTTTTTAGCTTATGAATTGAGATTCCATCAC
Found at i:45078922 original size:301 final size:292
Alignment explanation
Indices: 45078385--45079243 Score: 899
Period size: 301 Copynumber: 2.9 Consensus size: 292
45078375 TTGTTATGGG
* * * *
45078385 TTCAAATCTCAGCATATACATATTTTTATTAGTTTTTT-AGTGAAAAGAGTGAAATACCCTTAAA
1 TTCAAATCTCA-CATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAAA
* * * * * *
45078449 TAATATTACTTATTTTAATTACAAAATGACATTCTCGTAATTTTCTAACCGAGTTGTTACTCGGT
65 TAATATTACTTATTTTAATTACGAAAGGGCATTCTCGTACTTCT-TAACCGAGTTGTGACTCGGT
* * * *
45078514 TGAGGATGACACCGACTCAATAAAACAG-TTAAATAATAGCAAGTATAGATATACAACTGATAAA
129 TGAGGGTGACACCGACTCAA-ACAAGAGCTTAAATAATAG-AAGTA-AGATATACAACTGATGAA
* * * *
45078578 TGTAGTAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATAAAAAAAAAAGTTGTAGTTGAA
191 GGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAGTT-TAGTTGAA
* *
45078643 TGGTAAATTAAAGGTTTAACTAAAGTAATTGGTGTAAA
255 TGATAAATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
* *
45078681 TTCAAATCTCACTAAATTCATATTTTTA-TAGTTTTTTAAAGTGAAAAGACTAAAATACTCTCAA
1 TTCAAATCTCAC-ATATACATATTTTTATTAGTTTTTT-AAGTGAAAAGACTAAAATACTCTCAA
*
45078745 ATAATATTACTTATTTTAATTACGAAAGGGCATTCTCGTGACTTCTTAACCAAGTTGATGACTCG
64 ATAATATTACTTATTTTAATTACGAAAGGGCATTCTCGT-ACTTCTTAACCGAGTTG-TGACTCG
** *
45078810 GTTGAGGGTGACAATGACTCAACCAAGAGCTTAATTATAGTATAGAAGTAGAGATATACAA-TCG
127 GTTGAGGGTGACACCGACTCAAACAAGAGCTTAA--ATA--ATAGAAGTA-AGATATACAACT-G
** * *
45078874 ATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATTTTTTAAAACTTTAG
186 ATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATA-TAATAAAAAGTTTAG
* * * **
45078939 TTGAATGATAAATTAAAGGTTTTATTAATGCAATTGGTGTGGA
250 TTGAATGATAAATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
* * * * *
45078982 TTCAAACTTTGC-CATATGCATATATTTATTGGTTTTTTAAGTGAAAAGACTAAAATGCTCTCAA
1 TTCAAA-TCT-CACATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAA
* * *
45079046 ATAATATTACTTATTTTAATTAAATATTATGAAAGGGCATTCTCATAACTTCTTAATCGAGTTTG
64 ATAATATTACTTA--TT--TT--A-ATTACGAAAGGGCATTCTCGT-ACTTCTTAACCGAG-TT-
* * * * * *
45079111 GTGACCCGATTAAGGGTGACACCAATTCAATCAAGAGCTTAAATAATA-ATA-TAA-ATATACAA
119 GTGACTCGGTTGAGGGTGACACCGACTCAAACAAGAGCTTAAATAATAGA-AGTAAGATATACAA
* * * *
45079173 CTAATGGAGGTAATAAATTGTACATAATAAAATTAAAATGTATAAAAATAT-TAATAAAAAGTTT
183 CTGATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAG-TT
45079237 TAGTTGA
247 TAGTTGA
45079244 CAGAAGTTTT
Statistics
Matches: 473, Mismatches: 63, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
295 10 0.02
296 24 0.05
297 71 0.15
298 33 0.07
300 10 0.02
301 166 0.35
302 74 0.16
303 5 0.01
304 3 0.01
305 6 0.01
307 4 0.01
308 31 0.07
309 35 0.07
310 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (292 bp):
TTCAAATCTCACATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAAAT
AATATTACTTATTTTAATTACGAAAGGGCATTCTCGTACTTCTTAACCGAGTTGTGACTCGGTTG
AGGGTGACACCGACTCAAACAAGAGCTTAAATAATAGAAGTAAGATATACAACTGATGAAGGTAA
TAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAGTTTAGTTGAATGATAA
ATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
Found at i:45084754 original size:22 final size:23
Alignment explanation
Indices: 45084727--45084805 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 23
45084717 CACTAATGAA
45084727 CAGAGAGCACTGAAGTGCTATA-
1 CAGAGAGCACTGAAGTGCTATAT
*
45084749 CAGAGAGCACAGATA-TGCTA-AT
1 CAGAGAGCACTGA-AGTGCTATAT
*
45084771 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTGAAGTGCTA-T-AT
45084796 CAGAGAGCAC
1 CAGAGAGCAC
45084806 CAACGTCCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.02
22 34 0.71
23 1 0.02
25 12 0.25
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (23 bp):
CAGAGAGCACTGAAGTGCTATAT
Found at i:45084824 original size:25 final size:25
Alignment explanation
Indices: 45084771--45084824 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
45084761 ATATGCTAAT
** * * *
45084771 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACCAACGTCCTAATAAA
45084796 CAGAGAGCACCAACGTCCTAATAAA
1 CAGAGAGCACCAACGTCCTAATAAA
45084821 CAGA
1 CAGA
45084825 TAGCGAGCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (25 bp):
CAGAGAGCACCAACGTCCTAATAAA
Found at i:45124306 original size:57 final size:56
Alignment explanation
Indices: 45124202--45124379 Score: 233
Period size: 50 Copynumber: 3.2 Consensus size: 56
45124192 ACTTTTGATT
* *
45124202 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTGA-A
*
45124260 AGTGATAAGTGATAAGTGGCAGCTTAGCTACACTTATCTGATCAGTGACAAGTG--
1 AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGAA
* *
45124314 A-TG---AGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGATAAGAGATA
1 AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGA-A
*
45124367 AATGATAAGTGAT
1 AGTGATAAGTGAT
45124380 TCCGTGTAAG
Statistics
Matches: 107, Mismatches: 6, Indels: 15
0.84 0.05 0.12
Matches are distributed among these distances:
50 44 0.41
53 3 0.03
54 3 0.03
57 36 0.34
58 21 0.20
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (56 bp):
AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGAA
Found at i:45128617 original size:60 final size:60
Alignment explanation
Indices: 45128551--45128665 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
45128541 TTTTTTGAAA
* * * * * *
45128551 TTTTTAGAATTAT-AATTAAATTGTCAAATTTTATAAATATTGAGGGTTAAATTTATTAAT
1 TTTTTAGAATT-TGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTATTAAT
45128611 TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTA
1 TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTA
45128666 AAATCAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (60 bp):
TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTATTAAT
Found at i:45146602 original size:81 final size:81
Alignment explanation
Indices: 45146423--45146602 Score: 283
Period size: 81 Copynumber: 2.2 Consensus size: 81
45146413 GGGACGAAAT
**
45146423 TTTTTAGGGGGTCGGAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
1 TTTTTAGGGGGTCAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
45146488 AATAAAAAATTTATCA
66 AATAAAAAATTTATCA
*
45146504 TTTTT-GGGCGG-CTAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAATGAT
1 TTTTTAGGG-GGTC-AAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGAT
* *
45146567 TAAATCAAAATTTTATCA
64 TAAATAAAAAATTTATCA
45146585 TTTTTAGGGGGTCAAAAT
1 TTTTTAGGGGGTCAAAAT
45146603 GTAATTTTAC
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
80 4 0.04
81 82 0.91
82 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (81 bp):
TTTTTAGGGGGTCAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
AATAAAAAATTTATCA
Found at i:45148260 original size:2 final size:2
Alignment explanation
Indices: 45148253--45148277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45148243 CACAAAATGT
45148253 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 T
45148278 TGCTATGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45151855 original size:4 final size:4
Alignment explanation
Indices: 45151846--45151897 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
45151836 TAGAAATCTT
45151846 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45151894 ATAC
1 ATAC
45151898 TCTTTACCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:45153988 original size:45 final size:45
Alignment explanation
Indices: 45153924--45154017 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
45153914 AACAGATACT
* * *
45153924 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
45153969 CGGTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
45154014 CGGT
1 CGGT
45154018 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:45161786 original size:43 final size:42
Alignment explanation
Indices: 45161729--45161878 Score: 171
Period size: 42 Copynumber: 3.5 Consensus size: 42
45161719 AATGCCAACA
*
45161729 TCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATCAAAT-ACGATGCCACTG
* * *
45161772 TCCCAGACAG-GGTCTTACACGTAATCATATACGATGGCAATG
1 TCCCAGAC-GTGGTCTTACACGTAATCAAATACGATGCCACTG
* *
45161814 TCCCAGACATGATCTTACACGTAAATCTCAAATA-GATGCCAAC-G
1 TCCCAGACGTGGTCTTACACGT-AA--TCAAATACGATGCC-ACTG
45161858 TCCCAGACGTGGTCTTACACG
1 TCCCAGACGTGGTCTTACACG
45161879 ATATCACATA
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
42 29 0.32
43 28 0.31
44 26 0.29
45 7 0.08
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGTAATCAAATACGATGCCACTG
Found at i:45161819 original size:42 final size:42
Alignment explanation
Indices: 45161720--45161878 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 42
45161710 AGCTTGTACA
** *
45161720 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAAT-ACG
* *
45161763 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAATCAAATACG
* * *
45161805 ATGGCAATGTCCCAGACATGATCTTACACGTAAATCTCAAATA-G
