Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 160 of 259
Found at i:52310422 original size:14 final size:15
Alignment explanation
Indices: 52310395--52310430 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
52310385 ATTATATATG
52310395 TATATATCTTTAATA
1 TATATATCTTTAATA
52310410 TATATAT-TTTAATA
1 TATATATCTTTAATA
*
52310424 CATATAT
1 TATATAT
52310431 GTATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATCTTTAATA
Found at i:52310546 original size:21 final size:21
Alignment explanation
Indices: 52310495--52310550 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
52310485 ATATATATTG
* *
52310495 TATATATATATTTTTTAAATC
1 TATATATATATGTTTTAAATA
*
52310516 TAGTAT-TATATGTTTTATATA
1 TA-TATATATATGTTTTAAATA
52310537 TATATATATATGTT
1 TATATATATATGTT
52310551 CACTACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TATATATATATGTTTTAAATA
Found at i:52313756 original size:15 final size:14
Alignment explanation
Indices: 52313736--52313775 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 14
52313726 TGGAATTCTG
52313736 GAAAGAGAAAGCAAA
1 GAAAGA-AAAGCAAA
52313751 GAAAGAAAAAGCAAA
1 GAAAG-AAAAGCAAA
52313766 GAAAGAAAAG
1 GAAAGAAAAG
52313776 GAAAAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.21
15 18 0.75
16 1 0.04
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAGCAAA
Found at i:52313783 original size:21 final size:21
Alignment explanation
Indices: 52313735--52313783 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
52313725 ATGGAATTCT
*
52313735 GGAAAGAG-AAAGCAAAGAAA
1 GGAAAAAGCAAAGCAAAGAAA
52313755 -GAAAAAGCAAAG-AAAGAAAA
1 GGAAAAAGCAAAGCAAAG-AAA
52313775 GGAAAAAGC
1 GGAAAAAGC
52313784 TACGCGTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.67, C:0.06, G:0.27, T:0.00
Consensus pattern (21 bp):
GGAAAAAGCAAAGCAAAGAAA
Found at i:52322769 original size:77 final size:77
Alignment explanation
Indices: 52322584--52323062 Score: 653
Period size: 77 Copynumber: 6.1 Consensus size: 77
52322574 ATGTTTTAAT
* * * *
52322584 TTCTGTTTTTC--AAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCTCGGGTTACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
52322647 GGTA-TTTCAAA
66 GGTATTTTCAAA
* *
52322658 TTCTATTTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
52322723 GGTATTTTCAAA
66 GGTATTTTCAAA
*
52322735 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
52322800 GGTATTTTCAAA
66 GGTATTTTCAAA
* *
52322812 TTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
52322877 GGTATTTTCAAA
66 GGTATTTTCAAA
* * * **
52322889 TTCTGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTTGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
*
52322954 GGTATTTTCAAT
66 GGTATTTTCAAA
52322966 TTCTGTTTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTCTG----------T-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
* * *
52323031 G--ACACGCTGAGGTATTTTCAAT
54 GTCACATGCCGAGGTATTTTCAAA
52323053 TTCTGTTTTT
1 TTCTGTTTTT
52323063 TCAATTTATG
Statistics
Matches: 368, Mismatches: 22, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
74 10 0.03
75 3 0.01
76 52 0.14
77 232 0.63
87 25 0.07
88 1 0.00
89 45 0.12
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (77 bp):
TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGA
GGTATTTTCAAA
Found at i:52322874 original size:154 final size:154
Alignment explanation
Indices: 52322584--52323230 Score: 700
Period size: 154 Copynumber: 4.1 Consensus size: 154
52322574 ATGTTTTAAT
* * *
52322584 TTCTGTTTTTC--AAAAATCAACTCATATTGTGAGAGATGAGTTGAGCCTCGGGTTACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
* *
52322647 GGTA-TTTCAAATTCTATTTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCAG
66 GGTATTTTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
52322711 GTCACATGCCGAGGTATTTTCAAA
131 GTCACATGCCGAGGTATTTTCAAA
* *
52322735 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACATGCCGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
* *
52322800 GGTATTTTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGG
66 GGTATTTTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
52322865 GTCACATGCCGAGGTATTTTCAAA
131 GTCACATGCCGAGGTATTTTCAAA
* * **
52322889 TTCTGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTACATGTTGA
1 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
*
52322954 GGTATTTTCAATTTCTGTTTTTCAATTTATGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
66 GGTATTTTCAAATTCTG----------T-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
* * *
52323019 GTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAAT
119 GTTGAGCCTCAGGTCACATGCCGAGGTATTTTCAAA
52323053 TTCTGTTTTTTCAATTTATGTCTTTTTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTCTG---------TTT-T-TC--------AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * * * * *
52323118 GCCTCAGG--ACACGCTGAGGTATTTTTAATTTCTGTTTTTC--AAAAATCAACTCATACTGCTA
47 GCCTCAGGTTACATGCCGAGGTATTTTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGA
* * * * *
52323179 GAGGTGAGTTGAGTCTCGGGCCACATGCCAAGGTCTTTTCAAA
112 GAGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTTCAAA
52323222 TTCTGTTTT
1 TTCTGTTTT
52323231 AAATTTCTGT
Statistics
Matches: 425, Mismatches: 35, Indels: 64
0.81 0.07 0.12
Matches are distributed among these distances:
151 11 0.03
153 51 0.12
154 155 0.36
159 1 0.00
160 3 0.01
164 24 0.06
165 1 0.00
166 45 0.11
167 37 0.09
169 25 0.06
170 1 0.00
171 1 0.00
173 3 0.01
174 1 0.00
175 1 0.00
181 23 0.05
183 42 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (154 bp):
TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACATGCCGA
GGTATTTTCAAATTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
GTCACATGCCGAGGTATTTTCAAA
Found at i:52322977 original size:14 final size:14
Alignment explanation
Indices: 52322958--52322987 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52322948 TGTTGAGGTA
*
52322958 TTTTCAATTTCTGT
1 TTTTCAATTTATGT
52322972 TTTTCAATTTATGT
1 TTTTCAATTTATGT
52322986 TT
1 TT
52322988 CAAAAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:52323065 original size:15 final size:16
Alignment explanation
Indices: 52323045--52323079 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52323035 CGCTGAGGTA
*
52323045 TTTTCAATTTCTGT-T
1 TTTTCAATTTATGTCT
52323060 TTTTCAATTTATGTCT
1 TTTTCAATTTATGTCT
52323076 TTTT
1 TTTT
52323080 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTCAATTTATGTCT
Found at i:52323117 original size:94 final size:89
Alignment explanation
Indices: 52322881--52323159 Score: 418
Period size: 94 Copynumber: 3.1 Consensus size: 89
52322871 TGCCGAGGTA
* * *
52322881 TTTTCAAATTCTGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTATGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--A
* *
52322946 CATGTTGAGGTATTTTCAATTTCTGT
64 CACGCTGAGGTATTTTCAATTTCTGT
*
52322972 TTTTCAATTTATG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTATGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
52323035 CGCTGAGGTATTTTCAATTTCTGTT
66 CGCTGAGGTATTTTCAATTTCTG-T
52323060 TTTTCAATTTATGTCTTTTTAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTTTCAATTTATG--TTTTT--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
*
52323125 GACACGCTGAGGTATTTTTAATTTCTGT
62 GACACGCTGAGGTATTTTCAATTTCTGT
52323153 TTTTCAA
1 TTTTCAA
52323160 AAATCAACTC
Statistics
Matches: 173, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
87 24 0.14
88 14 0.08
89 45 0.26
91 11 0.06
92 3 0.02
93 8 0.05
94 68 0.39
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (89 bp):
TTTTCAATTTATGTTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTTCTGT
Found at i:52323249 original size:14 final size:14
Alignment explanation
Indices: 52323214--52323261 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
52323204 TGCCAAGGTC
*
52323214 TTTTCAAATTCTG-
1 TTTTCAATTTCTGT
*
52323227 TTTTAAATTTCTGT
1 TTTTCAATTTCTGT
52323241 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
52323255 TTTTCAA
1 TTTTCAA
52323262 AAAAAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:52323336 original size:14 final size:14
Alignment explanation
Indices: 52323317--52323351 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
52323307 CGCTGAGGTA
52323317 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
52323331 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
52323345 TTTTCAA
1 TTTTCAA
52323352 AAAATCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:52323387 original size:88 final size:87
Alignment explanation
Indices: 52323227--52323510 Score: 365
Period size: 88 Copynumber: 3.2 Consensus size: 87
52323217 TCAAATTCTG
* * *
52323227 TTTTAAATTTCTGTTTTTCAATTTCTGTTTTTCAAAAAAAAACAACTCATATTGCGAGAGGTGAG
1 TTTTCAATTTCTGTTTTTCAATTTATG-TTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAG
*
52323292 TTGAGCCTCGGGACACGCTGAGGTA
63 TTGAGCCTCAGGACACGCTGAGGTA
* * *
52323317 TTTTCAATTTCTGCTTTTCAATTTCTGCTTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTT
1 TTTTCAATTTCTGTTTTTCAATTTATG-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * *
52323382 AAGCCTCCGGACACACTGAGGTA
65 GAGCCTCAGGACACGCTGAGGTA
*
52323405 TTTTCAATTT-TGCTTTTCAATTTATGTGTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTT
1 TTTTCAATTTCTGTTTTTCAATTTATGT-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
*
52323468 GAGCCTCAGGTCACACGCCGAGGTA
65 GAGCCTCAGG--ACACGCTGAGGTA
* *
52323493 TTTCCAATTTCAGTTTTT
1 TTTTCAATTTCTGTTTTT
52323511 AAAAAAAATC
Statistics
Matches: 173, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
86 39 0.23
