Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 41 of 135
Found at i:16107162 original size:2 final size:2
Alignment explanation
Indices: 16107155--16107185 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16107145 CTTTGAAGTA
16107155 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16107186 TAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16110729 original size:18 final size:19
Alignment explanation
Indices: 16110702--16110737 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16110692 CTTGAAAAGT
*
16110702 ATATTGTGTGA-TGTGATG
1 ATATTATGTGATTGTGATG
16110720 ATATTATGTGATTGTGAT
1 ATATTATGTGATTGTGAT
16110738 TTTTGTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (19 bp):
ATATTATGTGATTGTGATG
Found at i:16110969 original size:22 final size:22
Alignment explanation
Indices: 16110937--16110978 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16110927 AAGAAAGATA
*
16110937 TGTGGCAGTTTATCTACAATCG
1 TGTGGCAGTTTATCGACAATCG
*
16110959 TGTGGCCGTTTATCGACAAT
1 TGTGGCAGTTTATCGACAAT
16110979 TATATGGTGG
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:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (22 bp):
TGTGGCAGTTTATCGACAATCG
Found at i:16114993 original size:7 final size:7
Alignment explanation
Indices: 16114971--16115005 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
16114961 TTTAATTGAC
16114971 ACCCTCAA
1 ACCCT-AA
16114979 ACCCTAA
1 ACCCTAA
*
16114986 ACCTTAA
1 ACCCTAA
16114993 ACCCTAA
1 ACCCTAA
16115000 ACCCTA
1 ACCCTA
16115006 CTCGGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:16119704 original size:39 final size:39
Alignment explanation
Indices: 16119647--16119721 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
16119637 TACTTTCTGT
** * *
16119647 TTGGCGTGATTCGGGTGGATCAGCTCTTATGAGCTTTTG
1 TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTTTTG
*
16119686 TTGGCGTGTTTCAAGTGGACCAACTCTTATGAGCTT
1 TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTT
16119722 CTATTTGGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.37
Consensus pattern (39 bp):
TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTTTTG
Found at i:16120278 original size:15 final size:17
Alignment explanation
Indices: 16120250--16120281 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16120240 TTCATTATTG
16120250 AAAGGTGATATGATGAA
1 AAAGGTGATATGATGAA
16120267 AAAGG-GAT-TGATGAA
1 AAAGGTGATATGATGAA
16120282 TTGAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (17 bp):
AAAGGTGATATGATGAA
Found at i:16125352 original size:124 final size:124
Alignment explanation
Indices: 16125127--16125406 Score: 499
Period size: 124 Copynumber: 2.3 Consensus size: 124
16125117 TTATTTCGAG
* * *
16125127 TTGACGTTTCTG-GTCAAATAGCATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGATGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGT
*
16125191 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAGATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
16125251 TTGATGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
16125316 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
16125375 TTGATGTTTCTGAGCAAATAGTATAAAATCGC
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGC
16125407 GCCCTCGTGG
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 148 0.99
125 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:16127384 original size:56 final size:56
Alignment explanation
Indices: 16127298--16127455 Score: 280
Period size: 56 Copynumber: 2.8 Consensus size: 56
16127288 NNNNNNNNNN
*
16127298 AAACTATGTAAAATTATTAAGCCCAAAAACTTCTGTTAATGGTTAGTAAAATTATC
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
** *
16127354 AAACTATGTAAAATTATTAATTCCAAAAACTTTTGTTAATGTTTAGTAAAATTATC
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
16127410 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAG
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAG
16127456 GGTTTTTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 95 1.00
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (56 bp):
AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
Found at i:16127488 original size:36 final size:36
Alignment explanation
Indices: 16127474--16128547 Score: 1149
Period size: 36 Copynumber: 32.3 Consensus size: 36
16127464 ATTAAATTAA
* *
16127474 GTTAGGGTTTATGGTTTTTAATTAAATTAGGTT-GCTAG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAG---G
16127512 GTTAGGGTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGG-T----TT-AAGGTGTTTAATTAAATTAGGTTAGG
16127554 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127590 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127626 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127662 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127698 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127734 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127770 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127806 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127842 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127878 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127914 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16127950 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* * *
16127986 GTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128022 GTTAGGGTTTAGGGTTTTTAATTAAATTAGGTT---
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128055 GTTAGGG--T----T-TTTAATTAAATTAAGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16128084 GTTAGGG--T----T-TTTAATT-AA--A--TTAG-
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128107 GTTAGGGTTTGA-GTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128142 TTTAGGG--T----T-TTTAATTAAATTAGGTTA--
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128169 G-T---GTTT-GGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128200 GTTA--G--T---GTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16128229 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16128265 GTTAGGG--T----T-TTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128294 GTTAGGGTTTAGGGTTTTTAATTAAATTAGGTT---
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128327 GTTAGGG--T----T-TTTAATTAAATTAAGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
16128356 GTTAGGG--T----T-TTTAATT-AA--A--TTAG-
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128379 GTTAGGGTTTGA-GTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128414 TTTAGGG--T----T-TTTAATTAAATTAGGTTA--
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
* *
16128441 G-T---GTTT-GGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128472 GTTA--G--T---GTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
*
16128501 GTTAGGGTTT-AGAGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTAAG-GTGTTTAATTAAATTAGGTTAGG
16128537 GTTAGGGTTTA
1 GTTAGGGTTTA
16128548 GNNNNNNNNN
Statistics
Matches: 944, Mismatches: 13, Indels: 159
0.85 0.01 0.14
Matches are distributed among these distances:
23 16 0.02
24 8 0.01
25 4 0.00
26 36 0.04
27 2 0.00
28 8 0.01
29 199 0.21
30 7 0.01
31 9 0.01
32 4 0.00
33 20 0.02
34 9 0.01
35 13 0.01
36 566 0.60
37 2 0.00
38 7 0.01
39 1 0.00
41 1 0.00
42 8 0.01
43 2 0.00
44 21 0.02
45 1 0.00
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.44
Consensus pattern (36 bp):
GTTAGGGTTTAAGGTGTTTAATTAAATTAGGTTAGG
Found at i:16128029 original size:29 final size:29
Alignment explanation
Indices: 16127985--16128546 Score: 695
Period size: 29 Copynumber: 18.6 Consensus size: 29
16127975 ATTAGGTTAG
16127985 GGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTA-GGGTTAGGGTTTTTAATT-AA--A--TTA
16128020 GGGTTAGGGTTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGG-TTAGGGTTTTTAATTAAATTA
16128051 GGTT---GTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128077 AGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
16128106 GGTTAGGGTTTGAGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128135 GGTTAGGTTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