1 ATGCCAATGTCCCAGACGTGGTCTTACACGT-AA--TCAAATACG
*
45161849 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
45161879 ATATCACATA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 29 0.30
43 34 0.35
44 28 0.29
45 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATACG
Found at i:45162971 original size:13 final size:13
Alignment explanation
Indices: 45162953--45162977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45162943 ACAAACGATA
45162953 AAATTTTCACACG
1 AAATTTTCACACG
45162966 AAATTTTCACAC
1 AAATTTTCACAC
45162978 ATTTTAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:45163479 original size:20 final size:18
Alignment explanation
Indices: 45163429--45163480 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
45163419 CTACAAGATA
45163429 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
45163446 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
45163466 AATATTAAATTAATA
1 AATATTAAATTAATA
45163481 AAATATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:45163537 original size:68 final size:71
Alignment explanation
Indices: 45163396--45163540 Score: 172
Period size: 68 Copynumber: 2.1 Consensus size: 71
45163386 TATTAAATCT
*
45163396 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAAAATATTTATCTA-AAGATAAATATTAAATTAAATTTAATATTAAGATAATC
***
45163461 ACTTTAA
65 AAAATAA
** * *
45163468 TATTAAATTAATAAAATATTT-T-T-AAGATACGTATTAAATTAAATTTAATATTAA-ATCTATT
1 TATTAAATTAATAAAATATTTATCTAAAGATAAATATTAAATTAAATTTAATATTAAGAT-AATC
45163529 AAAATAA
65 AAAATAA
45163536 TATTA
1 TATTA
45163541 TTTTTGTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
67 2 0.03
68 40 0.62
70 1 0.02
71 1 0.02
72 20 0.31
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (71 bp):
TATTAAATTAATAAAATATTTATCTAAAGATAAATATTAAATTAAATTTAATATTAAGATAATCA
AAATAA
Found at i:45165604 original size:25 final size:25
Alignment explanation
Indices: 45165516--45165605 Score: 126
Period size: 25 Copynumber: 3.6 Consensus size: 25
45165506 ACAAGCTATA
* *
45165516 AACGGGAAGCTCCTTCGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
* *
45165541 AACGGGAAGCTCTTGCGAGCTGTAT
1 AACGGGAAGCTCATGCGAGCTGAAT
*
45165566 AACAGGAAGCTCATGCGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
*
45165591 AACGGGAAGTTCATG
1 AACGGGAAGCTCATG
45165606 TGAGAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCTGAAT
Found at i:45168166 original size:25 final size:25
Alignment explanation
Indices: 45168092--45168436 Score: 272
Period size: 25 Copynumber: 14.6 Consensus size: 25
45168082 ATTATTCAGC
* *
45168092 AAATTGGACAGCAAT-AATATGCTCA
1 AAATTGGACAGC-ATCAATATACTTA
* *
45168117 AAA-TGGACAGCAT---TATACATC
1 AAATTGGACAGCATCAATATACTTA
*
45168138 AAATTAGACAGCATCAATATACTTA
1 AAATTGGACAGCATCAATATACTTA
*
45168163 AAATCGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* * *
45168186 AAAATGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
45168211 AAATTCGATAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
45168234 AAA-TGGGCAGCATCAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
45168258 AAATTGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
*
45168283 AAATTGAACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
45168306 AAA-TGGGCAGCATCAATATAATTA
1 AAATTGGACAGCATCAATATACTTA
45168330 AAATTGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
45168353 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
45168377 AAATTGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
*
45168400 AAA-TGGACAGCATCAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
45168424 AAA-TGGACAGCAT
1 AAATTGGACAGCAT
45168437 TATACATCAA
Statistics
Matches: 256, Mismatches: 37, Indels: 55
0.74 0.11 0.16
Matches are distributed among these distances:
21 7 0.03
22 65 0.25
23 38 0.15
24 39 0.15
25 103 0.40
26 4 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (25 bp):
AAATTGGACAGCATCAATATACTTA
Found at i:45168257 original size:47 final size:46
Alignment explanation
Indices: 45168096--45168271 Score: 210
Period size: 47 Copynumber: 3.7 Consensus size: 46
45168086 TTCAGCAAAT
* * * *
45168096 TGGACAGCAAT-AATATGCTCAAAATGGACAGCATTATACATCAAAT
1 TGGACAGC-ATCAATATACTCAAAATCGACAGCATTATACATTAAAA
* *
45168142 TAGACAGCATCAATATACTTAAAATCGGACAGCATTATACATTAAAAA
1 TGGACAGCATCAATATACTCAAAATC-GACAGCATTATACATT-AAAA
* *
45168190 TGGACAGCATCAATACACTCAAAATTCGATAGCATTATACATTAAAA
1 TGGACAGCATCAATATACTCAAAA-TCGACAGCATTATACATTAAAA
* *
45168237 TGGGCAGCATCAATATACTCAAAATTGGACAGCAT
1 TGGACAGCATCAATATACTCAAAA-TCGACAGCAT
45168272 CAATACACTC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.02
46 19 0.17
47 50 0.45
48 39 0.35
49 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (46 bp):
TGGACAGCATCAATATACTCAAAATCGACAGCATTATACATTAAAA
Found at i:45168273 original size:72 final size:70
Alignment explanation
Indices: 45168096--45168443 Score: 333
Period size: 72 Copynumber: 4.9 Consensus size: 70
45168086 TTCAGCAAAT
* * * *
45168096 TGGACAGCAATAATATGCTCAAAATGGACAGCAT-TATACA-TC-AAATTAGACAGCATCAATAT
1 TGGACAGC-ATAATATACTTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCAT---TAT
45168158 AC-TTAAAA
62 ACATTAAAA
* *
45168166 TCGGACAGCAT--TATACATTAAAAATGGACAGCATCAATACACTCAAAATTCGATAGCATTATA
1 T-GGACAGCATAATATAC-TT-AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATA
45168229 CATTAAAA
63 CATTAAAA
* * *
45168237 TGGGCAGCATCAATATACTCAAAATTGGACAGCATCAATACACTCAAAATTGAACAGCATTATAC
1 TGGACAGCAT-AATATACTTAAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCATTATAC
45168302 ATTAAAA
64 ATTAAAA
* * * * *
45168309 TGGGCAGCATCAATATAATTAAAATTGGACAGCAT-TATACA-TTAAAA-TGGACAGCATCAATA
1 TGGACAGCAT-AATATACTTAAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCAT-TATA
*
45168371 CACTCAAAA
63 CA-TTAAAA
*
45168380 TTGGACAGCAT--TATACATTAAAATGGACAGCATCAATATACTCAAAA-TGGACAGCATTATAC
1 -TGGACAGCATAATATAC-TTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATAC
45168442 AT
64 AT
45168444 CAAATTATAA
Statistics
Matches: 238, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
68 4 0.02
69 25 0.11
70 55 0.23
71 48 0.20
72 89 0.37
73 17 0.07
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.25
Consensus pattern (70 bp):
TGGACAGCATAATATACTTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACAT
TAAAA
Found at i:45168301 original size:47 final size:47
Alignment explanation
Indices: 45168116--45168443 Score: 309
Period size: 47 Copynumber: 7.0 Consensus size: 47
45168106 TAATATGCTC
* *
45168116 AAAATGGACAGCAT-TATACA-TC-AAATTAGACAGCATCAATATAC-TT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCAT---TATACATT
* * * * *
45168162 AAAATCGGACAGCAT-TATACA-TTAAAAATGGACAGCATCAATACACTC
1 AAAAT-GGACAGCATCAATACACTCAAAATTGGACAGCAT-TATACA-TT
* * * * * *
45168210 AAAATTCGATAGCAT-TATACA-TTAAAA-TGGGCAGCATCAATATAC-TC
1 AAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCAT---TATACATT
*
45168257 AAAATTGGACAGCATCAATACACTCAAAATTGAACAGCATTATACATT
1 AAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
* * * *
45168305 AAAATGGGCAGCATCAATATAATTAAAATTGGACAGCATTATACATT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
45168352 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
*
45168399 AAAATGGACAGCATCAATATACTCAAAA-TGGACAGCATTATACAT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACAT
45168444 CAAATTATAA
Statistics
Matches: 243, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
46 26 0.11
47 153 0.63
48 46 0.19
49 10 0.04
50 8 0.03
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (47 bp):
AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
Found at i:45179293 original size:33 final size:32
Alignment explanation
Indices: 45179158--45179296 Score: 93
Period size: 33 Copynumber: 4.2 Consensus size: 32
45179148 AGACCATATC
45179158 CCATAGCTGGAC-TATGGCATTCTGATGATAAGA
1 CCATAGCTGG-CTTATGGCATTCTGATG-TAAGA
* * * *
45179191 CCATAACTAGG-TTATGGCACTATGAACGTAAGA
1 CCATAGCT-GGCTTATGGCATTCTG-ATGTAAGA
* * * * * * *
45179224 TCATGGTTGGATTATGACAGTGTTTATATGTAAGA
1 CCATAGCTGGCTTATGGCA-T-TCT-GATGTAAGA
45179259 CCATAGCTGGCTTATGGCATTCTGATGATAAGA
1 CCATAGCTGGCTTATGGCATTCTGATG-TAAGA
45179292 CCATA
1 CCATA
45179297 ACACAGTTAT
Statistics
Matches: 78, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
32 5 0.06
33 45 0.58
34 5 0.06
35 23 0.29
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (32 bp):
CCATAGCTGGCTTATGGCATTCTGATGTAAGA
Found at i:45179344 original size:24 final size:24
Alignment explanation
Indices: 45179316--45179366 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
45179306 TGGCACTACG
45179316 AATGT-AAAGAATGAATTGACGAAA
1 AATGTAAAAG-ATGAATTGACGAAA
*
45179340 AATGTAAAAGATGAATTGACGACA
1 AATGTAAAAGATGAATTGACGAAA
45179364 AAT
1 AAT
45179367 TACCCAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.22
Consensus pattern (24 bp):
AATGTAAAAGATGAATTGACGAAA