87 19 0.11
88 80 0.46
89 5 0.03
90 30 0.17
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTTCAATTTCTGTTTTTCAATTTATGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCAGGACACGCTGAGGTA
Found at i:52324847 original size:29 final size:29
Alignment explanation
Indices: 52324814--52324869 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
52324804 GGAACCTGGA
52324814 CCTGCAGAGAAAACAAGGAAGAAATTTAG
1 CCTGCAGAGAAAACAAGGAAGAAATTTAG
52324843 CCTGCAGAGAAAACAAGGAAGAAATTT
1 CCTGCAGAGAAAACAAGGAAGAAATTT
52324870 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.14
Consensus pattern (29 bp):
CCTGCAGAGAAAACAAGGAAGAAATTTAG
Found at i:52325393 original size:21 final size:20
Alignment explanation
Indices: 52325347--52325488 Score: 65
Period size: 20 Copynumber: 7.2 Consensus size: 20
52325337 TTAATATTAT
52325347 TATTATTAATAT-TA-GTATA
1 TATT-TTAATATATATGTATA
* *
52325366 TGTTTTATTATATATGTATA
1 TATTTTAATATATATGTATA
*
52325386 TATCTT--TA-ATA--TATA
1 TATTTTAATATATATGTATA
52325401 TATTTTAATACATATATGTATA
1 TATTTTAAT--ATATATGTATA
52325423 TA-TTTATATATAGTTAT-TATTA
1 TATTTTA-ATATA--TATGTA-TA
*
52325445 GTTATTTTTATAT-TAT-TACTA
1 --TATTTTAATATATATGTA-TA
52325466 T-TTTTAATATATATTGTATA
1 TATTTTAATATATA-TGTATA
52325486 TAT
1 TAT
52325489 ATATTTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 38
0.67 0.06 0.27
Matches are distributed among these distances:
15 9 0.09
17 4 0.04
18 16 0.17
19 9 0.09
20 19 0.20
21 16 0.17
22 13 0.14
24 6 0.06
25 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TATTTTAATATATATGTATA
Found at i:52325475 original size:18 final size:18
Alignment explanation
Indices: 52325437--52325471 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52325427 TATATATAGT
*
52325437 TATTATTAGTTATTTTTA
1 TATTATTAGCTATTTTTA
52325455 TATTATTA-CTATTTTTA
1 TATTATTAGCTATTTTTA
52325472 ATATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TATTATTAGCTATTTTTA
Found at i:52336031 original size:48 final size:48
Alignment explanation
Indices: 52335956--52336341 Score: 652
Period size: 48 Copynumber: 8.0 Consensus size: 48
52335946 CAAGACAAAT
* *
52335956 ATATGTATATGTGGTAAATCCGTATGGCTAAG-GTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCT-AGTGTGAAATATGTATGAG
52336004 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
52336052 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
52336100 ATATATATATGTGGTAAAGCC-ATATGGCTAAG-GTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGA-ATGGCT-AGTGTGAAATATGTATGAG
52336148 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
52336196 ATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
52336244 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
52336292 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
52336340 AT
1 AT
52336342 GTGTGTATAT
Statistics
Matches: 322, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
47 5 0.02
48 314 0.98
49 3 0.01
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:52342489 original size:28 final size:28
Alignment explanation
Indices: 52342443--52342497 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
52342433 GTGAGCAACC
*
52342443 CAAATATCACAACTTGTGTGAGAAAATT
1 CAAATATCACAACTCGTGTGAGAAAATT
* *
52342471 CAAATATCATAGCTCGTGTGAGAAAAT
1 CAAATATCACAACTCGTGTGAGAAAAT
52342498 AAAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (28 bp):
CAAATATCACAACTCGTGTGAGAAAATT
Found at i:52343915 original size:38 final size:37
Alignment explanation
Indices: 52343871--52343981 Score: 97
Period size: 38 Copynumber: 3.0 Consensus size: 37
52343861 TAATTATGTA
52343871 AATATATATAATTTAATTATTAATTACTT-TTTTATTT
1 AATATATATAATTTAATTATTAATTA-TTATTTTATTT
* * *
52343908 AAGTATATAGATATTT-ATTATTTATTATTATTCTA-TT
1 AA-TATATATA-ATTTAATTATTAATTATTATTTTATTT
*
52343945 AA-AT-TATAATTTATATTATTAAATTATGATTATTATT
1 AATATATATAATTTA-ATTATT-AATTATTATT-TTATT
52343982 ATTATTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
33 4 0.07
34 3 0.05
35 8 0.14
36 8 0.14
37 10 0.17
38 22 0.37
39 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.57
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTATTATTTTATTT
Found at i:52343964 original size:20 final size:20
Alignment explanation
Indices: 52343931--52343985 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
52343921 TTTATTATTT
52343931 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
52343953 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
52343973 ATTATTATTATTA
1 ATTATTATTATTA
52343986 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 22 0.73
21 3 0.10
22 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:52343970 original size:25 final size:26
Alignment explanation
Indices: 52343922--52343988 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
52343912 ATATAGATAT
* **
52343922 TTATTATTTATTATTATTCTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
*
52343948 TTATAATTTA-TATTATTAAATTATGA
1 TTATAATTTATTATTATTAAATTA-AA
*
52343974 TTATTA-TTATTATTA
1 TTATAATTTATTATTA
52343989 AAAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:52344293 original size:13 final size:14
Alignment explanation
Indices: 52344275--52344312 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
52344265 TTATAAAGTT
52344275 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
52344288 AATAAAAGAAATGA
1 AATAAAATAAAAGA
52344302 AATAAAATAAA
1 AATAAAATAAA
52344313 GTAAAGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:52345425 original size:45 final size:45
Alignment explanation
Indices: 52345375--52345487 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
52345365 CGACTATTGT
52345375 TACTGTTACTGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAG-CACTTTGTGTGTCGAA
* ** *
52345420 TACTGTTACCGTTACTGTTATAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
52345465 TACTGTTACTGTTACTGTTACCG
1 TACTGTTACTGTTACTGTTACCG
52345488 TTACTATTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 59 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:52345476 original size:6 final size:6
Alignment explanation
Indices: 52345465--52345517 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
52345455 GTGTGTTGAA
* * * *
52345465 TACTGT TACTGT TACTGT TACCGT TACTAT TACTGC TACCGT TACTGAT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T
52345514 TACT
1 TACT
52345518 TATTAGATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:52345492 original size:18 final size:18
Alignment explanation
Indices: 52345469--52345517 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
52345459 GTTGAATACT
*
52345469 GTTACTGTTACTGTTACC
1 GTTACTGTTACTGCTACC
*
52345487 GTTACTATTACTGCTACC
1 GTTACTGTTACTGCTACC
52345505 GTTACTGATTACT
1 GTTACTG-TTACT
52345518 TATTAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (18 bp):
GTTACTGTTACTGCTACC
Found at i:52346263 original size:9 final size:9
Alignment explanation
Indices: 52346244--52346280 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
52346234 GTCGAAATTT
52346244 ATAAAAA-A
1 ATAAAAATA
52346252 ATAAAAATA
1 ATAAAAATA
52346261 ATAAAAAATA
1 AT-AAAAATA
52346271 ATAAAAATA
1 ATAAAAATA
52346280 A
1 A
52346281 AAATTTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.26
9 11 0.41
10 9 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
ATAAAAATA
Found at i:52346268 original size:16 final size:16
Alignment explanation
Indices: 52346247--52346283 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
52346237 GAAATTTATA
52346247 AAAAAATAA-AAATAAT
1 AAAAAATAATAAA-AAT
52346263 AAAAAATAATAAAAAT
1 AAAAAATAATAAAAAT
52346279 AAAAA
1 AAAAA
52346284 TTTGGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATAATAAAAAT
Found at i:52346269 original size:10 final size:10
Alignment explanation
Indices: 52346246--52346277 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
52346236 CGAAATTTAT
52346246 AAAAA-AAT-
1 AAAAATAATA
52346254 AAAAATAATA
1 AAAAATAATA
52346264 AAAAATAATA
1 AAAAATAATA
52346274 AAAA
1 AAAA
52346278 TAAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.23
9 3 0.14
10 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATAATA
Found at i:52357018 original size:33 final size:34
Alignment explanation
Indices: 52356975--52357047 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
52356965 GCATAGTCAA
* * *
52356975 ACAGTCTTGGGCC-TAAGCCCCTTTCAGTATCAGT
1 ACAGTCTTGGGCCTTAA-CCCATCTCAGCATCAGT
52357009 ACAGT-TTGGGCCTTAACCCATCTCAGCATCAGT
1 ACAGTCTTGGGCCTTAACCCATCTCAGCATCAGT
52357042 ATCAGT
1 A-CAGT
52357048 ATCAGTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (34 bp):
ACAGTCTTGGGCCTTAACCCATCTCAGCATCAGT
Found at i:52359687 original size:32 final size:33
Alignment explanation
Indices: 52359647--52359721 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
52359637 TGAATGTGGC
*
52359647 CGTGTGGGCCATACGGGC-TAGGCCAAGT-TGGG
1 CGTGTGGGCCATACGGGCAAAGGCCAA-TCTGGG
* *
52359679 TGTGTGGGCCATATGGGCAAAGGCCAATCTGGG
1 CGTGTGGGCCATACGGGCAAAGGCCAATCTGGG
52359712 CGTGTGGGCC
1 CGTGTGGGCC
52359722 CACAAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.16, C:0.21, G:0.43, T:0.20
Consensus pattern (33 bp):
CGTGTGGGCCATACGGGCAAAGGCCAATCTGGG
Found at i:52371672 original size:10 final size:10
Alignment explanation
Indices: 52371645--52371694 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
52371635 TTAAATTCTA
*
52371645 AAAGATAATT
1 AAAGATAAAT
52371655 ACAA-ATAAAT
1 A-AAGATAAAT
*
52371665 AAAGATAATT
1 AAAGATAAAT
52371675 AAAGATAAAT
1 AAAGATAAAT
52371685 GAAA-ATAAAT
1 -AAAGATAAAT