16128164 GGTTAGTGTTTGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128193 GGTTAGGGTTAGTGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
16128222 GGTTAGGGTTAGGGTTTAAGGTGTTTAATTAAATTA
1 GGTTAGGGTTAGGG--T----T-TTTAATTAAATTA
16128258 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTAGGGTTTTTAATT-AA--A--TTA
16128292 GGGTTAGGGTTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGG-TTAGGGTTTTTAATTAAATTA
16128323 GGTT---GTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128349 AGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
16128378 GGTTAGGGTTTGAGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128407 GGTTAGGTTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
* *
16128436 GGTTAGTGTTTGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
16128465 GGTTAGGGTTAGTGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
16128494 GGTTAGGGTTAGGGTTTAGAGTTTTTAATTAAATTA
1 GGTTAGGGTTA--G----G-GTTTTTAATTAAATTA
16128530 GGTTAGGGTTAGGGTTT
1 GGTTAGGGTTAGGGTTT
16128547 AGNNNNNNNN
Statistics
Matches: 470, Mismatches: 28, Indels: 63
0.84 0.05 0.11
Matches are distributed among these distances:
26 48 0.10
27 2 0.00
29 287 0.61
30 12 0.03
31 8 0.02
32 1 0.00
33 2 0.00
34 5 0.01
35 16 0.03
36 89 0.19
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (29 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:16130640 original size:22 final size:21
Alignment explanation
Indices: 16130615--16130665 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 21
16130605 TAATATGGAT
16130615 TTGAGAGATTTTTGGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
16130637 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
16130659 TTGAGAG
1 TTGAGAG
16130666 TTTGAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:16130671 original size:52 final size:52
Alignment explanation
Indices: 16130614--16130716 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
16130604 TTAATATGGA
*
16130614 TTTGAGAGATTTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAG
*
16130666 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAATGAAATTGAGA
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
16130717 TAGGATTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (52 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAG
Found at i:16130672 original size:30 final size:30
Alignment explanation
Indices: 16130637--16130695 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
16130627 TGGAAGGAAA
*
16130637 TTGAGAGGATTTTGGAAGGAAATTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
16130667 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
16130696 GATTTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:16130695 original size:22 final size:22
Alignment explanation
Indices: 16130667--16130716 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
16130657 AATTGAGAGT
16130667 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
16130689 TTGAGAGGATTTTGGAATGAAA
1 TTGAGAGAATTTTGGAAGGAAA
16130711 TTGAGA
1 TTGAGA
16130717 TAGGATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:16135599 original size:19 final size:19
Alignment explanation
Indices: 16135577--16135613 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16135567 TAAAATATTT
*
16135577 AAAAATTACAAAAAATATA
1 AAAAAATACAAAAAATATA
*
16135596 AAAAAATGCAAAAAATAT
1 AAAAAATACAAAAAATAT
16135614 TTTGAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAAAATACAAAAAATATA
Found at i:16136357 original size:30 final size:28
Alignment explanation
Indices: 16136287--16136360 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
16136277 TAGTAAATCT
*
16136287 GATTTATAAA-A-TTTTAAAAATATTAA
1 GATTTATAAATATTTTTAAAAAAATTAA
* *
16136313 GATTTATAATTATTTTTAAAAAAATTTA
1 GATTTATAAATATTTTTAAAAAAATTAA
*
16136341 GTAATTTTTAAATATTTTTA
1 G--ATTTATAAATATTTTTA
16136361 TAATGCTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 9 0.23
27 1 0.03
28 14 0.36
30 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
GATTTATAAATATTTTTAAAAAAATTAA
Found at i:16142312 original size:19 final size:19
