Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 178 of 230
Found at i:53290487 original size:35 final size:35
Alignment explanation
Indices: 53290436--53290512 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
53290426 AATTTCTATG
* *
53290436 TTTCAAAAATTTTCGTGTTTTCA-AAATTTTCGTGT
1 TTTCAAAAATTCTCGTG-TTTCACAAATTCTCGTGT
*
53290471 TTTCAACAATTCTCGTGTTTCACAAATTCTCGTGT
1 TTTCAAAAATTCTCGTGTTTCACAAATTCTCGTGT
53290506 TTT-AAAA
1 TTTCAAAA
53290513 TTTTTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (35 bp):
TTTCAAAAATTCTCGTGTTTCACAAATTCTCGTGT
Found at i:53290504 original size:52 final size:53
Alignment explanation
Indices: 53290406--53290516 Score: 147
Period size: 52 Copynumber: 2.1 Consensus size: 53
53290396 AAAAATTTCT
*
53290406 AATTTTCGTGTTTTTCTAAAAATTTCTATGTTTCAAAAATTTTCGTGTTTTCAA
1 AATTTTCGTGTTTTTCTAAAAATTTCTATGTTTCAAAAATTCTCGTGTTTT-AA
* * *
53290460 AATTTTCGTG-TTTTC-AACAA-TTCTCGTGTTTCACAAATTCTCGTGTTTTAA
1 AATTTTCGTGTTTTTCTAAAAATTTCT-ATGTTTCAAAAATTCTCGTGTTTTAA
53290511 AATTTT
1 AATTTT
53290517 TTATGTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
51 12 0.23
52 25 0.48
53 5 0.10
54 10 0.19
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (53 bp):
AATTTTCGTGTTTTTCTAAAAATTTCTATGTTTCAAAAATTCTCGTGTTTTAA
Found at i:53290534 original size:22 final size:23
Alignment explanation
Indices: 53290509--53290562 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
53290499 CTCGTGTTTT
* *
53290509 AAAATTTTTTATG-TTTTAAAAA
1 AAAATTTGTCATGTTTTTAAAAA
* *
53290531 AAAATTTGTCGTGTTTTTTAAAA
1 AAAATTTGTCATGTTTTTAAAAA
53290554 AAAATTTGT
1 AAAATTTGT
53290563 GTTTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (23 bp):
AAAATTTGTCATGTTTTTAAAAA
Found at i:53290577 original size:110 final size:112
Alignment explanation
Indices: 53290440--53290639 Score: 275
Period size: 110 Copynumber: 1.8 Consensus size: 112
53290430 TCTATGTTTC
* *
53290440 AAAAATTTTCGTGTTTTCAAAATTTTCGTGTTTTCAACAATTCTCGTG-TTTCACA-AATTCTCG
1 AAAAAATTTCGTGTTTTCAAAATTTTCGTATTTTCAA-AATTCTCGTGTTTTCA-ATAATTCTCG
*
53290503 TGTTTTA-AAATTTTTTATGTTTTAAAAAAAAATTTGTCGTGTTTTTTAA
64 TGTTTCACAAA-TTTTTATGTTTTAAAAAAAAATTTGTCGTGTTTTTTAA
* * *
53290552 AAAAAATTT-GTGTTTT-TAAATTTTCGTATTTTCAAATTTTTCGTGTTTTCAATAATTCTCGTG
1 AAAAAATTTCGTGTTTTCAAAATTTTCGTATTTTCAAAATTCTCGTGTTTTCAATAATTCTCGTG
*
53290615 TTTCACAAATTTTTGTGTTTTAAAA
66 TTTCACAAATTTTTATGTTTTAAAA
53290640 TTTTTTATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
109 9 0.12
110 51 0.65
111 10 0.13
112 8 0.10
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (112 bp):
AAAAAATTTCGTGTTTTCAAAATTTTCGTATTTTCAAAATTCTCGTGTTTTCAATAATTCTCGTG
TTTCACAAATTTTTATGTTTTAAAAAAAAATTTGTCGTGTTTTTTAA
Found at i:53290681 original size:127 final size:126
Alignment explanation
Indices: 53290442--53290681 Score: 349
Period size: 127 Copynumber: 1.9 Consensus size: 126
53290432 TATGTTTCAA
*
53290442 AAATTTTCGTGTTTTCAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTCACAAATTCTCGTGTT
1 AAATTTTCGTATTTTCAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTCACAAATTCTCGTGTT
*
53290507 TTAAAATTTTTTATGTTTTAAAAAAAAATTTGTCGTGTTTTTTAAAAAAAATTTGTGTTTTT
66 TTAAAATTTTTTATGTTTTAAAAAAAAATTTGTCGTG-TTTTCAAAAAAAATTTGTGTTTTT
* * * *
53290569 AAATTTTCGTATTTTCAAATTTTTCGTGTTTTCAATAATTCTCGTGTTTCACAAATTTTTGTGTT
1 AAATTTTCGTATTTTCAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTCACAAATTCTCGTGTT
* * *
53290634 TTAAAATTTTTTATATATTTTTTAAAAAAGA-TTGTCGTG-TTTCAAAAA
66 TTAAAA-TTTTT-TAT-GTTTTAAAAAAAAATTTGTCGTGTTTTCAAAAA
53290682 TTTTCATGTT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
127 74 0.73
128 5 0.05
129 11 0.11
130 11 0.11
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (126 bp):
AAATTTTCGTATTTTCAAAATTTTCGTGTTTTCAACAATTCTCGTGTTTCACAAATTCTCGTGTT
TTAAAATTTTTTATGTTTTAAAAAAAAATTTGTCGTGTTTTCAAAAAAAATTTGTGTTTTT
Found at i:53290735 original size:18 final size:18
Alignment explanation
Indices: 53290712--53290752 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
53290702 CGCGTTAAAA
*
53290712 AAAAATCTTCGTGTTTTC
1 AAAAATCCTCGTGTTTTC
*
53290730 AAAAATCCTCGTGTTTTT
1 AAAAATCCTCGTGTTTTC
53290748 AAAAA
1 AAAAA
53290753 AATTTCCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (18 bp):
AAAAATCCTCGTGTTTTC
Found at i:53303130 original size:141 final size:143
Alignment explanation
Indices: 53302638--53303646 Score: 1739
Period size: 141 Copynumber: 7.1 Consensus size: 143
53302628 TGAGCCTTTT
* * * *
53302638 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGGACACGCTG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACACGTTG
* * * *
53302703 AGGTAATTTTAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG
63 AGGTAATTTCAATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
*
53302768 GACACGCTGAGGTAATTTC
126 GACACGTTGAGGT-ATTTC
*
53302787 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG-TGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
53302851 TATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
66 TAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA
53302916 CGTTGAGGTATTTC
130 CGTTGAGGTATTTC
53302930 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53302995 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
53303059 GTTGAGGTATTTC
131 GTTGAGGTATTTC
53303072 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303136 TAATTTCAATTTCTGTTTTC-AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
53303200 GTTGAGGTATTTC
131 GTTGAGGTATTTC
53303213 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303277 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
53303342 GTTGAGGTATTTC
131 GTTGAGGTATTTC
53303355 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303420 T-ATTTCAATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
66 TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
53303483 GTTGAGGTATTTC
131 GTTGAGGTATTTC
*
53303496 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
* *
53303561 T-ATTTCAATTTCTGCTTTTCAAAACTT-AACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGC
66 TAATTTCAATTTCTG-TTTTCAAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
*
53303624 ACGCTGAGGTATTTC
129 ACGTTGAGGTATTTC
53303639 AATTTCTG
1 AATTTCTG
53303647 CTTTACTAAT
Statistics
Matches: 838, Mismatches: 14, Indels: 22
0.96 0.02 0.03
Matches are distributed among these distances:
140 37 0.04
141 319 0.38
142 105 0.13
143 227 0.27
144 71 0.08
145 20 0.02
146 9 0.01
148 42 0.05
149 8 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (143 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
GTTGAGGTATTTC
Found at i:53303650 original size:72 final size:71
Alignment explanation
Indices: 53302638--53303646 Score: 1717
Period size: 71 Copynumber: 14.1 Consensus size: 71
53302628 TGAGCCTTTT
* * * *
53302638 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGGACACGCTG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA--AGACACGTTG
*
53302703 AGGTAATTTT
63 AGGT-ATTTC
* * * *
53302713 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
53302778 GGTAATTTC
64 GGT-ATTTC
*
53302787 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG-TGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53302851 TATTTTC
66 TA-TTTC
53302858 AATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
53302923 GTATTTC
65 GTATTTC
53302930 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53302995 TAATTTC
66 T-ATTTC
53303002 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303066 TATTTC
66 TATTTC
53303072 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303136 TAATTTC
66 T-ATTTC
53303143 AATTTCTGTTTTC-AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303207 TATTTC
66 TATTTC
53303213 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303277 TAATTTC
66 T-ATTTC
53303284 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303349 TATTTC
66 TATTTC
53303355 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303420 TATTTC
66 TATTTC
53303426 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303490 TATTTC
66 TATTTC
*
53303496 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
53303561 TATTTC
66 TATTTC
* * *
53303567 AATTTCTGCTTTTCAAAACTT-AACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACGCTGA
1 AATTTCTG-TTTTCAAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
53303631 GGTATTTC
64 GGTATTTC
53303639 AATTTCTG
1 AATTTCTG
53303647 CTTTACTAAT
Statistics
Matches: 908, Mismatches: 11, Indels: 33
0.95 0.01 0.03
Matches are distributed among these distances:
69 46 0.05
70 163 0.18
71 321 0.35
72 288 0.32
73 11 0.01
74 31 0.03
75 10 0.01
76 38 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (71 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TATTTC
Found at i:53303711 original size:84 final size:87
Alignment explanation
Indices: 53303570--53303736 Score: 209
Period size: 84 Copynumber: 2.0 Consensus size: 87
53303560 GTATTTCAAT
* * * *
53303570 TTCTGCTTTTCAAAACTTAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACGCTGAGGT-
1 TTCTACTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTC
*
53303634 ATTTCAATTTCTGCTTTACTAA
66 ATTTCAAATTCTGCTTTACTAA
*
53303656 TTCTACTTTTC-AAA-TCAACTCATATTGCAAGAG-TGAGTTGAGTCTC-AGCCACACGCTGAGG
1 TTCTACTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAG--ACACGCTGAGG
* *
53303717 TCTTTTCAAATTCTGTTTTA
64 TCATTTCAAATTCTGCTTTA
53303737 ATTTCTGTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
82 2 0.03
83 12 0.17
84 28 0.40
85 18 0.26
86 10 0.14
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (87 bp):
TTCTACTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTC
ATTTCAAATTCTGCTTTACTAA
Found at i:53303882 original size:49 final size:49
Alignment explanation
Indices: 53303769--53303962 Score: 253
Period size: 49 Copynumber: 3.8 Consensus size: 49
53303759 TTCAAAAAAA
*
53303769 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC--TT--TTTCTATTTTTC
*
53303822 AAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTATTTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTATTTTTC
* *
53303871 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCTGTTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTC----TAT-TTTTC
*
53303925 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
53303963 GGCTCACGTG
Statistics
Matches: 129, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
49 51 0.40
51 2 0.02
53 35 0.27
54 5 0.04
55 36 0.28
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (49 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTCTATTTTTC
Found at i:53303894 original size:102 final size:103
Alignment explanation
Indices: 53303769--53303962 Score: 311
Period size: 104 Copynumber: 1.9 Consensus size: 103
53303759 TTCAAAAAAA
* *
53303769 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTT-AATTTCTATTTTTC-AAAACCAACT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTCAAATTCT-GTTTTCAAAAACCAACT
*
53303832 CATATTGCGAGAGGTGAGTTGAGCCTTTTTCTATTTTTC
65 CATATTGCGAGAAGTGAGTTGAGCCTTTTTCTATTTTTC