52371695 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:52371692 original size:20 final size:20
Alignment explanation
Indices: 52371645--52371684 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52371635 TTAAATTCTA
52371645 AAAGATAATTACAAATAAAT
1 AAAGATAATTACAAATAAAT
52371665 AAAGATAATTA-AAGATAAAT
1 AAAGATAATTACAA-ATAAAT
52371685 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAGATAATTACAAATAAAT
Found at i:52372545 original size:96 final size:96
Alignment explanation
Indices: 52372385--52372565 Score: 299
Period size: 96 Copynumber: 1.9 Consensus size: 96
52372375 TTTACCTTCA
* *
52372385 CTTAGGAAAATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
1 CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
52372450 TCAGCCCAACACATTCTTAATTTTTATTTTT
66 TCAGCCCAACACATTCTTAATTTTTATTTTT
* * * **
52372481 CTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTCACCCTGGTTAC
1 CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
52372546 TCAGCCCAACACATTCTTAA
66 TCAGCCCAACACATTCTTAA
52372566 AAATTAATAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (96 bp):
CTTAAGAAAATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
TCAGCCCAACACATTCTTAATTTTTATTTTT
Found at i:52373694 original size:15 final size:15
Alignment explanation
Indices: 52373676--52373760 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 15
52373666 TATCCAAAAT
52373676 TAAAATAATAAATAA
1 TAAAATAATAAATAA
52373691 TAAAATAA-AGTAA-AA
1 TAAAATAATA--AATAA
* *
52373706 TAAAATAAAAAAATAC
1 TAAAAT-AATAAATAA
52373722 TAATAA-AATAAAATGAAA
1 TAA-AATAAT-AAAT--AA
52373740 TAAAATAATAAATAA
1 TAAAATAATAAATAA
52373755 TAAAAT
1 TAAAAT
52373761 TAAGAAAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
14 1 0.02
15 28 0.49
16 12 0.21
17 9 0.16
18 7 0.12
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (15 bp):
TAAAATAATAAATAA
Found at i:52373729 original size:11 final size:9
Alignment explanation
Indices: 52373676--52373782 Score: 75
Period size: 10 Copynumber: 12.0 Consensus size: 9
52373666 TATCCAAAAT
52373676 TAAAAT-AA
1 TAAAATAAA
52373684 T-AAAT-AA
1 TAAAATAAA
52373691 TAAAATAAA
1 TAAAATAAA
52373700 GTAAAATAAAA
1 -TAAAAT-AAA
52373711 TAAAA-AAA
1 TAAAATAAA
*
52373719 TACTAATAAAA
1 TA-AAAT-AAA
52373730 TAAAATGAAA
1 TAAAAT-AAA
52373740 TAAAAT-AA
1 TAAAATAAA
52373748 T-AAAT-AA
1 TAAAATAAA
*
52373755 TAAAATTAA
1 TAAAATAAA
*
52373764 GAAAAGTAAA
1 TAAAA-TAAA
*
52373774 AAAAATAAA
1 TAAAATAAA
52373783 GGTTGGGTTG
Statistics
Matches: 83, Mismatches: 6, Indels: 19
0.77 0.06 0.18
Matches are distributed among these distances:
7 14 0.17
8 17 0.20
9 14 0.17
10 30 0.36
11 8 0.10
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:52373731 original size:34 final size:34
Alignment explanation
Indices: 52373671--52373782 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 34
52373661 ATTAATATCC
*
52373671 AAAATTAAAATAATAAATAATAAAATAAAGTAAAAT
1 AAAATAAAAATAAT--ATAATAAAATAAAGTAAAAT
* *
52373707 AAAATAAAAA-AATACTAATAAAATAAAATGAAAT
1 AAAATAAAAATAATA-TAATAAAATAAAGTAAAAT
* *
52373741 AAAATAATAAATAATAAAATTAAGA-AAAGTAAAA-
1 AAAATAA-AAATAATATAA-TAAAATAAAGTAAAAT
52373775 AAAATAAA
1 AAAATAAA
52373783 GGTTGGGTTG
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
33 2 0.03
34 31 0.48
35 15 0.23
36 17 0.26
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (34 bp):
AAAATAAAAATAATATAATAAAATAAAGTAAAAT
Found at i:52373777 original size:9 final size:9
Alignment explanation
Indices: 52373677--52373782 Score: 52
Period size: 9 Copynumber: 10.9 Consensus size: 9
52373667 ATCCAAAATT
52373677 AAAATAATAA
1 AAAATAA-AA
*
52373687 ATAATAAAA
1 AAAATAAAA
*
52373696 TAAAGTAAAA
1 -AAAATAAAA
52373706 TAAAAT-AAA
1 -AAAATAAAA
*
52373715 AAAATACTAAT
1 AAAATA--AAA
52373726 AAAATAAAA
1 AAAATAAAA
*
52373735 TGAAATAAAATA
1 -AAAAT-AAA-A
*
52373747 ATAAATAATA
1 A-AAATAAAA
* *
52373757 AAATTAAGA
1 AAAATAAAA
*
52373766 AAAGTAAAA
1 AAAATAAAA
52373775 AAAATAAA
1 AAAATAAA
52373783 GGTTGGGTTG
Statistics
Matches: 74, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
8 5 0.07
9 27 0.36
10 24 0.32
11 13 0.18
12 5 0.07
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAATAAAA
Found at i:52377519 original size:10 final size:10
Alignment explanation
Indices: 52377492--52377541 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
52377482 ATAAATTCTA
*
52377492 AAAGATAATT
1 AAAGATAAAT
52377502 ACAA-ATAAAT
1 A-AAGATAAAT
*
52377512 AAAGATAATT
1 AAAGATAAAT
52377522 AAAGATAAAT
1 AAAGATAAAT
52377532 GAAA-ATAAAT
1 -AAAGATAAAT
52377542 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:52377539 original size:20 final size:20
Alignment explanation
Indices: 52377492--52377531 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52377482 ATAAATTCTA
52377492 AAAGATAATTACAAATAAAT
1 AAAGATAATTACAAATAAAT
52377512 AAAGATAATTA-AAGATAAAT
1 AAAGATAATTACAA-ATAAAT
52377532 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAGATAATTACAAATAAAT
Found at i:52385314 original size:24 final size:24
Alignment explanation
Indices: 52385209--52385348 Score: 100
Period size: 24 Copynumber: 5.8 Consensus size: 24
52385199 TCAAACAAGG
* **
52385209 AAATTCGCACCCATAGTGCCATGT
1 AAATTCGCACACATAGTGCCATAC
* ** * *
52385233 TAACCCGCACACATAGTGCCTTAG
1 AAATTCGCACACATAGTGCCATAC
* * * * * * **
52385257 TAATTCACATACGTATTGACATTT
1 AAATTCGCACACATAGTGCCATAC
*
52385281 AAATCCGCACACATAGTGCCATAC
1 AAATTCGCACACATAGTGCCATAC
* * *
52385305 AATTTTGCACACATAGTGCCATTC
1 AAATTCGCACACATAGTGCCATAC
52385329 AAATTCGCACACATAGTGCC
1 AAATTCGCACACATAGTGCC
52385349 GAAGTCAATT
Statistics
Matches: 84, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (24 bp):
AAATTCGCACACATAGTGCCATAC
Found at i:52390452 original size:23 final size:23
Alignment explanation
Indices: 52390422--52390468 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52390412 GCTAAAGTCT
52390422 CACATACATATGAATGAGTAGAA
1 CACATACATATGAATGAGTAGAA
52390445 CACATACATATGAATGAGTAGAA
1 CACATACATATGAATGAGTAGAA
52390468 C
1 C
52390469 CAGGGTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (23 bp):
CACATACATATGAATGAGTAGAA
Found at i:52393365 original size:24 final size:24
Alignment explanation
Indices: 52393330--52393419 Score: 126
Period size: 24 Copynumber: 3.8 Consensus size: 24
52393320 ATTGACATTT
*
52393330 AAATCCGCACACATAGTGCTATAC
1 AAATCCGCACACATAGTGCCATAC
*
52393354 AAGTCCGCACACATAGTGCCATAC
1 AAATCCGCACACATAGTGCCATAC
* * *
52393378 AATTTCGCACACATAGTGCCATTC
1 AAATCCGCACACATAGTGCCATAC
*
52393402 AAATTCGCACACATAGTG
1 AAATCCGCACACATAGTG
52393420 ATGAAGTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.22
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCCATAC
Found at i:52398625 original size:43 final size:42
Alignment explanation
Indices: 52398560--52398681 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
52398550 AGTACCATGC
* * * *
52398560 CAATGCTATATCCTAGATATGGTCTTACATGAAATCTCGTAT
1 CAATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
* *
52398602 CAATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCGTAT
1 CAATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
* * * *
52398645 CGATGCCATATCCTAGATATGGTCTTACACGTAATCT
1 CAATGCCATAGCCCAGATATGGTCTTACACGAAATCT
52398682 TAGTAACCCT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 31 0.46
43 36 0.54
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
CAATGCCATAGCCCAGATATGGTCTTACACGAAATCTCGTAT
Found at i:52432707 original size:13 final size:13
Alignment explanation
Indices: 52432689--52432713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52432679 TGGCCACCAT
52432689 TTAACCCTAATTC
1 TTAACCCTAATTC
52432702 TTAACCCTAATT
1 TTAACCCTAATT
52432714 TCCCCCATTC
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAACCCTAATTC
Found at i:52438379 original size:19 final size:19
Alignment explanation
Indices: 52438351--52438388 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52438341 TAGTCAATCT
52438351 CGGTACGACCTACAAACTA
1 CGGTACGACCTACAAACTA
*
52438370 CGGTATGACCTACAAACTA
1 CGGTACGACCTACAAACTA
52438389 ACTCTTGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (19 bp):
CGGTACGACCTACAAACTA
Found at i:52439085 original size:13 final size:13
Alignment explanation
Indices: 52439067--52439122 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
52439057 TAGATTTTTC
52439067 CTAAATATTATCA
1 CTAAATATTATCA
52439080 CTAAATATTATCA
1 CTAAATATTATCA
* *
52439093 C-AAA-ATAAT-T
1 CTAAATATTATCA
52439103 CTAAATATTATCA
1 CTAAATATTATCA
52439116 CTAAATA
1 CTAAATA
52439123 AATCAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 1 0.03
11 7 0.19
12 7 0.19
13 21 0.58
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:52439107 original size:23 final size:23
Alignment explanation
Indices: 52439080--52439123 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
52439070 AATATTATCA
52439080 CTAAATATTATCACAAAATAATT
1 CTAAATATTATCACAAAATAATT
*
52439103 CTAAATATTATCACTAAATAA
1 CTAAATATTATCACAAAATAA
52439124 ATCAAATTTA
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:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (23 bp):
CTAAATATTATCACAAAATAATT
Found at i:52439757 original size:40 final size:40
Alignment explanation
Indices: 52439649--52439807 Score: 171
Period size: 40 Copynumber: 4.0 Consensus size: 40
52439639 TGTAAAACAT
***
52439649 AGAGCAATAGCGGCG-TTTTACCAAAAACGCCGCTAAAAAC
1 AGAGCAATAGCGGCGCTTTT-GGTAAAACGCCGCTAAAAAC
*
52439689 AGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAA-C
* *
52439730 AGAGCAATAGCGGTGCTTTTGGT-AAACGCCACTAAAAATC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAA-C