Found at i:45183169 original size:6 final size:6
Alignment explanation
Indices: 45183135--45183168 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
45183125 ACCTCATAGG
*
45183135 TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
45183169 CTTAACAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:45195210 original size:21 final size:20
Alignment explanation
Indices: 45195165--45195211 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
45195155 AGTTAATTAA
45195165 TTTAATTAAT--TTT-AATT
1 TTTAATTAATCATTTAAATT
45195182 TTTAATTAATCATTTAAATT
1 TTTAATTAATCATTTAAATT
*
45195202 ATTTGATTAA
1 -TTTAATTAA
45195212 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
19 3 0.12
20 4 0.16
21 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAATTAATCATTTAAATT
Found at i:45202539 original size:73 final size:71
Alignment explanation
Indices: 45202411--45202580 Score: 191
Period size: 73 Copynumber: 2.3 Consensus size: 71
45202401 NNNNNNNNNN
*
45202411 AGGTCTATCCCAACCTTTTTAAGGTTGCCATAGACGACTCTATCTCGACCTTTTTTAGA-GGTTG
1 AGGTCTAT-CCAACCTTTTTAAAGTTGCCATAGACGACTCTATCTCGACCTTTTTTA-ATGGTTG
*
45202475 CCTTGGAC
64 CCTTAGAC
* * * ** *
45202483 AAGGTATATGCCAACCTTTTTAAAGTTGTCTTAGACGGTTCTATCT-TACCCTTTTTTAATGGTT
1 -AGGTCTAT-CCAACCTTTTTAAAGTTGCCATAGACGACTCTATCTCGA-CCTTTTTTAATGGTT
45202547 GCCTTAGAC
63 GCCTTAGAC
45202556 AGGTCTATCTCAACCCTTTTTAAAG
1 AGGTCTATC-CAA-CCTTTTTAAAG
45202581 GTCGGTCTTG
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
71 1 0.01
72 12 0.14
73 70 0.84
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (71 bp):
AGGTCTATCCAACCTTTTTAAAGTTGCCATAGACGACTCTATCTCGACCTTTTTTAATGGTTGCC
TTAGAC
Found at i:45202555 original size:37 final size:37
Alignment explanation
Indices: 45202411--45202580 Score: 117
Period size: 37 Copynumber: 4.7 Consensus size: 37
45202401 NNNNNNNNNN
* * *
45202411 AGGTCTATCCCAA-CC-TTTTTAAGGTTGCCATAGAC
1 AGGTCTATCTCAACCCTTTTTTAAAGTTGCCTTAGAC
* * * *
45202446 -GACTCTATCTCGA-CCTTTTTTAGAGGTTGCCTTGGAC
1 AG-GTCTATCTCAACCCTTTTTTA-AAGTTGCCTTAGAC
* *
45202483 AAGGTATATGC-CAA-CC-TTTTTAAAGTTGTCTTAGAC
1 -AGGTCTAT-CTCAACCCTTTTTTAAAGTTGCCTTAGAC
* *
45202519 -GGTTCTATCT-TACCCTTTTTTAATGGTTGCCTTAGAC
1 AGG-TCTATCTCAACCCTTTTTTAA-AGTTGCCTTAGAC
45202556 AGGTCTATCTCAACCC-TTTTTAAAG
1 AGGTCTATCTCAACCCTTTTTTAAAG
45202581 GTCGGTCTTG
Statistics
Matches: 105, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
34 5 0.05
35 16 0.15
36 25 0.24
37 43 0.41
38 14 0.13
39 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (37 bp):
AGGTCTATCTCAACCCTTTTTTAAAGTTGCCTTAGAC
Found at i:45204048 original size:23 final size:23
Alignment explanation
Indices: 45204022--45204071 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
45204012 GCTCGATTTG
* *
45204022 TTTAGCGTTCGCAAACATGTTCA
1 TTTAACGTTCACAAACATGTTCA
* **
45204045 TTTAATGTTCATGAACATGTTCA
1 TTTAACGTTCACAAACATGTTCA
45204068 TTTA
1 TTTA
45204072 TAACATATTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (23 bp):
TTTAACGTTCACAAACATGTTCA
Found at i:45204240 original size:11 final size:11
Alignment explanation
Indices: 45204219--45204252 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
45204209 AATATCACAA
45204219 AAAACTAAGTTG
1 AAAA-TAAGTTG
45204231 AAAATAAGTTG
1 AAAATAAGTTG
45204242 AAAATAAGTTG
1 AAAATAAGTTG
45204253 TTTGATCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (11 bp):
AAAATAAGTTG
Found at i:45216902 original size:17 final size:16
Alignment explanation
Indices: 45216871--45216909 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
45216861 AATTTTTATT
*
45216871 TTTATTTTTATTTTAC
1 TTTATTTTTACTTTAC
*
45216887 TTTATTTGTTACTTTAT
1 TTTATTT-TTACTTTAC
45216904 TTTATT
1 TTTATT
45216910 ATACTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATTTTTACTTTAC
Found at i:45242296 original size:19 final size:19
Alignment explanation
Indices: 45242272--45242308 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
45242262 TTATTTTTTA
45242272 TTTTTTATTTTTAAAATAC
1 TTTTTTATTTTTAAAATAC
45242291 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
45242309 AATTTTTGGT
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAC
Found at i:45242314 original size:20 final size:19
Alignment explanation
Indices: 45242271--45242315 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
45242261 TTTATTTTTT
45242271 ATTTTTTATTTTTAAAATA
1 ATTTTTTATTTTTAAAATA
*
45242290 CTTTTTTATTTTTAAAATAA
1 ATTTTTTATTTTTAAAAT-A
45242310 ATTTTT
1 ATTTTT
45242316 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTTTTAAAATA
Found at i:45243804 original size:46 final size:46
Alignment explanation
Indices: 45243737--45243950 Score: 259
Period size: 46 Copynumber: 4.9 Consensus size: 46
45243727 NNNNNNNNNN
* *
45243737 TAGCTAAGGCTACCACTTATCACTTTGTCACTTGATCAGTTAAGTA
1 TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
45243783 TAGCTAAAGCTACCACTTATCACTTTCTCACTTGATCAGATAAGTG
1 TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* * *
45243829 TAGCTAAGGCTAACACTTATCACTGTGTCACTTGATCAGATAAG--
1 TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
45243873 TA--T--AG----CACTTATCACTTTTTCACTTGATCAGATAAGTG
1 TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
45243911 TAGCTAAAGCTACCACTTATCACTTTATCTCTTGATCAGA
1 TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
45243951 AGTACTCAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
36 29 0.20
38 2 0.01
40 2 0.01
42 3 0.02
44 2 0.01
46 107 0.74
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
TAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTA
Found at i:45243882 original size:36 final size:36
Alignment explanation
Indices: 45243842--45243914 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
45243832 CTAAGGCTAA
45243842 CACTTATCACTGTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTGTGTCACTTGATCAGATAAGTATAG
* * *
45243878 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTGTGTCACTTGATCAGATAAGTATAG
45243914 C
1 C
45243915 TAAAGCTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (36 bp):
CACTTATCACTGTGTCACTTGATCAGATAAGTATAG
Found at i:45243933 original size:82 final size:82
Alignment explanation
Indices: 45243796--45243950 Score: 256
Period size: 82 Copynumber: 1.9 Consensus size: 82
45243786 CTAAAGCTAC
* *
45243796 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTGTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTGTATCACT
45243861 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* * * *
45243878 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTGTATCACT
45243943 TGATCAGA
66 TGATCAGA
45243951 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTGTATCACT
TGATCAGATAAGTATAG
Found at i:45279382 original size:21 final size:21
Alignment explanation
Indices: 45279336--45279382 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
45279326 ATTTACAACT
*
45279336 TTATTTTTAGAAATTTAATCC
1 TTATTTTTAGAAATTTAATCA
* *
45279357 CTATTTCTTAGACATTTAAT-A
1 TTATTT-TTAGAAATTTAATCA
45279378 TTATT
1 TTATT
45279383 AAATTACATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATTTTTAGAAATTTAATCA
Found at i:45283884 original size:10 final size:10
Alignment explanation
Indices: 45283864--45283926 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 10
45283854 TGACCATGTT
45283864 AATTGATAAAA
1 AATT-ATAAAA
45283875 AATTATAAAA
1 AATTATAAAA
* *
45283885 ATTTAT-GAA
1 AATTATAAAA
45283894 AATTATTAAAA
1 AATTA-TAAAA
* *
45283905 AAATACTAAAT
1 AATTA-TAAAA
45283916 AATTATAAAA
1 AATTATAAAA
45283926 A
1 A
45283927 TAATTAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.15
10 17 0.41
11 18 0.44
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (10 bp):
AATTATAAAA
Found at i:45283908 original size:31 final size:31
Alignment explanation
Indices: 45283870--45283936 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
45283860 TGTTAATTGA
* * *
45283870 TAAAAAATTA-TAAA-AATTTATGAAAATTAT
1 TAAAAAAATACTAAATAA-TTATAAAAATAAT
45283900 TAAAAAAATACTAAATAATTATAAAAATAAT
1 TAAAAAAATACTAAATAATTATAAAAATAAT
45283931 TAAAAA
1 TAAAAA
45283937 GTGGTCTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.28
31 21 0.66
32 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (31 bp):
TAAAAAAATACTAAATAATTATAAAAATAAT
Found at i:45284097 original size:19 final size:18
Alignment explanation
Indices: 45284075--45284146 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
45284065 AAAGTTGTTG
45284075 AAATTTATAAAAAAATGTA
1 AAATTTATAAAAAAAT-TA
*
45284094 AAATATT-TAAAATATATTTA
1 AAAT-TTATAAAA-A-AATTA
45284114 AAATTTTATAAAAAATATTA
1 AAA-TTTATAAAAAA-ATTA
*
45284134 AAAATTATAAAAA
1 AAATTTATAAAAA
45284147 CATATACTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 19 0.43
20 17 0.39
21 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
AAATTTATAAAAAAATTA
Found at i:45284101 original size:21 final size:20