* *
53303871 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCTGTTTTCAAAAATCAACT
1 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTT-CAAATTCTGTTTTCAAAAACCAACT
53303936 CATATTGCGAGAAGTGAGTTGAGCCTT
65 CATATTGCGAGAAGTGAGTTGAGCCTT
53303963 GGCTCACGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
102 38 0.45
103 5 0.06
104 41 0.49
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (103 bp):
AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTTTCAAATTCTGTTTTCAAAAACCAACTC
ATATTGCGAGAAGTGAGTTGAGCCTTTTTCTATTTTTC
Found at i:53304235 original size:20 final size:21
Alignment explanation
Indices: 53304203--53304242 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
53304193 TTTAATTTTC
53304203 AAATTTCAAAAAAAAAAAATA
1 AAATTTCAAAAAAAAAAAATA
*
53304224 AAATTT-AAAAAATAAAAAT
1 AAATTTCAAAAAAAAAAAAT
53304243 TGCATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATTTCAAAAAAAAAAAATA
Found at i:53304302 original size:30 final size:29
Alignment explanation
Indices: 53304239--53304355 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 29
53304229 TAAAAAATAA
* *
53304239 AAATTGCATTTTGACACCTAAACTTT-TCCT
1 AAATTTCATTTTGAC-CCTAAACTTTCT-TT
53304269 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCTTT
* * *
53304299 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCTTT
* * *
53304329 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTGACCCTAAACTTTCT
53304356 AAAAATTACA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 57 0.78
31 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCTTT
Found at i:53304588 original size:20 final size:19
Alignment explanation
Indices: 53304566--53304622 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
53304556 AAAAAAATAA
53304566 AAAAAGAGAAAAGAAGAGG
1 AAAAAGAGAAAAGAAGAGG
*
53304585 AAAAGGAGAGAAAG-AGAGG
1 AAAAAGAGA-AAAGAAGAGG
* *
53304604 AGAAAG-GAGAAGAAGAGG
1 AAAAAGAGAAAAGAAGAGG
53304622 A
1 A
53304623 GAGCCTCCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 8 0.25
19 17 0.53
20 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (19 bp):
AAAAAGAGAAAAGAAGAGG
Found at i:53304664 original size:18 final size:17
Alignment explanation
Indices: 53304641--53304683 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
53304631 GACAGCGGCT
53304641 CGACGGCGAAGACGACGG
1 CGACGGCGAAG-CGACGG
*
53304659 CGACGGCACAAGCGACGG
1 CGACGGC-GAAGCGACGG
53304677 CG-CGGCG
1 CGACGGCG
53304684 CGACGGCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.18
18 15 0.68
19 3 0.14
ACGTcount: A:0.23, C:0.33, G:0.44, T:0.00
Consensus pattern (17 bp):
CGACGGCGAAGCGACGG
Found at i:53304709 original size:3 final size:3
Alignment explanation
Indices: 53304701--53304765 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
53304691 TAGGGCTCGT
* *
53304701 GAA GAA GAA GAA -AA GAA GAA GAA GAA GAA GAA GGA GAA GAA -AA AAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
53304747 GAA -AA GAA AAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA
53304766 AAGGAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 8 0.15
3 45 0.85
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53304718 original size:11 final size:11
Alignment explanation
Indices: 53304702--53304768 Score: 70
Period size: 11 Copynumber: 6.3 Consensus size: 11
53304692 AGGGCTCGTG
53304702 AAGAAGAAGAA
1 AAGAAGAAGAA
53304713 AAGAAGAAG--
1 AAGAAGAAGAA
53304722 AAGAAGAAGAA
1 AAGAAGAAGAA
* *
53304733 GGAGAAGAAAAA
1 -AAGAAGAAGAA
53304745 AAGAA-AAGAAA
1 AAGAAGAAG-AA
53304756 AAGAA-AAGAA
1 AAGAAGAAGAA
53304766 AAG
1 AAG
53304769 GAAAAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
9 9 0.19
10 7 0.15
11 23 0.48
12 9 0.19
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAAGAAGAA
Found at i:53304772 original size:6 final size:5
Alignment explanation
Indices: 53304702--53304773 Score: 58
Period size: 6 Copynumber: 13.4 Consensus size: 5
53304692 AGGGCTCGTG
*
53304702 AAGAA GAAGAA AAGAA GAAGAA GAAGAA GAAGGAG AAG-A AA-AA AAGAA
1 AAGAA -AAGAA AAGAA -AAGAA -AAGAA -AA-GAA AAGAA AAGAA AAGAA
53304750 AAGAAA AAGAA AAGAA AAGGAA AA
1 AAG-AA AAGAA AAGAA AA-GAA AA
53304774 AAATAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
4 5 0.09
5 20 0.34
6 31 0.53
7 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:53304841 original size:18 final size:18
Alignment explanation
Indices: 53304818--53304860 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
53304808 TCGGTCAAAC
53304818 CGACCCGATCCGGCGACA
1 CGACCCGATCCGGCGACA
* *
53304836 CGACCCGATCCGGTGACC
1 CGACCCGATCCGGCGACA
53304854 CGACCCG
1 CGACCCG
53304861 CAACCCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.47, G:0.28, T:0.07
Consensus pattern (18 bp):
CGACCCGATCCGGCGACA
Found at i:53336460 original size:25 final size:26
Alignment explanation
Indices: 53336425--53336480 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 26
53336415 AATCTATTTC
53336425 TTTTTATATAAAGTTTTAATAAATAA
1 TTTTTATATAAAGTTTTAATAAATAA
53336451 TTTTT-TATAAAGTTTTAATAAATAA
1 TTTTTATATAAAGTTTTAATAAATAA
53336476 TTTTT
1 TTTTT
53336481 GCTAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTTTATATAAAGTTTTAATAAATAA
Found at i:53340933 original size:33 final size:33
Alignment explanation
Indices: 53340894--53340964 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
53340884 AGAAGAAGTT
*
53340894 AGGGTTTTAATTGATTTAGAAAAAGTCTTTGGA
1 AGGGTTTTAATTGATTTAGAAAAAGTCTTCGGA
* * *
53340927 AGGGTTTTGATTGATTTAGCAAAAGTGTTCGGA
1 AGGGTTTTAATTGATTTAGAAAAAGTCTTCGGA
53340960 AGGGT
1 AGGGT
53340965 GACTGAGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (33 bp):
AGGGTTTTAATTGATTTAGAAAAAGTCTTCGGA
Found at i:53343678 original size:15 final size:15
Alignment explanation
Indices: 53343643--53343671 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53343633 AAAAAATTGA
53343643 AAAAATAAAGTGAAC
1 AAAAATAAAGTGAAC
53343658 AAAAATAAAGTGAA
1 AAAAATAAAGTGAA
53343672 AGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAAATAAAGTGAAC
Found at i:53346495 original size:18 final size:19
Alignment explanation
Indices: 53346445--53346497 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
53346435 AAAATTTCAC
53346445 AAAAAATATAAACATTATTT
1 AAAAAATATAAA-ATTATTT
* *
53346465 TAAAAAT-TTAAATTA-TT
1 AAAAAATATAAAATTATTT
53346482 AAAAAATATAAAATTA
1 AAAAAATATAAAATTA
53346498 AAATAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 8 0.29
18 11 0.39
19 3 0.11
20 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAAATATAAAATTATTT
Found at i:53346512 original size:37 final size:35
Alignment explanation
Indices: 53346445--53346525 Score: 83
Period size: 37 Copynumber: 2.3 Consensus size: 35
53346435 AAAATTTCAC
*** *
53346445 AAAAAATATAAACATTATTTTAAAAATTTAAATTATT
1 AAAAAATATAAACATTAAAATAAAAATTT-AATT-TA
*
53346482 AAAAAATATAAA-ATTAAAATAAATATTTTAATTTA
1 AAAAAATATAAACATTAAAATAAA-AATTTAATTTA
53346517 AAAAAATAT
1 AAAAAATAT
53346526 TTAATTGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 10 0.26
36 12 0.32
37 16 0.42
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (35 bp):
AAAAAATATAAACATTAAAATAAAAATTTAATTTA
Found at i:53346530 original size:17 final size:17
Alignment explanation
Indices: 53346482--53346531 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
53346472 TTAAATTATT
* *
53346482 AAAAAATA-TAAAATTA
1 AAAAAATATTTAATTTA
53346498 AAATAAATATTTTAATTTA
1 AAA-AAATA-TTTAATTTA
53346517 AAAAAATATTTAATT
1 AAAAAATATTTAATT
53346532 GCTAACGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
18 5 0.17
19 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAAATATTTAATTTA
Found at i:53354899 original size:22 final size:22
Alignment explanation
Indices: 53354859--53354900 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53354849 TTCATATTAT
* * *
53354859 TATATATATTTTTACTTATTCC
1 TATATATATATATAATTATTCC
53354881 TATATATATATATAATTATT
1 TATATATATATATAATTATT
53354901 TTCTTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATATATATAATTATTCC
Found at i:53361657 original size:43 final size:43
Alignment explanation
Indices: 53361585--53361724 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
53361575 TATCCCAAAT
* ** * *
53361585 ATGGTCTTACACATAATCTTGTATTGATGCCAATAGCCCAGCC
1 ATGGTCTTACACAAAATCTCATATCGATGCCAATAGCCCAGAC
* *
53361628 ATGGTCTTACACAAAATCACATATCGATGCCAAT-GTCCTAGAC
1 ATGGTCTTACACAAAATCTCATATCGATGCCAATAG-CCCAGAC
* * * *
53361671 ATGGTCTTACACGAAGTCTCATATCGATGCC-ATATCCCAGAT
1 ATGGTCTTACACAAAATCTCATATCGATGCCAATAGCCCAGAC
53361713 ATGGTCTTACAC
1 ATGGTCTTACAC
53361725 GTAATCTCGG
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 20 0.24
43 62 0.76
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACACAAAATCTCATATCGATGCCAATAGCCCAGAC
Found at i:53377950 original size:14 final size:14
Alignment explanation
Indices: 53377931--53377958 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53377921 CCAATTTATT
53377931 AATGAATTATTAAA
1 AATGAATTATTAAA
53377945 AATGAATTATTAAA
1 AATGAATTATTAAA
53377959 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:53384793 original size:27 final size:27
Alignment explanation
Indices: 53384265--53384783 Score: 616
Period size: 27 Copynumber: 19.2 Consensus size: 27
53384255 GTAATGGGCT
*
53384265 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
** * *
53384292 TAAAATGACCAAAATGCCATCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
53384319 TAAAATGACCT-ATATACCCTCGAAGGG
1 TAAAATGA-CTGAAATACCCTCGAAGGG
*
53384346 TAAAATGACTGAAATACCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
53384373 TAAAATGACTGAAATACCTTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
53384400 TAAAATGACTAAAATACCATCGAAGCG
1 TAAAATGACTGAAATACCCTCGAAGGG
* *
53384427 TAAAATGACCGAAATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
53384454 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * * *
53384481 TAAAATGACTGAAACACCCCCAAAAGG
1 TAAAATGACTGAAATACCCTCGAAGGG
** * *
53384508 TAAAATGACCAAAATACCC-CTTAAGTG
1 TAAAATGACTGAAATACCCTC-GAAGGG
*
53384535 TAAAATGA-TCGAAATACCCTCAAAGGG
1 TAAAATGACT-GAAATACCCTCGAAGGG
* *
53384562 TAAAATGACTAAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
53384589 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
* * *
53384616 TAAAATGACTAAAATACCCTCAAAAGG
1 TAAAATGACTGAAATACCCTCGAAGGG
53384643 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
53384670 TAAAATGACTGAAATACCC-CTAAAGGG
1 TAAAATGACTGAAATACCCTC-GAAGGG
** **
53384697 TAAAACAACCAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
*
53384724 TAAAATGACTGAAATACCC-CTAAAGGG
1 TAAAATGACTGAAATACCCTC-GAAGGG
** **
53384751 TAAAACAACCAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCTCGAAGGG
53384778 TAAAAT
1 TAAAAT
53384784 AATCGAAATA
Statistics
Matches: 419, Mismatches: 63, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
26 5 0.01
27 409 0.98
28 5 0.01
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGAAGGG
Found at i:53385020 original size:26 final size:26
Alignment explanation