* * * *
52439770 -GAAGCATTAGCGGCGCTTTCGATAAAACGCCTCTAAAA
1 AG-AGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
52439808 GTCATATAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 63 0.61
41 39 0.38
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
Found at i:52440134 original size:15 final size:15
Alignment explanation
Indices: 52440111--52440164 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
52440101 TATTTTAAGT
*
52440111 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
52440126 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
*
52440140 TTTAAGGG-TTAGGGG
1 TTT-AGGGATTATGGG
*
52440155 TCTA-GGATTA
1 TTTAGGGATTA
52440165 AGAGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 19 0.58
ACGTcount: A:0.22, C:0.02, G:0.35, T:0.41
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:52440137 original size:22 final size:21
Alignment explanation
Indices: 52440112--52440166 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
52440102 ATTTTAAGTT
*
52440112 TTATGGATTATGGGTTTAGGGA
1 TTATGGATTAAGGG-TTAGGGA
* *
52440134 TTATGGTTTAAGGGTTAGGGG
1 TTATGGATTAAGGGTTAGGGA
52440155 TCTA-GGATTAAG
1 T-TATGGATTAAG
52440167 AGTTTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTATGGATTAAGGGTTAGGGA
Found at i:52440206 original size:22 final size:22
Alignment explanation
Indices: 52440181--52440230 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
52440171 TATATTTTAT
* *
52440181 GATTTAGGATTTAGGGTCTAGG
1 GATTTAGGATTAAGAGTCTAGG
* *
52440203 GATTAAGGATTAAGAGTTTAGG
1 GATTTAGGATTAAGAGTCTAGG
52440225 G-TTTAG
1 GATTTAG
52440231 TTTATATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (22 bp):
GATTTAGGATTAAGAGTCTAGG
Found at i:52440430 original size:22 final size:21
Alignment explanation
Indices: 52440405--52440454 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
52440395 GAGTTACTAT
*
52440405 TTTAAGGTTTATGAATTATGGG
1 TTTAAGGTTTAGGAATTA-GGG
* **
52440427 TTTAGGGTTTAGGGTTTAGGG
1 TTTAAGGTTTAGGAATTAGGG
52440448 TTTAAGG
1 TTTAAGG
52440455 ACTGGGGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TTTAAGGTTTAGGAATTAGGG
Found at i:52440434 original size:7 final size:7
Alignment explanation
Indices: 52440424--52440451 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
52440414 TATGAATTAT
52440424 GGGTTTA
1 GGGTTTA
52440431 GGGTTTA
1 GGGTTTA
52440438 GGGTTTA
1 GGGTTTA
52440445 GGGTTTA
1 GGGTTTA
52440452 AGGACTGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:52442490 original size:46 final size:45
Alignment explanation
Indices: 52442437--52442611 Score: 167
Period size: 45 Copynumber: 3.8 Consensus size: 45
52442427 TATTTGGGCA
52442437 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
52442483 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * * * *
52442530 TCCGAGCTCGTTCAGTGGAGTCCGAGTTCACTTGTAGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
52442576 -CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52442612 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 32 0.31
46 31 0.30
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:52444107 original size:39 final size:40
Alignment explanation
Indices: 52444064--52444231 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
52444054 CTCGTTCAAG
* * * *
52444064 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
52444103 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
52444143 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
52444183 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
52444223 TGCCTTCGG
1 TGCCTTCGG
52444232 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:52444215 original size:80 final size:80
Alignment explanation
Indices: 52444099--52444284 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
52444089 AGTAACTCAT
* * *
52444099 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
52444163 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
52444178 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
52444242 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
52444259 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
52444285 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:52444244 original size:40 final size:40
Alignment explanation
Indices: 52444101--52444284 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
52444091 TAACTCATAC
* *
52444101 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
52444141 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
52444181 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
52444221 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
52444262 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52444285 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:52451208 original size:42 final size:43
Alignment explanation
Indices: 52451109--52451280 Score: 138
Period size: 42 Copynumber: 4.1 Consensus size: 43
52451099 ATTTTTAGCA
* * * *
52451109 GCGTTTGTGAGAAAAGCGTCGCTAAAAGTCATGTTCTTT-GATG
1 GCGTTTGTAAAAAAAGCGCCGCTAAAAGTCATGGTCTTTAG-TG
* *** * *
52451152 GC-TTTTTTGGAAAAGTGCCGCTAAAGGTCATGGTCTTTAGTG
1 GCGTTTGTAAAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGTG
* ** *
52451194 GCGTTTGT-AAAAAAGCGCTGCT-AAAGATCATAATCTTTAGGG
1 GCGTTTGTAAAAAAAGCGCCGCTAAAAG-TCATGGTCTTTAGTG
* * *
52451236 GCGTTTGTAAAAAAAACGTCGCTAAAAGTCAT-GTCTTTAGCG
1 GCGTTTGTAAAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGTG
52451278 GCG
1 GCG
52451281 CCTGCTATAA
Statistics
Matches: 103, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
41 3 0.03
42 74 0.72
43 22 0.21
44 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
GCGTTTGTAAAAAAAGCGCCGCTAAAAGTCATGGTCTTTAGTG
Found at i:52459019 original size:40 final size:41
Alignment explanation
Indices: 52458872--52459044 Score: 224
Period size: 41 Copynumber: 4.3 Consensus size: 41
52458862 GGGCACTAAA
*** * *
52458872 GTGC-ATTCAGGGGTGCCGAAGTACAAATAGGGGCACGTAT
1 GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCACGTAT
*
52458912 GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCATGTAT
1 GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCACGTAT
*
52458953 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCACGTAT
1 GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCACGTAT
* ** *
52458994 GTGCAATTCA-GGGTATTGAAGTACAAGCATAAGCATGTAT
1 GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCACGTAT
*
52459034 GTACAATTCAG
1 GTGCAATTCAG
52459045 TAATCATCAA
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
40 38 0.32
41 79 0.68
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (41 bp):
GTGCAATTCAGGGGTATTGAAGTACAAACATGGGCACGTAT
Found at i:52459033 original size:81 final size:82
Alignment explanation
Indices: 52458872--52459044 Score: 260
Period size: 82 Copynumber: 2.1 Consensus size: 82
52458862 GGGCACTAAA
* *
52458872 GTGC-ATTCAGGGGTGCCGAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGGTATTGAAGTA
1 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGGTATTGAAGTA
**
52458936 CAAACATGGGCATGTAT
66 CAAACATAAGCATGTAT
* *
52458953 GTGCAATTCAGGGGTATCGAAGTACAAACATGGGCACGTATGTGCAATTCA-GGGTATTGAAGTA
1 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGGTATTGAAGTA
*
52459017 CAAGCATAAGCATGTAT
66 CAAACATAAGCATGTAT
*
52459034 GTACAATTCAG
1 GTGCAATTCAG
52459045 TAATCATCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 41 0.49
82 42 0.51
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (82 bp):
GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAGGGGTATTGAAGTA
CAAACATAAGCATGTAT
Found at i:52460568 original size:15 final size:15
Alignment explanation
Indices: 52460551--52460601 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
52460541 CAGTTCGAAT
*
52460551 AATTTTTCGAAAAAT
1 AATTTTTCGAAAAAA
*
52460566 AATTTTAC-AAAAAA
1 AATTTTTCGAAAAAA
52460580 AATTATTT-GAACAAAA
1 AATT-TTTCGAA-AAAA
52460596 AATTTT
1 AATTTT
52460602 ATTTTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.30
15 13 0.43
16 8 0.27
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (15 bp):
AATTTTTCGAAAAAA
Found at i:52460582 original size:17 final size:18
Alignment explanation
Indices: 52460560--52460597 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52460550 TAATTTTTCG
*
52460560 AAAAATAATTT-TACAAA
1 AAAAATAATTTGAACAAA
*
52460577 AAAAATTATTTGAACAAA
1 AAAAATAATTTGAACAAA
52460595 AAA
1 AAA
52460598 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATAATTTGAACAAA
Found at i:52463702 original size:25 final size:26
Alignment explanation
Indices: 52463674--52463727 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
52463664 CTCTTTTATT
52463674 TATAAA-ATAAAATAATTATTGCAAA
1 TATAAAGATAAAATAATTATTGCAAA
* * * *
52463699 TATAAAGTTTAATTAATTATTTCAAA
1 TATAAAGATAAAATAATTATTGCAAA
52463725 TAT
1 TAT
52463728 CATTATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TATAAAGATAAAATAATTATTGCAAA
Found at i:52464622 original size:18 final size:17
Alignment explanation
Indices: 52464592--52464639 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
52464582 TTTATCATTT
*
52464592 TAATAATTTAAAATTTTA
1 TAAT-ATTTAAAATATTA
*
52464610 TAATATTTGAAAAGATTA
1 TAATATTT-AAAATATTA
*
52464628 TATTATTTAAAA
1 TAATATTTAAAA
52464640 ATCAAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TAATATTTAAAATATTA
Found at i:52468123 original size:20 final size:17
Alignment explanation
Indices: 52468083--52468150 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
52468073 ATTATTTCAT