Alignment explanation
Indices: 16142290--16142350 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
16142280 ATTAAAGTAG
16142290 GAAAGAAAGAGATATGGGA
1 GAAAGAAAGAGATATGGGA
*
16142309 GAAAGATAGAG--A-GGCGA
1 GAAAGAAAGAGATATGG-GA
* *
16142326 GAGAGAAAGAGATATGAGA
1 GAAAGAAAGAGATATGGGA
16142345 GAAAGA
1 GAAAGA
16142351 TAGAAAGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 12 0.36
19 18 0.55
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.08
Consensus pattern (19 bp):
GAAAGAAAGAGATATGGGA
Found at i:16142333 original size:36 final size:36
Alignment explanation
Indices: 16142293--16142366 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
16142283 AAAGTAGGAA
* * *
16142293 AGAAAGAGATATGGGAGAAAGATAGAGAGGCGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16142329 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16142365 AG
1 AG
16142367 GGAAAGGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.38, T:0.08
Consensus pattern (36 bp):
AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
Found at i:16144137 original size:50 final size:50
Alignment explanation
Indices: 16144082--16144275 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
16144072 CATTGAGGTT
* *
16144082 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * * *
16144132 ATGAGAGATCCCCCGTAAGACCATGTCTGGGAGATGGCATGGGCACCGAT
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * **
16144182 ATGAGA-ACTCCCATGTAAAACCATATCTGGGTTATGGCATTGGCA--GTAC
1 ATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * * * * *
16144231 AAGAAACATCCCATGTAAGACCATGTTTGGGACATGACTTTGGCA
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16144276 TGTTATTATC
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.31
50 81 0.69
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:16148560 original size:5 final size:5
Alignment explanation
Indices: 16148550--16148597 Score: 80
Period size: 5 Copynumber: 9.6 Consensus size: 5
16148540 GTAATTTGAT
16148550 AAATA AAATA AAATA AAATA AAAT- AAATA AAATA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
16148598 GCTATCATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.10
5 32 0.78
6 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:16148577 original size:14 final size:14
Alignment explanation
Indices: 16148550--16148590 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
16148540 GTAATTTGAT
16148550 AAATAAAATAAAATA
1 AAATAAAAT-AAATA
16148565 AAATAAAATAAATA
1 AAATAAAATAAATA
16148579 AAATAAAATAAA
1 AAATAAAATAAA
16148591 AATAAAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:16148577 original size:24 final size:25
Alignment explanation
Indices: 16148548--16148597 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
16148538 TGGTAATTTG
16148548 ATAAATAAAATAAAAT-AAAATAAA
1 ATAAATAAAATAAAATAAAAATAAA
16148572 ATAAATAAAATAAAATAAAAATAAA
1 ATAAATAAAATAAAATAAAAATAAA
16148597 A
1 A
16148598 GCTATCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (25 bp):
ATAAATAAAATAAAATAAAAATAAA
Found at i:16153559 original size:21 final size:21
Alignment explanation
Indices: 16153513--16153559 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
16153503 AAGTAGTTTT
*
16153513 GAAATGGAAAAGTAATGGATT
1 GAAATGGAAAAGTAATGGATG
16153534 GAAAT-GAAAAGT-ATGGTATG
1 GAAATGGAAAAGTAATGG-ATG
16153554 GTAAAT
1 G-AAAT
16153560 AGTTACATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (21 bp):
GAAATGGAAAAGTAATGGATG
Found at i:16158959 original size:38 final size:38
Alignment explanation
Indices: 16158917--16158990 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
16158907 CAGTTCAAGC
* *
16158917 TAATAAGCTCTTGAATCAAGGTTGTGAAGCTTTCCTGG
1 TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCTGG
*
16158955 TAATAAGTTCCTGAATCAAGGTTGTGAAGCATTCCT
1 TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCT
16158991 AGCCTACGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (38 bp):
TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCTGG
Found at i:16161207 original size:56 final size:50
Alignment explanation