Indices: 53384986--53385058 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
53384976 TTGCCACATA
* *
53384986 TACTATTACCGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCAT
* *
53385012 TACTGTTACTGGCAGCGTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCAT
* *
53385038 CACTATTACTGACAGCTTTGC
1 TACTATTACTGGCAGCTTTGC
53385059 CAATTTTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCAT
Found at i:53385174 original size:28 final size:28
Alignment explanation
Indices: 53385130--53385186 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
53385120 ACTGCATTGT
* *
53385130 ACTGTTACTGTATTGGGCCAAGGCCCAC
1 ACTGTTACTGAAATGGGCCAAGGCCCAC
*
53385158 ACTGTTACTGAAATGGGCTAAGGCCCAC
1 ACTGTTACTGAAATGGGCCAAGGCCCAC
53385186 A
1 A
53385187 TTGTACTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (28 bp):
ACTGTTACTGAAATGGGCCAAGGCCCAC
Found at i:53387578 original size:42 final size:43
Alignment explanation
Indices: 53387414--53387578 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 43
53387404 TACCATAACA
* * * ** *
53387414 ATGCC-ATATCCCAGATATGGCCTTACATGTAATCTTGTATTG
1 ATGCCAATATCCCAGACATGGTCTTACAAGTAATCTCATATCG
* * * * * *
53387456 ATGCCAATAGCCTAGCCATGGTCTTACACGAAATCACATATCG
1 ATGCCAATATCCCAGACATGGTCTTACAAGTAATCTCATATCG
*
53387499 ATGCCAATGTCCCAGACATGGTCTTACACA--AAGTCTCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACA-AGTAA-TCTCATATCG
*
53387542 ATGCC-ATATCCCAGATATGGTCTTACAAGTAATCTCA
1 ATGCCAATATCCCAGACATGGTCTTACAAGTAATCTCA
53387579 GTAACCCTAA
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 32 0.32
43 66 0.67
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACAAGTAATCTCATATCG
Found at i:53389677 original size:7 final size:7
Alignment explanation
Indices: 53389667--53389710 Score: 72
Period size: 7 Copynumber: 6.3 Consensus size: 7
53389657 TAAAATAAAT
53389667 AATATTA
1 AATATTA
53389674 AATATTA
1 AATATTA
53389681 AATATTA
1 AATATTA
53389688 AATATTAA
1 AATATT-A
53389696 AATATTA
1 AATATTA
53389703 AA-ATTA
1 AATATTA
53389709 AA
1 AA
53389711 GACAAAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AATATTA
Found at i:53389691 original size:21 final size:21
Alignment explanation
Indices: 53389654--53389706 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
53389644 TGACCCTTTT
* *
53389654 TATTAAAATAAATAATATTAAA
1 TATTAAAAT-ATTAAAATTAAA
53389676 TATT-AAATATTAAATATTAAAA
1 TATTAAAATATTAAA-ATT-AAA
53389698 TATTAAAAT
1 TATTAAAAT
53389707 TAAAGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 11 0.42
23 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAAATATTAAAATTAAA
Found at i:53401057 original size:16 final size:16
Alignment explanation
Indices: 53401036--53401103 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
53401026 TTTGGTTCGC
*
53401036 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
53401052 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
53401068 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
53401084 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53401100 TGTA
1 TGTA
53401104 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:53401380 original size:17 final size:18
Alignment explanation
Indices: 53401339--53401373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53401329 TTATTATTAA
*
53401339 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
53401357 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
53401374 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:53401491 original size:59 final size:55
Alignment explanation
Indices: 53401325--53401505 Score: 152
Period size: 54 Copynumber: 3.1 Consensus size: 55
53401315 ATATTTAAAC
* * *
53401325 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAAATTTTTA
1 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAATTTTAA
** * * *
53401379 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA-AAGATAATTTG
1 ATAATTAATATT-AAATAT--ATTT--T--AATTAAAATATATGAT--T-TAATAA-A-AATTTT
53401443 AA
54 AA
*
53401445 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAAT-AAAATTTAAA
1 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAATTTTAA
53401499 ATAATTA
1 ATAATTA
53401506 TAACTAATAA
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
54 25 0.25
55 5 0.05
56 4 0.04
57 5 0.05
59 15 0.15
61 14 0.14
63 5 0.05
64 4 0.04
65 5 0.05
66 18 0.18
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (55 bp):
ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAAATTTTAA
Found at i:53402143 original size:13 final size:13
Alignment explanation
Indices: 53402125--53402154 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53402115 TTAAAAGCTA
*
53402125 AATTCAGAAAATC
1 AATTCAGAAAAAC
53402138 AATTCAGAAAAAC
1 AATTCAGAAAAAC
53402151 AATT
1 AATT
53402155 ACATGACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:53405257 original size:20 final size:20
Alignment explanation
Indices: 53405215--53405259 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
53405205 TTTAAAATAC
*
53405215 TTTTAAAATAATTTTTTTAT
1 TTTTAAAATAATATTTTTAT
53405235 TTTTAAAATAA-ATTTTTAGT
1 TTTTAAAATAATATTTTTA-T
53405255 TTTTA
1 TTTTA
53405260 TTAAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAAATAATATTTTTAT
Found at i:53405258 original size:21 final size:20
Alignment explanation
Indices: 53405215--53405265 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
53405205 TTTAAAATAC
*
53405215 TTTTAAAATAATTTTTTTAT
1 TTTTAAAATAATTTTTGTAT
*
53405235 TTTTAAAATAAATTTTTAGTTT
1 TTTTAAAAT-AATTTTT-GTAT
53405257 TTATTAAAA
1 TT-TTAAAA
53405266 AATGGGTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 4 0.15
23 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAAAATAATTTTTGTAT
Found at i:53411895 original size:21 final size:21
Alignment explanation
Indices: 53411871--53411923 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
53411861 CATTGTTTCT
*
53411871 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
53411892 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
53411913 AATCTCACCGC
1 AATCTCACCGC
53411924 CATTGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:53416149 original size:2 final size:2
Alignment explanation
Indices: 53416142--53416166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53416132 ATTATTATTT
53416142 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
53416167 TTTAAGCTTG
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:53425871 original size:26 final size:26
Alignment explanation
Indices: 53425842--53425893 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53425832 TGATAAGAGG
53425842 ACATTGAGGAGACTAGCTATTGACTA
1 ACATTGAGGAGACTAGCTATTGACTA
53425868 ACATTGAGGAGACTAGCTATTGACTA
1 ACATTGAGGAGACTAGCTATTGACTA
53425894 TGTCTTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (26 bp):
ACATTGAGGAGACTAGCTATTGACTA
Found at i:53428249 original size:44 final size:45
Alignment explanation
Indices: 53428199--53428880 Score: 291
Period size: 45 Copynumber: 15.7 Consensus size: 45
53428189 TAATAGATCG
** *
53428199 AGTCTTATCTCCCAAAAGTTCCAGTGGAGCAGACT-AAG-TAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-GGCA
53428243 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATGGCA
* * * ** *
53428288 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * * ** *
53428333 A-TCCTATCTCGCTGAAGTTGCAGT-GAGCGGA-TTAA-A-ACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A
* * * * *
53428374 AGATCTTATCTCTCTAAAGTTGCAG-AGAGTAGA-T--AGCAT--CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-ATGGCA
*
53428415 AGTCTTATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATGGCA
* * * * ** *
53428460 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* ** * * ** *
53428505 A-TCCTATCTCGTTGAAGTTGCAGT-GAGCGGA-TTAA-A-ACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A
* * * *
53428546 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCG--CAT--CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATGGCA
53428587 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATGGCA
* * * * *
53428632 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * * * * ** *
53428677 A-TCCTATCTCGCTAAAGTTACAGT-GAGCGGA-TTAA-A-ACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A
* * * ** * * *
53428718 AGATCCTATCTCTCTAAAGTTGCA-AAGAGCAGA-T-CACAT--CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
*
53428759 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACT-AAG-TGGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-GGCA
*
53428803 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATGGCA
* *
53428848 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
53428881 TTAAAGCCGA
Statistics
Matches: 496, Mismatches: 85, Indels: 113
0.71 0.12 0.16
Matches are distributed among these distances:
39 2 0.00
40 59 0.12
41 31 0.06
42 17 0.03
43 108 0.22
44 118 0.24
45 147 0.30
46 14 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
Found at i:53428529 original size:172 final size:171
Alignment explanation
Indices: 53428243--53429127 Score: 1024
Period size: 172 Copynumber: 5.1 Consensus size: 171
53428233 TAAGTAGGCA
53428243 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
*
53428308 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACCT
65 GCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACCT
* *
53428373 TAGATCTTATCTCTCTAAAGTTGCAGAGAGTAGATAGCATCT
130 TAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATAGCATCT
* *
53428415 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAAGTT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* *
53428480 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGTTGAAGTTGCAGTGAGCGGATTAAAACCT
65 GCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACCT
*
53428545 TAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
130 TAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATAGCATCT
53428587 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* * *
53428652 GCAGTGGAGCAGATTAAAGTTGGTAATCCTATCTCGCTAAAGTTACAGTGAGCGGATTAAAACCT
65 GCAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACCT
* * *
53428717 TAGATCCTATCTCTCTAAAGTTGCAAAGAGCAGATCA-CATCT
130 TAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGAT-AGCATCT
*
53428759 AGTCTTATCTCCTTGAAGTTGCAGTG-GAGCAGACT-AAG-TGGGCAAGTCTTATC-CTCCTGAA
1 AGTCTTATCTCC-TGAAGTTGCAGTGAG-GCAGACTGAAGAT-GGCAAATCTTATCTC-CCTGAA
* * * * * * * *
53428820 GTTGCAGT-GAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTA
62 GTTGCAGTGGA-GCAGATTAAAGCTGG-TAATCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTA
* * * * * ** ** *
53428884 AAGCCGATA-ATCCTATCT-TCCTGAAGTTGTAAGTGGAGTGGATTAAAACCTT
124 AAACC-TTAGATCTTATCTCT-CTGAAGTTG-CAG-AGAGCAGA-TAGCATC-T
* * * ** * * * ** *
53428936 GGATCTTATCTCTCTAAAGTTACA-AAAAGCAGA-T-CATAT--TTAGTCTTATCTCCCTGAAGT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
* * *
53428996 TGCAGTGGAGCAGATTAAAGCTGATAATCCTATCTTC-CTGAAGTTACAGTGGAGTGGATTAAAA
64 TGCAGTGGAGCAGATTAAAGCTGGTAATCCTATC-TCGCTGAAGTTGCAGT-GAGCGGATTAAAA
* * *
