Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 64 of 199
Found at i:19033617 original size:42 final size:42
Alignment explanation
Indices: 19033565--19033832 Score: 359
Period size: 42 Copynumber: 6.3 Consensus size: 42
19033555 ACGTCGCTAA
*
19033565 CTTTTGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
19033607 CTTTAGCGGCGCTTAGGAAAAAAACGCCG-TAAAAGATCATGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCT-AAAGATCATGTT
19033650 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
19033692 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * *
19033734 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
**
19033777 -TTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTT-TAGCGGCGCTTAG-GAAAAAACGCCGCTAAAGA-TCA-TGTT
19033819 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
19033833 GTTTCACAAA
Statistics
Matches: 208, Mismatches: 9, Indels: 18
0.89 0.04 0.08
Matches are distributed among these distances:
41 1 0.00
42 133 0.64
43 74 0.36
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:19033713 original size:85 final size:85
Alignment explanation
Indices: 19033565--19033832 Score: 379
Period size: 85 Copynumber: 3.2 Consensus size: 85
19033555 ACGTCGCTAA
*
19033565 CTTTTGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-GAAAAAA
19033630 ACGCCG-TAAAAGATCATGTT
65 ACGCCGCTAAAAGATCATGTT
19033650 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
19033715 CGCCGCT-AAAGATCATGTT
66 CGCCGCTAAAAGATCATGTT
* * * **
19033734 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT-TTATAGCGGCGCTT-GTTCA
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTTCTT-TAGCGGCGCTTAG-AAA
19033796 AAAACGCCGCTAAAAG-T-AGTGTT
62 AAAACGCCGCTAAAAGATCA-TGTT
19033819 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
19033833 GTTTCACAAA
Statistics
Matches: 170, Mismatches: 6, Indels: 14
0.89 0.03 0.07
Matches are distributed among these distances:
84 48 0.28
85 118 0.69
86 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAA
CGCCGCTAAAAGATCATGTT
Found at i:19033713 original size:127 final size:127
Alignment explanation
Indices: 19033565--19033832 Score: 384
Period size: 127 Copynumber: 2.1 Consensus size: 127
19033555 ACGTCGCTAA
* *
19033565 CTTTTGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
* *
19033630 ACGCC-GTAAAAGATCATGTTCTT-TAGCGGCGCTTAG-GAAAAAACGCCGCT-AAAGATCA-TG
66 ACGCCTCTAAAAG-TAATGTT-TTATAGCGGCGCTT-GTGAAAAAACGCCGCTAAAAG-T-AGTG
19033690 TT
126 TT
* *
19033692 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAAGAAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
**
19033757 ACGCCTCTAAAAGTAATGTTTTATAGCGGCGCTTGTTCAAAAACGCCGCTAAAAGTAGTGTT
66 ACGCCTCTAAAAGTAATGTTTTATAGCGGCGCTTGTGAAAAAACGCCGCTAAAAGTAGTGTT
19033819 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
19033833 GTTTCACAAA
Statistics
Matches: 128, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
126 4 0.03
127 114 0.89
128 10 0.08
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (127 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
ACGCCTCTAAAAGTAATGTTTTATAGCGGCGCTTGTGAAAAAACGCCGCTAAAAGTAGTGTT
Found at i:19034312 original size:21 final size:21
Alignment explanation
Indices: 19034268--19034312 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19034258 GCTTCTATCA
* *
19034268 CTGCTTCTCTCGCTGCGGCAT
1 CTGCTTCCCTCGCTGCCGCAT
*
19034289 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCCGCAT
19034310 CTG
1 CTG
19034313 ATTTAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.44, G:0.22, T:0.31
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCCGCAT
Found at i:19039916 original size:9 final size:9
Alignment explanation
Indices: 19039902--19040147 Score: 156
Period size: 9 Copynumber: 28.2 Consensus size: 9
19039892 TTAAGTAAAT
19039902 TTATGTAAG
1 TTATGTAAG
*
19039911 TTATGTACG
1 TTATGTAAG
19039920 TGTA--TAAG
1 T-TATGTAAG
*
19039928 TTATTTAAG
1 TTATGTAAG
*
19039937 TTTTGT-A-
1 TTATGTAAG
* *
19039944 TTAAGTAAA
1 TTATGTAAG
*
19039953 CTATGTAAG
1 TTATGTAAG
*
19039962 TTGTGT-A-
1 TTATGTAAG
* *
19039969 TTATATAAC
1 TTATGTAAG
19039978 TTATGTAAG
1 TTATGTAAG
**
19039987 TTATCAAAG
1 TTATGTAAG
* *
19039996 TAATGTATG
1 TTATGTAAG
19040005 TTATGTAAG
1 TTATGTAAG
19040014 -T-TGTAAG
1 TTATGTAAG
*
19040021 TTAT-TATG
1 TTATGTAAG
* *
19040029 TATTATATAAC
1 --TTATGTAAG
*
19040040 TTCTGTAAG
1 TTATGTAAG
19040049 TTATGTAAG
1 TTATGTAAG
19040058 TTATGTAAG
1 TTATGTAAG
*
19040067 TTGTGTAAG
1 TTATGTAAG
* * *
19040076 CTATTTCAG
1 TTATGTAAG
19040085 TTATGTAAG
1 TTATGTAAG
19040094 CTT-TGT-A-
1 -TTATGTAAG
19040101 TTATGTAAG
1 TTATGTAAG
*
19040110 TTATGTAGG
1 TTATGTAAG
19040119 TTATGTAAG
1 TTATGTAAG
* *
19040128 TTGTGTAAA
1 TTATGTAAG
19040137 TTATGTAAG
1 TTATGTAAG
19040146 TT
1 TT
19040148 CTTGTACATA
Statistics
Matches: 177, Mismatches: 44, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
6 2 0.01
7 19 0.11
8 15 0.08
9 131 0.74
10 8 0.05
11 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:19039968 original size:25 final size:25
Alignment explanation
Indices: 19039902--19039988 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
19039892 TTAAGTAAAT
* * * *
19039902 TTATGTAAGTTATGTACGTGTATAAG
1 TTATGTAAGTTGTGTA-TTATATAAC
* *
19039928 TTATTTAAGTTTTGTATTA-AGTAAAC
1 TTATGTAAGTTGTGTATTATA-T-AAC
19039954 -TATGTAAGTTGTGTATTATATAAC
1 TTATGTAAGTTGTGTATTATATAAC
19039978 TTATGTAAGTT
1 TTATGTAAGTT
19039989 ATCAAAGTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
24 4 0.08
25 29 0.58
26 17 0.34
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATATAAC
Found at i:19040361 original size:53 final size:53
Alignment explanation
Indices: 19040291--19040693 Score: 247
Period size: 53 Copynumber: 7.6 Consensus size: 53
19040281 ATTTATAGCG
*
19040291 AGTAATGTATTTAAGTAACATACTTAAGTAAAAAATTTAACCAAATTTTAGTA
1 AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTA
* * * *
19040344 ATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTTAGTA
1 AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTA
* * * * ** *
19040397 AGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTA--A
1 AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAA-ATTTTAGTA
* * ** * * * * *
19040449 GAGTAA--AATTT-AGTAAAAATATGTTTTATTTATTAATATTGTAA-GACA---T-CTA
1 -AGTAATGTATTTAAGT-AACATA---TTTAAGTA-AAAAATT-TAACCAAATTTTAGTA
* * * * ** * * **
19040501 A--AATATACTTAA-AAATATTTATTTAAGTAATGTAATATATACTTAAATTTATAGCG
1 AGTAATGTATTTAAGTAACA--TATTTAAGTAA-AAAATTTA-AC-CAAATTT-TAGTA
* *
19040557 GGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAAACAAATTTTAGTA
1 AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTA
* * * *
19040610 ATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAAATTTTAGTA
1 AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTA
*
19040663 AGTAATGTATTTAAGTAACTTATTTAAGTAA
1 AGTAATGTATTTAAGTAACATATTTAAGTAA
19040694 TATATTCAAG
Statistics
Matches: 260, Mismatches: 63, Indels: 54
0.69 0.17 0.14
Matches are distributed among these distances:
48 2 0.01
49 11 0.04
50 6 0.02
51 15 0.06
52 5 0.02
53 165 0.63
54 18 0.07
55 8 0.03
56 7 0.03
57 11 0.04
58 9 0.03
59 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (53 bp):
AGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTA
Found at i:19040413 original size:13 final size:13
Alignment explanation
Indices: 19040395--19040446 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
19040385 GAAATTTTAG
*
19040395 TAAGTAATGTATT
1 TAAGTAATATATT
19040408 TAAGTAACT-TATT
1 TAAGTAA-TATATT
19040421 TAAGTAATATATT
1 TAAGTAATATATT
*
19040434 CAAGTAATATATT
1 TAAGTAATATATT
19040447 AAGAGTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 1 0.03
13 34 0.94
14 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:19040580 original size:13 final size:13
Alignment explanation
Indices: 19040558--19040712 Score: 75
Period size: 13 Copynumber: 11.8 Consensus size: 13
19040548 TTTATAGCGG
*
19040558 GTAATGTATTTAA
1 GTAATATATTTAA
*
19040571 GTAACATATTTAA
1 GTAATATATTTAA
* *
19040584 GTAAAAAATTTAA
1 GTAATATATTTAA
** *
19040597 ACAA-ATTTTAGTAA
1 GTAATATATT--TAA
* * * *
19040611 TTAATGTATCTGA
1 GTAATATATTTAA
*
19040624 GTAACATATTTAA
1 GTAATATATTTAA
* *
19040637 GTAAAAAATTTAA
1 GTAATATATTTAA
*
19040650 CG-AA-ATTTTAGTAA
1 -GTAATATATT--TAA
*
19040664 GTAATGTATTTAA
1 GTAATATATTTAA
19040677 GTAACT-TATTTAA
1 GTAA-TATATTTAA
*
19040690 GTAATATATTCAA
1 GTAATATATTTAA
19040703 GTAATATATT
1 GTAATATATT
19040713 AAGAGTAAAA
Statistics
Matches: 106, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
12 7 0.07
13 82 0.77
14 12 0.11
15 5 0.05
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (13 bp):
GTAATATATTTAA
Found at i:19040732 original size:266 final size:273
Alignment explanation
Indices: 19040258--19040953 Score: 1199
Period size: 266 Copynumber: 2.5 Consensus size: 273
19040248 ACAAGTTCTG
* *
19040258 TAAGTAATGTAATATATACTTAAATTTATAGCGAGTAATGTATTTAAGTAACATACTTAAGTAAA
1 TAAGTAATGTAATATATACTTAAATTTATAGCGGGTAATGTATTTAAGTAACATATTTAAGTAAA
19040323 AAATTTAACCAAATTTTAGTAATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAA
66 AAATTTAACCAAATTTTAGTAATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAA
19040388 ATTTTAGTAAGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTAAGAGT
131 ATTTTAGTAAGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTAAGAGT
19040453 AAAATTTAGTAAAAATATG-TTTTATTTATTA-ATATT-GTAAG-AC-ATCTAAAATATAC-TT-
196 AAAATTTAGTAAAAATATGTTTTTATTTATTATATATTGGTAAGAACAATCTAAAATATACTTTA
19040511 AAAAATATTTATT
261 AAAAATATTTATT
19040524 TAAGTAATGTAATATATACTTAAATTTATAGCGGGTAATGTATTTAAGTAACATATTTAAGTAAA
1 TAAGTAATGTAATATATACTTAAATTTATAGCGGGTAATGTATTTAAGTAACATATTTAAGTAAA
*
19040589 AAATTTAAACAAATTTTAGTAATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAA
66 AAATTTAACCAAATTTTAGTAATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAA
19040654 ATTTTAGTAAGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTAAGAGT
131 ATTTTAGTAAGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTAAGAGT
19040719 AAAATTTAGTAAAAATATGTTTTTATTTATTATATATTGGTAAGAACAATCTAAAATATACTTTA
196 AAAATTTAGTAAAAATATGTTTTTATTTATTATATATTGGTAAGAACAATCTAAAATATACTTTA
19040784 AAAAATATTTATT
261 AAAAATATTTATT
19040797 TAAGTAAATGTAATATAATACTTAAATTTATAGCCGGAGTAATGTATTTAAGTAACATATTTAAG
1 TAAGT-AATGTAATAT-ATACTTAAATTTATAG-CGG-GTAATGTATTTAAGTAACATATTTAAG
19040862 TAAAAAAATTTAACCAAATTTTTAGTAAATTTAAATGTATCTGAGTAACATATTTAAGTAAAAAA
62 T-AAAAAATTTAACCAAA-TTTTAGT-AA-TT-AATGTATCTGAGTAACATATTTAAGTAAAAAA
*
19040927 TTTAACCGAAAATTTAAGTAATGTAAT