Alignment explanation
Indices: 45284077--45284146 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
45284067 AGTTGTTGAA
45284077 ATTTATAAAAAAATGTAAAAT
1 ATTTATAAAAAAAT-TAAAAT
* *
45284098 ATTTA-AAATATATTTAAAAT
1 ATTTATAAA-AAAATTAAAAT
45284118 -TTTATAAAAAATATTAAAA-
1 ATTTATAAAAAA-ATTAAAAT
45284137 A-TTATAAAAA
1 ATTTATAAAAA
45284147 CATATACTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 15 0.37
20 18 0.44
21 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (20 bp):
ATTTATAAAAAAATTAAAAT
Found at i:45284146 original size:20 final size:20
Alignment explanation
Indices: 45284079--45284151 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
45284069 TTGTTGAAAT
*
45284079 TTATAAAAAAAT-GTAAAATA
1 TTATAAAAAAATATTAAAA-A
* *
45284099 TT-T-AAAATATATTTAAAA
1 TTATAAAAAAATATTAAAAA
*
45284117 TTTTATAAAAAATATTAAAAA
1 TTATA-AAAAAATATTAAAAA
*
45284138 TTATAAAAACATAT
1 TTATAAAAAAATAT
45284152 ACTTCATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 10 0.24
21 17 0.40
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
TTATAAAAAAATATTAAAAA
Found at i:45284330 original size:109 final size:110
Alignment explanation
Indices: 45284183--45284418 Score: 433
Period size: 109 Copynumber: 2.2 Consensus size: 110
45284173 CCATAGTCAA
45284183 ATTTTCTTT-TTCTTTTTTACAAATTGTAAAGAAAGCCAAAAGAAAAAAAAAACTCACTAGTCAT
1 ATTTT-TTTATTCTTTTTTAC-AATTGTAAAGAAAGCCAAAAGAAAAAAAAAACTCACTAGTCAT
45284247 TATTGAATGATATAACCTTCTAAATCACAAGTTTTAATTATTTTAAT
64 TATTGAATGATATAACCTTCTAAATCACAAGTTTTAATTATTTTAAT
45284294 ATTTTTTTATTCTTTTTTAC-ATTGTAAAGAAAGCCAAAAGAAAAAAAAAACTCACTAGTCATTA
1 ATTTTTTTATTCTTTTTTACAATTGTAAAGAAAGCCAAAAGAAAAAAAAAACTCACTAGTCATTA
45284358 TTGAATGATATAACCTTCTAAATCACAAGTTTTAATTATTTTAAT
66 TTGAATGATATAACCTTCTAAATCACAAGTTTTAATTATTTTAAT
45284403 ATTTTTTTATT-TTTTT
1 ATTTTTTTATTCTTTTT
45284419 CATATTTCTA
Statistics
Matches: 124, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
108 5 0.04
109 100 0.81
110 3 0.02
111 16 0.13
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.42
Consensus pattern (110 bp):
ATTTTTTTATTCTTTTTTACAATTGTAAAGAAAGCCAAAAGAAAAAAAAAACTCACTAGTCATTA
TTGAATGATATAACCTTCTAAATCACAAGTTTTAATTATTTTAAT
Found at i:45288483 original size:1 final size:1
Alignment explanation
Indices: 45288443--45288470 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
45288433 AAAGAAAACT
45288443 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
45288471 CCACCCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45297791 original size:125 final size:124
Alignment explanation
Indices: 45297563--45297841 Score: 441
Period size: 125 Copynumber: 2.2 Consensus size: 124
45297553 GCCCATGTTT
45297563 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
* * * *
45297628 TAAAATCGCTTCTAGCAGGATGATGTTTGATAATAATTTGGGAAATCGTGGCCTCGTGG
66 TAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
* * *
45297687 ACGCGCTTTTGCTACGGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGT
* *
45297752 ATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGTGCCCTCGTGG
65 ATAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
* * *
45297812 ACCCGCTTTTGCTACAATAAGTCCTGAAAA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAA
45297842 TTGAGAGAGG
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
124 28 0.20
125 112 0.80
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
TAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
Found at i:45302479 original size:45 final size:45
Alignment explanation
Indices: 45302415--45302504 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
45302405 GTTATGCCCT
**
45302415 TGAGCTATATGGCATCAATTTCATCACCCTTTTTTCTTTCCTACC
1 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
45302460 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
1 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
45302505 ATCAAAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (45 bp):
TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
Found at i:45303396 original size:1 final size:1
Alignment explanation
Indices: 45303390--45303426 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
45303380 GTGGGGTGCC
* *
45303390 GGGGGGGGGGGGGGGGNGCGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
45303427 AGAGAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.95, T:0.00
Consensus pattern (1 bp):
G
Found at i:45305638 original size:34 final size:35
Alignment explanation
Indices: 45305583--45305649 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
45305573 TAAACATCAG
*
45305583 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
45305618 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
45305650 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:45308538 original size:21 final size:21
Alignment explanation
Indices: 45308504--45308544 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45308494 AGAAGAAGAA
*
45308504 CCCAAGAAGTCTAATATCAAG
1 CCCAAGAAGTCTAAGATCAAG
45308525 CCCAAGAAAG-CTAAGATCAA
1 CCCAAG-AAGTCTAAGATCAA
45308545 CTAGTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (21 bp):
CCCAAGAAGTCTAAGATCAAG
Found at i:45312220 original size:22 final size:21
Alignment explanation
Indices: 45312187--45312227 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
45312177 TTTTCGTTTA
*
45312187 AATCTTTTAAAATTTTAAATT
1 AATCTTTTAAAATTATAAATT
45312208 AATCTTTTAAAAATTATAAA
1 AATCTTTT-AAAATTATAAA
45312228 GATATAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATCTTTTAAAATTATAAATT
Found at i:45318276 original size:10 final size:11
Alignment explanation
Indices: 45318245--45318277 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
45318235 CGACCCACCC
45318245 ATATTAATGTTT
1 ATATTAAT-TTT
45318257 ATATTAATTTT
1 ATATTAATTTT
45318268 ATA-TAATTTT
1 ATATTAATTTT
45318278 TAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:45320244 original size:49 final size:49
Alignment explanation
Indices: 45320085--45320247 Score: 240
Period size: 49 Copynumber: 3.4 Consensus size: 49
45320075 TGTTAAGCCA
* *
45320085 TGTG-GGGGCACAC-GGTGTGTGTGATTACACGGGTAAATCAGGTAGGT
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
* *
45320132 TGTGTGGGGCACACGGGCGTGTGTGATTACATGGGTAAATCAGGTAGGC
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
* * *
45320181 CGTGTGGGGCACACAGGCGTATGAGATTACATGGGTAAATCAGGTAGGT
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
*
45320230 TGTGTAGGGCACACAGGC
1 TGTGTGGGGCACACAGGC
45320248 AAATCAGGTA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
47 4 0.04
48 9 0.09
49 91 0.88
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.23
Consensus pattern (49 bp):
TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
Found at i:45320604 original size:18 final size:18
Alignment explanation
Indices: 45320583--45320635 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
45320573 TCTATTCTAA
45320583 TATGATATATGATTCGAC
1 TATGATATATGATTCGAC
45320601 TATG-TGATATG--T--A-
1 TATGAT-ATATGATTCGAC
45320614 TATGATATATGATTCGAC
1 TATGATATATGATTCGAC
45320632 TATG
1 TATG
45320636 TGATATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
15 1 0.04
16 1 0.04
17 2 0.07
18 13 0.46
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (18 bp):
TATGATATATGATTCGAC
Found at i:45320620 original size:31 final size:31
Alignment explanation
Indices: 45320582--45320645 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
45320572 ATCTATTCTA
45320582 ATATGATATATGATTCGACTATGTGATATGT
1 ATATGATATATGATTCGACTATGTGATATGT
45320613 ATATGATATATGATTCGACTATGTGATATGT
1 ATATGATATATGATTCGACTATGTGATATGT
45320644 AT
1 AT
45320646 GTATGTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (31 bp):
ATATGATATATGATTCGACTATGTGATATGT
Found at i:45320641 original size:18 final size:18
Alignment explanation
Indices: 45320589--45320642 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
45320579 CTAATATGAT
45320589 ATATGATTCGACTATGTG
1 ATATGATTCGACTATGTG
45320607 ATATG--T--A-TATGAT-
1 ATATGATTCGACTATG-TG
45320620 ATATGATTCGACTATGTG
1 ATATGATTCGACTATGTG
45320638 ATATG
1 ATATG
45320643 TATGTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 14 0.48
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (18 bp):
ATATGATTCGACTATGTG
Found at i:45325544 original size:5 final size:5
Alignment explanation
Indices: 45325534--45325559 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45325524 TGAGCATTCG
45325534 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
45325560 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:45326266 original size:9 final size:9
Alignment explanation
Indices: 45326252--45326288 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
45326242 TATAGTTTGA
45326252 TATTCGAAT
1 TATTCGAAT
45326261 TATTCGAAT
1 TATTCGAAT
*
45326270 TATTCGAGT
1 TATTCGAAT
45326279 TATTCGAAT
1 TATTCGAAT