53429060 CCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGAATTT
127 CCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATAGCATCT
53429105 AGTCTTATCTCCCTGAAGTTGCA
1 AGTCTTATCT-CCTGAAGTTGCA
53429128 CCAGGAGTGG
Statistics
Matches: 616, Mismatches: 72, Indels: 54
0.83 0.10 0.07
Matches are distributed among these distances:
168 17 0.03
169 3 0.00
170 7 0.01
171 51 0.08
172 380 0.62
173 78 0.13
174 40 0.06
175 9 0.01
176 5 0.01
177 8 0.01
178 17 0.03
179 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (171 bp):
AGTCTTATCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACCTT
AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATAGCATCT
Found at i:53428822 original size:216 final size:218
Alignment explanation
Indices: 53428587--53429009 Score: 674
Period size: 216 Copynumber: 1.9 Consensus size: 218
53428577 GATCGCATCT
*
53428587 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
* ** *
53428652 GCAGTGGAGCAGATTAAAGTTGGTAATCCTATC-TCGCTAAAG-T-TACAGT-GAGCGGATTAAA
66 GCAGTGGAACAGATTAAAGCCGATAATCCTATCTTC-CTAAAGTTGTA-AGTGGAGCGGATTAAA
* * *
53428713 ACCTTAGATCCTATCTCTCTAAAGTTGCAAAGAGCAGATCACATCTAGTCTTATCTCCTTGAAGT
129 ACCTTAGATCCTATCTCTCTAAAGTTACAAAAAGCAGATCACATCTAGTCTTATCTCCCTGAAGT
53428778 TGCAGTGGAGCAGACTAAGTGGGCA
194 TGCAGTGGAGCAGACTAAGTGGGCA
53428803 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
* *
53428868 GCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGTAAGTGGAGTGGATTAAAAC
66 GCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTAAAGTTGTAAGTGGAGCGGATTAAAAC
* * * *
53428933 CTTGGATCTTATCTCTCTAAAGTTACAAAAAGCAGATCATATTTAGTCTTATCTCCCTGAAGTTG
131 CTTAGATCCTATCTCTCTAAAGTTACAAAAAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTG
53428998 CAGTGGAGCAGA
196 CAGTGGAGCAGA
53429010 TTAAAGCTGA
Statistics
Matches: 189, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
216 98 0.52
217 6 0.03
218 85 0.45
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (218 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
GCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTAAAGTTGTAAGTGGAGCGGATTAAAAC
CTTAGATCCTATCTCTCTAAAGTTACAAAAAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTG
CAGTGGAGCAGACTAAGTGGGCA
Found at i:53428983 original size:129 final size:128
Alignment explanation
Indices: 53428850--53429127 Score: 452
Period size: 128 Copynumber: 2.2 Consensus size: 128
53428840 AGATGGAAAA
53428850 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTGAAG-T-TA
*
53428915 -AGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTAAAGTTACAAAAAGCAGATC-ATATTTA
64 CAGTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTAAAGTTACAAAAAGCAGATCGA-ATTTA
53428978 G
128 G
* *
53428979 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAATCCTATCTTCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTACA
* * * *
53429044 GTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGAATTTAG
66 GTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTAAAGTTACAAAAAGCAGATCGAATTTAG
53429107 TCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
53429128 CCAGGAGTGG
Statistics
Matches: 140, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
127 2 0.01
128 79 0.56
129 59 0.42
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTACA
GTGGAGTGGATTAAAACCTTAGATCTTATCTCTCTAAAGTTACAAAAAGCAGATCGAATTTAG
Found at i:53429074 original size:44 final size:44
Alignment explanation
Indices: 53428289--53429097 Score: 172
Period size: 44 Copynumber: 18.8 Consensus size: 44
53428279 AAGATGGCAA
* * * *
53428289 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTA-
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACC-TTAG
* * *
53428333 ATCCTATC-TCGCTGAAGTTGCAGT-GAGCGGATTAAAACCTTAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * * * ** *
53428376 ATCTTATC-TCTCTAAAGTTGCAG-AGAGTAGA-TAGCATC-TAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * * * * **** *
53428417 -TCTTATCCTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTTCCTGAAGTTACAGTGGA-GCAGA-TTAAAACCTTAG
* * * * *
53428461 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGGTA-
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACC-TTAG
* * * *
53428505 ATCCTATC-TCGTTGAAGTTGCAGT-GAGCGGATTAAAACCTTAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * *** *
53428548 ATCTTATC-TCTCTGAAGTTGCAG-AGAGCAGA-TCGCATC-TAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * * * **** *
53428589 -TCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTTCCTGAAGTTACAGTGGA-GCAGA-TTAAAACCTTAG
* * * *
53428633 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAA-GTTGG
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * *
53428675 TAATCCTATC-TCGCTAAAGTTACAGT-GAGCGGATTAAAACCTTAG
1 --ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * * ** * * *
53428720 ATCCTATC-TCTCTAAAGTTGCA-AAGAGCAGA-TCACATC-TAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * *** *
53428761 -TCTTATC-TCCTTGAAGTTGCAGTGGAGCAGACTAAGTGGGC-AAG
1 ATCTTATCTTCC-TGAAGTTACAGTGGAGCAGATTAA--AACCTTAG
* * * * **** *
53428805 -TCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAAA
1 ATCTTATCTTCCTGAAGTTACAGTGGA-GCAGA-TTAAAACCTTAG
* * * * *
53428849 ATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATA-
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACC-TTAG
* ** *
53428893 ATCCTATCTTCCTGAAGTTGTA-AGTGGAGTGGATTAAAACCTTGG
1 ATCTTATCTTCCTGAAG-T-TACAGTGGAGCAGATTAAAACCTTAG
* *** * * *
53428938 ATCTTATC-TCTCTAAAGTTACA-AAAAGCAGA-TCATA-TTTAG
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* * *
53428979 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTGATA-
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACCT--TAG
* **
53429022 ATCCTATCTTCCTGAAGTTACAGTGGAGTGGATTAAAACCTTAG
1 ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
* *
53429066 ATCTTATC-TCTCTGAAGTTGCAG-AGAGCAGAT
1 ATCTTATCTTC-CTGAAGTTACAGTGGAGCAGAT
53429098 CGAATTTAGT
Statistics
Matches: 573, Mismatches: 136, Indels: 113
0.70 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 75 0.13
41 41 0.07
42 23 0.04
43 140 0.24
44 165 0.29
45 121 0.21
46 7 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTAAAACCTTAG
Found at i:53432360 original size:60 final size:60
Alignment explanation
Indices: 53432294--53432463 Score: 297
Period size: 60 Copynumber: 2.8 Consensus size: 60
53432284 CCGAAAAATG
*
53432294 GATGAATGTATGT-GACAATATTTACAATGTACGATGATGGCGAAAATATGTTGAAAAACA
1 GATGAATGTATGTAG-CAATATTTACCATGTACGATGATGGCGAAAATATGTTGAAAAACA
* *
53432354 GATGAATGTATGTAGCAATATTTACCATGTACGATGATGGCGAAAATATTTTGAAAAACG
1 GATGAATGTATGTAGCAATATTTACCATGTACGATGATGGCGAAAATATGTTGAAAAACA
53432414 GATGAATGTATGTAGCAATATTTACCATGTACGATGATGGCGAAAATATG
1 GATGAATGTATGTAGCAATATTTACCATGTACGATGATGGCGAAAATATG
53432464 ATATTAACAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
60 104 0.99
61 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (60 bp):
GATGAATGTATGTAGCAATATTTACCATGTACGATGATGGCGAAAATATGTTGAAAAACA
Found at i:53432390 original size:32 final size:32
Alignment explanation
Indices: 53432354--53432450 Score: 78
Period size: 32 Copynumber: 3.2 Consensus size: 32
53432344 TTGAAAAACA
53432354 GATGAATGTATGTAGCAATATTTACCATGTAC
1 GATGAATGTATGTAGCAATATTTACCATGTAC
** * ** ***
53432386 GATG-ATG-GCG-A-AAATATTT-TGAAAAAC
1 GATGAATGTATGTAGCAATATTTACCATGTAC
53432413 GGATGAATGTATGTAGCAATATTTACCATGTAC
1 -GATGAATGTATGTAGCAATATTTACCATGTAC
53432446 GATGA
1 GATGA
53432451 TGGCGAAAAT
Statistics
Matches: 43, Mismatches: 16, Indels: 12
0.61 0.23 0.17
Matches are distributed among these distances:
27 3 0.07
28 11 0.26
29 4 0.09
30 2 0.05
31 4 0.09
32 16 0.37
33 3 0.07
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (32 bp):
GATGAATGTATGTAGCAATATTTACCATGTAC
Found at i:53441112 original size:16 final size:15
Alignment explanation
Indices: 53441091--53441120 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
53441081 CTAGCTATTC
53441091 TGTTTCTTTTCTTTTT
1 TGTTTC-TTTCTTTTT
53441107 TGTTTCTTTCTTTT
1 TGTTTCTTTCTTTT
53441121 ACTTTATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TGTTTCTTTCTTTTT
Found at i:53441143 original size:3 final size:3
Alignment explanation
Indices: 53441135--53441160 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53441125 TATTCCTAGT
53441135 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
53441161 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53441309 original size:14 final size:14
Alignment explanation
Indices: 53441290--53441335 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
53441280 TATTTAAAAT
53441290 ATAATAATAATTTA
1 ATAATAATAATTTA
*
53441304 ATAATACTAATTTA
1 ATAATAATAATTTA
53441318 ATAATAATAATTTA
1 ATAATAATAATTTA
53441332 ATAA
1 ATAA
53441336 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:53447305 original size:23 final size:22
Alignment explanation
Indices: 53447238--53447311 Score: 100
Period size: 21 Copynumber: 3.5 Consensus size: 22
53447228 CCTGATCAGT
* *
53447238 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
53447259 A-ACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
53447279 ATACGACACACGAGGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
53447301 TATACGACACA
1 -ATACGACACA
53447312 TAAAGTGCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.19
21 28 0.60
23 10 0.21
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:53447319 original size:23 final size:23
Alignment explanation
Indices: 53447237--53447324 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 23
53447227 ACCTGATCAG
*
53447237 TATACGACACA-TAAGTGCCTGA
1 TATACGACACACGAAGTGCCTGA
*
53447259 -A-ACGACACACGAGGTGCCTG-
1 TATACGACACACGAAGTGCCTGA
*
53447279 -ATACGACACACGAGGTGCCTGA
1 TATACGACACACGAAGTGCCTGA
**
53447301 TATACGACACATAAAGTGCCTGA
1 TATACGACACACGAAGTGCCTGA
53447324 T
1 T
53447325 CGGCAAAGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.16
21 28 0.49
23 20 0.35
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
TATACGACACACGAAGTGCCTGA
Found at i:53447320 original size:44 final size:41
Alignment explanation
Indices: 53447238--53447324 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
53447228 CCTGATCAGT
* * *
53447238 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACAGAAGTGCCTGAAACGACACACAAAGTGCCTG
* *
53447279 ATACGACACACGAGGTGCCTGATATACGACACATAAAGTGCCTG
1 ATACGACACA-GAAGTGCCTGA-A-ACGACACACAAAGTGCCTG
53447323 AT
1 AT
53447325 CGGCAAAGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 10 0.26
42 9 0.24
43 1 0.03
44 18 0.47
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (41 bp):
ATACGACACAGAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:53448321 original size:3 final size:3
Alignment explanation
Indices: 53448313--53448338 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53448303 TATTCCTAGT
53448313 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
53448339 TATTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:53448487 original size:14 final size:14
Alignment explanation