122 TTTAA-CG-AAATTTTAGTAA-GTAAT
19040954 ATATAAAATT
Statistics
Matches: 406, Mismatches: 5, Indels: 19
0.94 0.01 0.04
Matches are distributed among these distances:
266 211 0.52
267 12 0.03
268 5 0.01
269 5 0.01
270 2 0.00
271 13 0.03
272 2 0.00
273 18 0.04
274 10 0.02
275 16 0.04
276 3 0.01
277 28 0.07
278 15 0.04
279 7 0.02
280 2 0.00
281 2 0.00
282 37 0.09
283 2 0.00
284 11 0.03
285 5 0.01
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (273 bp):
TAAGTAATGTAATATATACTTAAATTTATAGCGGGTAATGTATTTAAGTAACATATTTAAGTAAA
AAATTTAACCAAATTTTAGTAATTAATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACGAA
ATTTTAGTAAGTAATGTATTTAAGTAACTTATTTAAGTAATATATTCAAGTAATATATTAAGAGT
AAAATTTAGTAAAAATATGTTTTTATTTATTATATATTGGTAAGAACAATCTAAAATATACTTTA
AAAAATATTTATT
Found at i:19040909 original size:58 final size:58
Alignment explanation
Indices: 19040837--19040947 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
19040827 TAGCCGGAGT
* * *
19040837 AATGTATTTAAGTAACATATTTAAGTAAAAAAATTTAACC-AAATTTTTAGTAAATTTA
1 AATGTATCTAAGTAACATATTTAAGT-AAAAAATTTAACCGAAAATTTAAGTAAATTTA
*
19040895 AATGTATCTGAGTAACATATTTAAGTAAAAAATTTAACCGAAAATTTAAGTAA
1 AATGTATCTAAGTAACATATTTAAGTAAAAAATTTAACCGAAAATTTAAGTAA
19040948 TGTAATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 13 0.27
58 35 0.73
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (58 bp):
AATGTATCTAAGTAACATATTTAAGTAAAAAATTTAACCGAAAATTTAAGTAAATTTA
Found at i:19043128 original size:198 final size:198
Alignment explanation
Indices: 19042789--19043159 Score: 613
Period size: 198 Copynumber: 1.9 Consensus size: 198
19042779 NNNNNNNNNN
* * * * *
19042789 CGCCACTAGTAATATGATCAAACGCTGTCGTTTCTCGATCAATTAACTCAAAGTCATTGCGTTTT
1 CGCCACTAGTAATATGATCAAACGCTGTCGTTTCCCGATCAATTAACTAAAACTCATGGCGTATT
* *
19042854 AGAGAAAACGGCATCGTCTCCATAAAAATTAAAACATTTTTGCGGCGTTTACTAAAAGCGCCACT
66 AGAGAAAACGACATCATCTCCATAAAAATTAAAACATTTTTGCGGCGTTTACTAAAAGCGCCACT
19042919 AAAAGTAAATAAGAAAAC-GAAGCCGTTTTCCTAAACAATTTCTGTAATTTACAGCGCTTATATA
131 AAAAGTAAATAAGAAAACAG-AGCCGTTTTCCTAAACAATTTCTGTAATTTACAGCGCTTATATA
19042983 CCAA
195 CCAA
* *
19042987 CGCCACTAGTAATATGATCAAACGCTGTCGTTTCCCGATTAGTTAACTAAAACTCATGGCGTATT
1 CGCCACTAGTAATATGATCAAACGCTGTCGTTTCCCGATCAATTAACTAAAACTCATGGCGTATT
19043052 AGAGAAAACGACATCATCTCCATAAAAATTAAAACCA-TTTTGCGGCGTTTACTAAAAGCGCCAC
66 AGAGAAAACGACATCATCTCCATAAAAATTAAAA-CATTTTTGCGGCGTTTACTAAAAGCGCCAC
19043116 T-AAAGTTAAATAAGAAAACAGAGCCGTTTTCCTAAACAATTTCT
130 TAAAAG-TAAATAAGAAAACAGAGCCGTTTTCCTAAACAATTTCT
19043160 ATAAATTGCG
Statistics
Matches: 161, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
197 4 0.02
198 154 0.96
199 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (198 bp):
CGCCACTAGTAATATGATCAAACGCTGTCGTTTCCCGATCAATTAACTAAAACTCATGGCGTATT
AGAGAAAACGACATCATCTCCATAAAAATTAAAACATTTTTGCGGCGTTTACTAAAAGCGCCACT
AAAAGTAAATAAGAAAACAGAGCCGTTTTCCTAAACAATTTCTGTAATTTACAGCGCTTATATAC
CAA
Found at i:19043692 original size:13 final size:13
Alignment explanation
Indices: 19043674--19043699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19043664 NNNNNNNNNA
19043674 TTTTATTTTTTGT
1 TTTTATTTTTTGT
19043687 TTTTATTTTTTGT
1 TTTTATTTTTTGT
19043700 AATTTTGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTGT
Found at i:19043930 original size:89 final size:88
Alignment explanation
Indices: 19043822--19043991 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 88
19043812 TATAAAGAAC
* * ** * * * * *
19043822 TTATTTAATATGTTAATTAAAAAGTAGTAATTAATCCAAATCTTAATCCCTAACCCGA-CTCCAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAAGCTTAAACCATAACCCAATC-CCAA
19043886 ATCCATAACCCCTAACCCCTAAACT
65 A-CCATAACCCCTAACCCCTAAACT
* *
19043911 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAGCTTAAACCATAACCCAATCCCTAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAAGCTTAAACCATAACCCAATCCCAAA
*
19043976 CCCTAACCCCTAACCC
66 CCATAACCCCTAACCC
19043992 TTAACCCTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
88 15 0.22
89 52 0.76
90 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.29
Consensus pattern (88 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAAGCTTAAACCATAACCCAATCCCAAA
CCATAACCCCTAACCCCTAAACT
Found at i:19043988 original size:7 final size:7
Alignment explanation
Indices: 19043973--19044106 Score: 182
Period size: 7 Copynumber: 19.3 Consensus size: 7
19043963 ACCCAATCCC
19043973 TAACCC-
1 TAACCCT
*
19043979 TAACCCC
1 TAACCCT
19043986 TAACCCT
1 TAACCCT
19043993 TAACCCT
1 TAACCCT
19044000 TAACCCT
1 TAACCCT
19044007 TAACCCT
1 TAACCCT
19044014 TAACCCT
1 TAACCCT
19044021 TAACCCT
1 TAACCCT
19044028 TAACCCT
1 TAACCCT
19044035 TAACCCT
1 TAACCCT
19044042 TAACCCT
1 TAACCCT
19044049 TAACCCT
1 TAACCCT
*
19044056 AAACCCT
1 TAACCCT
*
19044063 TAACCCA
1 TAACCCT
*
19044070 TGA-CCT
1 TAACCCT
19044076 CTAACCCT
1 -TAACCCT
*
19044084 TAACCCC
1 TAACCCT
*
19044091 TAACCCC
1 TAACCCT
*
19044098 TAAACCT
1 TAACCCT
19044105 TA
1 TA
19044107 TTTAATATAT
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
6 8 0.07
7 104 0.90
8 3 0.03
ACGTcount: A:0.31, C:0.44, G:0.01, T:0.25
Consensus pattern (7 bp):
TAACCCT
Found at i:19044210 original size:7 final size:7
Alignment explanation
Indices: 19044200--19044243 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
19044190 CTCTTAACAT
19044200 CTAACCC
1 CTAACCC
19044207 CTAA--C
1 CTAACCC
19044212 CTAACCC
1 CTAACCC
19044219 CTAACCC
1 CTAACCC
19044226 CTAACCC
1 CTAACCC
19044233 CTAACCC
1 CTAACCC
19044240 CTAA
1 CTAA
19044244 TCTATAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
7 30 0.86
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:19044211 original size:14 final size:12
Alignment explanation
Indices: 19044200--19044238 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
19044190 CTCTTAACAT
19044200 CTAACCCCTAAC
1 CTAACCCCTAAC
19044212 CTAACCCCTAACCC
1 CTAACCCCTAA--C
19044226 CTAACCCCTAAC
1 CTAACCCCTAAC
19044238 C
1 C
19044239 CCTAATCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.52
14 12 0.48
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:19044223 original size:26 final size:26
Alignment explanation
Indices: 19044185--19044238 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
19044175 ACCCTAAATC
* * *
19044185 CCTAACTCTTAACATCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
*
19044211 CCTAACCCCTAACCCCTAACCCCTAA
1 CCTAACCCCTAACACCTAACCCCTAA
19044237 CC
1 CC
19044239 CCTAATCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.20
Consensus pattern (26 bp):
CCTAACCCCTAACACCTAACCCCTAA
Found at i:19045182 original size:113 final size:112
Alignment explanation
Indices: 19044897--19045219 Score: 348
Period size: 113 Copynumber: 2.9 Consensus size: 112
19044887 TATACCTCAA
* * *
19044897 AACCAAGCCCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAAACGCCACTAATGATGT
1 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTAC-AATAAACGCCACTAATGATAT
* * *
19044962 TCTTTTACGGCGTTTGTTTAAAAACGCCACTAATACTAATCTACCTCG
65 TCTTTTACGGCGTTTGTTCAAAAACGCCACTAATACTAATATACATCG
* * **** * *
19045010 AGACCAAACGCTGCGTTTTCGTTAAGATA-TTTGCGGCGCTTTTTGTAAAATGCCGCTAAT-ACT
1 A-ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAT-AAACGCCACTAATGA-T
* * *
19045073 ATTC-TTTAGCGGCGTTT-TATCGAAAACGCCACTAATTCTAATATACAATTG
63 ATTCTTTTA-CGGCGTTTGT-TCAAAAACGCCACTAATACTAATATAC-ATCG
* *
19045124 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTATGTT
1 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATGATATT
* * * *
19045189 CTTTTACAGCGTTTTTTTAGAAACGCCACTA
66 CTTTTACGGCGTTTGTTCAAAAACGCCACTA
19045220 GTTGTTCAGG
Statistics
Matches: 170, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
112 7 0.04
113 118 0.69
114 45 0.26
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (112 bp):
AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATGATATT
CTTTTACGGCGTTTGTTCAAAAACGCCACTAATACTAATATACATCG
Found at i:19045397 original size:41 final size:41
Alignment explanation
Indices: 19045352--19045443 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
19045342 CATTTTTAAT
* *
19045352 GAAGCGCTGCTAAAGTTAAGGTTTTTAGCGACGTTTTT-TG
1 GAAGCGCCGCTAAAGTTAAGGGTTTTAGCGACGTTTTTGTG
* * *
19045392 AGAAGCGCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTTGTG
1 -GAAGCGCCGCTAAAGTTAAGGGTTTTAGCGACGTTTTTGTG
19045434 GAAGCGCCGC
1 GAAGCGCCGC
19045444 AAAAAACATT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.32
Consensus pattern (41 bp):
GAAGCGCCGCTAAAGTTAAGGGTTTTAGCGACGTTTTTGTG
Found at i:19046401 original size:7 final size:7
Alignment explanation
Indices: 19046389--19046447 Score: 64
Period size: 7 Copynumber: 7.9 Consensus size: 7
19046379 AGATTAAGGT
19046389 TTAGGGG
1 TTAGGGG
19046396 TTAGGGG
1 TTAGGGG
19046403 TTAGTGGG
1 TTAG-GGG
19046411 ATTTAGGGG
1 --TTAGGGG
19046420 TTAGGGG
1 TTAGGGG
*
19046427 TTAGGGAT
1 TTAGGG-G
*
19046435 TTAGGGT
1 TTAGGGG
19046442 TTAGGG
1 TTAGGG
19046448 TATCAAGGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
7 31 0.66
8 9 0.19
9 3 0.06
10 4 0.09
ACGTcount: A:0.17, C:0.00, G:0.49, T:0.34
Consensus pattern (7 bp):
TTAGGGG
Found at i:19046436 original size:22 final size:23
Alignment explanation
Indices: 19046388--19046447 Score: 95
Period size: 24 Copynumber: 2.6 Consensus size: 23
19046378 GAGATTAAGG
19046388 TTTAGGGGTTAGGGGTTAGTGGGA
1 TTTAGGGGTTAGGGGTTAG-GGGA
19046412 TTTAGGGGTTAGGGGTTA-GGGA
1 TTTAGGGGTTAGGGGTTAGGGGA
*
19046434 TTTAGGGTTTAGGG
1 TTTAGGGGTTAGGG
19046448 TATCAAGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 17 0.49
24 18 0.51
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.35
Consensus pattern (23 bp):
TTTAGGGGTTAGGGGTTAGGGGA
Found at i:19048745 original size:12 final size:12
Alignment explanation
Indices: 19048728--19048753 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19048718 TAGTTTGAAA
19048728 TTGTTCATAATT
1 TTGTTCATAATT
19048740 TTGTTCATAATT
1 TTGTTCATAATT
19048752 TT
1 TT
19048754 CACTATCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTGTTCATAATT
Found at i:19049359 original size:25 final size:26
Alignment explanation
Indices: 19049325--19049382 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
19049315 CTCGTTGCAT
*
19049325 AATAATTCTTACTCTAT-GCGTATCA
1 AATAATTCTTACTCTATAGCGTATAA
*
19049350 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCGTATAA
19049376 AATAATT
1 AATAATT
19049383 AAATTCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCGTATAA
Found at i:19050238 original size:21 final size:21
Alignment explanation
Indices: 19050214--19050253 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19050204 ATTGTAAATG