** *
52468083 ATTTTTTTCGAATTATA
1 ATTTTTTTATAATTTTA
52468100 ATTTTTATATATAATTTTTA
1 ATTTTT-T-TATAA-TTTTA
52468120 ATTTTTTTATAATTTTA
1 ATTTTTTTATAATTTTA
*
52468137 ATTTATTTACTAAT
1 ATTTTTTTA-TAAT
52468151 GCCAGCAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 19 0.44
18 10 0.23
19 4 0.09
20 10 0.23
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (17 bp):
ATTTTTTTATAATTTTA
Found at i:52469622 original size:19 final size:19
Alignment explanation
Indices: 52469595--52469646 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
52469585 TAGATTTTTT
* *
52469595 AATTTTTTTGGAATTTTATA
1 AATTATTTT-GAATTTTAAA
*
52469615 AA-TATTTTTAATTTTAAA
1 AATTATTTTGAATTTTAAA
*
52469633 AATTATTTTAAATT
1 AATTATTTTGAATT
52469647 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.37
19 15 0.56
20 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTATTTTGAATTTTAAA
Found at i:52469627 original size:18 final size:19
Alignment explanation
Indices: 52469606--52469646 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
52469596 ATTTTTTTGG
* *
52469606 AATTTTATAAA-TATTTTT
1 AATTTTAAAAATTATTTTA
52469624 AATTTTAAAAATTATTTTA
1 AATTTTAAAAATTATTTTA
52469643 AATT
1 AATT
52469647 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTA
Found at i:52470503 original size:55 final size:55
Alignment explanation
Indices: 52470435--52470676 Score: 305
Period size: 55 Copynumber: 4.5 Consensus size: 55
52470425 GATAGCCTGT
** * * * *
52470435 GAATACTGTTTCTTTTGAATCGATTGTTTGTATGTTTAAATCAATTGTCATGTT-
1 GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
52470489 GTAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATAG-T-
1 G-AATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTAT-GTTA
* * * *
52470544 GGA-ACTTCTTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTA
1 GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
* * *
52470598 GAATATTACTTCTTTTAAATCAATTATTTATATGTTTAAATCGATTGTTATGTTA
1 GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
*
52470653 GAATACTGCTTC-TTTGAATCAATT
1 GAATACTACTTCTTTTGAATCAATT
52470677 ATTATGTTAG
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
52 1 0.01
53 45 0.28
54 15 0.09
55 101 0.62
56 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.50
Consensus pattern (55 bp):
GAATACTACTTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTA
Found at i:52470567 original size:108 final size:108
Alignment explanation
Indices: 52470444--52470648 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
52470434 TGAATACTGT
* *
52470444 TTCTTTTGAATCGATTGTTTGTATGTTTAAATCAATTGTCATGTT-GTAATACTACTTCTTTTGA
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAG-AATACTACTTCTTTTAA
*
52470508 ATCAATTGTTTATATGTTTAAATCGATTGTTATAGTGGAACTTC
65 ATCAATTATTTATATGTTTAAATCGATTGTTATAGTGGAACTTC
** * *
52470552 TTCTTTTGAATCGATTGTTTATATGTTTAAATTGATTGTTATGTTAGAATATTACTTCTTTTAAA
1 TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAGAATACTACTTCTTTTAAA
52470617 TCAATTATTTATATGTTTAAATCGATTGTTAT
66 TCAATTATTTATATGTTTAAATCGATTGTTAT
52470649 GTTAGAATAC
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 88 0.99
109 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.51
Consensus pattern (108 bp):
TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTAGAATACTACTTCTTTTAAA
TCAATTATTTATATGTTTAAATCGATTGTTATAGTGGAACTTC
Found at i:52470687 original size:33 final size:33
Alignment explanation
Indices: 52470636--52470700 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
52470626 TATATGTTTA
* * *
52470636 AATCGATTGTTATGTTAGAATACTGCTTCTTTG
1 AATCAATTATTATGTTAGAATACTACTTCTTTG
52470669 AATCAATTATTATGTTAGAATACTACTTCTTT
1 AATCAATTATTATGTTAGAATACTACTTCTTT
52470701 TTAATCGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (33 bp):
AATCAATTATTATGTTAGAATACTACTTCTTTG
Found at i:52479159 original size:21 final size:22
Alignment explanation
Indices: 52479135--52479184 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
52479125 AAACCTTGAA
52479135 TTTTCCCCTTTTTC-TTCTTTC
1 TTTTCCCCTTTTTCTTTCTTTC
*
52479156 TTTT-CTCTTTTTCTTTCTTTC
1 TTTTCCCCTTTTTCTTTCTTTC
*
52479177 -CTTCCCCT
1 TTTTCCCCT
52479185 GCTCTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCCCCTTTTTCTTTCTTTC
Found at i:52479411 original size:3 final size:3
Alignment explanation
Indices: 52479385--52479471 Score: 53
Period size: 3 Copynumber: 30.3 Consensus size: 3
52479375 TTATTTAATT
* * *
52479385 TAA TAA T-A TAA T-A TCAA TTA -AA TAA TAA TAA CAA TAA CAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
52479428 TAA TTA -AA T-A TAA -AA CT-A TAA TAA TAAA TAA TAA GAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA
52479471 T
1 T
52479472 TTAATATATT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
2 11 0.17
3 48 0.75
4 5 0.08
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:52479431 original size:21 final size:19
Alignment explanation
Indices: 52479405--52479471 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
52479395 ATATCAATTA
52479405 AATAATAATAACAATAACAAT
1 AATAATAATAA-AATAA-AAT
52479426 AATAAT--TAAATATAAAACT
1 AATAATAATAAA-ATAAAA-T
*
52479445 -ATAATAAT-AAATAATAAG
1 AATAATAATAAAATAA-AAT
52479463 AATAATAAT
1 AATAATAAT
52479472 TTAATATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
18 12 0.31
19 20 0.51
20 1 0.03
21 6 0.15
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (19 bp):
AATAATAATAAAATAAAAT
Found at i:52481610 original size:12 final size:12
Alignment explanation
Indices: 52481595--52481630 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
52481585 ATTTTCCCTT
52481595 TTTTCTTCTTTC
1 TTTTCTTCTTTC
52481607 TTTTC-TCTTT-
1 TTTTCTTCTTTC
52481617 TTTT-TTCTTTC
1 TTTTCTTCTTTC
52481628 TTT
1 TTT
52481631 CCCCTGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.41
11 8 0.36
12 5 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:52481610 original size:21 final size:21
Alignment explanation
Indices: 52481586--52481635 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
52481576 AAACCTTGAA
52481586 TTTTCCCTTTTTTCTTCTTTC
1 TTTTCCCTTTTTTCTTCTTTC
* *
52481607 TTTTCTCTTTTTTTTTCTTTC
1 TTTTCCCTTTTTTCTTCTTTC
*
52481628 TTTCCCCT
1 TTTTCCCT
52481636 GCTCTCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCCCTTTTTTCTTCTTTC
Found at i:52481862 original size:3 final size:3
Alignment explanation
Indices: 52481836--52481922 Score: 60
Period size: 3 Copynumber: 30.3 Consensus size: 3
52481826 TTATTTAATT
* * * *
52481836 TAA TAA T-A TAA TAT TAA TTA -AA TAA TAA TAA CAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
52481882 TTA -AA T-A TAA -AA CT-A TAA TAA TAAA TAA TAA GAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA T
52481923 TTAATATATT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
2 9 0.14
3 52 0.81
4 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:52481889 original size:40 final size:40
Alignment explanation
Indices: 52481836--52481929 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
52481826 TTATTTAATT
52481836 TAATAA-TATAATATTAATTAA-ATAATAAT-AACAATAAAAA
1 TAATAATTA-AATATTAA--AACATAATAATAAACAATAAAAA
* *
52481876 TAATAATTAAATA-TAAAACTATAATAATAAATAATAAGAA
1 TAATAATTAAATATTAAAAC-ATAATAATAAACAATAAAAA
*
52481916 TAATAATTTAATAT
1 TAATAATTAAATAT
52481930 ATTTTAACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
37 2 0.04
39 11 0.24
40 31 0.67
41 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (40 bp):
TAATAATTAAATATTAAAACATAATAATAAACAATAAAAA
Found at i:52482792 original size:22 final size:22
Alignment explanation
Indices: 52482767--52482817 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
52482757 ATGCCAGAAC
* *
52482767 TTAAATCGAGCTTAGAGATCAT
1 TTAAATAGAGCTTAGAGAACAT
*
52482789 TTAAATTAGAGCTTAGGGAACAT
1 TTAAA-TAGAGCTTAGAGAACAT
52482812 TTAAAT
1 TTAAAT
52482818 TAACTCAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (22 bp):
TTAAATAGAGCTTAGAGAACAT
Found at i:52482802 original size:23 final size:23
Alignment explanation
Indices: 52482774--52482819 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52482764 AACTTAAATC
*
52482774 GAGCTTAGAGATCATTTAAATTA
1 GAGCTTAGAGAACATTTAAATTA
*
52482797 GAGCTTAGGGAACATTTAAATTA
1 GAGCTTAGAGAACATTTAAATTA
52482820 ACTCAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (23 bp):
GAGCTTAGAGAACATTTAAATTA
Found at i:52484065 original size:41 final size:41
Alignment explanation
Indices: 52484005--52484098 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
52483995 ACAAGTTACC
* * * * * *
52484005 TGATACGACACACCGGCACGAAGCTTGCTAGGCTCGAGGCT
1 TGATACGATACACCAGCACGAAGCCTACTAAGCTCAAGGCT
*
52484046 TGATACAATACACCAGCACGAAGCCTACTAAGCTCAAGGCT
1 TGATACGATACACCAGCACGAAGCCTACTAAGCTCAAGGCT
*
52484087 CGATACGATACA
1 TGATACGATACA
52484099 TCTAGTACAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (41 bp):
TGATACGATACACCAGCACGAAGCCTACTAAGCTCAAGGCT
Found at i:52490930 original size:16 final size:16
Alignment explanation
Indices: 52490911--52490950 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
52490901 TTTAGTAATT
52490911 TTTTTATAATAT-TATA
1 TTTTTA-AATATATATA
*
52490927 TTTTTAATTATATATA
1 TTTTTAAATATATATA
52490943 TTTTTAAA
1 TTTTTAAA
52490951 ATTAGTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAATATATATA
Found at i:52493270 original size:28 final size:28
Alignment explanation
Indices: 52493230--52493287 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
52493220 AGTCACGAGA
52493230 CTAAAATTTTACATTACACTAAAACATC
1 CTAAAATTTTACATTACACTAAAACATC
52493258 CTAAAATTTTACATTACACTAAAACATC