Indices: 53448468--53448513 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
53448458 TATTTAAAAT
53448468 ATAATAATAATTTA
1 ATAATAATAATTTA
*
53448482 ATAATACTAATTTA
1 ATAATAATAATTTA
53448496 ATAATAATAATTTA
1 ATAATAATAATTTA
53448510 ATAA
1 ATAA
53448514 CATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:53449075 original size:23 final size:23
Alignment explanation
Indices: 53449049--53449093 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
53449039 ATGTTTTGGG
*
53449049 TGTAATATCCCGAAAATTACTAC
1 TGTAATAACCCGAAAATTACTAC
53449072 TGTAATAACCCGAAAATTACTA
1 TGTAATAACCCGAAAATTACTA
53449094 AAGTGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (23 bp):
TGTAATAACCCGAAAATTACTAC
Found at i:53452171 original size:50 final size:50
Alignment explanation
Indices: 53452104--53452442 Score: 387
Period size: 50 Copynumber: 6.8 Consensus size: 50
53452094 AGATTATAAA
*
53452104 AGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
* * *
53452154 AGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
*
53452204 AGGTCCCATGTAAGACCATGTCTGTGACATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
*
53452254 AGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
** *** * *
53452304 AGGTCCCCCGTAA-ATCCATGTCTGGGACATGGCACGGGCACCAATATGAG
1 AGGTCCCATGTAAGA-CCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
** * * ** * * * * *
53452354 AACTCCCATATAAGACCATATCTGGGGTATGGCATTTGCA--GTACAGGAA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATGAG
** * *
53452403 ACATCCCATGTAAGACCATGTCTGGTACATGGCTTTGGCA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
53452443 TGTTATTATT
Statistics
Matches: 244, Mismatches: 42, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
49 36 0.15
50 207 0.85
51 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
Found at i:53452235 original size:100 final size:99
Alignment explanation
Indices: 53452056--53452442 Score: 409
Period size: 100 Copynumber: 3.8 Consensus size: 99
53452046 TGTGAGCCAG
* *
53452056 TGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTATAAAAGGTCCCATGTAAGACC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAAAGGTCCCATGTAAGACC
*
53452121 ATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCTCA
60 ATGTCT-GGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
*
53452162 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTAAGACCATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAAAGGTCCCATGTAAGACCATGTCT
53452227 GTGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
66 G-GACATGGCGTTGGCACCGAGATGAGAGGTCCCA
** * * **
53452262 TGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCCGTAA-ATCCATGTC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAAAGGTCCCATGTAAGA-CCATGTC
*** * * **
53452326 TGGGACATGGCACGGGCACCAATATGAGAACTCCCA
65 T-GGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
* * ** * * * * **
53452362 TATAAGACCATATCTGGGGTATGGCATTTGCAGT-ACAGGAAACATCCCATGTAAGACCATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAAAGGTCCCATGTAAGACCATGTCT
*
53452426 GGTACATGGCTTTGGCA
66 GG-ACATGGCGTTGGCA
53452443 TGTTATTATT
Statistics
Matches: 241, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
98 2 0.01
99 34 0.14
100 168 0.70
101 1 0.00
103 4 0.02
105 1 0.00
106 31 0.13
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (99 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAAAGGTCCCATGTAAGACCATGTCT
GGACATGGCGTTGGCACCGAGATGAGAGGTCCCA
Found at i:53453958 original size:23 final size:23
Alignment explanation
Indices: 53453923--53453966 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53453913 GGGAGAAATG
* *
53453923 TAATATCCTGAAAATTACTACTA
1 TAATACCCCGAAAATTACTACTA
53453946 TAATACCCCGAAAATTACTAC
1 TAATACCCCGAAAATTACTAC
53453967 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (23 bp):
TAATACCCCGAAAATTACTACTA
Found at i:53464973 original size:24 final size:24
Alignment explanation
Indices: 53464921--53464994 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
53464911 TCTAGGCTTA
*
53464921 TTAACGGGAAGCTCACAAAAAGC-C
1 TTAACGGGAAGCTC-CGAAAAGCAC
* *
53464945 TTTAACGGGTAGCTCTGAAAAGCAC
1 -TTAACGGGAAGCTCCGAAAAGCAC
*
53464970 TTAACGGGAAGCTCCGAAGAGCAC
1 TTAACGGGAAGCTCCGAAAAGCAC
53464994 T
1 T
53464995 ATACCCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 28 0.67
25 14 0.33
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (24 bp):
TTAACGGGAAGCTCCGAAAAGCAC
Found at i:53469822 original size:10 final size:10
Alignment explanation
Indices: 53469807--53469833 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
53469797 TTCCATGCAC
53469807 AAAAAAAAGA
1 AAAAAAAAGA
53469817 AAAAAAAAGA
1 AAAAAAAAGA
53469827 AAAAAAA
1 AAAAAAA
53469834 GATTAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:53471944 original size:20 final size:20
Alignment explanation
Indices: 53471904--53471954 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
53471894 GTAACCCTTA
53471904 TTTTT-AAAATTTTCAATTTT
1 TTTTTCAAAATTTTC-ATTTT
53471924 TTTTTCAAAATTTTC-TGTTT
1 TTTTTCAAAATTTTCAT-TTT
*
53471944 TGTTTCAAAAT
1 TTTTTCAAAAT
53471955 GAACCCCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTCAAAATTTTCATTTT
Found at i:53473079 original size:6 final size:6
Alignment explanation
Indices: 53473068--53473113 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
53473058 ATCTTAACTC
* *
53473068 TATTAA TATTAA TATTAA TATTAA TAATAA TATTAT TATTATA TAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTA-A TAT
53473114 AAACAAGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
6 32 0.91
7 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:53476558 original size:22 final size:21
Alignment explanation
Indices: 53476519--53476562 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
53476509 AACAATACAA
* *
53476519 AATTTATCATGATTAAATATT
1 AATTTATCATAATGAAATATT
53476540 AATTTATCATAAATGAAATATT
1 AATTTATCAT-AATGAAATATT
53476562 A
1 A
53476563 TTAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
AATTTATCATAATGAAATATT
Found at i:53479909 original size:5 final size:5
Alignment explanation
Indices: 53479899--53479932 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
53479889 AAGCTAGTTT
53479899 TTTTG TTTTG TTTTG TTTTTG TTTTG TTTT- TTTT
1 TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG TTTT
53479933 TCCCTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:53479917 original size:16 final size:15
Alignment explanation
Indices: 53479896--53479933 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
53479886 TTAAAGCTAG
53479896 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
53479911 TTGTTTTTGTTTTGTT
1 TT-TTTTTGTTTTGTT
53479927 TTTTTTT
1 TTTTTTT
53479934 CCCTCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
TTTTTTTGTTTTGTT
Found at i:53479918 original size:11 final size:11
Alignment explanation
Indices: 53479899--53479933 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
53479889 AAGCTAGTTT
53479899 TTTTG-TTTTG
1 TTTTGTTTTTG
53479909 TTTTGTTTTTG
1 TTTTGTTTTTG
53479920 TTTTGTTTTT-
1 TTTTGTTTTTG
53479930 TTTT
1 TTTT
53479934 CCCTCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:53484104 original size:19 final size:19
Alignment explanation
Indices: 53484062--53484107 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53484052 ATTGTAACAT
*
53484062 TATTTATAATTTTAAATATC
1 TATTTA-AATTTTAAATATA
53484082 TATTTAAATTTT-AATAATA
1 TATTTAAATTTTAAAT-ATA
53484101 TATTTAA
1 TATTTAA
53484108 TTTGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 15 0.62
20 6 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTAAATTTTAAATATA
Found at i:53484119 original size:19 final size:18
Alignment explanation
Indices: 53484068--53484119 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
53484058 ACATTATTTA
* *
53484068 TAATTTTAAATATCTATT
1 TAATTTTAAAAATATATT
*
53484086 TAAATTTTAATAATATATT
1 T-AATTTTAAAAATATATT
53484105 TAATTTGTAAAAATA
1 TAATTT-TAAAAATA
53484120 GCAATAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTTTAAAAATATATT
Found at i:53485175 original size:16 final size:14
Alignment explanation
Indices: 53485154--53485188 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53485144 ATTTATAAAA
53485154 AAATTATGAAAATTAT
1 AAATTAT-AAAA-TAT
53485170 AAATTATAAAATAT
1 AAATTATAAAATAT
53485184 AAATT
1 AAATT
53485189 TTTTATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 4 0.21
16 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AAATTATAAAATAT
Found at i:53485319 original size:9 final size:9
Alignment explanation
Indices: 53485298--53485327 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53485288 TTTTTTAATA
53485298 AAAAATTTT
1 AAAAATTTT
53485307 -AAAATTTT
1 AAAAATTTT
53485315 AAAAATTTT
1 AAAAATTTT
53485324 AAAA
1 AAAA
53485328 CCTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:53485880 original size:103 final size:104
Alignment explanation
Indices: 53485727--53485919 Score: 291
Period size: 103 Copynumber: 1.9 Consensus size: 104
53485717 GCCCTCAAAC
* * * * *
53485727 TTTTTCAAAATAAGCAATTAAGCTCCTGCTTTATTTTTTCACTCATTTGGGTACTTGAACTTTCA
1 TTTTTCAAAAAAAGCAATTAAGCCCCTACTTTATTTTTGCACTCAATTGGGTACTTGAACTTTCA
53485792 AAATACATC-AAAAGGACCCTCAAACCTTCTTCTTTTTTT
66 AAATACATCTAAAA-GACCCTCAAACCTTCTTCTTTTTTT
* *
53485831 TTTTTTAAAAAAAGCAATTAAGCCCCTACTTT-TTTTTGCACTCAATTGGGTACTTGAACTTTTA
1 TTTTTCAAAAAAAGCAATTAAGCCCCTACTTTATTTTTGCACTCAATTGGGTACTTGAACTTTCA
*
53485895 AAATCCATCTAAAAGACCCTCAAAC
66 AAATACATCTAAAAGACCCTCAAAC
53485920 TTTTTCAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
103 48 0.60
104 32 0.40
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (104 bp):
TTTTTCAAAAAAAGCAATTAAGCCCCTACTTTATTTTTGCACTCAATTGGGTACTTGAACTTTCA
AAATACATCTAAAAGACCCTCAAACCTTCTTCTTTTTTT
Found at i:53485969 original size:9 final size:9
Alignment explanation
Indices: 53485955--53486161 Score: 73
Period size: 9 Copynumber: 22.4 Consensus size: 9
53485945 CTGCATTTAT
53485955 TAAAAATTA
1 TAAAAATTA
*
53485964 TAAAAAAT-
1 TAAAAATTA
**
53485972 TAAAAGCTA
1 TAAAAATTA
**
53485981 TAAAAGCTA
1 TAAAAATTA
*
53485990 TAAATATTA
1 TAAAAATTA
**
53485999 TTAAATTTTAA
1 -TAAAAATT-A
53486010 TAAAAATT-
1 TAAAAATTA
* *
53486018 CAAATATTA
1 TAAAAATTA
*
53486027 -AAAATTTA
1 TAAAAATTA
53486035 TTAAAAATTA
1 -TAAAAATTA
* *
53486045 GAAAAAATA
1 TAAAAATTA
**
53486054 TAAAAATCG
1 TAAAAATTA
*
53486063 TAAAATTTTA
1 TAAAA-ATTA
*
53486073 TAAAAATCA
1 TAAAAATTA
53486082 T-AAAATATA
1 TAAAAAT-TA
*
53486091 TAGAAATATA
1 TAAAAAT-TA
*
53486101 AAAAAATTA
1 TAAAAATTA
*
53486110 T-AAAATTT
1 TAAAAATTA
* *
53486118 TATAAAGTCA
1 TA-AAAATTA
53486128 TAAGAAAATTA
1 T-A-AAAATTA
*
53486139 TAAAAAATA
1 TAAAAATTA
*
53486148 TAAAGAACTA
1 TAAA-AATTA
53486158 TAAA
1 TAAA
53486162 TTTCGTAAAA
Statistics
Matches: 146, Mismatches: 39, Indels: 25
0.70 0.19 0.12
Matches are distributed among these distances:
8 30 0.21
9 56 0.38
10 52 0.36
11 8 0.05
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:53486077 original size:37 final size:38
Alignment explanation