* *
19050214 CTATTTTTTAAATATTAAAAC
1 CTATATTTTAAATAATAAAAC
*
19050235 CTATATTTTCAATAATAAA
1 CTATATTTTAAATAATAAA
19050254 TTTTATAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
CTATATTTTAAATAATAAAAC
Found at i:19050256 original size:69 final size:69
Alignment explanation
Indices: 19050176--19050386 Score: 377
Period size: 69 Copynumber: 3.1 Consensus size: 69
19050166 AAATTTTATT
* * *
19050176 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGCTATTTTTTAAATATTAAAACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
19050241 TTTC
66 TTTC
*
19050245 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAGCACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
19050310 TTTC
66 TTTC
19050314 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
*
19050379 TTTT
66 TTTC
19050383 AATA
1 AATA
19050387 TATCACCCCA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 136 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (69 bp):
AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
TTTC
Found at i:19050693 original size:16 final size:16
Alignment explanation
Indices: 19050672--19050949 Score: 169
Period size: 16 Copynumber: 16.8 Consensus size: 16
19050662 CTTATATATA
19050672 AACTTACATAATACAT
1 AACTTACATAATACAT
*
19050688 AACTTACATAATATAT
1 AACTTACATAATACAT
* * *
19050704 AGCCTACATAAATTGCAT
1 AACTTACAT-AA-TACAT
* * *
19050722 AACTCACAAAATACAC
1 AACTTACATAATACAT
*
19050738 AACTTACATAACTTAAAT
1 AACTTACATAA--TACAT
19050756 AACTTACATAATACAT
1 AACTTACATAATACAT
19050772 AACTTA-ATTAATTA-AT
1 AACTTACA-TAA-TACAT
*
19050788 -ATTATACATAACTTACAT
1 AACT-TACATAA--TACAT
* *
19050806 AGCTTACA-ACTTACAT
1 AACTTACATA-ATACAT
19050822 AACTTA-ATTAATTA-AT
1 AACTTACA-TAA-TACAT
* *
19050838 -ATTATACACAACTTACAT
1 AACT-TACATAA--TACAT
*
19050856 AACATACATAATACAT
1 AACTTACATAATACAT
*
19050872 AACTTACATAATACAC
1 AACTTACATAATACAT
*
19050888 AACTTACATAGCTTACAT
1 AACTTACATA--ATACAT
19050906 AA--TACATAACTTACAT
1 AACTTACATAA--TACAT
*
19050922 AACTTATATAATACAT
1 AACTTACATAATACAT
19050938 AACTTACATAAT
1 AACTTACATAAT
19050950 TTACGTAATA
Statistics
Matches: 202, Mismatches: 34, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
15 6 0.03
16 128 0.63
17 18 0.09
18 48 0.24
19 2 0.01
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.32
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:19050725 original size:34 final size:34
Alignment explanation
Indices: 19050676--19050770 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 34
19050666 TATATAAACT
* * *
19050676 TACAT-AA-TACATAACTTACATAATATATAGCC
1 TACATAAATTACATAACTTACATAATACACAACC
* * * *
19050708 TACATAAATTGCATAACTCACAAAATACACAACT
1 TACATAAATTACATAACTTACATAATACACAACC
* *
19050742 TACATAACTTAAATAACTTACATAATACA
1 TACATAAATTACATAACTTACATAATACA
19050771 TAACTTAATT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 5 0.10
33 2 0.04
34 42 0.86
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.28
Consensus pattern (34 bp):
TACATAAATTACATAACTTACATAATACACAACC
Found at i:19050770 original size:25 final size:24
Alignment explanation
Indices: 19050742--19050991 Score: 149
Period size: 25 Copynumber: 10.0 Consensus size: 24
19050732 ATACACAACT
*
19050742 TACATAACTTAAATAACTTACATAA
1 TACATAACTTACATAA-TTACATAA
19050767 TACATAACTTA-ATTAATTA-ATATTA
1 TACATAACTTACA-TAATTACATA--A
* *
19050792 TACATAACTTACATAGCTTACA-ACT
1 TACATAACTTACATA-ATTACATA-A
19050817 TACATAACTTA-ATTAATTA-ATATTA
1 TACATAACTTACA-TAATTACATA--A
* *
19050842 TACACAACTTACATAACATACATAA
1 TACATAACTTACATAA-TTACATAA
*
19050867 TACATAACTTACATAA-TACACAA
1 TACATAACTTACATAATTACATAA
*
19050890 CTTACATAGCTTACATAA-TACATAA
1 --TACATAACTTACATAATTACATAA
*
19050915 CTTACATAACTTATATAA-TACATAA
1 --TACATAACTTACATAATTACATAA
* *
19050940 CTTACATAATTTACGTAA-TACATAAA
1 --TACATAACTTACATAATTACAT-AA
* * *
19050966 TATATATCATATCATAACTTACATAA
1 TACATAACTTA-CATAA-TTACATAA
19050992 CTCATATATA
Statistics
Matches: 185, Mismatches: 22, Indels: 35
0.76 0.09 0.14
Matches are distributed among these distances:
23 10 0.05
24 16 0.09
25 138 0.75
26 12 0.06
27 9 0.05
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (24 bp):
TACATAACTTACATAATTACATAA
Found at i:19050798 original size:75 final size:74
Alignment explanation
Indices: 19050719--19050953 Score: 207
Period size: 75 Copynumber: 3.1 Consensus size: 74
19050709 ACATAAATTG
*
19050719 CATAACTCACAAAATACACAACTTACATAACTTAAATAACTTACATAATACATAACTTA-ATTAA
1 CATAACTTACAAAATACACAACTTACATAACTTAAATAA-TTACATAATACATAACTTACA-TAA
*
19050783 -TTA-ATATTATA
64 CATACATA--ATA
** * * *
19050794 CATAACTTACATAGCT-TACAACTTACATAACTTAATTAATTA-ATATTATACACAACTTACATA
1 CATAACTTACA-AAATACACAACTTACATAACTTAAATAATTACATA--ATACATAACTTACATA
19050857 ACATACATAATA
63 ACATACATAATA
* * * *
19050869 CATAACTTACATAATACACAACTTACATAGCTTACATAA-TACATAACTTACATAACTTATAT-A
1 CATAACTTACAAAATACACAACTTACATAACTTAAATAATTACATAA--TACATAACTTACATAA
19050932 -ATACATAACTTA
64 CATACATAA--TA
*
19050944 CATAATTTAC
1 CATAACTTAC
19050954 GTAATACATA
Statistics
Matches: 131, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
73 12 0.09
74 7 0.05
75 104 0.79
76 5 0.04
77 3 0.02
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.33
Consensus pattern (74 bp):
CATAACTTACAAAATACACAACTTACATAACTTAAATAATTACATAATACATAACTTACATAACA
TACATAATA
Found at i:19051179 original size:66 final size:66
Alignment explanation
Indices: 19051097--19051248 Score: 216
Period size: 66 Copynumber: 2.3 Consensus size: 66
19051087 GTCAAGGGTA
* *
19051097 AGCATCGAGAGAAGCTGAGGTTCAAAA-AAGATATGAAGAACTTCAGCTACAACTTAAAGCAGAA
1 AGCAGCGAGAGAAGCTGAGGTTCAAAAGAAG-TATGAAGAACTCCAGCTACAACTTAAAGCAGAA
19051161 GC
65 GC
* * *
19051163 AGCAGCGAGAGAAGCTGAGGTTCAAAAGAAGTATGAAGAACTCCAGCTTCAGCTTAAAGCAGAGG
1 AGCAGCGAGAGAAGCTGAGGTTCAAAAGAAGTATGAAGAACTCCAGCTACAACTTAAAGCAGAAG
19051228 C
66 C
* * *
19051229 GGCAGCGAGGGAAGCAGAGG
1 AGCAGCGAGAGAAGCTGAGG
19051249 CAGCAGCGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
66 74 0.96
67 3 0.04
ACGTcount: A:0.39, C:0.17, G:0.30, T:0.14
Consensus pattern (66 bp):
AGCAGCGAGAGAAGCTGAGGTTCAAAAGAAGTATGAAGAACTCCAGCTACAACTTAAAGCAGAAG
C
Found at i:19051243 original size:21 final size:21
Alignment explanation
Indices: 19051219--19051268 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
19051209 CTTCAGCTTA
* *
19051219 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
19051240 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
19051261 AAACAGAG
1 AAGCAGAG
19051269 CAGAGCAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.44, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:19051626 original size:43 final size:43
Alignment explanation
Indices: 19051591--19051795 Score: 302
Period size: 43 Copynumber: 4.8 Consensus size: 43
19051581 CGTTTTTAAA
* * * *
19051591 AAAAACGCCACTAAAGGTCATGGCCTATAGCGGCGTTTGTGTG
1 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
* *
19051634 AAAAGCACCGATAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
1 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
*
19051677 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
* * *
19051720 AAAAGCGCCGCCAAAGGTCGTGGCCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
**
19051763 AAAAGCGCCGCTAAAGGTTGTGGCCTATAGCGG
1 AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGG
19051796 AGGCGTTTAT
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 149 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTTTGGG
Found at i:19054257 original size:66 final size:67
Alignment explanation
Indices: 19054098--19054290 Score: 239
Period size: 66 Copynumber: 2.9 Consensus size: 67
19054088 AAAAGTATTT
* ** *
19054098 TTAT-TTTTTACATCAAGAATATACTTATTTACAATTTACGAAAAAATGAAAAATTGTTGGTATA
1 TTATATTTTTACATCAACAATATACTTATTTACAATTTACGAAAAAATGAAAAA--AAT-GCATA
19054162 TTGTA
63 TTGTA
* *
19054167 TTGTATTTTTACATCAACAATATACTTATTTATAATTTACGAAAAAAATGAAAAAAAT-CAT-TT
1 TTATATTTTTACATCAACAATATACTTATTTACAATTTACG-AAAAAATGAAAAAAATGCATATT
19054230 GTA
65 GTA
* ** *
19054233 TTATATTTTTACATCAATAATATACTTATTTACAATTTACCCAAAAATGGAAAAAATG
1 TTATATTTTTACATCAACAATATACTTATTTACAATTTACGAAAAAATGAAAAAAATG
19054291 AATTATTTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
65 14 0.13
66 42 0.39
67 2 0.02
69 4 0.04
70 34 0.31
71 13 0.12
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (67 bp):
TTATATTTTTACATCAACAATATACTTATTTACAATTTACGAAAAAATGAAAAAAATGCATATTG
TA
Found at i:19059715 original size:26 final size:27
Alignment explanation
Indices: 19059673--19059744 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
19059663 TCTTATCCCT
* *
19059673 ATTTTA-CCCTCAATAAAA-AATTGACG
1 ATTTTACCCCT-AGTAAAATAATTAACG
**
19059699 ATTTTACCCCTAGTAAAATTTTTAACG
1 ATTTTACCCCTAGTAAAATAATTAACG
* *
19059726 ATTTTACCCTTGGTAAAAT
1 ATTTTACCCCTAGTAAAAT
19059745 TTTAAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 12 0.32
27 26 0.68
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (27 bp):
ATTTTACCCCTAGTAAAATAATTAACG
Found at i:19059749 original size:26 final size:27
Alignment explanation
Indices: 19059696--19059747 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
19059686 TAAAAAATTG
19059696 ACGATTTTACCCCTAGTAAAATTTTTA
1 ACGATTTTACCCCTAGTAAAATTTTTA
* *
19059723 ACGATTTTACCCTTGGTAAAATTTT
1 ACGATTTTACCCCTAGTAAAATTTT
19059748 AAGAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (27 bp):
ACGATTTTACCCCTAGTAAAATTTTTA
Found at i:19065653 original size:18 final size:18
Alignment explanation
Indices: 19065630--19065665 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19065620 AAACCCTAGA
19065630 ATTCTTT-TGAGTCTGATT
1 ATTCTTTGTGA-TCTGATT
19065648 ATTCTTTGTGATCTGATT
1 ATTCTTTGTGATCTGATT
19065666 TTTTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (18 bp):
ATTCTTTGTGATCTGATT
Found at i:19073816 original size:21 final size:21
Alignment explanation
Indices: 19073785--19073841 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
19073775 ATTGTTGTTG
*
19073785 AGAAGGAAGTTGCTGCTGCAGA
1 AGAA-GAAGTTGCTGCTGAAGA
* *
19073807 AG-AGAAAGTTGTTTCTGAAGA
1 AGAAG-AAGTTGCTGCTGAAGA
19073828 AGAAGAAGTTGCTG
1 AGAAGAAGTTGCTG
19073842 AAAATGAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (21 bp):
AGAAGAAGTTGCTGCTGAAGA
Found at i:19074317 original size:17 final size:17
Alignment explanation
Indices: 19074295--19074328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19074285 GATAAATATA
* *
19074295 TATTGTGATTGCATTTT
1 TATTGTCATTACATTTT
19074312 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