45326288 T
1 T
45326289 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:45326359 original size:9 final size:9
Alignment explanation
Indices: 45326342--45326372 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
45326332 TCGAGTTGAT
45326342 TCGAATAAC
1 TCGAATAAC
*
45326351 TCGATTAAC
1 TCGAATAAC
45326360 TCGAATAAC
1 TCGAATAAC
45326369 TCGA
1 TCGA
45326373 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:45327108 original size:25 final size:25
Alignment explanation
Indices: 45327080--45327128 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45327070 GGTTTGCAGC
45327080 TCGTAAGAACTTACCG-ATTCTCAGT
1 TCGTAAGAACTTACCGTATT-TCAGT
* *
45327105 TCGTATGAGCTTACCGTATTTCAG
1 TCGTAAGAACTTACCGTATTTCAG
45327129 CTCGGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (25 bp):
TCGTAAGAACTTACCGTATTTCAGT
Found at i:45341768 original size:27 final size:27
Alignment explanation
Indices: 45341720--45341784 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
45341710 AAAAATAACT
*
45341720 AAAATATTAT-AATTTTTTTATTTATC
1 AAAATATTATAAATTTTTTTATTTACC
45341746 AAAATATTATAAATTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTATTTACC
45341773 AAAATA-TATAAA
1 AAAATATTATAAA
45341785 AACAAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATATTATAAATTTTTTTATTTACC
Found at i:45342532 original size:18 final size:18
Alignment explanation
Indices: 45342496--45342533 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
45342486 ACCAAAATAG
*
45342496 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
45342514 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
45342532 AG
1 AG
45342534 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:45345532 original size:18 final size:18
Alignment explanation
Indices: 45345497--45345535 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
45345487 ATTACTTTTT
* **
45345497 AAAAATATTTTTGGGATA
1 AAAAATACTTTTAAGATA
45345515 AAAAATACTTTTAAGATA
1 AAAAATACTTTTAAGATA
45345533 AAA
1 AAA
45345536 GTATTCCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAAATACTTTTAAGATA
Found at i:45345815 original size:14 final size:14
Alignment explanation
Indices: 45345782--45345821 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
45345772 TCCAAGTCAC
45345782 ATAAAA-AAGTTAAA
1 ATAAAATAAG-TAAA
45345796 AT-AAATAAGTAAA
1 ATAAAATAAGTAAA
45345809 ATAAAATAA-TAAA
1 ATAAAATAAGTAAA
45345822 TCAAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
ATAAAATAAGTAAA
Found at i:45346035 original size:26 final size:27
Alignment explanation
Indices: 45346006--45346058 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
45345996 AAACTCTTCT
* *
45346006 AAAAGAAACTCA-AGAGAAATTCTTAA
1 AAAAAAAACTCAGAGAGAAATTATTAA
45346032 AAAAAAAACTCAGAGAGAAATTATTAA
1 AAAAAAAACTCAGAGAGAAATTATTAA
45346059 CTCAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (27 bp):
AAAAAAAACTCAGAGAGAAATTATTAA
Found at i:45347328 original size:52 final size:52
Alignment explanation
Indices: 45347220--45347350 Score: 142
Period size: 53 Copynumber: 2.6 Consensus size: 52
45347210 CTTTTAAAAT
* * * *** *
45347220 TTTAAAAAAATTGGATGTTGGGACACTGACGTCCGACATCTTTATACCAGTT
1 TTTAAAAAAATTGGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
*
45347272 TTTAAAAAAATTGGGATATTGGGACACTGATGGCCGACACCCCAATACCAG-A
1 TTTAAAAAAATT-GGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
* *
45347324 TTTAAAAAAA-T-AATGTTGGGACACTGA
1 TTTAAAAAAATTGGATATTGGGACACTGA
45347351 TAGTCGGCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 14 0.21
51 1 0.01
52 22 0.32
53 31 0.46
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (52 bp):
TTTAAAAAAATTGGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
Found at i:45347868 original size:90 final size:90
Alignment explanation
Indices: 45347713--45347915 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 90
45347703 ACTACAATTC
* * * **
45347713 AAAATGTTGGTATTATTTTTGTATCTGTAAATCAATTTTAGTCCGTATTATTTGTTGGTTGAATT
1 AAAATGTTGGTATTATTTTTGTATCTATAAATAAATTTTAGTCCATATTATTTGTTGGTAAAATT
* *
45347778 TTATATTTTCGAATATCAGTTTTGT
66 TTATATTTTAGAATATCAATTTTGT
45347803 AAAATGGTT-GTATTATTTTTAG-ATCTATAAA-AATATTTTAGTCCATATTATTTGTTGGTAAA
1 AAAAT-GTTGGTATTATTTTT-GTATCTATAAATAA-ATTTTAGTCCATATTATTTGTTGGTAAA
* *
45347865 ATTTTATATTTTAGTATATCAATTTTCT
63 ATTTTATATTTTAGAATATCAATTTTGT
* * *
45347893 AAGATGTTCGTATT-TTCTTGTAT
1 AAAATGTTGGTATTATTTTTGTAT
45347916 ATGTAAAAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
88 1 0.01
89 10 0.10
90 82 0.85
91 4 0.04
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (90 bp):
AAAATGTTGGTATTATTTTTGTATCTATAAATAAATTTTAGTCCATATTATTTGTTGGTAAAATT
TTATATTTTAGAATATCAATTTTGT
Found at i:45349871 original size:15 final size:17
Alignment explanation
Indices: 45349851--45349882 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45349841 CTTTTTTTAA
45349851 TTAAA-TTAT-ATTATT
1 TTAAATTTATAATTATT
45349866 TTAAATTTATAATTATT
1 TTAAATTTATAATTATT
45349883 CTTTTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAATTTATAATTATT
Found at i:45350010 original size:13 final size:14
Alignment explanation
Indices: 45349966--45350010 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
45349956 ATTTTTTAAA
45349966 TTAAATTCTATTCTT
1 TTAAATT-TATTCTT
*
45349981 TTAAATTTATTCAT
1 TTAAATTTATTCTT
*
45349995 TTAAA-TTATTTTT
1 TTAAATTTATTCTT
45350008 TTA
1 TTA
45350011 TTAAACTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 9 0.33
14 11 0.41
15 7 0.26
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAAATTTATTCTT
Found at i:45350236 original size:17 final size:18
Alignment explanation
Indices: 45350214--45350249 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
45350204 CTTTTTTATC
45350214 TTTAC-ATACAAAATTGA
1 TTTACAATACAAAATTGA
45350231 TTTACAGATACAAAATTGA
1 TTTACA-ATACAAAATTGA
45350250 ATCACATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (18 bp):
TTTACAATACAAAATTGA
Found at i:45352344 original size:16 final size:16
Alignment explanation
Indices: 45352307--45352346 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
45352297 TAAATAAAAT
* *
45352307 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
45352323 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
45352339 TAAAATTA
1 TAAAATTA
45352347 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:45352431 original size:9 final size:9
Alignment explanation
Indices: 45352419--45352462 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
45352409 TTTATCAAAT
45352419 TATTAATTG
1 TATTAATTG
45352428 TATTAATTG
1 TATTAATTG
45352437 --TTAATTG
1 TATTAATTG
*
45352444 TATTAATTA
1 TATTAATTG
45352453 TATTAATTG
1 TATTAATTG
45352462 T
1 T
45352463 TGTAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.23
9 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:45352435 original size:16 final size:16
Alignment explanation
Indices: 45352416--45352453 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
45352406 AAATTTATCA
45352416 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
45352432 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
45352448 AATTAT
1 AATTAT
45352454 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:45353561 original size:18 final size:17
Alignment explanation
Indices: 45353538--45353578 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
45353528 TACAGTGAAT
45353538 AAAAATATATTAGAAGTA
1 AAAAATATATTA-AAGTA
* *
45353556 AAAAATCTATTACAGTA
1 AAAAATATATTAAAGTA
45353573 AAAAAT
1 AAAAAT
45353579 CTATGAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (17 bp):
AAAAATATATTAAAGTA
Found at i:45353572 original size:17 final size:17
Alignment explanation
Indices: 45353520--45353582 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
45353510 GAAATTAATG
45353520 AAATCTATTACAGTGAATAA
1 AAATCTATTACAGT--A-AA
* *
45353540 AAATATATTAGAAGTAAA
1 AAATCTATTA-CAGTAAA
45353558 AAATCTATTACAGTAAA
1 AAATCTATTACAGTAAA
45353575 AAATCTAT
1 AAATCTAT
45353583 GAGGACTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 14 0.37
18 11 0.29
19 1 0.03
20 9 0.24
21 3 0.08
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (17 bp):
AAATCTATTACAGTAAA
Found at i:45357158 original size:126 final size:126
Alignment explanation
Indices: 45356933--45357475 Score: 865
Period size: 126 Copynumber: 4.3 Consensus size: 126
45356923 CCAAACATGT
*
45356933 GCCACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCAT-CA
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATAC-
* *
45356997 TGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAAGA
65 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* *
45357059 GCCACTGTAGCAAAAGCGCGTCTACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATATT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