Indices: 53486025--53486097 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
53486015 ATTCAAATAT
*
53486025 TAAAAATTTATTAAAAATTAGAAAAAATATAAAAATCG
1 TAAAAATTTATTAAAAATCAGAAAAAATATAAAAATCG
* * * *
53486063 TAAAATTTTA-TAAAAATCATAAAATATATAGAAAT
1 TAAAAATTTATTAAAAATCAGAAAAAATATAAAAAT
53486098 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 21 0.70
38 9 0.30
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (38 bp):
TAAAAATTTATTAAAAATCAGAAAAAATATAAAAATCG
Found at i:53486121 original size:29 final size:28
Alignment explanation
Indices: 53486074--53486151 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
53486064 AAAATTTTAT
*
53486074 AAAAATCATAAAATATATAGAAAT-ATAA
1 AAAAATTATAAAATATATA-AAATCATAA
* *
53486102 AAAAATTATAAAATTTTATAAAGTCATAA
1 AAAAATTATAAAA-TATATAAAATCATAA
* *
53486131 GAAAATTATAAAAAATATAAA
1 AAAAATTATAAAATATATAAA
53486152 GAACTATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAATCATAA
Found at i:53486163 original size:47 final size:46
Alignment explanation
Indices: 53486037--53486186 Score: 130
Period size: 47 Copynumber: 3.2 Consensus size: 46
53486027 AAAATTTATT
*
53486037 AAAAATTAGAAAAAATATAAAAATCGTA-AAATTTTATAAAAATCATA
1 AAAAATTATAAAAAATATAAAAA-C-TATAAATTTTATAAAAATCATA
* * * * *
53486084 AAATA-TATAGAAATATAAAAAAATTATAAAATTTTAT-AAAGTCATA
1 AAAAATTATA-AAAAATATAAAAACTAT-AAATTTTATAAAAATCATA
*
53486130 AGAAAATTATAAAAAATATAAAGAACTATAAATTTCGTAAAAAAAT-AT-
1 A-AAAATTATAAAAAATATAAA-AACTATAAATTT--TATAAAAATCATA
53486178 AAAAATTAT
1 AAAAATTAT
53486187 CATACCAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
45 2 0.02
46 12 0.15
47 50 0.61
48 10 0.12
49 4 0.05
50 4 0.05
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (46 bp):
AAAAATTATAAAAAATATAAAAACTATAAATTTTATAAAAATCATA
Found at i:53486348 original size:19 final size:19
Alignment explanation
Indices: 53486326--53486411 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
53486316 TTTTTTTATG
53486326 ATTTTTATAAAATTTTAGA
1 ATTTTTATAAAATTTTAGA
***
53486345 ATTTTT-TATTTTTTTACG-
1 ATTTTTATAAAATTTTA-GA
**
53486363 ATTTTTATAAAATAATTTCTA
1 ATTTTTATAAAAT--TTTAGA
* *
53486384 ATTTTTATTAAATTTTAAA
1 ATTTTTATAAAATTTTAGA
53486403 ATTTTTATA
1 ATTTTTATA
53486412 TTTTATTAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
18 13 0.26
19 22 0.44
21 15 0.30
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTTATAAAATTTTAGA
Found at i:53486433 original size:19 final size:19
Alignment explanation
Indices: 53486396--53486445 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
53486386 TTTTATTAAA
*
53486396 TTTTAAAATTT-TTATATT
1 TTTTAAAATTTAATATATT
53486414 TTATTAAAATTTAATA-ATT
1 TT-TTAAAATTTAATATATT
53486433 TTTCTAAAATTTA
1 TTT-TAAAATTTA
53486446 TTTTTATCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 23 0.82
20 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAAATTTAATATATT
Found at i:53487905 original size:18 final size:18
Alignment explanation
Indices: 53487869--53487903 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53487859 TTTACGATAA
53487869 CATTGATTTCTCATTTTT
1 CATTGATTTCTCATTTTT
*
53487887 CATTGA-TTCTTATTTTT
1 CATTGATTTCTCATTTTT
53487904 TCCATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (18 bp):
CATTGATTTCTCATTTTT
Found at i:53488740 original size:33 final size:35
Alignment explanation
Indices: 53488695--53488783 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 35
53488685 GTTTTTTTTT
* *
53488695 TAAATTAATTAAATTAGATTTTTTGGG-TTTTAA-A
1 TAAATTAATTAAATTAG-GTTTTAGGGTTTTTAAGA
53488729 TAAA-TAATTAAATTAGGTTTTAGGGTTTTTAAGA
1 TAAATTAATTAAATTAGGTTTTAGGGTTTTTAAGA
53488763 -AAATTAATTAAATTATGGTTT
1 TAAATTAATTAAATTA-GGTTT
53488784 ATTTTTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
32 7 0.14
33 21 0.43
34 16 0.33
35 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (35 bp):
TAAATTAATTAAATTAGGTTTTAGGGTTTTTAAGA
Found at i:53489324 original size:251 final size:250
Alignment explanation
Indices: 53488856--53489752 Score: 1300
Period size: 251 Copynumber: 3.6 Consensus size: 250
53488846 AAAAAATTGT
** *
53488856 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAGGTAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
* * *
53488921 ACGCTTCAAGTAGGATGCATTGTCAGCAAAATTATGTAAAAAAAGCTCCCACGTGGACGCTCTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA-CT-AAAAAAGCTCCCACGTGGACGCTCTTT
*
53488986 TTCTACAGTAGTTCCT-AAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACG
129 TTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACG
* *
53489050 CTTCAAGCAGGATGCATTGTCAGCAAAATTAGTGAAAAAAGCTCTCATGTGGACGCTA
194 CTTCAAGCAGGATGCACTGTCAGCAAAATTAGTGAAAAAAGCTC-CATGTGGACGCTC
* *
53489108 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTAAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
* * * * * *
53489173 ATGCTTCAAGCAGGATGCACTATCA-TAAAATTACTGAAAAAAGCTCCTACGCGAACGCTCTTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTCTTTT
* *
53489237 TCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTTTGAACAAATAATGTCAAAAACGC
130 TCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGC
53489302 TTCAAGCAGGATGCACTGTCAGCAAAATTAGTGAAAAAAGCTCCCATGTGGACGCTC
195 TTCAAGCAGGATGCACTGTCAGCAAAATTAGTGAAAAAAGCT-CCATGTGGACGCTC
* * *
53489359 TTTTTCTACAGTAGTTCCTGAGAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
* * *
53489424 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCATGTGGACACTTTTTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTCTTTTT
* * * * * *
53489489 CTACAGTAATTCTTGAAAAAATAATTTTGACAAGATGGTTCTGAACAAATAGTGTAAAAAATGCT
131 CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCT
* * * * *
53489554 TCAAGCA-GATGCACTGTCAG-AAAATT-GCTAAAAAAAGCTCCTACGCGAATGCTC
196 TCAAGCAGGATGCACTGTCAGCAAAATTAG-TGAAAAAAGCTCC-ATGTGGACGCTC
* * * * *
53489608 TTTTCCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
* * *
53489673 ACACTTCAATCAGGATGCACTGTTAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTCTTTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTCTTTTT
53489738 CTACAGTAGTTCTTG
131 CTACAGTAGTTCTTG
53489753 TTTGGCCTTA
Statistics
Matches: 580, Mismatches: 60, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
248 3 0.01
249 156 0.27
250 53 0.09
251 277 0.48
252 91 0.16
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (250 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTAAAAAAGCTCCCACGTGGACGCTCTTTTT
CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCT
TCAAGCAGGATGCACTGTCAGCAAAATTAGTGAAAAAAGCTCCATGTGGACGCTC
Found at i:53489752 original size:125 final size:126
Alignment explanation
Indices: 53488856--53489749 Score: 1248
Period size: 125 Copynumber: 7.1 Consensus size: 126
53488846 AAAAAATTGT
*
53488856 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AA-AAAGGTAATGTCAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAA--TAGTGTCAA
* *
53488919 AAACGCTTCAAGTAGGATGCATTGTCAGCAAAATTA-TGTAAAAAAAGCTCCCACGTGGACGCTC
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTG--AAAAAAGCTCCCACGTGGACGCTC
*
53488983 TTTTTCTACAGTAGTTCCT-AAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * * *
53489047 ACGCTTCAAGCAGGATGCATTGTCAGCAAAATTAGTGAAAAAAGCTCTCATGTGGACGCTA
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * *
53489108 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTAAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * * * *
53489173 ATGCTTCAAGCAGGATGCACTATCA-TAAAATTACTGAAAAAAGCTCCTACGCGAACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * *
53489233 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTTTGAACAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* *
53489298 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTAGTGAAAAAAGCTCCCATGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * *
53489359 TTTTTCTACAGTAGTTCCTGAGAAAATAATTTTGAGAAAACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * *
53489424 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCATGTGGACACTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * * * *
53489484 TTTTTCTACAGTAATTCTTGAAAAAATAATTTTGACAAGATGGTTCTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * * * * *
53489549 ATGCTTCAAGCA-GATGCACTGTCAG-AAAATTGCTAAAAAAAGCTCCTACGCGAATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * *
53489608 TTTTCCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * *
53489673 ACACTTCAATCAGGATGCACTGTTAGCAAAATTACT-AAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
53489733 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
53489750 TTGTTTGGCC
Statistics
Matches: 683, Mismatches: 76, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
123 8 0.01
124 98 0.14
125 287 0.42
126 264 0.39
127 23 0.03
128 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:53490232 original size:125 final size:126
Alignment explanation
Indices: 53490007--53491074 Score: 1407
Period size: 125 Copynumber: 8.5 Consensus size: 126
53489997 AATCTTCAGA
* *
53490007 ATGCACTGTCAGCAAAATTACT-AAAAAATCTCCCATGTGGACGCT-TTCTTTCTACAGTAGTTC
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTT-TTTCTACAGTAGTTC
* * *
53490070 CTGAAAAAATAATTTTTAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTAAAGCAGG
65 CTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * ** * *
53490132 ATACACTGTCAG-AAAATTATTGAAAAATGCTCCCACACGAACGCTCTTTTTCTATAGTAGTTCC
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* *
53490196 TGAAAAAATAATTTTGAGAAGACGATTTTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * ** * *
53490257 ATGCATTGTTAGCAAAATTAGTGAAAAAAGCTCTAATGTGGACACTC-TTTTCTACAGTAGTTCC
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* * *
53490321 TGAGAAAATAATTTTGAGAAGACTGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * *
53490382 ATGCACTGTCAGCAAAATTACT-AAAAAAGCTTCCATGTGGAAGCTCTTTTTCTACAGTAGTTCT
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* * *
53490446 TG-AAAAATAATTTTGAGAAGACGGTTCTGAACAAATACTGTAAAAAACGCGTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * * * *
53490506 ATGCACTGTCAACAAAATTAGTGAAAAAAGCTCCCATGTGGACGCTATTTTTCTATAGTAGTTCT
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* *
53490571 TGAAAAAATAATTTTGAGAAAACGGTTCTAGAA-AAATAGTGTCAAATACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCT-GAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * ** *
53490632 ATGCACTGTCAGCAAAATTACT-AAAAAAGCTCCCATGTGGACGCTTTTTTTCTGTAATAGTTCC
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* *
53490696 TGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTCAAACAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * *
53490757 ATGCACTGTCAG-AAAATTGCTGAAAAAAGCTCCCACGTGAACGCTCTTTTTCTACATTAGTTCT
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* *
53490821 TGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATGGTGTCAAAAACGCTTCAAGCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * * * * * * * *
53490882 ATGTATTGTCAGTAAAATTATTGAAAAAAACTCCCACGTGTACGTTATTTTTCTAGAGTAGTTCT
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