Indices: 16161127--16161317 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
16161117 GGAATGAGAT
*
16161127 TCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---GAGA-TATGAGAGG
* *
16161182 TCTCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAG--ATGAGAGG
1 TC-CATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAGATATGAGAGG
** * * **
16161232 TCCCCGTAAGACCATGTCTGGGACATGGCATGGGCAC-CGATATGAGAAC
1 TCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGG
* *
16161281 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 T-CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16161318 GTATAGAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 36 0.31
50 40 0.35
53 3 0.03
55 2 0.02
56 32 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGG
Found at i:16161310 original size:50 final size:50
Alignment explanation
Indices: 16161128--16161366 Score: 216
Period size: 49 Copynumber: 4.7 Consensus size: 50
16161118 GAATGAGATT
* * **
16161128 CCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAACTC
* * * * **
16161184 TCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
* *
16161234 CC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
* * *
16161283 CCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TATAGAAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATAT-GAGAAC-TC
* * *
16161332 CCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16161367 TGTATTATCA
Statistics
Matches: 156, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
47 3 0.02
48 6 0.04
49 74 0.47
50 39 0.25
51 2 0.01
55 1 0.01
56 31 0.20
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
Found at i:16161583 original size:12 final size:12
Alignment explanation
Indices: 16161566--16161604 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16161556 ATGAGTTATT
16161566 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
16161578 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
16161590 TAAGTGAGTAAG
1 TAAGTAAGCAAG
16161602 TAA
1 TAA
16161605 ACAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:16161592 original size:20 final size:20
Alignment explanation
Indices: 16161567--16161609 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16161557 TGAGTTATTT
16161567 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
**
16161587 AAGTAAGTGAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
16161607 AAG
1 AAG
16161610 CGAGTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.16
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:16167554 original size:50 final size:50
Alignment explanation
Indices: 16167479--16167822 Score: 465
Period size: 50 Copynumber: 6.8 Consensus size: 50
16167469 NNNNNNNNNN
16167479 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
*
16167529 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCT
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
* **
16167579 AACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCA-CTTTGATGCC
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG-TGCC
* * * * * *
16167629 AACACCATGTCCCAGACATGGTATTACATGGAACCTCTTATCTCGGTACC
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
* *
16167679 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
* *
16167729 AACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGAATTCC
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-AG--TGCC
* * *
16167785 AATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16167823 TTACCTAAAT
Statistics
Matches: 259, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
49 3 0.01
50 211 0.81
51 3 0.01
53 4 0.02
54 1 0.00
56 37 0.14
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (50 bp):
AACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCC
Found at i:16174675 original size:19 final size:19
Alignment explanation
Indices: 16174651--16174690 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16174641 CCGGCCCATT
* * *
16174651 TTTTAATAAACATTAAAAA
1 TTTTAAAAAAAATAAAAAA
16174670 TTTTAAAAAAAATAAAAAA
1 TTTTAAAAAAAATAAAAAA
16174689 TT