45357124 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTC-AGAA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAG-A
* * *
45357185 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGATTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
* * *
45357250 GCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGGAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* * * * *
45357311 GCCACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTTAGTACTTCTGTTGACAAATCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
* * *
45357376 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTACTTGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* *
45357437 GCTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
45357476 AAATTAACAA
Statistics
Matches: 388, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
125 2 0.01
126 385 0.99
127 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
Found at i:45357635 original size:96 final size:97
Alignment explanation
Indices: 45357504--45357711 Score: 260
Period size: 96 Copynumber: 2.2 Consensus size: 97
45357494 ATTAACCATA
* * *
45357504 AACCCCAAACCTTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAACCCCTAATCAAAT
1 AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
* *
45357569 TTTATAAA-AA-ATTATAATTAATTTACTCAATT
66 TTT-TAAATAATATT-TAATTAAATTACTCAAGT
* * * * * * **
45357601 AATCCTGAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTTAACTCTAAACCCTTATCTGAT
1 AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
45357665 TTTTAAATAATATTTAATTAAATTACTCAAGT
66 TTTTAAATAATATTTAATTAAATTACTCAAGT
45357697 AACCCTAAACCCTAA
1 AACCCTAAACCCTAA
45357712 ATCCTAATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
95 4 0.04
96 67 0.71
97 23 0.24
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (97 bp):
AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
TTTTAAATAATATTTAATTAAATTACTCAAGT
Found at i:45358744 original size:77 final size:76
Alignment explanation
Indices: 45358616--45358764 Score: 264
Period size: 77 Copynumber: 1.9 Consensus size: 76
45358606 ATAGAGTTAG
45358616 AACTTGGAACTACCCATTTTTTCTGTTCACCAAGTTCTAGATAATCGGAGATATGGCTTTGG-TA
1 AACTTGGAACTACCCATTTTTTCTGTTCACCAAGTTCTAGATAATCGGAGATATGGC-TTGGATA
45358680 AAACGATTTTTT
65 AAACGATTTTTT
45358692 ANACTTGGAACTACCCATTTTTTCTGTTCACCAAGTTCTAGATAATCGGAGATATGGCTTGGATA
1 A-ACTTGGAACTACCCATTTTTTCTGTTCACCAAGTTCTAGATAATCGGAGATATGGCTTGGATA
*
45358757 ACACGATT
65 AAACGATT
45358765 CTTAACGGCG
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
76 5 0.07
77 65 0.93
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (76 bp):
AACTTGGAACTACCCATTTTTTCTGTTCACCAAGTTCTAGATAATCGGAGATATGGCTTGGATAA
AACGATTTTTT
Found at i:45366811 original size:10 final size:10
Alignment explanation
Indices: 45366780--45366878 Score: 73
Period size: 10 Copynumber: 10.0 Consensus size: 10
45366770 TATTTAAAAA
45366780 ATTAAATATT
1 ATTAAATATT
45366790 A-TAAATAGTT
1 ATTAAATA-TT
45366800 ATTAAATATT
1 ATTAAATATT
45366810 ATTAAAATATT
1 ATT-AAATATT
45366821 -TTAAA-ATT
1 ATTAAATATT
* *
45366829 ATTAAAAATC
1 ATTAAATATT
* *
45366839 ATAAAAGATT
1 ATTAAATATT
45366849 ATTTAAA-ATT
1 A-TTAAATATT
*
45366859 -TGTAAAAATT
1 AT-TAAATATT
*
45366869 ATTGAATATT
1 ATTAAATATT
45366879 GTGAAATCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
8 4 0.05
9 18 0.25
10 33 0.45
11 18 0.25
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (10 bp):
ATTAAATATT
Found at i:45366835 original size:9 final size:9
Alignment explanation
Indices: 45366756--45366871 Score: 58
Period size: 10 Copynumber: 12.0 Consensus size: 9
45366746 AAAAATGTAA
*
45366756 AAAAATATT
1 AAAATTATT
*
45366765 TAAATTATTT
1 AAAATTA-TT
*
45366775 AAAA-AATT
1 AAAATTATT
45366783 AAATATTA-T
1 AAA-ATTATT
45366792 AAATAGTTATT
1 AAA-A-TTATT
45366803 AAATATTATT
1 AAA-ATTATT
*
45366813 AAAATATTTT
1 AAAAT-TATT
45366823 AAAATTATT
1 AAAATTATT
* *
45366832 AAAAATCATA
1 -AAAATTATT
45366842 AAAGATTATTT
1 AAA-ATTA-TT
45366853 AAAATT-TGT
1 AAAATTAT-T
45366862 AAAAATTATT
1 -AAAATTATT
45366872 GAATATTGTG
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
8 6 0.07
9 22 0.26
10 45 0.54
11 11 0.13
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (9 bp):
AAAATTATT
Found at i:45367177 original size:20 final size:20
Alignment explanation
Indices: 45367138--45367187 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
45367128 AATAATTTGT
45367138 TAATTATTTATATTTTTTTAA
1 TAATTATTTATA-TTTTTTAA
45367159 TAATTATTTATGA-TTTTTAA
1 TAATTATTTAT-ATTTTTTAA
45367179 TAATT-TTTA
1 TAATTATTTA
45367188 AAAAATTATN
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 11 0.39
22 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TAATTATTTATATTTTTTAA
Found at i:45369405 original size:24 final size:25
Alignment explanation
Indices: 45369363--45369409 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
45369353 GGCCTTGAGT
45369363 CGGTGTTATCTATCAGGCTTTGTAC
1 CGGTGTTATCTATCAGGCTTTGTAC
* *
45369388 CGGTG-TATTTATCGGGCTTTGT
1 CGGTGTTATCTATCAGGCTTTGT
45369410 GCCTAGCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (25 bp):
CGGTGTTATCTATCAGGCTTTGTAC
Found at i:45369515 original size:25 final size:25
Alignment explanation
Indices: 45369468--45369527 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
45369458 GGCTTTGTGT
** *
45369468 TGGTGTTATCTATCAGGCCTTGAGC
1 TGGTGTTATCTATCAAACATTGAGC
* *
45369493 TGGTGTTGTCTATCAAACATTGAGT
1 TGGTGTTATCTATCAAACATTGAGC
45369518 TGGTGATTAT
1 TGGTG-TTAT
45369528 TTAGCAAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (25 bp):
TGGTGTTATCTATCAAACATTGAGC
Found at i:45376959 original size:18 final size:19
Alignment explanation
Indices: 45376927--45376964 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
45376917 TTTATATTCT
45376927 TTGAGAGTGAATAC-TAAA
1 TTGAGAGTGAATACTTAAA
**
45376945 TTGAGAGTGTTTACTTAAA
1 TTGAGAGTGAATACTTAAA
45376964 T
1 T
45376965 ACCTATTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGAGAGTGAATACTTAAA
Found at i:45386875 original size:12 final size:12
Alignment explanation
Indices: 45386860--45386891 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
45386850 AACTAAGTTG
45386860 TAAATATTTTTA
1 TAAATATTTTTA
45386872 TAAATATTTTTA
1 TAAATATTTTTA
45386884 TAAATATT
1 TAAATATT
45386892 ACGGAGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:45389253 original size:108 final size:107
Alignment explanation
Indices: 45388952--45389498 Score: 766
Period size: 108 Copynumber: 5.1 Consensus size: 107
45388942 GATTAAGATA
* * *
45388952 TAAAATGATATTTGGCTATTTGGTCCG-ACG-GGAAATCGAGACCCAATACATTAGGGCACGTTT
1 TAAAAGGATATTTGGCTATTTGGT-CGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTT
45389015 TCTCGAATTTCCAAACGCAAAACA---CCTTATTTTGAAAATT
65 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* * * * *
45389055 TAAAAGGATATTCGGCTATTTGGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCATGTTTC
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
*
45389120 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* *
45389162 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAA-ATCGAAACCCAACACATTAGGGCACGTTT
** *
45389227 TCTTAAATTTCCAAACGCAAAACATTGCTTTATTTTGAAAATT
65 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* * * *
45389270 TAAAAGGATATTCGGCTATTTGGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTC
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
* *
45389335 CTCGAATTTCCAAACGCAAAACATTGCTTTATTTTGAAATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* *
45389377 TAAAAGGATATTTAGCTATTTGGTCGAACGA-GAATGATCGAAACCCAACACATTAGGGCACATT
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAA--ATCGAAACCCAACACATTAGGGCACGTT
45389441 TTCTCGAACTTT-CAAACGCAAAACATTGCCTTATTTTTGAAAAATT
64 TTCTCGAA-TTTCCAAACGCAAAACATTGCCTTA-TTTTG-AAAATT
**
45389487 TTTAAGGATATT
1 TAAAAGGATATT
45389499 AATATGCATA
Statistics
Matches: 394, Mismatches: 39, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
102 2 0.01
103 25 0.06
104 51 0.13
106 2 0.01
107 142 0.36
108 149 0.38
109 8 0.02
110 15 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (107 bp):
TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
Found at i:45389369 original size:215 final size:215
Alignment explanation
Indices: 45388952--45389498 Score: 874
Period size: 215 Copynumber: 2.6 Consensus size: 215
45388942 GATTAAGATA
* * * * *
45388952 TAAAATGATATTTGGCTATTTGGTCCG-ACG-GGAA-ATCGAGACCCAATACATTAGGGCACGTT
1 TAAAAGGATATTTAGCTATTTGGT-CGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTT
*
45389014 TTCTCGAATTTCCAAACGCAAAACA---CCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTT
65 TTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTT
*
45389076 GGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCATGTTTCCTCGAATTTCCAAACGCAAAA
130 GGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAA
45389141 CATTGCCTTATTTTGAAATTT