19074329 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:19077211 original size:23 final size:22
Alignment explanation
Indices: 19077168--19077211 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
19077158 ATATTTTTAA
19077168 AATTTTAATTTTTTTAATATATG
1 AATTTTAATTTTTTT-ATATATG
19077191 AATTTTATATTCTTTTT-TATA
1 AATTTTA-ATT-TTTTTATATA
19077212 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
AATTTTAATTTTTTTATATATG
Found at i:19078513 original size:15 final size:16
Alignment explanation
Indices: 19078490--19078522 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19078480 ATAAATGTCT
19078490 TTAAAAATAAAA-AAA
1 TTAAAAATAAAATAAA
*
19078505 TTAACAATAAAATAAA
1 TTAAAAATAAAATAAA
19078521 TT
1 TT
19078523 TTATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAAAATAAAATAAA
Found at i:19079174 original size:30 final size:30
Alignment explanation
Indices: 19079140--19079199 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19079130 ACTTAACAAG
19079140 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
19079170 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
19079200 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:19090187 original size:33 final size:34
Alignment explanation
Indices: 19090111--19090187 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
19090101 TTTTAATTTC
*
19090111 TTTGGGTTTTTTATTTGATTTAAATGTTTTCAAG
1 TTTGGATTTTTTATTTGATTTAAATGTTTTCAAG
** *
19090145 TTTATATTTTTTATTTGATTTAAATGTTTT-GAG
1 TTTGGATTTTTTATTTGATTTAAATGTTTTCAAG
19090178 TTTGGATTTT
1 TTTGGATTTT
19090188 GAATTTAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 10 0.27
34 27 0.73
ACGTcount: A:0.21, C:0.01, G:0.16, T:0.62
Consensus pattern (34 bp):
TTTGGATTTTTTATTTGATTTAAATGTTTTCAAG
Found at i:19091706 original size:2 final size:2
Alignment explanation
Indices: 19091687--19091727 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
19091677 AGAATGACCT
*
19091687 TA TA T- TA TA TG T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19091727 T
1 T
19091728 TAGTAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:19092252 original size:43 final size:43
Alignment explanation
Indices: 19092201--19092314 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
19092191 TGTGTTATCG
* * *
19092201 TGTAAGACCACGTCTGGGACGTTGGCATCGACT-TGTGTTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATC-AATGCGTGATTACA
19092244 TGTAAGACC-CTGTCTGGGACAG-TGGCATCAATGCGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAATGCGTGATTACA
19092287 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
19092315 TGTAAGAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
42 4 0.06
43 57 0.90
44 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAATGCGTGATTACA
Found at i:19093195 original size:23 final size:23
Alignment explanation
Indices: 19093168--19093314 Score: 143
Period size: 23 Copynumber: 6.3 Consensus size: 23
19093158 ATGAGTTGAA
*
19093168 CCAATTTGTTACATACATGCTGT
1 CCAATTTGTTACATATATGCTGT
* * * * *
19093191 CCAATTTTGATGA-TTAAATGTTGC
1 CCAA-TTTG-TTACATATATGCTGT
19093215 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
19093238 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
* * * * *
19093261 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGTTACATATATGCTGT
* *
19093285 CCAGTTTGTTGCATATATGCTGT
1 CCAATTTGTTACATATATGCTGT
19093308 CCAATTT
1 CCAATTT
19093315 TGGTGTAAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
22 2 0.02
23 63 0.64
24 32 0.32
25 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (23 bp):
CCAATTTGTTACATATATGCTGT
Found at i:19093286 original size:70 final size:70
Alignment explanation
Indices: 19093168--19093314 Score: 249
Period size: 70 Copynumber: 2.1 Consensus size: 70
19093158 ATGAGTTGAA
*
19093168 CCAATTTGTTACATACATGCTGTCCAATTTTGATGATTAAATGTTGCCCAATTTGTTACATATAT
1 CCAATTTGTTACATACATGCTGTCCAATTTTGATGATTAAATGCTGCCCAATTTGTTACATATAT
19093233 GCTGT
66 GCTGT
* * * *
19093238 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAGTTTGTTGCATATAT
1 CCAATTTGTTACATACATGCTGTCCAATTTTGATGATTAAATGCTGCCCAATTTGTTACATATAT
19093303 GCTGT
66 GCTGT
19093308 CCAATTT
1 CCAATTT
19093315 TGGTGTAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (70 bp):
CCAATTTGTTACATACATGCTGTCCAATTTTGATGATTAAATGCTGCCCAATTTGTTACATATAT
GCTGT
Found at i:19093327 original size:47 final size:47
Alignment explanation
Indices: 19093231--19093324 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
19093221 TGTTACATAT
* *
19093231 ATGCTGTCCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCTAAA
* * *
19093278 ATGCTGCCCAGTTTGTTGCATATATGCTGTCCAATTTTGGTG-TAAA
1 ATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCTAAA
19093324 A
1 A
19093325 ATGTTGCTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 4 0.10
47 38 0.90
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.40
Consensus pattern (47 bp):
ATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGATGCTAAA
Found at i:19093342 original size:47 final size:47
Alignment explanation
Indices: 19093244--19093358 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
19093234 CTGTCCAATT
* * ***
19093244 TGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAGTT
1 TGTTGCATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
* * *
19093291 TGTTGCATATATGCTGTCCAATTTTGGTG-TAAAAATGTTGCTCAAAC
1 TGTTGCATATATGCTGTCCAATTTTGATGCT-AAAATGCTGCCCAAAC
* *
19093338 TGTTGTATATATGCTGCCCAA
1 TGTTGCATATATGCTGTCCAA
19093359 ATTGATGTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 1 0.02
47 56 0.98
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (47 bp):
TGTTGCATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
Found at i:19093383 original size:23 final size:23
Alignment explanation
Indices: 19093227--19093384 Score: 75
Period size: 23 Copynumber: 6.8 Consensus size: 23
19093217 AATTTGTTAC
* * * **
19093227 ATATATGCTGTCCAATTTGTTAC
1 ATATATGCTGCCCAAATTGATGT
* *
19093250 ATATATGCTGTCCAATTTTGATGCT
1 ATATATGCTGCCCAA-ATTGATG-T
* ** * *
19093275 -TAAATGCTGCCCAGTTTGTTGC
1 ATATATGCTGCCCAAATTGATGT
* * *
19093297 ATATATGCTGTCCAATTTTGGTGT
1 ATATATGCTGCCCAA-ATTGATGT
* * * * * *
19093321 AAAAATGTTGCTCAAACTGTTGT
1 ATATATGCTGCCCAAATTGATGT
19093344 ATATATGCTGCCCAAATTGATGT
1 ATATATGCTGCCCAAATTGATGT
* *
19093367 ATTTATGCTGTCCAAATT
1 ATATATGCTGCCCAAATT
19093385 TTAGCGTGAA
Statistics
Matches: 102, Mismatches: 29, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
23 70 0.69
24 32 0.31
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (23 bp):
ATATATGCTGCCCAAATTGATGT
Found at i:19098364 original size:45 final size:45
Alignment explanation
Indices: 19098300--19098388 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
19098290 AACAGATACT
* *
19098300 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
19098345 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
19098389 TCAGTTCACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:19098464 original size:51 final size:51
Alignment explanation
Indices: 19098395--19098535 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 51
19098385 ATGTTCAGTT
* * * *
19098395 CACATAGTAGCATTCACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
* * * *
19098446 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCGATA
*
19098497 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
19098536 CACTTTCACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.03
51 73 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
Found at i:19101174 original size:24 final size:24
Alignment explanation
Indices: 19101147--19101205 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
19101137 ATTGCCTTTG
19101147 TGGCATATTCTGTAAATGCCTCTA
1 TGGCATATTCTGTAAATGCCTCTA
* * * * *
19101171 TGGCGTATTTTGTAATTGCCTTTG
1 TGGCATATTCTGTAAATGCCTCTA
*
19101195 TGGAATATTCT
1 TGGCATATTCT
19101206 ATGATGTCTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (24 bp):
TGGCATATTCTGTAAATGCCTCTA
Found at i:19103797 original size:21 final size:20
Alignment explanation
Indices: 19103773--19103812 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19103763 AGGAAATTAC
19103773 TTTAAATGATTTCAAAATGTG
1 TTTAAA-GATTTCAAAATGTG
* *
19103794 TTTAAAGCTTTGAAAATGT
1 TTTAAAGATTTCAAAATGT
19103813 TGGAAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTAAAGATTTCAAAATGTG
Found at i:19106351 original size:143 final size:132
Alignment explanation
Indices: 19106186--19106461 Score: 354
Period size: 143 Copynumber: 2.0 Consensus size: 132
19106176 CATCATGTGC
** * **
19106186 AAGATCATGTGAAACAATTTACACGAGCCTTGAGGGGTGATATGGATATGAAACAAATCGAATCG
1 AAGATCATGCAAAACAATTTACACGAGCCTCGAGGGCCGATATGGATATG----AAA-CGAATCG
* *
19106251 ACTGATTCAAAAATGAAATGAGATAATGGAATGAATATATATATACACACATATATGATTGTTGC
61 ACCGATTCAAAAATGAAATGAGATAATGAAATG-A-ATATATAT----ACATATATGATTGTTGC
*
19106316 AAACTAACTATCG
120 AAACTAACAATCG
* *
19106329 AAGATCATGCAAAACGATTTACAGGAGCCTCGAGGGCCGATATGGATATGAAACGAATCGACCGA
1 AAGATCATGCAAAACAATTTACACGAGCCTCGAGGGCCGATATGGATATGAAACGAATCGACCGA
*
19106394 TTCAGAAATGAAATGAGATAATGAAATGAATATATATACATATATGATTGTTGCAAACTAACAAT
66 TTCAAAAATGAAATGAGATAATGAAATGAATATATATACATATATGATTGTTGCAAACTAACAAT
19106459 CG
131 CG
19106461 A
1 A
19106462 GGTAAGCATA
Statistics
Matches: 122, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
132 30 0.25
136 8 0.07
137 1 0.01
138 37 0.30
139 3 0.02
143 43 0.35
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (132 bp):
AAGATCATGCAAAACAATTTACACGAGCCTCGAGGGCCGATATGGATATGAAACGAATCGACCGA
TTCAAAAATGAAATGAGATAATGAAATGAATATATATACATATATGATTGTTGCAAACTAACAAT
CG
Found at i:19111409 original size:18 final size:18
Alignment explanation
Indices: 19111379--19111413 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19111369 ATGTTGTACA
19111379 TGTTATGACATTGTGATT
1 TGTTATGACATTGTGATT
19111397 TGTTGATGA-ATTGTGAT
1 TGTT-ATGACATTGTGAT
19111414 GATCAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (18 bp):
TGTTATGACATTGTGATT
Found at i:19116674 original size:388 final size:388
Alignment explanation
Indices: 19115958--19116738 Score: 1526
Period size: 388 Copynumber: 2.0 Consensus size: 388
19115948 GGTTTTAGAA
* *
19115958 AATGAGGTATCGGGACCTCGTTTCTATAAACTGAGCCATAAATATTTTTATAAATATTTAGAGAA
1 AATGAGGTATCGGGACCTCATTTCTATAAACTGAGCCATAAATATTTTTATAAATATTTACAGAA
19116023 TGTTATTAAGGTGGTATTAAATTTTCGTTAAAAAATTTTAACGTTTCGATAGTTAATTAAGCGAA
66 TGTTATTAAGGTGGTATTAAATTTTCGTTAAAAAATTTTAACGTTTCGATAGTTAATTAAGCGAA
19116088 AAGGACTAAATCTTAAAAAGTGTAAAATGTGATCCCTATTTGATTAGAGTGATTAAATGGCTTAT