1 TT
16174691 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTAAAAAAAATAAAAAA
Found at i:16174699 original size:11 final size:11
Alignment explanation
Indices: 16174685--16174713 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16174675 AAAAAAATAA
16174685 AAAATTATTTT
1 AAAATTATTTT
16174696 AAAATTATTTT
1 AAAATTATTTT
16174707 AAAATTA
1 AAAATTA
16174714 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:16183032 original size:26 final size:26
Alignment explanation
Indices: 16182996--16183047 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
16182986 TTGCCAACTG
*
16182996 AGTTATAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16183022 AGTTAGAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16183048 TATGTGTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (26 bp):
AGTTAGAGAAGATTCATAATGTATTC
Found at i:16184348 original size:92 final size:93
Alignment explanation
Indices: 16184231--16184417 Score: 322
Period size: 92 Copynumber: 2.0 Consensus size: 93
16184221 ACAATCGGCA
* * *
16184231 AAAATACTTAATTTTCATAAGTAAGTGTTAGAGTAAGAATTTGATGTTGTCATAGAAGGGAAAAA
1 AAAATACCTAATGTTCATAAGTAAGTGTTAGAGTAAGAATTTGATGTTCTCATAGAAGGGAAAAA
*
16184296 TGTTCAG-ATGTTATAAAACATAATAAT
66 TGTTCAGCATGTTATAAAACATAAGAAT
16184323 AAAATACCTAATGTTCATAAGTAAGTGTTAGAGTAAGAATTTGATGTTCTCATAGAAGGGAAAAA
1 AAAATACCTAATGTTCATAAGTAAGTGTTAGAGTAAGAATTTGATGTTCTCATAGAAGGGAAAAA
*
16184388 TGTTTAGCATGTTATAAAACATAAGAAT
66 TGTTCAGCATGTTATAAAACATAAGAAT
16184416 AA
1 AA
16184418 GAGATGAAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 68 0.76
93 21 0.24
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (93 bp):
AAAATACCTAATGTTCATAAGTAAGTGTTAGAGTAAGAATTTGATGTTCTCATAGAAGGGAAAAA
TGTTCAGCATGTTATAAAACATAAGAAT
Found at i:16184895 original size:81 final size:81
Alignment explanation
Indices: 16184758--16184914 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 81
16184748 TTAAGTGTGA
* * ** *
16184758 GATGATAGAGAATCAGTGATTAAAGCCCCGTTGAAACATTTGGAGTGTATTGGATACAAATGTCC
1 GATGACAGAGAATCAGTGATAAAAGCCCCGTTGAAACATTACGAGTGTATTGGATACAAATGTCA
16184823 TGAAATTTGGGGAAAC
66 TGAAATTTGGGGAAAC
*
16184839 GATGACAGAGAATCAGTGATAAAAGCCCCGTTGAAACATTACGAGTGTATTTGATACAAATGTCA
1 GATGACAGAGAATCAGTGATAAAAGCCCCGTTGAAACATTACGAGTGTATTGGATACAAATGTCA
*
16184904 TGACATTTGGG
66 TGAAATTTGGG
16184915 TAAAGAGATC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (81 bp):
GATGACAGAGAATCAGTGATAAAAGCCCCGTTGAAACATTACGAGTGTATTGGATACAAATGTCA
TGAAATTTGGGGAAAC
Found at i:16185044 original size:50 final size:50
Alignment explanation
Indices: 16184981--16185147 Score: 144
Period size: 50 Copynumber: 3.4 Consensus size: 50
16184971 ATGAGAGGTC
* * * ** *
16184981 CCATGTATGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCT-TAAGA
1 CCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACT-CCCATGTAAGA
*
16185031 CCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGA
1 CCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGA
* * * * * * *
16185081 CCATATCTGGGATATGGCAT-TG-ACAGTACAAGA-AACATCCTATGTAAGA
1 CCATGTCTGGGACATGGCATGGGCACCG-AGATGAGAAC-TCCCATGTAAGA
*
16185130 CCATGTCTGAGACATGGC
1 CCATGTCTGGGACATGGC
16185148 TTTGGAATGC
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
48 6 0.06
49 35 0.36
50 56 0.58
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
CCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCATGTAAGA
Found at i:16207143 original size:13 final size:13
Alignment explanation
Indices: 16207122--16207153 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16207112 GCTTGGATCA
*
16207122 TCATCAAATAAAT
1 TCATAAAATAAAT
16207135 TCATAAAATAAAT
1 TCATAAAATAAAT
16207148 TCATAA
1 TCATAA
16207154 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16210289 original size:41 final size:45
Alignment explanation
Indices: 16210215--16210298 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
16210205 TTTAAAAATC
*
16210215 TATATTTAAATTAAAATATTAATAAATAAAAATGTTACAAAAAGTT
1 TATATTTAAATTAAAATATTAATAAAT-AAAATGTAACAAAAAGTT
*