1 CTAAAATTTTACATTACACTAAAACATC
52493286 CT
1 CT
52493288 TAAGACAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (28 bp):
CTAAAATTTTACATTACACTAAAACATC
Found at i:52495379 original size:47 final size:46
Alignment explanation
Indices: 52495303--52495624 Score: 183
Period size: 47 Copynumber: 6.8 Consensus size: 46
52495293 TTGGGTTATG
*
52495303 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA
1 TGAGGGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA
* * *
52495351 TGAGGGCTAGTGTAAGACGTGTCTGGGACATGCATCAGCCACATT-ATGA
1 TGAGGGCCAGTGTAAGACATGTCTGGGACATGCATC-G--GCATTGA-GA
* * * *
52495400 T-A--TCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGTAGAGA
1 TGAGGGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA
* * ** * *
52495445 TGAGTGCCAGTGTAAGACGTGTCTGGGACATGCATTAGC-CTCA-A
1 TGAGGGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
* * * *
52495489 TGATGGTAGCCAATGTAAGACGTGTCTGGGACATGCATCGGC--TAAGC
1 TGA-GG--GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
** * * * * * * *
52495536 TTCGTGCTAATGTAAGACATGTTTGGGACATGCATCAGCACTTATACA
1 TGAGGGCCAGTGTAAGACATGTCTGGGACATGCATCGGCA-TT-GAGA
* * *
52495584 CGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGAGGGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
52495625 CTCGATGAAA
Statistics
Matches: 214, Mismatches: 40, Indels: 38
0.73 0.14 0.13
Matches are distributed among these distances:
44 34 0.16
45 8 0.04
46 25 0.12
47 74 0.35
48 46 0.21
49 20 0.09
50 7 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
TGAGGGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
Found at i:52495418 original size:94 final size:93
Alignment explanation
Indices: 52495307--52495720 Score: 363
Period size: 94 Copynumber: 4.4 Consensus size: 93
52495297 GTTATGTGAG
*
52495307 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGGGCTAGTGTAAGACGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGAGTGCTAGTGTAAGACGTG
52495372 TCTGGGACATGCATCAGCCACATTATGAT
65 TCTGGGACATGCATCAGCCACATTATGAT
* * * *
52495401 ATCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGTAGAGATGAGTGCCAGTGTAAGACGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGAGTGCTAGTGTAAGACGTG
* * * *
52495466 TCTGGGACATGCATTAGCCTCAATGATGGT
65 TCTGGGACATGCATCAGCCAC-ATTATGAT
* * * * ** * *
52495496 AGCCAATGTAAGA-CGTGTCTGGGACAT-GCATCGGC-TAAGCTTCGTGCTAATGTAAGACATGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAGTGCTAGTGTAAGACGTGT
* *
52495558 TTGGGACATGCATCAG-CAC-TTATACACGAG
66 CTGGGACATGCATCAGCCACATTAT----GAT
* * * * * * *
52495588 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGA-AAATAACCATTGTAAGACC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGA-GATGAGT-GCTAGTGTAAGA-C
* ** * * * *
52495652 ATGTCTAAGACATGGCATCGGCCTCGATGAAGAT
62 GTGTCTGGGACAT-GCATCAGCCAC-ATTATGAT
*
52495686 AGCCAGTGTAAGACCTTGTCTGGGACATGGCATCG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
52495721 ACAACTTAAC
Statistics
Matches: 254, Mismatches: 50, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
88 3 0.01
90 2 0.01
91 33 0.13
92 12 0.05
93 20 0.08
94 98 0.39
95 18 0.07
96 2 0.01
97 10 0.04
98 46 0.18
99 6 0.02
100 2 0.01
102 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (93 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAGTGCTAGTGTAAGACGTGT
CTGGGACATGCATCAGCCACATTATGAT
Found at i:52495647 original size:49 final size:49
Alignment explanation
Indices: 52495592--52495720 Score: 204
Period size: 49 Copynumber: 2.6 Consensus size: 49
52495582 CACGAGAGCT
52495592 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAAAATAACC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAAAATAACC
* ** * *
52495641 ATTGTAAGACCATGTCTAAGACATGGCATCGGCCTCGATGAAGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAAAATAACC
*
52495690 AGTGTAAGACCTTGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
52495721 ACAACTTAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAAAATAACC
Found at i:52495647 original size:141 final size:141
Alignment explanation
Indices: 52495304--52495722 Score: 368
Period size: 141 Copynumber: 2.9 Consensus size: 141
52495294 TGGGTTATGT
* * ** * *
52495304 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GATGAGGGCTAGTGTAAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCCAATGTAAGA
* *
52495368 CGTGTCTGGGACATGCATCAGCCACATTATGATATCCAGTGTAAGACCATGTCTGGGACATGGCA
66 CGTGTCTGGGACATGCATCGGCAACATTATGATA--CAGTGTAAGACCATGTCTGGGACATGGCA
* *
52495433 TCGACGTAGAGAT
129 TCGACGTAGACAC
* * ** * *
52495446 GAGTGCCAGTGTAAGA-CGTGTCTGGGACAT-GCATTAGCCTCAATGATGGTAGCCAATGTAAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCCAATGTAAGA
* * *
52495509 CGTGTCTGGGACATGCATCGGCTAAGC-TTCGTGCTA-A-TGTAAGA-CATGTTTGGGACAT-GC
66 CGTGTCTGGGACATGCATCGGC-AA-CATT-ATGATACAGTGTAAGACCATGTCTGGGACATGGC
* *
52495569 ATCAGCACTTATACAC
128 ATC-G-ACGTAGACAC
* ** * *
52495585 GAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAAAATAACCATTGTAAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCCAATGTAAGA
* ** ** * * *
52495650 CCATGTCTAAGACATGGCATCGGCCTCGATGAAGATAGCCAGTGTAAGACCTTGTCTGGGACATG
66 -CGTGTCTGGGACAT-GCATCGGCAAC-ATTATGATA--CAGTGTAAGACCATGTCTGGGACATG
52495715 GCATCGAC
126 GCATCGAC
52495723 AACTTAACCC
Statistics
Matches: 216, Mismatches: 43, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
137 5 0.02
138 14 0.06
139 27 0.12
140 22 0.10
141 74 0.34
142 32 0.15
143 14 0.06
145 1 0.00
146 9 0.04
147 13 0.06
148 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (141 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGATGATAGCCAATGTAAGA
CGTGTCTGGGACATGCATCGGCAACATTATGATACAGTGTAAGACCATGTCTGGGACATGGCATC
GACGTAGACAC
Found at i:52502521 original size:39 final size:39
Alignment explanation
Indices: 52502467--52502682 Score: 267
Period size: 39 Copynumber: 5.5 Consensus size: 39
52502457 TGATATTTGA
* * * *
52502467 GAATTATATCTGGACTAAAAGTCCGCAGGCTATATGCGG
1 GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGCAG
*
52502506 GAATTACATCCGGACTTAAAGTCCGTAGGCTATATGC-G
1 GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGCAG
*
52502544 AGAATTATATCCGGACTTAAAGTCTGTAGGCTATATGCAAG
1 -GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGC-AG
* *
52502585 G-ATTATATCCGGACTTAAAGTCCGCAGGCTATGTGCAG
1 GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGCAG
* ** *
52502623 GAATTATATCCGGACTTAAGGTCCGTAGGCTACGTGCTGG
1 GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGC-AG
*
52502663 GAA-TATATCCGGGCTTAAAG
1 GAATTATATCCGGACTTAAAG
52502683 CCCCGAAGGC
Statistics
Matches: 157, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
38 4 0.03
39 147 0.94
40 5 0.03
41 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (39 bp):
GAATTATATCCGGACTTAAAGTCCGTAGGCTATATGCAG
Found at i:52502680 original size:117 final size:117
Alignment explanation
Indices: 52502469--52502682 Score: 322
Period size: 117 Copynumber: 1.8 Consensus size: 117
52502459 ATATTTGAGA
* *
52502469 ATTATATCTGGACTAAAAGTCCGCAGGCTATATGCGGGAATTACATCCGGACTTAAAGTCCGTAG
1 ATTATATCCGGACTAAAAGTCCGCAGGCTATATGCAGGAATTACATCCGGACTTAAAGTCCGTAG
*
52502534 GCTATATGCGAGAATTATATCCGGACTTAAAGTCTGTAGGCTATATGCAAGG
66 GCTACATGCGAGAATTATATCCGGACTTAAAGTCTGTAGGCTATATGCAAGG
* * * *
52502586 ATTATATCCGGACTTAAAGTCCGCAGGCTATGTGCAGGAATTATATCCGGACTTAAGGTCCGTAG
1 ATTATATCCGGACTAAAAGTCCGCAGGCTATATGCAGGAATTACATCCGGACTTAAAGTCCGTAG
* * *
52502651 GCTACGTGCTGGGAA-TATATCCGGGCTTAAAG
66 GCTACATGC-GAGAATTATATCCGGACTTAAAG
52502683 CCCCGAAGGC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 82 0.95
118 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (117 bp):
ATTATATCCGGACTAAAAGTCCGCAGGCTATATGCAGGAATTACATCCGGACTTAAAGTCCGTAG
GCTACATGCGAGAATTATATCCGGACTTAAAGTCTGTAGGCTATATGCAAGG
Found at i:52503935 original size:31 final size:31
Alignment explanation
Indices: 52503900--52503961 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
52503890 ATGAAAAGAG
52503900 ACATTTTGGAGTTTGTCTCTAAGTGTTTAGT
1 ACATTTTGGAGTTTGTCTCTAAGTGTTTAGT
52503931 ACATTTTGGAGTTTGTCTCTAAGTGTTTAGT
1 ACATTTTGGAGTTTGTCTCTAAGTGTTTAGT
52503962 GTGTCAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (31 bp):
ACATTTTGGAGTTTGTCTCTAAGTGTTTAGT
Found at i:52508683 original size:47 final size:46
Alignment explanation
Indices: 52508605--52508963 Score: 232
Period size: 47 Copynumber: 7.6 Consensus size: 46
52508595 TGGGTTATGT
52508605 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATT-AGAC
* * * * *
52508653 GAGGGCTAGTGTAAGA-CGTGCCTGGGACATGCATCAGCCACATT--AC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGCATC-G--GCATTAGAC
* * * *
52508699 GATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAAAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCAT-TAGAC
* * * * * *
52508747 GAGTGCCAGTGTAAGA-CGTGTCTGGGACATGCATCAGCCTCA-AT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTAGAC
* * * * *
52508791 GATGGTAGCCAGTGTAAGA-CGTGTCTAGGACATGCACCGGC-TAAGAT
1 GA--G-AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTAGAC
* * * * *
52508838 GAGTGCCAGTGTAAGA-CATGTCTGGGACATACGTCAGCACTTATAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCA-TTAGAC
* * * *
52508884 -ATGAGCACTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGTTGAA
1 GA-GAGC-C-AGTGTAAGACCATGTCTGGGACAT-GCATCGGCAT--TAGAC
*
52508935 GATAGCCAGTGTAAGACCATGTCTGGGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGAC
52508964 TTGGTATCGG
Statistics
Matches: 243, Mismatches: 46, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
44 32 0.13
45 5 0.02
46 37 0.15
47 75 0.31