131 AAGGACTAAATCTTAAAAAGTGTAAAATGTGATCCCTATTTGATTAGAGTGATTAAATGGCTTAT
19116153 TGAATAAAGGAAAAGTGACCTAGATGGTAATTGGACCATTATTATAAATAGTGGACAAAGGTGGA
196 TGAATAAAGGAAAAGTGACCTAGATGGTAATTGGACCATTATTATAAATAGTGGACAAAGGTGGA
19116218 CATTAAATAGGTGATTTTTGATATTATAAAAAAGGTTGATTTAGTAATTTATTTATTAAAAGAAA
261 CATTAAATAGGTGATTTTTGATATTATAAAAAAGGTTGATTTAGTAATTTATTTATTAAAAGAAA
*
19116283 TTTAAAACAAATAAAAAAATGGCATCATCTTTTTTAAATTTAGTTCCACAAAATTTGTTGAAG
326 TTTAAAACAAATAAAAAAATGGCATCATCTTCTTTAAATTTAGTTCCACAAAATTTGTTGAAG
19116346 AATGAGGTATCGGGACCTCATTTCTATAAACTGAGCCATAAATATTTTTATAAATATTTACAGAA
1 AATGAGGTATCGGGACCTCATTTCTATAAACTGAGCCATAAATATTTTTATAAATATTTACAGAA
19116411 TGTTATTAAGGTGGTATTAAATTTTCGTTAAAAAATTTTAACGTTTCGATAGTTAATTAAGCGAA
66 TGTTATTAAGGTGGTATTAAATTTTCGTTAAAAAATTTTAACGTTTCGATAGTTAATTAAGCGAA
19116476 AAGGACTAAATCTTAAAAAGTGTAAAATGTGATCCCTATTTGATTAGAGTGATTAAATGGCTTAT
131 AAGGACTAAATCTTAAAAAGTGTAAAATGTGATCCCTATTTGATTAGAGTGATTAAATGGCTTAT
*
19116541 TGAATAAAGGAAAAGTGACCTAGATGGTAATTGGACCATTATTATAAATAGTGGACAAGGGTGGA
196 TGAATAAAGGAAAAGTGACCTAGATGGTAATTGGACCATTATTATAAATAGTGGACAAAGGTGGA
19116606 CATTAAATAGGTGATTTTTGATATTATAAAAAAGGTTGATTTAGTAATTTATTTATTAAAAGAAA
261 CATTAAATAGGTGATTTTTGATATTATAAAAAAGGTTGATTTAGTAATTTATTTATTAAAAGAAA
19116671 TTTAAAACAAATAAAAAAATGGCATCATCTTCTTTAAATTTAGTTCCACAAAATTTGTTGAAG
326 TTTAAAACAAATAAAAAAATGGCATCATCTTCTTTAAATTTAGTTCCACAAAATTTGTTGAAG
19116734 AATGA
1 AATGA
19116739 AGCCATAGCT
Statistics
Matches: 389, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
388 389 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (388 bp):
AATGAGGTATCGGGACCTCATTTCTATAAACTGAGCCATAAATATTTTTATAAATATTTACAGAA
TGTTATTAAGGTGGTATTAAATTTTCGTTAAAAAATTTTAACGTTTCGATAGTTAATTAAGCGAA
AAGGACTAAATCTTAAAAAGTGTAAAATGTGATCCCTATTTGATTAGAGTGATTAAATGGCTTAT
TGAATAAAGGAAAAGTGACCTAGATGGTAATTGGACCATTATTATAAATAGTGGACAAAGGTGGA
CATTAAATAGGTGATTTTTGATATTATAAAAAAGGTTGATTTAGTAATTTATTTATTAAAAGAAA
TTTAAAACAAATAAAAAAATGGCATCATCTTCTTTAAATTTAGTTCCACAAAATTTGTTGAAG
Found at i:19117499 original size:33 final size:33
Alignment explanation
Indices: 19117462--19117571 Score: 89
Period size: 33 Copynumber: 3.3 Consensus size: 33
19117452 GAAAAATGTA
19117462 TAAGACCATGGTTGGACCATGGTAATGTTTACG
1 TAAGACCATGGTTGGACCATGGTAATGTTTACG
*** * * * *
19117495 TAAGACCATAGCAAGG-CTATGGCAGT-TTTCAGACA
1 TAAGACCAT-GGTTGGACCATGGTAATGTTT---ACG
* *
19117530 CAAGACTATGGTTGGACCATGGTAATGTTTACG
1 TAAGACCATGGTTGGACCATGGTAATGTTTACG
19117563 TAAGACCAT
1 TAAGACCAT
19117572 AGCGAGGCTA
Statistics
Matches: 53, Mismatches: 18, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
32 3 0.06
33 25 0.47
34 6 0.11
35 16 0.30
36 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (33 bp):
TAAGACCATGGTTGGACCATGGTAATGTTTACG
Found at i:19117572 original size:68 final size:68
Alignment explanation
Indices: 19117463--19117626 Score: 240
Period size: 68 Copynumber: 2.4 Consensus size: 68
19117453 AAAAATGTAT
*
19117463 AAGACCATGGTTGGACCATGGTAATGTTTACGTAAGACCATAGCAAGGCTATGGCAGTT-TTCAG
1 AAGA-CATGGTTGGACCATGGTAATGTTTACGTAAGACCATAGCAAGGCTATGACAGTTGTTCAG
19117527 ACAC
65 ACAC
* *
19117531 AAGACTATGGTTGGACCATGGTAATGTTTACGTAAGACCATAGCGAGGCTATGACATTTGTTCAG
1 AAGAC-ATGGTTGGACCATGGTAATGTTTACGTAAGACCATAGCAAGGCTATGACAGTTGTTCAG
**
19117596 ACGT
65 ACAC
*
19117600 AAGAACATGGTTGGACCATGGCAATGT
1 AAG-ACATGGTTGGACCATGGTAATGT
19117627 ATATATATAT
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
67 1 0.01
68 54 0.62
69 30 0.34
70 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (68 bp):
AAGACATGGTTGGACCATGGTAATGTTTACGTAAGACCATAGCAAGGCTATGACAGTTGTTCAGA
CAC
Found at i:19117838 original size:29 final size:30
Alignment explanation
Indices: 19117805--19117864 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
19117795 TTGCAGTGTT
*
19117805 CATCGAAT-ATGAAAATGGATGGTTTAGAC
1 CATCGAATAAAGAAAATGGATGGTTTAGAC
* *
19117834 CATCGATTAAAGAAAATGGATGGTTTCGAC
1 CATCGAATAAAGAAAATGGATGGTTTAGAC
19117864 C
1 C
19117865 TTCATTTAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (30 bp):
CATCGAATAAAGAAAATGGATGGTTTAGAC
Found at i:19123058 original size:24 final size:22
Alignment explanation
Indices: 19123017--19123060 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
19123007 CATTATTCCA
*
19123017 ATTTCATATACATGTATCATAT
1 ATTTCATATACATATATCATAT
19123039 ATTTCATATATCAATATATCAT
1 ATTTCATATA-C-ATATATCAT
19123061 GTAACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCATATACATATATCATAT
Found at i:19123317 original size:25 final size:24
Alignment explanation
Indices: 19123289--19123366 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
19123279 TCATACGAGT
19123289 TGAATATTGTTAAGCTCTCTTGAGC
1 TGAATATTG-TAAGCTCTCTTGAGC
* *
19123314 TGAATATTAGAAAGCTCAT-GTGAGC
1 TGAATATT-GTAAGCTC-TCTTGAGC
* * *
19123339 TAAATATCGGTAAGCTCTCTCGAGC
1 TGAATAT-TGTAAGCTCTCTTGAGC
19123364 TGA
1 TGA
19123367 GAATCGGTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 1 0.02
25 38 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (24 bp):
TGAATATTGTAAGCTCTCTTGAGC
Found at i:19127346 original size:52 final size:52
Alignment explanation
Indices: 19127284--19127386 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
19127274 GCCAAAGACC
*
19127284 ATCCATGGTTAAAGCTGCCCATGAAGAAGACAAATACCAACAAAATTTGGAT
1 ATCCATGGTTAAAGCTGCCCATGAAGAAGAAAAATACCAACAAAATTTGGAT
19127336 ATCCATGGTTAAAGCTGCCCATGAAGAAGAAAAATACCAACAAAATTTGGA
1 ATCCATGGTTAAAGCTGCCCATGAAGAAGAAAAATACCAACAAAATTTGGA
19127387 CAGACTTAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (52 bp):
ATCCATGGTTAAAGCTGCCCATGAAGAAGAAAAATACCAACAAAATTTGGAT
Found at i:19128500 original size:30 final size:31
Alignment explanation
Indices: 19128464--19128522 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
19128454 TTCGAGCTTG
19128464 GGGACAAAAAT-GTAATTATG-CAAAAGTTTA
1 GGGAC-AAAATCGTAATTATGACAAAAGTTTA
*
19128494 GGGACAAAATCGTAATTTTGACAAAAGTT
1 GGGACAAAATCGTAATTATGACAAAAGTT
19128523 GAGTCGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 5 0.19
30 13 0.50
31 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (31 bp):
GGGACAAAATCGTAATTATGACAAAAGTTTA
Found at i:19137838 original size:20 final size:20
Alignment explanation
Indices: 19137813--19137865 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
19137803 AAGTTTATGC
*
19137813 TAAGTAAATTGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
* *
19137833 TAAGTAAATGGAATGGTAAT
1 TAAGTAAATGGAATGGAAAG
19137853 TAAGTAAATGGAA
1 TAAGTAAATGGAA
19137866 CGGTTCTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.26
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:19148901 original size:89 final size:89
Alignment explanation
Indices: 19148688--19149037 Score: 402
Period size: 89 Copynumber: 3.9 Consensus size: 89
19148678 AAGGTTGGTG
* * * ** *
19148688 TCTTCGATCTGCTTTGTTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAGTCTACTCCGCTGC
1 TCTTCGATCTACTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
** * * * * *
19148753 AACTTAGGGAGATAAGACTAG-TG
66 TTCTCAGAGAGATAAGGCTGGCTA
* *
19148776 TCTTCGATCTACTTCGCTACCAGTAC-AGAAAGACAAGACCTGCTATCTTCAACCTACTCCACTG
1 TCTTCGATCTACTTCGCTGCCAGTACAAG-AAGACAAGATCTGCTATCTTCAACCTACTCCACTG
19148840 CTTCTCAGAGAGATAAGGCTGGCTA
65 CTTCTCAGAGAGATAAGGCTGGCTA
* * * * *
19148865 TCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATTTGCTATCTTCAACCTATTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
* *
19148930 TTCACA-AGGAGATAAGGCTGACTA
66 TTCTCAGA-GAGATAAGGCTGGCTA
* * * *
19148954 TCTTTGATCTACTTTGCTGCCAGTACAAGAAGACAAGATCTGCTATTTTCAATCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
*
19149019 TGT-TCAGGGAGATAAGGCT
66 T-TCTCAGAGAGATAAGGCT
19149038 TTGTGGTTTC
Statistics
Matches: 221, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
87 2 0.01
88 70 0.32
89 147 0.67
90 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
TTCTCAGAGAGATAAGGCTGGCTA
Found at i:19149018 original size:178 final size:177
Alignment explanation
Indices: 19148688--19149037 Score: 443
Period size: 178 Copynumber: 2.0 Consensus size: 177
19148678 AAGGTTGGTG
* * * ** *
19148688 TCTTCGATCTGCTTTGTTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAGTCTACTCCGCTGC
1 TCTTCGATCTGCTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
** * * *
19148753 AACTTAGGGAGATAAGACTAGTGTCTTCGATCTACTTCGCTACCAGTACAGAAAGACAAGACCTG
66 AACACAAGGAGATAAGACTACTATCTTCGATCTACTTCGCTACCAGTACAGAAAGACAAGACCTG
19148818 CTATCTTCAACCTACTCCACTGCT-TCTCAGAGAGATAAGGCTGGCTA
131 CTATCTTCAACCTACTCCACTGCTGT-TCAGAGAGATAAGGCTGGCTA
* * *
19148865 TCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATTTGCTATCTTCAACCTATTCCACTGC
1 TCTTCGATCTGCTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
** * * * * *
19148930 TTCACAAGGAGATAAGGCTGACTATCTTTGATCTACTTTGCTGCCAGTACA-AGAAGACAAGATC
66 AACACAAGGAGATAAGACT-ACTATCTTCGATCTACTTCGCTACCAGTACAGA-AAGACAAGACC
* * *
19148994 TGCTATTTTCAATCTACTCCACTGCTGTTCAGGGAGATAAGGCT
129 TGCTATCTTCAACCTACTCCACTGCTGTTCAGAGAGATAAGGCT
19149038 TTGTGGTTTC
Statistics
Matches: 146, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
177 70 0.48
178 75 0.51
179 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (177 bp):
TCTTCGATCTGCTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGC
AACACAAGGAGATAAGACTACTATCTTCGATCTACTTCGCTACCAGTACAGAAAGACAAGACCTG
CTATCTTCAACCTACTCCACTGCTGTTCAGAGAGATAAGGCTGGCTA
Found at i:19161651 original size:48 final size:48
Alignment explanation
Indices: 19161565--19161706 Score: 176
Period size: 48 Copynumber: 3.0 Consensus size: 48
19161555 GATTTCTCGA
* * * * ** * *
19161565 TGGCCTATACATAGTCCGTACCACCTTTGTGTAATAACAGACTCTCAG
1 TGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATCAG
**
19161613 TGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATTGG
1 TGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATCAG
* *
19161661 TGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATC
1 TGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATC
19161707 GGTACGCATA
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
TGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATCAG
Found at i:19167278 original size:48 final size:48
Alignment explanation
Indices: 19167208--19167406 Score: 218
Period size: 48 Copynumber: 4.1 Consensus size: 48
19167198 AAAACATATT
* * * * *
19167208 TCTCGGTGGCCTATACACAGTCCGTACCACCTTTGTGTAATAACAGAC
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* **
19167256 TCTCGGTGGCCTACACATAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * * * **
19167304 TATTGGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * * **
19167352 TATTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
*
19167400 TATCGGT
1 TCTCGGT
19167407 ACGCATAGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 136 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
Found at i:19172536 original size:15 final size:16
Alignment explanation
Indices: 19172505--19172537 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19172495 AGTGCTTTTC
*
19172505 AAAAGCACTTTTGAAA
1 AAAAGCACTTCTGAAA
19172521 AAAAGCACTTCT-AAA
1 AAAAGCACTTCTGAAA
19172536 AA
1 AA
19172538 GGAGAAGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAGCACTTCTGAAA
Found at i:19173025 original size:13 final size:13
Alignment explanation
Indices: 19173009--19173061 Score: 97
Period size: 13 Copynumber: 4.1 Consensus size: 13
19172999 TTTAAACCAA
19173009 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
19173022 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
19173035 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
19173048 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
19173061 A
1 A
19173062 TTGCCAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:19173405 original size:41 final size:42
Alignment explanation
Indices: 19173348--19173434 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 42
19173338 TAGCTAAACG
19173348 ATATTTGATATGAAATGTGATTGAAATTGGTATACTATGTA-
1 ATATTTGATATGAAATGTGATTGAAATTGGTATACTATGTAT
*
19173389 ATATTTTATATGAAATGTGATTGAAATTGGTATACTATGTAT
1 ATATTTGATATGAAATGTGATTGAAATTGGTATACTATGTAT
19173431 ATAT
1 ATAT
19173435 GTACATGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 40 0.91
42 4 0.09
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (42 bp):
ATATTTGATATGAAATGTGATTGAAATTGGTATACTATGTAT
Found at i:19173443 original size:41 final size:41
Alignment explanation
Indices: 19173357--19173447 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
19173347 GATATTTGAT
* *
19173357 ATGAAATGTGATTGAAATTGGTATACTATGTAATATTTTAT
1 ATGAAATGTGATTGAAATTGGTATACTATGTAATATTGTAC
19173398 ATGAAATGTGATTGAAATTGGTATACTATGT-ATATATGTAC
1 ATGAAATGTGATTGAAATTGGTATACTATGTAATAT-TGTAC
19173439 ATG-AATGTG
1 ATGAAATGTG
19173448 GAAAATTACA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 10 0.21
41 37 0.79
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (41 bp):
ATGAAATGTGATTGAAATTGGTATACTATGTAATATTGTAC
Found at i:19174577 original size:75 final size:75
Alignment explanation
Indices: 19174491--19174715 Score: 369
Period size: 75 Copynumber: 3.0 Consensus size: 75
19174481 GAAAAACGAA
* *
19174491 GATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAAGAAATTATATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAA
*
19174556 AAGATTATTG
66 AAGAATATTG
* *
19174566 TATTATTCCCTTATTAATAAAGAAGACAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAA
1 GATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAA
19174631 AAGAATATTG
66 AAGAATATTG
* * *
19174641 GATTATTCCCTAATTAATAGAAAAGACAAATGGAAAGTTAGAAAAAAGGAATTACATTCTTTCCA
1 GATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAG-AAAAAGGAATTATATTCTTTCCA
19174706 AAAGAATATT
65 AAAGAATATT
19174716 AATTTTCATA
Statistics
Matches: 139, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
75 107 0.77
76 32 0.23
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAA
AAGAATATTG
Found at i:19174936 original size:138 final size:138
Alignment explanation
Indices: 19174690--19175110 Score: 650
Period size: 138 Copynumber: 3.1 Consensus size: 138
19174680 AGAAAAAAGG
* * * *
19174690 AATTACATTCTTTCCAAAAGAATATTAATTTTCATATC--TTGTATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
*
19174753 TATAACTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
19174818 CATATATT
131 CATATATT
19174826 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
** *
19174891 TGCAACTGTTTATATTAATAAGA-TCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
66 TATAACTGTTTATATTAATAA-ATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
19174955 TCATATATT
130 TCATATATT
* * * *
19174964 AGTTATATTCCTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
* * * * * *
19175029 TATAACTATTTATATTAATAAATTTGGTTAAACATATACAATAAATATTTTGTATGAATCAAATG
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
19175094 CATATATT
131 CATATATT
19175102 AATTATATT
1 AATTATATT
19175111 TATGTTCTCT
Statistics
Matches: 259, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
136 36 0.14
137 1 0.00
138 221 0.85
139 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.43
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:19177403 original size:14 final size:14
Alignment explanation
Indices: 19177384--19177410 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19177374 CATTTCTTGG
19177384 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
19177398 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
19177411 ACTGGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:19180296 original size:31 final size:30
Alignment explanation
Indices: 19180238--19180300 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
19180228 GCTTTTTGAA
* *
19180238 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
19180268 AATATTTACAAAAA-AGAGCAACCAAATTTTT
1 AATATTTACAAAAAGAG-GC-ACCAAATTTTT
19180299 AA
1 AA
19180301 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 16 0.55
31 11 0.38
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:19188077 original size:27 final size:27
Alignment explanation
Indices: 19188039--19188234 Score: 193
Period size: 27 Copynumber: 7.3 Consensus size: 27
19188029 GCAAGTGATC
* *
19188039 GAAATACCCTCGAAGGGTAAAATAACT
1 GAAATACCCTCAAAGGGTAAAATGACT
* *
19188066 GAAATACCCTCGAAGGGTAAAATGACC
1 GAAATACCCTCAAAGGGTAAAATGACT
* ** * *
19188093 AAAATATCCC-CAAAATGTAAAATAACC
1 GAAATA-CCCTCAAAGGGTAAAATGACT
* * *
19188120 AAAATACCTTTAAAGGGTAAAATGACT
1 GAAATACCCTCAAAGGGTAAAATGACT
* *
19188147 GAAATACCCT-TAAGGGTAAAATGATT
1 GAAATACCCTCAAAGGGTAAAATGACT
19188173 GAAATAACCC-CAAAGGGTAAAATGACT
1 GAAAT-ACCCTCAAAGGGTAAAATGACT
* *
19188200 GAAA-ACCCTCATAGGGTAAAATGGCT
1 GAAATACCCTCAAAGGGTAAAATGACT
*
19188226 GATATACCC
1 GAAATACCC
19188235 CTAAGAGATG
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
25 4 0.03
26 39 0.28
27 95 0.67
28 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (27 bp):
GAAATACCCTCAAAGGGTAAAATGACT
Found at i:19188249 original size:53 final size:53
Alignment explanation
Indices: 19188039--19188251 Score: 148
Period size: 53 Copynumber: 4.0 Consensus size: 53
19188029 GCAAGTGATC
* * * *
19188039 GAAATACCCTCGAAGGGTAAAATAACTGAAAT-ACCCTCGAAGGGTAAAATGACC
1 GAAATACCCTC-AAGGGTAAAATGACTGAAATAACCC-CAAAGGATAAAATGACT
* ** * ** ** *
19188093 AAAATATCCC-CAAAATGTAAAATAACCAAAAT-ACCTTTAAAGGGTAAAATGACT
1 GAAATA-CCCTC-AAGGGTAAAATGACTGAAATAACC-CCAAAGGATAAAATGACT
* * *
19188147 GAAATACCCTTAAGGGTAAAATGATTGAAATAACCCCAAAGGGTAAAATGACT
1 GAAATACCCTCAAGGGTAAAATGACTGAAATAACCCCAAAGGATAAAATGACT
* * * *
19188200 GAAA-ACCCTCATAGGGTAAAATGGCTGATAT-ACCCCTAAGAGATGAAATGAC
1 GAAATACCCTCA-AGGGTAAAATGACTGAAATAACCCCAAAG-GATAAAATGAC
19188252 CATTATAGCC
Statistics
Matches: 126, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
52 14 0.11
53 62 0.49
54 47 0.37
55 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (53 bp):
GAAATACCCTCAAGGGTAAAATGACTGAAATAACCCCAAAGGATAAAATGACT
Found at i:19197975 original size:50 final size:50
Alignment explanation
Indices: 19197900--19198144 Score: 312
Period size: 50 Copynumber: 4.9 Consensus size: 50
19197890 TTTCTTGTAC
* * * * ** * *
19197900 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
19197950 TGACC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
19198000 TGCCAACGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
19198050 TGTTAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
19198100 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
19198145 AATCTCAATG
Statistics
Matches: 171, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 2 0.01
50 167 0.98
51 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:19199626 original size:51 final size:51
Alignment explanation
Indices: 19199552--19199894 Score: 295
Period size: 51 Copynumber: 6.6 Consensus size: 51
19199542 CGATGAACAT
* ** * *
19199552 GTGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCAC
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATATTGGTCAC
* * * * *
19199603 ATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGTCAC
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAA-ATATTGGTCAC
** * * *
19199654 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCAC
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATATTGGTCAC
* * *
19199705 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACC-AAAAAGCT-TTGGTCAC
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAA--TATTGGTCAC
* * * *
19199756 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGATCAC
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATA-TTGGTCAC
* * * *
19199806 GTGTGTAGTACTATGTGAAGGCGAAGGCTACTACTTGAACCG-TAAA-ACTTGATCAC
1 GTGTGTAGTAC----T-AA-GTGAAGGCTACTACGTGTACCGATAAATA-TTGGTCAC
*
19199862 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GTGTGTAGTACTAAGTGAAGGCTACTACGTGTA
19199895 TCGAATGATA
Statistics
Matches: 237, Mismatches: 42, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
50 39 0.16
51 148 0.62
52 3 0.01
54 1 0.00
55 1 0.00
56 45 0.19
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
GTGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGATAAATATTGGTCAC
Found at i:19199728 original size:102 final size:102
Alignment explanation
Indices: 19199552--19199827 Score: 421
Period size: 102 Copynumber: 2.7 Consensus size: 102
19199542 CGATGAACAT
* *
19199552 GTGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAA
* *
19199617 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCAC
66 GTGAAGGCTACAATGTGTACCAAAAAGCTTTGGTCAC
19199654 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAA
*
19199719 GTGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCAC
66 GTGAAGGCTACAATGTGTACCAAAAAGCTTTGGTCAC
* * * * * *
19199756 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTACTA
*
19199819 TGTGAAGGC
65 AGTGAAGGC
19199828 GAAGGCTACT
Statistics
Matches: 161, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 30 0.19
102 130 0.81
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAA
GTGAAGGCTACAATGTGTACCAAAAAGCTTTGGTCAC
Found at i:19199858 original size:56 final size:56
Alignment explanation
Indices: 19199772--19199883 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