195 CATTGCCTTATTTTGAAATTT
45389162 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
1 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
* *
45389227 TCTTAAATTTCCAAACGCAAAACATTGCTTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
66 TCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
45389292 GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
131 GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
*
45389357 ATTGCTTTATTTTGAAATTT
196 ATTGCCTTATTTTGAAATTT
* *
45389377 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAATGATCGAAACCCAACACATTAGGGCACATTT
1 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
* **
45389442 TCTCGAACTTT-CAAACGCAAAACATTGCCTTATTTTTGAAAAATTTTTAAGGATATT
66 TCTC-AAATTTCCAAACGCAAAACATTGCCTTA-TTTTG-AAAATTTAAAAGGATATT
45389499 AATATGCATA
Statistics
Matches: 311, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
209 2 0.01
210 25 0.08
211 3 0.01
212 49 0.16
215 206 0.66
216 10 0.03
217 16 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (215 bp):
TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
TCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
ATTGCCTTATTTTGAAATTT
Found at i:45389703 original size:4 final size:4
Alignment explanation
Indices: 45389694--45389743 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
45389684 CAATAATGAG
45389694 AATA AATA AATA AATA AATA AA-A TAATA AA-A TAATAA AATA AAT- AATA
1 AATA AATA AATA AATA AATA AATA -AATA AATA -AAT-A AATA AATA AATA
45389742 AA
1 AA
45389744 ATCTATGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
3 5 0.12
4 30 0.75
5 4 0.10
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:45389744 original size:12 final size:11
Alignment explanation
Indices: 45389694--45389745 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 11
45389684 CAATAATGAG
45389694 AATAAATAAATA
1 AATAAATAAA-A
45389706 AATAAATAAAA
1 AATAAATAAAA
45389717 TAATAAAATAATAA
1 -AAT-AAATAA-AA
45389731 AATAAATAATAA
1 AATAAATAA-AA
45389743 AAT
1 AAT
45389746 CTATGTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.03
12 25 0.68
13 9 0.24
14 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:45390039 original size:3 final size:3
Alignment explanation
Indices: 45390031--45390081 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
45390021 TAAATAAACA
*
45390031 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
45390079 AAT
1 AAT
45390082 GATGATGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:45390082 original size:6 final size:6
Alignment explanation
Indices: 45390035--45390123 Score: 63
Period size: 6 Copynumber: 15.0 Consensus size: 6
45390025 TAAACAAATA
* * * * * *
45390035 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATG ATAATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
* * * * * *
45390083 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG -TAATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
45390124 TGATAACAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
5 4 0.05
6 76 0.95
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:45390086 original size:3 final size:3
Alignment explanation
Indices: 45390074--45390118 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
45390064 AATAATAATA
*
45390074 ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
45390119 TAATGTGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:45391481 original size:37 final size:38
Alignment explanation
Indices: 45391416--45391495 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
45391406 TGTCAATTTA
* *
45391416 TTACTTCGGATTTATTCGATGAGGCACTAGGTGGCAAC
1 TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
* *
45391454 TTACTTCGG-TTTAATCGATGAGACACTAGGTGTCAAT
1 TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
45391491 TTACT
1 TTACT
45391496 ACTTCAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 29 0.76
38 9 0.24
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (38 bp):
TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
Found at i:45393897 original size:40 final size:40
Alignment explanation
Indices: 45393803--45393903 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
45393793 TGGCGTTTGG
*
45393803 ACAAAAAAGCGCCGCTAAAAATCGAGCATTAGCGACGCTTT
1 ACAAAAAA-CGCCGCTAAAAATCGAACATTAGCGACGCTTT
* *
45393844 ACATAAAAA-GCCGCTAAAAAT-GAACATTAGCGGCGTTTTT
1 ACA-AAAAACGCCGCTAAAAATCGAACATTAGCGACG-CTTT
* *
45393884 CCAAAAAACGCCGCAAAAAA
1 ACAAAAAACGCCGCTAAAAA
45393904 CCTAAGCCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 17 0.33
40 27 0.52
41 3 0.06
42 5 0.10
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (40 bp):
ACAAAAAACGCCGCTAAAAATCGAACATTAGCGACGCTTT
Found at i:45398783 original size:87 final size:87
Alignment explanation
Indices: 45398683--45398843 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
45398673 GTGTTTGTTA
* * * * *
45398683 AAAAGCGCCGCTAAGAGTCAT-CTTTATTGTGGCATTTTGTTGTAGAAGAGTCGCTAAAAGTCAT
1 AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTT-TAGTAGAAGAGTCGCTAAAAGTCAT
* *
45398747 TGTCTTTAGCCACATTTTTTGAG
65 GGTCTATAGCCACATTTTTTGAG
* * * *
45398770 AAAAGCGCCGCTAAAAATTATGGTCTATAGTGGCATTTTTAGTAGAAGCGTCGCTAAAGGTCATG
1 AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTTTAGTAGAAGAGTCGCTAAAAGTCATG
45398835 GTCTATAGC
66 GTCTATAGC
45398844 GACGTTTGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
87 48 0.77
88 14 0.23
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (87 bp):
AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTTTAGTAGAAGAGTCGCTAAAAGTCATG
GTCTATAGCCACATTTTTTGAG
Found at i:45398870 original size:87 final size:88
Alignment explanation
Indices: 45398711--45398883 Score: 197
Period size: 87 Copynumber: 2.0 Consensus size: 88
45398701 CATCTTTATT
* * * * * * *
45398711 GTGGCATTTTGTTGTAGAAGAGTCGCTAAAAGTCATTGTCTTTAGCCACATTTTTTGAGAAAAGC
1 GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAAGC
*
45398776 GCCGCTAAAAATTATGGTCTATA
66 GCCGCTAAAAATTATGATCTATA
* * *
45398799 GTGGCATTTT-TAGTAGAAGCGTCGCTAAAGGTCATGGTCTATAGCGAC-GTTTGTAAAAAAAGG
1 GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAA-G
* * *
45398862 TGCTGCTAAAGATTATGATCTA
65 CGCCGCTAAAAATTATGATCTA
45398884 GCGTTTGTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
86 9 0.13
87 51 0.73
88 10 0.14
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (88 bp):
GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAAGC
GCCGCTAAAAATTATGATCTATA
Found at i:45401594 original size:93 final size:93
Alignment explanation
Indices: 45401435--45401614 Score: 324
Period size: 93 Copynumber: 1.9 Consensus size: 93
45401425 CCACAAAAAA
*
45401435 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTAGATGGATATG
1 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
45401500 ATATTTAGACTACTAATACATTAAGCAT
66 ATATTTAGACTACTAATACATTAAGCAT
* * *
45401528 TACAAGATAGGTTAAGTACTTATGACGCTTACATGTACAAGTTTAATTATTATTACATGGATATG
1 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
45401593 ATATTTAGACTACTAATACATT
66 ATATTTAGACTACTAATACATT
45401615 GAGAAAGCAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (93 bp):
TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
ATATTTAGACTACTAATACATTAAGCAT
Found at i:45403176 original size:2 final size:2
Alignment explanation
Indices: 45403136--45403167 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
45403126 AACGCATTTT
*
45403136 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
45403168 CGGGAGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:45404391 original size:21 final size:21
Alignment explanation
Indices: 45404367--45404422 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
45404357 AATAGTGGTG
* *
45404367 GCGGTGAGATTAGTTATTGCA
1 GCGGTGAGATTAGATACTGCA
* *
45404388 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGCA
*
45404409 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
45404423 AACAATGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGCA
Found at i:45409187 original size:9 final size:9
Alignment explanation
Indices: 45409173--45409230 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
45409163 TTTGGTTAAA
45409173 AATTAACCG
1 AATTAACCG
*
45409182 AATTAATCG
1 AATTAACCG
45409191 AATTAACCG
1 AATTAACCG
45409200 AATTAACCG
1 AATTAACCG
45409209 AATT-ACCGG
1 AATTAACC-G
*
45409218 AATTAACCT
1 AATTAACCG
45409227 AATT
1 AATT
45409231 GAATCATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.07
9 38 0.86
10 3 0.07
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:45409372 original size:18 final size:18
Alignment explanation
Indices: 45409333--45409392 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
45409323 ATTTTTATGA
** *
45409333 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGAATAC
45409351 TTGGGTTGGGTTGAATAC
1 TTGGGTTGGGTTGAATAC