* * * * * *
53490947 TGAAAAAATAATTTTGAGAAGATGGTTTTGAACAAATGGTGTCAAAAACACATCAATCAGG
66 TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
* * * *
53491008 ATGTACTGTCAGCAAAATTACTAAAAAAATCTCCCACGTGGACGTTCTTTTTCTACAGTAGTTCC
1 ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
53491073 TG
66 TG
53491075 TTTGGCCTTA
Statistics
Matches: 832, Mismatches: 101, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
124 110 0.13
125 464 0.56
126 255 0.31
127 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (126 bp):
ATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCC
TGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGG
Found at i:53494177 original size:21 final size:21
Alignment explanation
Indices: 53494105--53494183 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
53494095 TTCTATTGCC
* *
53494105 TTATTCAAAAGAACTTTTA-T
1 TTATTAAAAACAACTTTTATT
* * *
53494125 TTATTAAAAATAAATTACTATT
1 TTATTAAAAACAACTT-TTATT
53494147 AATATATTAAAAACAACTTTTATT
1 --T-TATTAAAAACAACTTTTATT
53494171 TTATTAAATAACA
1 TTATTAAA-AACA
53494184 CAATATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 13 0.28
21 9 0.20
22 6 0.13
24 5 0.11
25 13 0.28
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (21 bp):
TTATTAAAAACAACTTTTATT
Found at i:53495631 original size:18 final size:16
Alignment explanation
Indices: 53495608--53495641 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
53495598 TTCTTGTTGA
53495608 AAAATAATTAAATATTAT
1 AAAATAA-TAAA-ATTAT
53495626 AAAATAATAAAATTAT
1 AAAATAATAAAATTAT
53495642 GTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATAAAATTAT
Found at i:53504926 original size:12 final size:11
Alignment explanation
Indices: 53504901--53504938 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
53504891 GAACATGAAG
53504901 AATTTTA-ATT
1 AATTTTATATT
53504911 AATTTTATAGTT
1 AATTTTATA-TT
53504923 AATTTT-TATT
1 AATTTTATATT
53504933 AATTTT
1 AATTTT
53504939 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:53510843 original size:11 final size:11
Alignment explanation
Indices: 53510827--53510865 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
53510817 TATATAAATA
53510827 TATAAATTAAT
1 TATAAATTAAT
53510838 TATAAATTATAT
1 TATAAATTA-AT
53510850 TATTAAATTAAT
1 TA-TAAATTAAT
53510862 TATA
1 TATA
53510866 TTATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:53510863 original size:12 final size:12
Alignment explanation
Indices: 53510829--53510864 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
53510819 TATAAATATA
53510829 TAAATTAATTA-
1 TAAATTAATTAT
53510840 TAAATTATATTAT
1 TAAATTA-ATTAT
53510853 TAAATTAATTAT
1 TAAATTAATTAT
53510865 ATTATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.30
12 9 0.39
13 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATTAATTAT
Found at i:53510864 original size:17 final size:15
Alignment explanation
Indices: 53510842--53510882 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
53510832 ATTAATTATA
53510842 AATTATATTATTAAATT
1 AATTATATTA-TAAA-T
53510859 AATTATATTATAAAT
1 AATTATATTATAAAT
53510874 -ATTATATTA
1 AATTATATTA
53510883 AGAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 1 0.04
16 4 0.17
17 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTATATTATAAAT
Found at i:53510877 original size:14 final size:14
Alignment explanation
Indices: 53510832--53510882 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
53510822 AAATATATAA
53510832 ATTA-ATTAT-AA-
1 ATTATATTATAAAT
53510843 ATTATATTATTAAATT
1 ATTATATTA-TAAA-T
53510859 AATTATATTATAAAT
1 -ATTATATTATAAAT
53510874 ATTATATTA
1 ATTATATTA
53510883 AGAAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.12
12 4 0.12
13 1 0.03
14 11 0.32
15 1 0.03
16 4 0.12
17 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATTATAAAT
Found at i:53510894 original size:31 final size:28
Alignment explanation
Indices: 53510814--53510895 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
53510804 TACATGATTT
* * *
53510814 AATTATATAAATATATAAATTAATTATA
1 AATTATATTAAGAAATAAATTAATTATA
** *
53510842 AATTATATTATTAAATTAATTATATTATAA
1 AATTATATTAAGAAATAAATTA-ATTAT-A
53510872 ATATTATATTAAGAAATAAATTAA
1 A-ATTATATTAAGAAATAAATTAA
53510896 ATAAAGACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.41
29 5 0.11
30 3 0.07
31 18 0.41
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
AATTATATTAAGAAATAAATTAATTATA
Found at i:53511914 original size:21 final size:22
Alignment explanation
Indices: 53511886--53511949 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
53511876 GCTTTGCCGA
53511886 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* **
53511908 T-AGGCACCACGTGTGTCGT-T
1 TCAGGCACTATATGTGTCGTAT
* *
53511928 TCAGGCACTTTATGTGTTGTAT
1 TCAGGCACTATATGTGTCGTAT
53511950 ACTGCTTCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:53517336 original size:124 final size:125
Alignment explanation
Indices: 53517116--53517464 Score: 601
Period size: 124 Copynumber: 2.8 Consensus size: 125
53517106 CCCAAACATG
*
53517116 CTACTGTAGCAAAAGCACGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
53517181 TAGAAACGATTTTATATTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
* * * * *
53517240 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCAATTTCATAAATTCTTCTTAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
53517305 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
* *
53517365 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTATCAAACAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
53517430 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC
53517465 GATTTTATAC
Statistics
Matches: 209, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
124 107 0.51
125 102 0.49
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTCTTCCAGGAC
Found at i:53517468 original size:28 final size:28
Alignment explanation
Indices: 53517436--53517492 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
53517426 CTGCTAGAAG
53517436 CGATTTTATACTATTTGCTCAGAAACGT
1 CGATTTTATACTATTTGCTCAGAAACGT
53517464 CGATTTTATACTATTTGCTCAGAAACGT
1 CGATTTTATACTATTTGCTCAGAAACGT
53517492 C
1 C
53517493 AACTCGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (28 bp):
CGATTTTATACTATTTGCTCAGAAACGT
Found at i:53517506 original size:28 final size:28
Alignment explanation
Indices: 53517445--53517507 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
53517435 GCGATTTTAT
* * ** *
53517445 ACTATTTGCTCAGAAACGTCGATTTTAT
1 ACTATTTGCTCAGAAACGTCAACTCGAA
53517473 ACTATTTGCTCAGAAACGTCAACTCGAA
1 ACTATTTGCTCAGAAACGTCAACTCGAA
*
53517501 ATTATTT
1 ACTATTT
53517508 TTTCAAGACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (28 bp):
ACTATTTGCTCAGAAACGTCAACTCGAA
Found at i:53519313 original size:20 final size:20
Alignment explanation
Indices: 53519280--53519317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53519270 AATACTTTTT
53519280 TTTTAAATATATTTTTATAC
1 TTTTAAATATATTTTTATAC
53519300 TTTTATAATA-ATTTTTAT
1 TTTTA-AATATATTTTTAT
53519318 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAATATATTTTTATAC
Found at i:53519331 original size:20 final size:19
Alignment explanation
Indices: 53519277--53519332 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
53519267 TTAAATACTT
*
53519277 TTTTTTTAAATATATTTTTA
1 TTTTTTAAAATA-ATTTTTA
* *
53519297 TACTTTTATAATAATTTTTA
1 T-TTTTTAAAATAATTTTTA
53519317 TTTTTTAAAATTAATT
1 TTTTTTAAAA-TAATT
53519333 AATTGTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.24
20 14 0.48
21 8 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTAAAATAATTTTTA
Found at i:53519634 original size:9 final size:9
Alignment explanation
Indices: 53519620--53519650 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53519610 GTTAAACGAA
53519620 TCGAGTTAT
1 TCGAGTTAT
*
53519629 TCGAGTTAA
1 TCGAGTTAT
53519638 TCGAGTTAT
1 TCGAGTTAT
53519647 TCGA
1 TCGA
53519651 ATCAACTTGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53519720 original size:9 final size:9
Alignment explanation
Indices: 53519703--53519739 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53519693 TGAGTTTTCA
53519703 AATTCGAAT
1 AATTCGAAT
*
53519712 AACTCGAAT
1 AATTCGAAT
53519721 AATTCGAAT
1 AATTCGAAT
53519730 AATTCGAAT
1 AATTCGAAT
53519739 A
1 A
53519740 TCAAACTATA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53519987 original size:30 final size:31
Alignment explanation
Indices: 53519953--53520012 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
53519943 AAACCTTTTA
*
53519953 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
53519983 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
53520013 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:53520281 original size:9 final size:9
Alignment explanation
Indices: 53520267--53520295 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53520257 AATTTCACAT
53520267 TTTATATTA
1 TTTATATTA
53520276 TTTATATTA
1 TTTATATTA
53520285 TTTATATTA
1 TTTATATTA
53520294 TT
1 TT
53520296 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:53520776 original size:5 final size:5
Alignment explanation
Indices: 53520766--53520796 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
53520756 CTCGAAAATT
53520766 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
53520797 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:53520859 original size:7 final size:7
Alignment explanation
Indices: 53520832--53520872 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
53520822 CCCGAAAGTT
53520832 TAAAATAA
1 TAAAAT-A
* *
53520840 TATAATT
1 TAAAATA
53520847 TAAAATA
1 TAAAATA
53520854 TAAAATA
1 TAAAATA
53520861 TAAAATA
1 TAAAATA
53520868 TAAAA
1 TAAAA
53520873 GTAGTTTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 24 0.83
8 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAAATA
Found at i:53527877 original size:7 final size:7
Alignment explanation
Indices: 53527862--53527906 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
53527852 AAAATGAGAG
53527862 AAAAAGA
1 AAAAAGA
*
53527869 AAGAAGA
1 AAAAAGA
53527876 AAAAAGAA
1 AAAAAG-A
53527884 AAAAAGA
1 AAAAAGA
53527891 AAAAAG-
1 AAAAAGA
53527897 AAAAAGA
1 AAAAAGA
53527904 AAA
1 AAA
53527907 GAAAAGGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.18
7 21 0.62
8 7 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:53527890 original size:15 final size:15
Alignment explanation
Indices: 53527862--53527901 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
53527852 AAAATGAGAG
*
53527862 AAAAAG-AAAGAAGA
1 AAAAAGAAAAAAAGA
53527876 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
53527891 AAAAAGAAAAA
1 AAAAAGAAAAA
53527902 GAAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:53527890 original size:22 final size:21
Alignment explanation
Indices: 53527862--53527906 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
53527852 AAAATGAGAG
*
53527862 AAAAAGAAAGAAGAAAAAAGAA
1 AAAAAGAAAAAAG-AAAAAGAA
53527884 AAAAAGAAAAAAGAAAAAGAA
1 AAAAAGAAAAAAGAAAAAGAA
53527905 AA