48 43 0.18
49 39 0.16
50 6 0.02
51 5 0.02
52 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTAGAC
Found at i:52508722 original size:94 final size:93
Alignment explanation
Indices: 52508608--52508925 Score: 376
Period size: 94 Copynumber: 3.4 Consensus size: 93
52508598 GTTATGTGAG
* * * *
52508608 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTAAGATGAGTGCCAGTGTAAGACGTG
*
52508673 CCTGGGACATGCATCAGCCACATTACGAT
65 TCTGGGACATGCATCAGCCACATTACGAT
*
52508702 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAAAGATGAGTGCCAGTGTAAGACGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTAAGATGAGTGCCAGTGTAAGACGTG
* * * *
52508767 TCTGGGACATGCATCAGCCTCAATGATGGT
65 TCTGGGACATGCATCAGCCAC-ATTACGAT
* * * *
52508797 AGCCAGTGTAAGA-CGTGTCTAGGACAT-GCACCGGC-TAAGATGAGTGCCAGTGTAAGACATGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTAAGATGAGTGCCAGTGTAAGACGTGT
* * *
52508859 CTGGGACATACGTCAG-CACTTATAC-AT
66 CTGGGACATGCATCAGCCACAT-TACGAT
*
52508886 GAGCACTAGTGTAAGACCATGTTTGGGACATGGCATCGGC
1 -AGC-C-AGTGTAAGACCATGTCTGGGACATGGCATCGGC
52508926 CTCGTTGAAG
Statistics
Matches: 190, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
89 2 0.01
90 6 0.03
91 40 0.21
92 9 0.05
93 18 0.09
94 97 0.51
95 18 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (93 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTAAGATGAGTGCCAGTGTAAGACGTGT
CTGGGACATGCATCAGCCACATTACGAT
Found at i:52509836 original size:55 final size:53
Alignment explanation
Indices: 52509720--52509839 Score: 134
Period size: 55 Copynumber: 2.2 Consensus size: 53
52509710 ACTTAAACTT
* * * * *
52509720 TAAAGTCAGTATTGTCCACGGGTATGTCACACGGGCGTGTGCTGTAGCCGCGTC
1 TAAAGTCAGTATTGTCCACGAGTAGGCCACACGGGCATGTGCTG-AGCCGCGCC
*
52509774 TATAAGTCAGTATTGTCCACGAGTAGGCCACACGGGCATGTGTCATG-GCCGTGCCC
1 TA-AAGTCAGTATTGTCCACGAGTAGGCCACACGGGCATGTG-C-TGAGCCGCG-CC
52509830 TAAAGTCAGT
1 TAAAGTCAGT
52509840 GTTGCACACG
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
54 2 0.04
55 48 0.86
56 4 0.07
57 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (53 bp):
TAAAGTCAGTATTGTCCACGAGTAGGCCACACGGGCATGTGCTGAGCCGCGCC
Found at i:52511706 original size:12 final size:11
Alignment explanation
Indices: 52511687--52511716 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
52511677 TGTAAAAAAC
52511687 TTATTTTGTTA
1 TTATTTTGTTA
52511698 TTAATTTTGTTA
1 TT-ATTTTGTTA
52511710 TTATTTT
1 TTATTTT
52511717 AAAGGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:52517485 original size:42 final size:42
Alignment explanation
Indices: 52517438--52517518 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 42
52517428 AAATTATAAT
52517438 ATTATTTAACTATAT-AATCAATATAATTGTTTTGTCTTTAAA
1 ATTATTTAACTATATAAAT-AATATAATTGTTTTGTCTTTAAA
52517480 ATTATTTAACTATATAAATAATATAATTGTTTTGTCTTT
1 ATTATTTAACTATATAAATAATATAATTGTTTTGTCTTT
52517519 TCACTTAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (42 bp):
ATTATTTAACTATATAAATAATATAATTGTTTTGTCTTTAAA
Found at i:52517674 original size:40 final size:40
Alignment explanation
Indices: 52517619--52517699 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
52517609 TCAAAACGAC
52517619 ATAGTTTTGCCTTTTCTTATTTGAATTTTCGAATAACTCG
1 ATAGTTTTGCCTTTTCTTATTTGAATTTTCGAATAACTCG
*
52517659 ATAGTTTTGCCTTTTCTTATTTGGATTTTCGAATAACTCG
1 ATAGTTTTGCCTTTTCTTATTTGAATTTTCGAATAACTCG
52517699 A
1 A
52517700 ATTGTGTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.49
Consensus pattern (40 bp):
ATAGTTTTGCCTTTTCTTATTTGAATTTTCGAATAACTCG
Found at i:52518344 original size:22 final size:23
Alignment explanation
Indices: 52518314--52518356 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
52518304 ATCCTGGTTT
52518314 AATTAATAAAA-ATATATATTTTA
1 AATTAATAAAATATAT-TATTTTA
52518337 AATT-ATAAAATATATTATTT
1 AATTAATAAAATATATTATTT
52518357 AATACATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTAATAAAATATATTATTTTA
Found at i:52518690 original size:44 final size:44
Alignment explanation
Indices: 52518627--52518716 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
52518617 TTTTTATTGC
52518627 ATTTCTCTTCTTTTCTATCATCATTACAAGTAGTATACTCTTAT
1 ATTTCTCTTCTTTTCTATCATCATTACAAGTAGTATACTCTTAT
52518671 ATTTCTCTTCTTTTCTATCATCATTACAAGTAGTATACTCTTAT
1 ATTTCTCTTCTTTTCTATCATCATTACAAGTAGTATACTCTTAT
52518715 AT
1 AT
52518717 ACATATGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (44 bp):
ATTTCTCTTCTTTTCTATCATCATTACAAGTAGTATACTCTTAT
Found at i:52518800 original size:24 final size:24
Alignment explanation
Indices: 52518773--52518830 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
52518763 GGGGTTACAA
*
52518773 GAAGATGAAATGTG-AAGAGTTAAG
1 GAAGATGAAAGGTGAAAG-GTTAAG
*
52518797 GAAGATGGAAGGTGAAAGGTTAAG
1 GAAGATGAAAGGTGAAAGGTTAAG
*
52518821 AAAGATGAAA
1 GAAGATGAAA
52518831 AGTTGAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
GAAGATGAAAGGTGAAAGGTTAAG
Found at i:52528525 original size:16 final size:17
Alignment explanation
Indices: 52528504--52528538 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
52528494 TAATGTCTAG
52528504 GAAAATTA-TTAATTGA
1 GAAAATTAGTTAATTGA
52528520 GAAAATTAGTTTAATTGA
1 GAAAATTAG-TTAATTGA
52528538 G
1 G
52528539 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
GAAAATTAGTTAATTGA
Found at i:52542968 original size:126 final size:126
Alignment explanation
Indices: 52542743--52542994 Score: 504
Period size: 126 Copynumber: 2.0 Consensus size: 126
52542733 AAGTGATCAT
52542743 ATAATTTATTATATTTATTGCAAACATTCACTTTAAGGAATCTATAAGAAATAATTCAGAAAATA
1 ATAATTTATTATATTTATTGCAAACATTCACTTTAAGGAATCTATAAGAAATAATTCAGAAAATA
52542808 ATGTAAACTTATCTCATATTCTTTGCCAATAAGATCATAAGGTATTATCCGCTCCAAAGAA
66 ATGTAAACTTATCTCATATTCTTTGCCAATAAGATCATAAGGTATTATCCGCTCCAAAGAA
52542869 ATAATTTATTATATTTATTGCAAACATTCACTTTAAGGAATCTATAAGAAATAATTCAGAAAATA
1 ATAATTTATTATATTTATTGCAAACATTCACTTTAAGGAATCTATAAGAAATAATTCAGAAAATA
52542934 ATGTAAACTTATCTCATATTCTTTGCCAATAAGATCATAAGGTATTATCCGCTCCAAAGAA
66 ATGTAAACTTATCTCATATTCTTTGCCAATAAGATCATAAGGTATTATCCGCTCCAAAGAA
52542995 TGATTAATTA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (126 bp):
ATAATTTATTATATTTATTGCAAACATTCACTTTAAGGAATCTATAAGAAATAATTCAGAAAATA
ATGTAAACTTATCTCATATTCTTTGCCAATAAGATCATAAGGTATTATCCGCTCCAAAGAA
Found at i:52543519 original size:48 final size:49
Alignment explanation
Indices: 52543448--52543549 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 49
52543438 TTAGGGAACG
*
52543448 AAACTGATCTAATGTGA-ATTTTTTTTCATTATCATAATTTTCTTTCAA
1 AAACTGATCTAATGAGATATTTTTTTTCATTATCATAATTTTCTTTCAA
*
52543496 AAACTGATCTAATGAGATTTTTTTTTTCATTATCATAATTTTCTTTCAA
1 AAACTGATCTAATGAGATATTTTTTTTCATTATCATAATTTTCTTTCAA
52543545 AAACT
1 AAACT
52543550 AATTCATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 16 0.31
49 35 0.69
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (49 bp):
AAACTGATCTAATGAGATATTTTTTTTCATTATCATAATTTTCTTTCAA
Found at i:52546328 original size:19 final size:20
Alignment explanation
Indices: 52546291--52546328 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52546281 AAGGTATACC
*
52546291 AATTTTTAACAGTAGAAATA
1 AATTTTTAACAGTAAAAATA
52546311 AATTTTTAACAG-AAAAAT
1 AATTTTTAACAGTAAAAAT
52546329 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (20 bp):
AATTTTTAACAGTAAAAATA
Found at i:52546972 original size:3 final size:3
Alignment explanation
Indices: 52546964--52546999 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
52546954 AGGATGTCGC
* *
52546964 GGT GGT GGT GGT GGT GGT GGT GGT TGT GCT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
52547000 TGTAGGGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.61, T:0.36
Consensus pattern (3 bp):
GGT
Found at i:52551292 original size:24 final size:24
Alignment explanation
Indices: 52551263--52551311 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
52551253 GTAGACTAAG
*
52551263 TAGATATACTCATAAACTAAGCAA
1 TAGATATACTCATAAACCAAGCAA
*
52551287 TAGATATACTCATAATCCAAGCAA
1 TAGATATACTCATAAACCAAGCAA
52551311 T
1 T
52551312 GAGCATACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (24 bp):
TAGATATACTCATAAACCAAGCAA
Found at i:52551319 original size:24 final size:24
Alignment explanation
Indices: 52551263--52551319 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
52551253 GTAGACTAAG
* *
52551263 TAGATATACTCATAAACTAAGCAA
1 TAGACATACTCATAAACCAAGCAA
* *
52551287 TAGATATACTCATAATCCAAGCAA
1 TAGACATACTCATAAACCAAGCAA
52551311 T-GAGCATAC
1 TAGA-CATAC
52551320 CTTAAAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.25
Consensus pattern (24 bp):
TAGACATACTCATAAACCAAGCAA
Found at i:52554379 original size:5 final size:5
Alignment explanation
Indices: 52554357--52554415 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
52554347 AAAATTAGCC
* * *
52554357 TAAAC TAAAT TAATA TAAAA TAAAAA TAAAAA TAAAA -AATAA -AAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA T-AAAA TAAAA TAA-AA TAAAA
52554403 TAAAA TAAAA TAA
1 TAAAA TAAAA TAA
52554416 GATTCTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 32 0.68
6 11 0.23
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:52554384 original size:6 final size:6
Alignment explanation
Indices: 52554368--52554412 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
52554358 AAACTAAATT
52554368 AATATAA AATAAA AATAAA AATAAAA AATAAA AA-ATAA AATAAA A
1 AATA-AA AATAAA AATAAA AAT-AAA AATAAA AATA-AA AATAAA A
52554413 TAAGATTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 23 0.66
7 11 0.31
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:52554388 original size:7 final size:7