19199762 AGTACTATGT
19199772 GAAGGCTACTACATGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
1 GAAGGCTACTACATGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
*
19199828 GAAGGCTACTACTTGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
1 GAAGGCTACTACATGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
19199884 TACTACGTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (56 bp):
GAAGGCTACTACATGAACCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGC
Found at i:19199877 original size:106 final size:102
Alignment explanation
Indices: 19199552--19199889 Score: 362
Period size: 102 Copynumber: 3.3 Consensus size: 102
19199542 CGATGAACAT
* * * * * *
19199552 GTGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAATAATGATCACATGTGTAGTACTAA
* * * * * *
19199617 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCAC
66 GCGAAGGCTACTATGTGAACCAAAAAGCTTTGATCAC
* * * *
19199654 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAATAATGATCACATGTGTAGTACTAA
* * *
19199719 GTGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCAC
66 GCGAAGGCTACTATGTGAACCAAAAAGCTTTGATCAC
* *
19199756 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCG-TAAA-ACTTGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAATA-ATGATCACATGTGTAGTAC--
*
19199819 TGTGAAGGCGAAGGCTACTACT-TGAACCGTAAAA-C-TTGATCAC
63 --T-AA-GCGAAGGCTACTA-TGTGAACC-AAAAAGCTTTGATCAC
19199862 GTGTGTAGTACTATGTGAAGGCTACTAC
1 GTGTGTAGTACTATGTGAAGGCTACTAC
19199890 GTGTATCGAA
Statistics
Matches: 212, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
100 1 0.00
101 20 0.09
102 130 0.61
105 1 0.00
106 37 0.17
107 18 0.08
108 5 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
GTGTGTAGTACTATGTGAAGGCTACTACATGAACCGATAAATAATGATCACATGTGTAGTACTAA
GCGAAGGCTACTATGTGAACCAAAAAGCTTTGATCAC
Found at i:19206549 original size:102 final size:101
Alignment explanation
Indices: 19206370--19206713 Score: 451
Period size: 102 Copynumber: 3.4 Consensus size: 101
19206360 TATCGATGAA
* * * *
19206370 CACGTGTGTAGTACTGTGTGAAGGCTACTACCTGTATTGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
19206435 TAAGTGAAGGCTACAATGTCTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
* * *
19206472 CATGTGTGTAGTACTCTATGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
19206537 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * * * *
19206574 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTGTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * *
19206637 CTATGTGAAGGCTACTATGTGAACCGTAAAAC-TTGAT
65 CTAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* *
19206674 CACGTGTGTAGTGCTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
19206714 ATGATAAAAG
Statistics
Matches: 215, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
100 41 0.19
101 46 0.21
102 127 0.59
103 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:19206640 original size:50 final size:50
Alignment explanation
Indices: 19206370--19206707 Score: 315
Period size: 51 Copynumber: 6.7 Consensus size: 50
19206360 TATCGATGAA
* * * ** * *
19206370 CACGTGTGTAGTACTGTGTGAAGGCTACTACCTGTATTGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * ** * *
19206421 CACATGTGTAGTACTAAGTGAAGGCTACAATGTCTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
* * * * * *
19206472 CATGTGTGTAGTACTCTATGAAGGCTACTACGTGAATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * *
19206523 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
19206574 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* *
19206624 CACGTGTGTACTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
19206674 CACGTGTGTAGTGCTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
19206708 TATCGAATGA
Statistics
Matches: 235, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.00
49 4 0.02
50 85 0.36
51 138 0.59
52 6 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:19213524 original size:18 final size:18
Alignment explanation
Indices: 19213491--19213539 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
19213481 GGGCTTGACC
* *
19213491 TTGCCATTGTCCTTAGGCT
1 TTGCCTTTG-CCTTAGCCT
19213510 TTGCCTTTGCCTTAGCCT
1 TTGCCTTTGCCTTAGCCT
*
19213528 TAGCCTTT-CCTT
1 TTGCCTTTGCCTT
19213540 TGCCCTTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 4 0.15
18 15 0.56
19 8 0.30
ACGTcount: A:0.08, C:0.31, G:0.16, T:0.45
Consensus pattern (18 bp):
TTGCCTTTGCCTTAGCCT
Found at i:19216951 original size:50 final size:50
Alignment explanation
Indices: 19216856--19217000 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 50
19216846 CATTGAGGTT
* * * ** *
19216856 ATGAGAGGTCTCATGTAAGATCATGTCTGGGACATGGTGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* *
19216906 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-G
** * * * * *
19216957 -TGAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCA
19217001 GTACAAGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 77 0.99
51 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:19218428 original size:22 final size:22
Alignment explanation
Indices: 19218403--19218446 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19218393 AAATTAAATC
*
19218403 AAAATTTATGAAAATTTAATAT
1 AAAATTAATGAAAATTTAATAT
*
19218425 AAAATTAATTAAAATTTAATAT
1 AAAATTAATGAAAATTTAATAT
19218447 GTTAACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATTAATGAAAATTTAATAT
Found at i:19218443 original size:11 final size:11
Alignment explanation
Indices: 19218393--19218444 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
19218383 AAATCTGTCG
* *
19218393 AAATTAAATCA
1 AAATTTAATTA
*
19218404 AAATTT-ATGA
1 AAATTTAATTA
19218414 AAATTTAATATA
1 AAATTTAAT-TA
19218426 AAA-TTAATTA
1 AAATTTAATTA
19218436 AAATTTAAT
1 AAATTTAAT
19218445 ATGTTAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 14 0.40
11 17 0.49
12 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
AAATTTAATTA
Found at i:19221559 original size:5 final size:5
Alignment explanation
Indices: 19221549--19221586 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
19221539 GTAATTAGTT
19221549 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
19221587 CAAAATGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:19232329 original size:6 final size:6
Alignment explanation
Indices: 19232318--19232390 Score: 132
Period size: 6 Copynumber: 12.5 Consensus size: 6
19232308 AAACCATTCT
19232318 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT-C -TTTCC TTTTCC
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC
19232364 TTTTCC TTTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTT
19232391 ACATCGATGC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
4 3 0.05
5 2 0.03
6 60 0.92
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCC
Found at i:19232358 original size:34 final size:34
Alignment explanation
Indices: 19232319--19232386 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
19232309 AACCATTCTT
19232319 TTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTC
1 TTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTC
19232353 TTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTC
1 TTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTC
19232387 CTTTACATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (34 bp):
TTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTC
Found at i:19237497 original size:144 final size:144
Alignment explanation
Indices: 19237222--19237499 Score: 342
Period size: 144 Copynumber: 1.9 Consensus size: 144
19237212 TTTAGGGTGG
* * * * *
19237222 CAAGCTTAACTCAATTTACTCAAATAAATGAAGGTTGTGAGTATAACTCATTTAACTTTTAAACA
1 CAAGCTTAACTCAACTTACTCAAATAAATAAAGGTTGTAAGTATAACTCATCTAACCTTTAAACA
* * * * **
19237287 TTGGCTGGGAGAGTAAGACCGCGAGCTATGTTGAAGTTTATCAGCTGGAAGAGTAGGTCTGCGAG
66 TAGGCTGAGAGAGTAAGACCACGAGCTATGTTGAAGTTTATCAGCTGGAAGAGTAGATCCACGAG
19237352 CTGTTCTAGAGTAA
131 CTGTTCTAGAGTAA
* *
19237366 CAAGCTTAACTCAGCTTACTCAAATAAATAAAGGTTTTAAGTATAACTCATCTAACCTTTAAACA
1 CAAGCTTAACTCAACTTACTCAAATAAATAAAGGTTGTAAGTATAACTCATCTAACCTTTAAACA
* * ** * * * * *
19237431 TCAGTCT-AGAGCGTAAGTTCACGAGCTGTGTTGAAGTTTTTCAGCTGGGAGCGTAGATCCATGA
66 T-AGGCTGAGAGAGTAAGACCACGAGCTATGTTGAAGTTTATCAGCTGGAAGAGTAGATCCACGA
19237495 GCTGT
130 GCTGT
19237500 CAGCTGGGAG
Statistics
Matches: 111, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
144 108 0.97
145 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (144 bp):
CAAGCTTAACTCAACTTACTCAAATAAATAAAGGTTGTAAGTATAACTCATCTAACCTTTAAACA
TAGGCTGAGAGAGTAAGACCACGAGCTATGTTGAAGTTTATCAGCTGGAAGAGTAGATCCACGAG
CTGTTCTAGAGTAA
Found at i:19237524 original size:28 final size:28
Alignment explanation
Indices: 19237471--19237525 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
19237461 TTGAAGTTTT
* *
19237471 TCAGCTGGGAGCGTAGATCCATGAGCTG
1 TCAGCTGGGAGCATAGATCCACGAGCTG
* *
19237499 TCAGCTGGGAGCATAGGTCCGCGAGCT
1 TCAGCTGGGAGCATAGATCCACGAGCT
19237526 ATTCCAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (28 bp):
TCAGCTGGGAGCATAGATCCACGAGCTG
Found at i:19237733 original size:104 final size:104
Alignment explanation
Indices: 19237499--19237735 Score: 357
Period size: 104 Copynumber: 2.3 Consensus size: 104
19237489 CCATGAGCTG
* *
19237499 TCAGCTGGGAGCATAGGTCCGCGAGCTATTCCAAAGTAGCGAGCTTAACGCAGCTTACTCAAATA
1 TCAGCTGGGAACATAGGTCCGCGAGCTATTCCAAAGTAGCAAGCTTAACGCAGCTTACTCAAATA
19237564 AATGAAGGTTGTGAGTATAACTCATCTAACCTTTAAACA
66 AATGAAGGTTGTGAGTATAACTCATCTAACCTTTAAACA
* * ** * * * * *
19237603 TCAACTGGGAACGTAATTCTGTGAGCTGTTCCAGAGTAGCAAGCTTAACTCAGCTTACTCAAATA
1 TCAGCTGGGAACATAGGTCCGCGAGCTATTCCAAAGTAGCAAGCTTAACGCAGCTTACTCAAATA
* *
19237668 AATGAATGTTTTGAGTATAACTCATCTAACCTTTAAACA
66 AATGAAGGTTGTGAGTATAACTCATCTAACCTTTAAACA
19237707 TCAGCTGGGAACATAGGTCCGCGAGCTAT
1 TCAGCTGGGAACATAGGTCCGCGAGCTAT
19237736 GTTGACAAAC
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 113 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (104 bp):
TCAGCTGGGAACATAGGTCCGCGAGCTATTCCAAAGTAGCAAGCTTAACGCAGCTTACTCAAATA
AATGAAGGTTGTGAGTATAACTCATCTAACCTTTAAACA
Found at i:19239345 original size:20 final size:20
Alignment explanation
Indices: 19239320--19239361 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19239310 GCTACGATTG
19239320 AATGACACTTCTTCAGAACT
1 AATGACACTTCTTCAGAACT
19239340 AATGACACTTCTTCAGAACT
1 AATGACACTTCTTCAGAACT
19239360 AA
1 AA
19239362 CTCTTTCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (20 bp):
AATGACACTTCTTCAGAACT
Found at i:19246969 original size:30 final size:30
Alignment explanation