1 AA
53527907 GAAAAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAGAAAAAGAA
Found at i:53528870 original size:51 final size:52
Alignment explanation
Indices: 53528781--53528879 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
53528771 AGAAGGGACT
* *
53528781 AAGGTGAAAACCCGCAAAGGGCACCTTGATTTCTAAAAA-AAAAAAAAGACC
1 AAGGTGAAAACCCGCAAAAGGCACCTTGATGTCTAAAAATAAAAAAAAGACC
* * *
53528832 AAGGTGAAAACCTGCAAAAGGCACTTTGA-GTCTAAAAAATTAAAAAAA
1 AAGGTGAAAACCCGCAAAAGGCACCTTGATGTCT-AAAAATAAAAAAAA
53528880 TAAATCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 3 0.07
51 31 0.76
52 7 0.17
ACGTcount: A:0.51, C:0.16, G:0.17, T:0.16
Consensus pattern (52 bp):
AAGGTGAAAACCCGCAAAAGGCACCTTGATGTCTAAAAATAAAAAAAAGACC
Found at i:53530313 original size:44 final size:44
Alignment explanation
Indices: 53530259--53530531 Score: 307
Period size: 44 Copynumber: 6.2 Consensus size: 44
53530249 TGACCCCAGC
** * *
53530259 CCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGGTTGTGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGTGAAT
* * * * * *
53530303 CCTATATCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGAGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGTGAAT
* * *
53530347 TCTATCTCTCTGTG-CAACAGTGGAATAGATTGAAGGTTGTGAAT
1 CCTATCTCCCTG-GACAACAGTGGAATAGATTGAAGATTGTGAAT
* * *
53530391 CCTATCTCCCTGGTCAACAGTGGAATAGATTAAAGATTGAGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGTGAAT
* * * *
53530435 TCTATCTCTCTGGGCAGCAGTGGAATAGATTGAAGATTGTGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGTGAAT
* *
53530479 TCTATCTCCCTGGACAATAGTGGAATAGATTGAAGATT-TAGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGT-GAAT
*
53530523 TCTATCTCC
1 CCTATCTCC
53530532 TTAAGCAGCA
Statistics
Matches: 197, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.01
44 194 0.98
45 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
CCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTGTGAAT
Found at i:53530374 original size:88 final size:88
Alignment explanation
Indices: 53530277--53530530 Score: 384
Period size: 88 Copynumber: 2.9 Consensus size: 88
53530267 CCTGGACAGT
* * * *
53530277 AGTGGAATAGGTTGAAGGTTGTGAATCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAAAATTG
1 AGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATTGAAAATTG
*
53530342 AGAATTCTATCTCTCTGTGCAAC
66 AGAATTCTATCTCTCTGGGCAAC
53530365 AGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATT-AAAGATT
1 AGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATTGAAA-ATT
*
53530429 GAGAATTCTATCTCTCTGGGCAGC
65 GAGAATTCTATCTCTCTGGGCAAC
* * * * * *
53530453 AGTGGAATAGATTGAAGATTGTGAATTCTATCTCCCTGGACAATAGTGGAATAGATTGAAGATTT
1 AGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATTGAAAATTG
53530518 AGAATTCTATCTC
66 AGAATTCTATCTC
53530531 CTTAAGCAGC
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
87 3 0.02
88 147 0.97
89 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (88 bp):
AGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATTGAAAATTG
AGAATTCTATCTCTCTGGGCAAC
Found at i:53530453 original size:132 final size:132
Alignment explanation
Indices: 53530259--53530531 Score: 352
Period size: 132 Copynumber: 2.1 Consensus size: 132
53530249 TGACCCCAGC
** * * * * *
53530259 CCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGGTTGTGAATCCTATATCCCTGGTCAGCAGT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTAAAGATTGAGAATCCTATATCCCTGGGCAGCAGT
* * *
53530324 GGAATAGGTTGAAAATTGAGAATTCTATCTCTCTGTG-CAACAGTGGAATAGATTGAAGGTTGT-
66 GGAATAGATTGAAAATTGAGAATTCTATCTCCCTG-GACAACAGTGGAATAGATTGAAGATT-TA
53530387 GAAT
129 GAAT
* * * *
53530391 CCTATCTCCCTGGTCAACAGTGGAATAGATTAAAGATTGAGAATTCTATCTCTCTGGGCAGCAGT
1 CCTATCTCCCTGGACAACAGTGGAATAGATTAAAGATTGAGAATCCTATATCCCTGGGCAGCAGT
* * *
53530456 GGAATAGATTGAAGATTGTGAATTCTATCTCCCTGGACAATAGTGGAATAGATTGAAGATTTAGA
66 GGAATAGATTGAAAATTGAGAATTCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTTAGA
53530521 AT
131 AT
*
53530523 TCTATCTCC
1 CCTATCTCC
53530532 TTAAGCAGCA
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
131 2 0.02
132 119 0.98
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (132 bp):
CCTATCTCCCTGGACAACAGTGGAATAGATTAAAGATTGAGAATCCTATATCCCTGGGCAGCAGT
GGAATAGATTGAAAATTGAGAATTCTATCTCCCTGGACAACAGTGGAATAGATTGAAGATTTAGA
AT
Found at i:53530556 original size:88 final size:87
Alignment explanation
Indices: 53530260--53530546 Score: 364
Period size: 88 Copynumber: 3.3 Consensus size: 87
53530250 GACCCCAGCC
* * * *
53530260 CTATCTCC-CTGGACAGTAGTGGAATAGGTTGAAGGTTGTGAATCCTATATCCCTGGTCAGCAGT
1 CTATCTCCTCT-G-CAGCAGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGT
* *
53530324 GGAATAGGTTGAAAATTGAGAATT
64 GGAATAGATTGAAGATTGAGAATT
* *
53530348 CTATCTCTCTGTGCAACAGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTG
1 CTATCTC-CTCTGCAGCAGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTG
*
53530413 GAATAGATTAAAGATTGAGAATT
65 GAATAGATTGAAGATTGAGAATT
* * * *
53530436 CTATCT-CTCTGGGCAGCAGTGGAATAGATTGAAGATTGTGAATTCTATCTCCCTGGACAATAGT
1 CTATCTCCTCT--GCAGCAGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGT
*
53530500 GGAATAGATTGAAGATTTAGAATT
64 GGAATAGATTGAAGATTGAGAATT
53530524 CTATCTCCT-TAAGCAGCAGTGGA
1 CTATCTCCTCT--GCAGCAGTGGA
53530547 GTAAGTTGAA
Statistics
Matches: 175, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
86 3 0.02
88 167 0.95
89 4 0.02
90 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (87 bp):
CTATCTCCTCTGCAGCAGTGGAATAGATTGAAGGTTGTGAATCCTATCTCCCTGGTCAACAGTGG
AATAGATTGAAGATTGAGAATT
Found at i:53530589 original size:132 final size:132
Alignment explanation
Indices: 53530320--53530602 Score: 292
Period size: 132 Copynumber: 2.1 Consensus size: 132
53530310 CCCTGGTCAG
* * * *
53530320 CAGTGGAATAGGTTGAAAATTGAGAATTCTATCTCTCTGTGCAACAGTGGAATAGATTGAAGGTT
1 CAGTGGAATAGATTGAAGATTGAGAATTCTATCTCCCTGTGCAACAGTGGAATAGATTGAAGATT
* * **
53530385 GTGAATCCTATCTCCCTGGTCAACAGTGGAATAGATTAAAGATTGAGAATTCTATCTCTCTGGGC
66 GTGAATCCTATCTCCCTAGTCAACAGTGGAATAGATTAAAGATTCAGAATTCTATCTCTCTAAGC
*
53530450 AG
131 AA
* *
53530452 CAGTGGAATAGATTGAAGATTGTGAATTCTATCTCCCTG-GACAATAGTGGAATAGATTGAAGAT
1 CAGTGGAATAGATTGAAGATTGAGAATTCTATCTCCCTGTG-CAACAGTGGAATAGATTGAAGAT
* * * *
53530516 T-TAGAATTCTATCTCCTTAAG-CAGCAGTGGAGTA-AGTTGAAA-ATTACAG-A-TCTTATCTC
65 TGT-GAATCCTATCTCCCT-AGTCAACAGTGGAATAGA-TT-AAAGATT-CAGAATTC-TATCTC
53530575 TCTAAGCAA
124 TCTAAGCAA
* * *
53530584 TAGTGGAACAGATCGAAGA
1 CAGTGGAATAGATTGAAGA
53530603 CCCTAGCCTT
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
131 5 0.04
132 115 0.91
133 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (132 bp):
CAGTGGAATAGATTGAAGATTGAGAATTCTATCTCCCTGTGCAACAGTGGAATAGATTGAAGATT
GTGAATCCTATCTCCCTAGTCAACAGTGGAATAGATTAAAGATTCAGAATTCTATCTCTCTAAGC
AA
Found at i:53530862 original size:220 final size:220
Alignment explanation
Indices: 53530460--53530885 Score: 504
Period size: 220 Copynumber: 1.9 Consensus size: 220
53530450 AGCAGTGGAA
* * * * *
53530460 TAGATTGAAGATTGTGAATTCTATCTCCCTGGACAATAGTGGAATAGATTGAAGATTTAGAATTC
1 TAGATCGAAGATTGTGAATCCTATCTCCCTGGACAACAGTGGAATAGATTGAAAATTTAGAATCC
* * * * * *
53530525 TATCTCCTTAAGCAGCAGTGGAGTAAGTTGAAAATTACAGATCTTATCTCTCTAAGCAATAGTGG
66 TATCTCCTGAAGCAGCAGTAGAATAAGGTCAAAATTACAGATCTTATCTCTCTAAACAATAGTGG
*** *
53530590 AACAGATCGAAGACCCTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAACAGAGC
131 AACAGATCGAAGACCCTAGCCTTGCCTCCCTGGACAGCAGCGGAACAGGTTGAAAATAACAGAGC
*
53530655 TTTCCTTCCTGTACTGACGGTGAAG
196 TTGCCTTCCTGTACTGACGGTGAAG
* *
53530680 TAGATCGAAGATTGT-AAGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTGTA-AAT
1 TAGATCGAAGATTGTGAA-TCCTATCTCCCTGGACAACAGTGGAATAGATTGAAAATT-TAGAAT
* * *
53530743 CCTCTCTCTCTGGA-CAGCAGTAGAAT-AGGTCAAAGATTACAGATCTTATCTC-CTTAAACAGT
64 CCTATCTC-CTGAAGCAGCAGTAGAATAAGGTCAAA-ATTACAGATCTTATCTCTC-TAAACAAT
* * * * * *
53530805 AGTGGAGCAGATCGAAGACACC-AGCCTTGCCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTA
126 AGTGGAACAGATCGAAGAC-CCTAGCCTTGCCTCCCTGGACAGCAGCGGAACAGGTTGAAAATAA
*
53530869 CAGATCTTGCCTTCCTG
190 CAGAGCTTGCCTTCCTG
53530886 CACCGACAGC
Statistics
Matches: 172, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
219 9 0.05
220 156 0.91
221 7 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (220 bp):
TAGATCGAAGATTGTGAATCCTATCTCCCTGGACAACAGTGGAATAGATTGAAAATTTAGAATCC
TATCTCCTGAAGCAGCAGTAGAATAAGGTCAAAATTACAGATCTTATCTCTCTAAACAATAGTGG
AACAGATCGAAGACCCTAGCCTTGCCTCCCTGGACAGCAGCGGAACAGGTTGAAAATAACAGAGC
TTGCCTTCCTGTACTGACGGTGAAG
Found at i:53530940 original size:88 final size:88
Alignment explanation
Indices: 53530848--53531058 Score: 235
Period size: 88 Copynumber: 2.4 Consensus size: 88
53530838 CCTGGACAGT
* * * *
53530848 AGTGGAATAGGTTGAAGATTA-CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCAAAGAC
1 AGTGGAACAGGTTGAA-AATAGCAAATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCAAAGAC
53530912 ACTAACCTTGCCTCCTTGGGTTAC
65 ACTAACCTTGCCTCCTTGGGTTAC
* * * **
53530936 AGTGGAGCAGGTTGAAAATAGCAAATTTTGCCTTCCTGTACCAACAGCGAAGCAGATTGAAGACA
1 AGTGGAACAGGTTGAAAATAGCAAATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCAAAGACA
* * * * *
53531001 CTAGCCTTGCCTCCCTAGTTTGC
66 CTAACCTTGCCTCCTTGGGTTAC
* * * * *
53531024 AGTGGAGCAGGCTGAAAACACCAGATCTTGCCTTC
1 AGTGGAACAGGTTGAAAATAGCAAATCTTGCCTTC
53531059 TTGTATTGGC
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 3 0.03
88 100 0.97
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (88 bp):
AGTGGAACAGGTTGAAAATAGCAAATCTTGCCTTCCTGCACCAACAGCGAAGCAGATCAAAGACA
CTAACCTTGCCTCCTTGGGTTAC
Found at i:53531226 original size:44 final size:45
Alignment explanation
Indices: 53531174--53531260 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
53531164 TGAATTGCAT
* * * *
53531174 CAAGTCTTAT-CTCCCTGAGGTTGCAGCGGTGCAGACTGAGAAAG
1 CAAGTCTTATCCCCCCTGAAGTTACAGCGGGGCAGACTGAGAAAG
* *
53531218 CAAGTCTTATCCCCCCTGAAGTTACGGTGGGGCAGACTGAGAA
1 CAAGTCTTATCCCCCCTGAAGTTACAGCGGGGCAGACTGAGAA
53531261 TAGCGAATCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 10 0.28
45 26 0.72
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (45 bp):
CAAGTCTTATCCCCCCTGAAGTTACAGCGGGGCAGACTGAGAAAG
Found at i:53531702 original size:9 final size:9
Alignment explanation
Indices: 53531690--53531721 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
53531680 CCATTTAAAA
53531690 CCCAATTAG
1 CCCAATTAG
53531699 CCCAATTAG
1 CCCAATTAG
53531708 CCCAATTAG
1 CCCAATTAG
53531717 CCCAA
1 CCCAA
53531722 ACCTGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (9 bp):
CCCAATTAG
Found at i:53532249 original size:16 final size:15
Alignment explanation
Indices: 53532228--53532266 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
53532218 ATTTGAATTT
53532228 TTTTCTTTTTCTTCTC
1 TTTTCTTTTTCTT-TC
*
53532244 TTTTCTTTTTTCTTTT
1 TTTTC-TTTTTCTTTC
53532260 TTTTCTT
1 TTTTCTT
53532267 GGCTCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 11 0.52
17 8 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTCTTTC
Done.