Alignment explanation
Indices: 52554368--52554407 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
52554358 AAACTAAATT
*
52554368 AATATAA
1 AATAAAA
52554375 AAT-AAA
1 AATAAAA
52554381 AAT-AAA
1 AATAAAA
52554387 AATAAAA
1 AATAAAA
52554394 AATAAAA
1 AATAAAA
52554401 AATAAAA
1 AATAAAA
52554408 TAAAATAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AATAAAA
Found at i:52554395 original size:19 final size:19
Alignment explanation
Indices: 52554368--52554412 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
52554358 AAACTAAATT
*
52554368 AATATAAAAT-AAAAATAAA
1 AATAAAAAATAAAAAAT-AA
52554387 AATAAAAAATAAAAAATAA
1 AATAAAAAATAAAAAATAA
52554406 AATAAAA
1 AATAAAA
52554413 TAAGATTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (19 bp):
AATAAAAAATAAAAAATAA
Found at i:52555768 original size:21 final size:22
Alignment explanation
Indices: 52555725--52555769 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52555715 GACGAAATAC
*
52555725 ATGAGATTTATTTGTTTATAAT
1 ATGAGATTTATTTATTTATAAT
52555747 ATGAG-TTTAATTTATTTA-AAT
1 ATGAGATTT-ATTTATTTATAAT
52555768 AT
1 AT
52555770 TGTGATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
ATGAGATTTATTTATTTATAAT
Found at i:52556645 original size:87 final size:86
Alignment explanation
Indices: 52556491--52556653 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 86
52556481 TGTGTAAGGA
* * *
52556491 TGAGTTTTTACTCTTAATGAATTTATAGCCTAGAAATTGGGTGGTCTTATTGAGACGTACTTAAT
1 TGAGTTTTTACTCTTAATGAATTCATAGCCTAGAAATTGGGTGGTCCTATTGAGAAGTACTTAAT
52556556 GAATTCACCGACTTGAGAGGT
66 GAATTCACCGACTTGAGAGGT
* * * * *
52556577 TGAGTTTATTACTCTTAATGAGTTCATATCCTAGAATTTGGGTGTTCCTATTGAGATAG-ACTTG
1 TGAGTTT-TTACTCTTAATGAATTCATAGCCTAGAAATTGGGTGGTCCTATTGAGA-AGTACTTA
52556641 ATGAATTCACCGA
64 ATGAATTCACCGA
52556654 ACTTAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 7 0.10
87 59 0.88
88 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (86 bp):
TGAGTTTTTACTCTTAATGAATTCATAGCCTAGAAATTGGGTGGTCCTATTGAGAAGTACTTAAT
GAATTCACCGACTTGAGAGGT
Found at i:52558168 original size:12 final size:12
Alignment explanation
Indices: 52558151--52558190 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
52558141 GATTTGCACA
*
52558151 CTATTCCAACAT
1 CTATTCCAATAT
*
52558163 CTATTCCAATGT
1 CTATTCCAATAT
*
52558175 CTATCCCAATAT
1 CTATTCCAATAT
52558187 CTAT
1 CTAT
52558191 GCATGCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (12 bp):
CTATTCCAATAT
Found at i:52565031 original size:21 final size:20
Alignment explanation
Indices: 52564994--52565035 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
52564984 TACTCAAGGA
*
52564994 AAGCCGATTGATCCATCTAAG
1 AAGCCGATTCATCCATC-AAG
52565015 AAGCCGAATTCAT-CATCAAG
1 AAGCCG-ATTCATCCATCAAG
52565035 A
1 A
52565036 CTGAAGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAGCCGATTCATCCATCAAG
Found at i:52587190 original size:30 final size:30
Alignment explanation
Indices: 52587156--52587215 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52587146 ATTTAATATG
52587156 AACTTTGGAAAAATTACACTTTTACCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
* * * *
52587186 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
52587216 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTACCCCTA
Found at i:52601589 original size:93 final size:93
Alignment explanation
Indices: 52601457--52601627 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
52601447 GCCCCTAAGT
* *
52601457 GAACTCGGACTCAACTCAATGAGCTCGAGCGTTCACATCCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCATTCACATCCATAAGTGAACTCGAACTCAACTCAA
52601522 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * *
52601550 GAACTCGGACTCAACTCAACGAGTTC-AGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CATTCACATCCATAAGTGAACTCGAACTCAACTCA
52601614 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
52601628 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCATTCACATCCATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:52601613 original size:46 final size:46
Alignment explanation
Indices: 52601452--52601621 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
52601442 AACCCGCCCC
* * *
52601452 TAAGTGAACTCGGACTCAACTCAATGAGCTC-GAGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGA-CATTCACATCCA
* * *
52601498 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-A-TTCACATCCA
* * *
52601546 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCACATCCA
52601591 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
52601622 GGATGCTCAA
Statistics
Matches: 100, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 3 0.03
46 54 0.54
47 25 0.25
48 2 0.02
49 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCACATCCA
Found at i:52604665 original size:18 final size:18
Alignment explanation
Indices: 52604642--52604690 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
52604632 ATGATGTGCC
52604642 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
52604660 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
*
52604678 AAACCATTTTCAT
1 AAACTATTTTCAT
52604691 ACTTACCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:52607766 original size:47 final size:48
Alignment explanation
Indices: 52607695--52607868 Score: 164
Period size: 48 Copynumber: 3.7 Consensus size: 48
52607685 ATGGATGTGT
52607695 GCTAGTGTAAGACATGTCTGGGACAT-ACATCGGCCACATTATG-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGACATCGGCCACATTATGAAGA
* *
52607741 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G--ACATTAAGACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGACATCGGCCACATTATG--AAGA
* * * * * *
52607789 GCTAGTGTAAGACATGTCTGGGGCATG-CATTGACCTCGAGATATGCA-A
1 GCTAGTGTAAGACATGTCTGGGACATGACATCGGCCAC-A-TTATGAAGA
* *
52607837 GCTAGTGTAAGACCTGTCTAGGACATGACATC
1 GCTAGTGTAAGACATGTCTGGGACATGACATC
52607869 AGCTTCACAT
Statistics
Matches: 104, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
45 7 0.07
46 15 0.14
47 29 0.28
48 44 0.42
49 5 0.05
50 1 0.01
51 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGACATCGGCCACATTATGAAGA
Found at i:52607794 original size:48 final size:45
Alignment explanation
Indices: 52607695--52607810 Score: 146
Period size: 47 Copynumber: 2.5 Consensus size: 45
52607685 ATGGATGTGT
*
52607695 GCTAGTGTAAGACATGTCTGGGACATACATCGGCCACATTATG--AGA
1 GCTAGTGTAAGACATGTCTGGGACATACATC-G--ACATTAAGAAAGA
*
52607741 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGACAAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-ACATCGACATTAAGA-AAGA
52607789 GCTAGTGTAAGACATGTCTGGG
1 GCTAGTGTAAGACATGTCTGGG
52607811 GCATGCATTG
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
45 7 0.11
46 12 0.19
47 25 0.40
48 19 0.30
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.23
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATACATCGACATTAAGAAAGA
Found at i:52607941 original size:49 final size:48
Alignment explanation
Indices: 52607698--52608059 Score: 228
Period size: 49 Copynumber: 7.6 Consensus size: 48
52607688 GATGTGTGCT
* * * * *
52607698 AGTGTAAGACATGTCTGGGACAT-ACATCGGCCA-C-ATTATGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GACATCGATGATGAGAGCC
* * ** *
52607744 AGTGTAAGACCATGTCTGGGACATGGCATCGACAT-TAAGACAAGAGCT
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGACATCGATGATGAGAGCC
* * * * *
52607792 AGTGTAAGACATGTCTGGGGCAT-GCATTGACCTCGA-GAT-ATGCAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATGATGA-G--AGCC
* * * * ***
52607840 AGTGTAAGACCTGTCTAGGACATGACATC-AGCTTC-A-CAT--GTTTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGA-CATCGATGATGAGAGCC
*
52607884 AGTGTAAGACCTATCTGGGACATGGCATCGACATCGATGGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGAT-GATGAGAGCC
* * * * * * *
52607933 AATGTAAGAGCTGTCTGGGACATGGCATCGGCGTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGAT-GATGAGAGCC
* * * *
52607982 AGTGTAAGACCTGTCTGGGACATGGCATTGACTTAGATG-TGTGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATGATGAGAGCC
* *
52608029 AGTGTAAGACCATGTTTGGAACATGGCATCG
1 AGTGTAAGACC-TGTCTGGGACATGGCATCG
52608060 GCATTGTACC
Statistics
Matches: 245, Mismatches: 54, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
44 29 0.12
45 3 0.01
46 22 0.09
47 45 0.18
48 66 0.27
49 80 0.33
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATGATGAGAGCC
Found at i:52607975 original size:142 final size:140
Alignment explanation
Indices: 52607744--52608005 Score: 332
Period size: 142 Copynumber: 1.9 Consensus size: 140
52607734 TATGAGAGCT
* * * *
52607744 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGACAAGAGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACCATATCTGGGACATGGCATCGACATGAAGACAAGAGCCAATGTAAGACATGTCTG
* * *
52607809 GGGCATGCATTGACCTCGAGATATGCAAG-CTAGTGTAAGACCTGTCTAGGACATGACATCAGCT
66 GGACATGCATCGACCTCGAGATATGAAAGTC-AGTGTAAGACCTGTCTAGGACATGACATCAGCT
52607873 TCACATGTTTC
130 TCACATGTTTC
* **
52607884 AGTGTAAGACC-TATCTGGGACATGGCATCGACATCGATGGATGAGAGCCAATGTAAGAGC-TGT
1 AGTGTAAGACCATATCTGGGACATGGCATCGACAT-GA-AGACAAGAGCCAATGTAAGA-CATGT
* * * *
52607947 CTGGGACATGGCATCGGCGTCGATATATGAAAGTCAGTGTAAGACCTGTCTGGGACATG
63 CTGGGACAT-GCATCGACCTCGAGATATGAAAGTCAGTGTAAGACCTGTCTAGGACATG
52608006 GCATTGACTT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
139 22 0.21
140 12 0.12
141 26 0.25
142 42 0.41
143 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACCATATCTGGGACATGGCATCGACATGAAGACAAGAGCCAATGTAAGACATGTCTG
GGACATGCATCGACCTCGAGATATGAAAGTCAGTGTAAGACCTGTCTAGGACATGACATCAGCTT
CACATGTTTC
Done.