Indices: 19246934--19246992 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
19246924 TATTTTATTG
*
19246934 TTAATTTTTTTATTATTTTAAAGACATTTA
1 TTAATTTTGTTATTATTTTAAAGACATTTA
* *
19246964 TTAATTTTGTTATTATTTTAGAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGACATTT
19246993 GCTTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.59
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTA
Found at i:19253933 original size:14 final size:14
Alignment explanation
Indices: 19253911--19253940 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19253901 GAGAATCTAC
*
19253911 AAAGTAAAAAAAAG
1 AAAGAAAAAAAAAG
19253925 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
19253939 AA
1 AA
19253941 CTTTTTCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:19255999 original size:96 final size:96
Alignment explanation
Indices: 19255834--19256011 Score: 297
Period size: 96 Copynumber: 1.9 Consensus size: 96
19255824 GAAATAGTGG
*
19255834 CCTCGTGGACGCGATTTCGCTACAGTGGTCATGTGAGAAATAATTTTTTTTGACGTTTTCTGAGG
1 CCTCGTGGACGCGATTTCGCTACAGTGGTCATGTGAGAAATAATTTTTTTTGACGTTTTCTGAGC
19255899 AAATAGTATAAAATCGCTGATATCAGGATGC
66 AAATAGTATAAAATCGCTGATATCAGGATGC
19255930 CCTCGTGGACGCGATTTCGCTACAGTTGGTCATGT-AGGAAATAATTTTTTTTGACG-TTTCTGA
1 CCTCGTGGACGCGATTTCGCTACAG-TGGTCATGTGA-GAAATAATTTTTTTTGACGTTTTCTGA
* *
19255993 GCAAATAGTGTCAAATCGC
64 GCAAATAGTATAAAATCGC
19256012 GCCCTCATGG
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
96 49 0.64
97 28 0.36
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (96 bp):
CCTCGTGGACGCGATTTCGCTACAGTGGTCATGTGAGAAATAATTTTTTTTGACGTTTTCTGAGC
AAATAGTATAAAATCGCTGATATCAGGATGC
Found at i:19257915 original size:28 final size:29
Alignment explanation
Indices: 19257877--19257932 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
19257867 NNNNNNNATT
*
19257877 AAAAATTTTAAAATTAT-TTAAAAAAATA
1 AAAAAATTTAAAATTATCTTAAAAAAATA
*
19257905 AAAAAATTTAAAATTTTCTTAAAAAAAT
1 AAAAAATTTAAAATTATCTTAAAAAAAT
19257933 GAAATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAAATTTAAAATTATCTTAAAAAAATA
Found at i:19258004 original size:22 final size:22
Alignment explanation
Indices: 19257974--19258015 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19257964 ATTTGGAGAT
*
19257974 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
19257996 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
19258016 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:19258036 original size:52 final size:51
Alignment explanation
Indices: 19257965--19258067 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
19257955 TTAATATGGA
* * *
19257965 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
19258016 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
19258068 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:19258042 original size:22 final size:23
Alignment explanation
Indices: 19258017--19258108 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
19258007 ATTTGAGAGT
19258017 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
19258039 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
19258061 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
19258083 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
19258105 TTGA
1 TTGA
19258109 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:19258066 original size:44 final size:44
Alignment explanation
Indices: 19258017--19258108 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
19258007 ATTTGAGAGT
* * * *
19258017 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
19258061 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
19258105 TTGA
1 TTGA
19258109 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:19260308 original size:27 final size:26
Alignment explanation
Indices: 19260250--19260320 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
19260240 AAGTTAATAT
* *
19260250 TTTTACTATTA-AATATTATTTTTTAA
1 TTTTAC-ATTATAATATAATTATTTAA
19260276 TATTTACATTATAATATAATATATTTAA
1 T-TTTACATTATAATATAAT-TATTTAA
19260304 TTTT--A-TATAATATAATT
1 TTTTACATTATAATATAATT
19260321 TACATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 1 0.03
26 5 0.12
27 15 0.38
28 7 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTACATTATAATATAATTATTTAA
Found at i:19260311 original size:19 final size:21
Alignment explanation
Indices: 19260275--19260344 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 21
19260265 TTATTTTTTA
19260275 ATATTTACATTATAATATAAT
1 ATATTTACATTATAATATAAT
*
19260296 ATATTTA-ATT-TTATATAAT
1 ATATTTACATTATAATATAAT
19260315 ATAATTTACA-TA-AA-ATAAT
1 AT-ATTTACATTATAATATAAT
19260334 ATAATTTACAT
1 AT-ATTTACAT
19260345 AAAATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
19 25 0.58
20 10 0.23
21 8 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTTACATTATAATATAAT
Found at i:19260345 original size:19 final size:19
Alignment explanation
Indices: 19260310--19260350 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19260300 TTAATTTTAT
19260310 ATAATATAATTTACATAAA
1 ATAATATAATTTACATAAA
19260329 ATAATATAATTTACATAAA
1 ATAATATAATTTACATAAA
19260348 ATA
1 ATA
19260351 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATATAATTTACATAAA
Found at i:19260968 original size:30 final size:31
Alignment explanation
Indices: 19260901--19260968 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
19260891 ATATTTATTT
*
19260901 ATTTTTTAAATTTTAAAATATTTTTAAAATAC
1 ATTTTTTAAATTTT-AAATATTTTTAAAATAA
* **
19260933 TTTTTTTAAATTTT-TTTATTTTTAAAATAA
1 ATTTTTTAAATTTTAAATATTTTTAAAATAA
19260963 ATTTTT
1 ATTTTT
19260969 AGTGTTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 18 0.58
32 13 0.42
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTTTAAATTTTAAATATTTTTAAAATAA
Found at i:19261541 original size:15 final size:16
Alignment explanation
Indices: 19261516--19261546 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
19261506 TGAGTGAGTT
19261516 TTTTATTATATTTTAA
1 TTTTATTATATTTTAA
19261532 TTTT-TTATATTTTAA
1 TTTTATTATATTTTAA
19261547 ATGTGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATATTTTAA
Found at i:19261616 original size:18 final size:18
Alignment explanation
Indices: 19261593--19261627 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19261583 TTTTTTAAAG
19261593 AAAAAAT-TTAAAATTTTT
1 AAAAAATGTT-AAATTTTT
19261611 AAAAAATGTTAAATTTT
1 AAAAAATGTTAAATTTT
19261628 ACTTTCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAAAAATGTTAAATTTTT
Found at i:19262167 original size:11 final size:12
Alignment explanation
Indices: 19262134--19262161 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19262124 CGGCCCACCC
19262134 ATATTAATTTTT
1 ATATTAATTTTT
19262146 ATATTAATTTTT
1 ATATTAATTTTT
19262158 ATAT
1 ATAT
19262162 AGTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:19262325 original size:30 final size:30
Alignment explanation
Indices: 19262289--19262353 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
19262279 CAACTTAACA
*
19262289 AACAAATGCCTCTAAAATAATAATAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
19262319 AACAAATGCCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
19262349 AACAA
1 AACAA
19262354 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:19262408 original size:22 final size:22
Alignment explanation
Indices: 19262383--19262425 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19262373 TATCCAAACA
19262383 ATAAAAACAAAATAGTAGCAAC
1 ATAAAAACAAAATAGTAGCAAC
* **
19262405 ATAATAGTAAAATAGTAGCAA
1 ATAAAAACAAAATAGTAGCAA
19262426 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAAAAACAAAATAGTAGCAAC
Found at i:19262429 original size:11 final size:11
Alignment explanation
Indices: 19262390--19262430 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
19262380 ACAATAAAAA
19262390 CAAAATAGTAG
1 CAAAATAGTAG
* *
19262401 CAACATAATAG
1 CAAAATAGTAG
*
19262412 TAAAATAGTAG
1 CAAAATAGTAG
19262423 CAAAATAG
1 CAAAATAG
19262431 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:19264032 original size:3 final size:3
Alignment explanation
Indices: 19264024--19264249 Score: 140
Period size: 3 Copynumber: 75.7 Consensus size: 3
19264014 CTTTGTCCTT
*
19264024 TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
19264072 TTA CTA GTA TTA TTA TTA GTT- TTA TTG CTA TT- TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * ** * * *
19264116 ACA TCA TTA TTA GAA TTA TTA TTA ATG TTA TTA CTA TT- TT- TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * * * **
19264160 TT- TTA TTTC TTA TTA TTA ATA CTA TTA ATA TTA TTA TTG CCA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
19264205 TTA TTA TAA TTA TAA TTA TTA TT- TTCA TTA CCA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TT
19264250 TATTTATTTT
Statistics
Matches: 167, Mismatches: 46, Indels: 20
0.72 0.20 0.09
Matches are distributed among these distances:
2 12 0.07
3 144 0.86
4 11 0.07
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:19264178 original size:19 final size:19
Alignment explanation
Indices: 19264131--19264179 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
19264121 ATTATTAGAA
19264131 TTATTATTAATGTTATTAC
1 TTATTATTAATGTTATTAC
* * *
19264150 -TATTTTTTAATTTTATTTC
1 TTA-TTATTAATGTTATTAC
19264169 TTATTATTAAT
1 TTATTATTAAT
19264180 ACTATTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTATTAATGTTATTAC
Found at i:19269405 original size:19 final size:19
Alignment explanation
Indices: 19269381--19269427 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19269371 AACATCTCTT
*
19269381 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
19269400 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
19269419 TATGCATTA
1 TTTGCATTA
19269428 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:19272225 original size:17 final size:17
Alignment explanation
Indices: 19272203--19272242 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
19272193 AAAAAATAGG
*
19272203 GAAAAAAATAAACAAAT
1 GAAAAAAATAAAAAAAT
19272220 GAAAAAAATAAAAAAAT
1 GAAAAAAATAAAAAAAT
19272237 -AAAAAA
1 GAAAAAA
19272243 CAAAAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (17 bp):
GAAAAAAATAAAAAAAT
Found at i:19272232 original size:8 final size:8
Alignment explanation
Indices: 19272204--19272242 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
19272194 AAAAATAGGG
19272204 AAAAAAAT
1 AAAAAAAT
*
19272212 AAACAAAT
1 AAAAAAAT
19272220 GAAAAAAAT
1 -AAAAAAAT
19272229 AAAAAAAT
1 AAAAAAAT
19272237 AAAAAA
1 AAAAAA
19272243 CAAAAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Done.