**
45409369 TT-GGTTGAATTGAATAC
1 TTGGGTTGGGTTGAATAC
45409386 TTGGGTT
1 TTGGGTT
45409393 TAGATTGAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
17 15 0.42
18 21 0.58
ACGTcount: A:0.17, C:0.03, G:0.38, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGAATAC
Found at i:45410768 original size:2 final size:2
Alignment explanation
Indices: 45410761--45410798 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
45410751 TATGTAAGAG
*
45410761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45410799 CACATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:45411634 original size:17 final size:18
Alignment explanation
Indices: 45411612--45411649 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
45411602 CCGTTTAAAA
*
45411612 AAAGAAAAT-AGAATAAC
1 AAAGAAAATAAAAATAAC
45411629 AAAGAAAATAAAAATAAC
1 AAAGAAAATAAAAATAAC
45411647 AAA
1 AAA
45411650 AAACGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAGAAAATAAAAATAAC
Found at i:45416120 original size:423 final size:419
Alignment explanation
Indices: 45415209--45416472 Score: 2140
Period size: 423 Copynumber: 3.0 Consensus size: 419
45415199 GGGAGAATAT
* * *
45415209 TTAGATGGGTTACCTTAGATTCAAAGGATTTATCTCTGTTCTTGGTAAGGAAGTAGGGAGAAGTA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
* *
45415274 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACCTTTGTGAAGATTTTC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
*
45415339 CCAAATCTGAAAACAAATAA-AGTTGAGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAA
131 CCAAATCTGAAAACAAATAAGA-TTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAA
* *
45415403 AATAATAAATGAAAATATGGGCATTTTTGTTTGCAAAAAAACTTGACTGCCCACTGTGTTTAAGC
195 AATAATAAATGAAAATAT-GGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGC
*
45415468 TGGAGCTTTTA-T-CTCCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTCAACTGCACCT
259 TGGAGCTTTTACTCCT-CGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCT
* *
45415531 CACCATTGTTCCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCT
323 CACTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCT
45415596 CACCATGGTTGATTCTACATCCAAAGGAAGCC
388 CACCATGGTTGATTCTACATCCAAAGGAAGCC
* *
45415628 TTAGATGGGTTACCTTGGATTCAAATGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
*
45415693 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTATC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
45415758 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
131 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
* * *
45415823 ATAATAAATGAAAATATGTGCATTTTTGTCTGTAACAAAACTTGACTGCACACTCTGTTTAAGCT
196 ATAATAAATGAAAATATG-GCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCT
* * *
45415888 GAAGCTTTTACGTACCTCTGGTTGGAAATGAGGCTGGTAGTGAGGTTCAAATTTTTAACTGCACC
260 GGAGCTTTTAC-T-CCTC-GATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACC
* * *
45415953 TCACTATTGTTTCTCCAAACACCAACACAATGCAGGGAAAAAGAATATTCCTTCAAAATTTCATC
322 TCACTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATC
*
45416018 TCACCATGGTTGATTCTGCATCCAAAGGAAGCC
387 TCACCATGGTTGATTCTACATCCAAAGGAAGCC
*
45416051 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAATA
1 TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
*
45416116 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTATGAAGATTTTC
66 AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
*
45416181 CCAAATCTGAAAACAAATAAGGTTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
131 CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
* *
45416246 ATAATAAATGAAAATATAGGCATTTTTGTCTGCAACAAAACTTGATTGCCCACAGTGTTTAAGCT
196 ATAATAAATGAAAATAT-GGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCT
* *
45416311 GGAGCTTTTAC-CTTCAATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCA
260 GGAGCTTTTACTCCTCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCA
*
45416375 CTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAGTATTCCTTCAAAATTCCATCTCA
325 CTATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCTCA
45416440 CCATGGTTGATTCTACATCCAAAGGAAGCC
390 CCATGGTTGATTCTACATCCAAAGGAAGCC
45416470 TTA
1 TTA
45416473 ATGAAGCCAT
Statistics
Matches: 793, Mismatches: 44, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
418 1 0.00
419 391 0.49
420 4 0.01
421 1 0.00
422 1 0.00
423 394 0.50
424 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (419 bp):
TTAGATGGGTTACCTTAGATTCAAAAGATTTATCTCTGTTCTTGGTGAGGAAGTAAGGAGAAGTA
AATTTCTGGCATAGAATTGAGGGAACCTAACCTCAATGAAAAAGAAAACATCTGTGAAGATTTTC
CCAAATCTGAAAACAAATAAGATTGGGAAAGAAAATACTTTAACTTTCAAGGATAAAATTGTAAA
ATAATAAATGAAAATATGGCATTTTTGTCTGCAACAAAACTTGACTGCCCACTGTGTTTAAGCTG
GAGCTTTTACTCCTCGATTGGAAATGAGGCTGGCAGTGAGGTTCAAATTTTTAACTGCACCTCAC
TATTGTTTCTCCAAACACCAACACAGTGTAGGGAAAAAGAATATTCCTTCAAAATTCCATCTCAC
CATGGTTGATTCTACATCCAAAGGAAGCC
Found at i:45422443 original size:7 final size:7
Alignment explanation
Indices: 45422372--45422462 Score: 51
Period size: 7 Copynumber: 12.9 Consensus size: 7
45422362 TATCACTATA
45422372 GTTTAGG
1 GTTTAGG
**
45422379 GTTTTTG
1 GTTTAGG
*
45422386 GTATAGG
1 GTTTAGG
* *
45422393 GTATATG
1 GTTTAGG
45422400 GTTTAGAG
1 GTTTAG-G
*
45422408 G-TTATGT
1 GTTTA-GG
*
45422415 GTTAAGG
1 GTTTAGG
45422422 GTTTATGG
1 GTTTA-GG
*
45422430 CTTTAGG
1 GTTTAGG
45422437 GTTTA-G
1 GTTTAGG
**
45422443 GTTTATA
1 GTTTAGG
45422450 GTTTAGG
1 GTTTAGG
45422457 GTTTAG
1 GTTTAG
45422463 ATTAACTAGT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
6 6 0.10
7 45 0.73
8 11 0.18
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:45422456 original size:20 final size:21
Alignment explanation
Indices: 45422421--45422462 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
45422411 ATGTGTTAAG
*
45422421 GGTTTATGGCTTTAGGGTTTA
1 GGTTTATAGCTTTAGGGTTTA
45422442 GGTTTATAG-TTTAGGGTTTA
1 GGTTTATAGCTTTAGGGTTTA
45422462 G
1 G
45422463 ATTAACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (21 bp):
GGTTTATAGCTTTAGGGTTTA
Found at i:45422500 original size:16 final size:16
Alignment explanation
Indices: 45422479--45422511 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45422469 TAGTGTTTTC
45422479 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
45422495 TAATTTATTATATAAT
1 TAATTTATTATATAAT
45422511 T
1 T
45422512 GTAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:45422764 original size:28 final size:28
Alignment explanation
Indices: 45422733--45422790 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
45422723 AGTGATTTAA
45422733 AATTTTAAAATTAATTTT-AAAAGATTTT
1 AATTTT-AAATTAATTTTAAAAAGATTTT
***
45422761 AATTTTTTTTTAATTTTAAAAAGATTTT
1 AATTTTAAATTAATTTTAAAAAGATTTT
45422789 AA
1 AA
45422791 ACTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTTTAAATTAATTTTAAAAAGATTTT
Found at i:45422796 original size:27 final size:27
Alignment explanation
Indices: 45422743--45422796 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
45422733 AATTTTAAAA
**
45422743 TTAATTTTAAAAGATTTTAATTTTTTT
1 TTAATTTTAAAAGATTTTAATACTTTT
45422770 TTAATTTTAAAAAGATTTTAA-ACTTTT
1 TTAATTTT-AAAAGATTTTAATACTTTT
45422797 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
TTAATTTTAAAAGATTTTAATACTTTT
Found at i:45422796 original size:28 final size:27
Alignment explanation
Indices: 45422743--45422796 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
45422733 AATTTTAAAA
**
45422743 TTAATTTTAAAAGATTTTAATTTTTTT
1 TTAATTTTAAAAGATTTTAAACTTTTT
45422770 TTAATTTTAAAAAGATTTTAAACTTTT
1 TTAATTTT-AAAAGATTTTAAACTTTT
45422797 ATTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (27 bp):
TTAATTTTAAAAGATTTTAAACTTTTT
Found at i:45426870 original size:43 final size:43
Alignment explanation
Indices: 45426795--45426952 Score: 208
Period size: 43 Copynumber: 3.7 Consensus size: 43
45426785 AAATATTTTT
* * * * *
45426795 TAAATGTCTTGTTCTTTAGCGGAGTTTGTGGGAAAAGCGCTGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
* *
45426838 TAAAGGTCTTGTTTTTTAGCGGCGTTTATGGGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
* * **
45426881 TAAAGGTCTTGTTCTATAACGGCGTTTGTATGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
*
45426924 TAAAGGTCTTGTTCTATAGCGACGTTTAT
1 TAAAGGTCTTGTTCTATAGCGGCGTTTAT
45426953 TTCTAAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAAGCGCCGC
Found at i:45427198 original size:43 final size:43
Alignment explanation
Indices: 45427086--45427198 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
45427076 AAATATTTTT
* *
45427086 TAAATGTCGTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* ** * **
45427129 TAAAGGTCTTGTTCTTTAAAGACGTTTGTGTTAAAAGCGCCGC
1 TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
45427172 TAAAATTCTTGTTCTATAGCGGCGTTT
1 TAAAAGTCTTGTTCTTTAGCGGCGTTT
45427199 ATTTTTAAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (43 bp):
TAAAAGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Done.