16210261 TATATTTAAATTCAAA-A-T-ATAAAT-AAATGTAACAAAAA
1 TATATTTAAATTAAAATATTAATAAATAAAATGTAACAAAAA
16210299 TCTAATCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 13 0.36
43 6 0.17
44 1 0.03
45 1 0.03
46 15 0.42
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (45 bp):
TATATTTAAATTAAAATATTAATAAATAAAATGTAACAAAAAGTT
Found at i:16210838 original size:32 final size:32
Alignment explanation
Indices: 16210798--16210868 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
16210788 CTTTTAGGTC
*
16210798 ACCA-AACCCTACCTGAACGCAAGCAATCCAT
1 ACCACAACCCTACCTGAACGCAAGCAACCCAT
*
16210829 ACCACAACCCTACCTGAATGCAAGCAACCCAT
1 ACCACAACCCTACCTGAACGCAAGCAACCCAT
*
16210861 ACCGCAAC
1 ACCACAAC
16210869 TCAGAAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.38, C:0.41, G:0.10, T:0.11
Consensus pattern (32 bp):
ACCACAACCCTACCTGAACGCAAGCAACCCAT
Found at i:16214099 original size:9 final size:9
Alignment explanation
Indices: 16214082--16214118 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16214072 TGAGTTTTCG
16214082 AATTCGAAT
1 AATTCGAAT
*
16214091 AACTCGAAT
1 AATTCGAAT
16214100 AATTCGAAT
1 AATTCGAAT
16214109 AATTCGAAT
1 AATTCGAAT
16214118 A
1 A
16214119 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16214861 original size:5 final size:5
Alignment explanation
Indices: 16214851--16214876 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16214841 CTCAAAAATT
16214851 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
16214877 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:16219703 original size:7 final size:7
Alignment explanation
Indices: 16219684--16219716 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16219674 GCAGACCAGA
16219684 AAAAAAT
1 AAAAAAT
16219691 AGAAAAAT
1 A-AAAAAT
16219699 AAAAAAT
1 AAAAAAT
16219706 -AAAAAT
1 AAAAAAT
16219712 AAAAA
1 AAAAA
16219717 GCCAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:16224143 original size:29 final size:29
Alignment explanation
Indices: 16224101--16224168 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
16224091 TATTTAATTA
16224101 ATGTTAAATGATTTTATTGAGTTGTTTTG
1 ATGTTAAATGATTTTATTGAGTTGTTTTG
16224130 ATGTTAAATGATTTTATTGAGTTGTTTTG
1 ATGTTAAATGATTTTATTGAGTTGTTTTG
16224159 ATGTTAAATG
1 ATGTTAAATG
16224169 TTACACCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (29 bp):
ATGTTAAATGATTTTATTGAGTTGTTTTG
Found at i:16238549 original size:14 final size:14
Alignment explanation
Indices: 16238517--16238543 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16238507 CAAATTTAAC
16238517 TATACTAAAATGAA
1 TATACTAAAATGAA
16238531 TATACTAAAATGA
1 TATACTAAAATGA
16238544 TCATACAAAC
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:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
TATACTAAAATGAA
Found at i:16239004 original size:24 final size:24
Alignment explanation
Indices: 16238958--16239004 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16238948 GGCTCTTCAG
* *
16238958 TAGCAGTTAGATTGGGCTGCTCGA
1 TAGCAGTTAGAGTGGCCTGCTCGA
* *
16238982 TAGCAGTTTGAGTGGCCTTCTCG
1 TAGCAGTTAGAGTGGCCTGCTCG
16239005 GCAGCATAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (24 bp):
TAGCAGTTAGAGTGGCCTGCTCGA
Found at i:16240726 original size:79 final size:80
Alignment explanation
Indices: 16240612--16240774 Score: 319
Period size: 79 Copynumber: 2.0 Consensus size: 80
16240602 AACTGCTCAA
16240612 AAATAAAAATAGAAACGGAAAAAATATTAAAAAATAAAAAATAATAAATTAAAAGTAATTAAAGA
1 AAATAAAAATAGAAACGGAAAAAATATTAAAAAATAAAAAATAATAAATTAAAAGTAATTAAAGA
16240677 AAAG-AAGATAAAAG
66 AAAGAAAGATAAAAG
16240691 AAATAAAAATAGAAACGGAAAAAATATTAAAAAATAAAAAATAATAAATTAAAAGTAATTAAAGA
1 AAATAAAAATAGAAACGGAAAAAATATTAAAAAATAAAAAATAATAAATTAAAAGTAATTAAAGA
16240756 AAAGAAAGATAAAAG
66 AAAGAAAGATAAAAG
16240771 AAAT
1 AAAT
16240775 TGTTAGCTCA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 69 0.83
80 14 0.17
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (80 bp):
AAATAAAAATAGAAACGGAAAAAATATTAAAAAATAAAAAATAATAAATTAAAAGTAATTAAAGA
AAAGAAAGATAAAAG
Found at i:16243730 original size:27 final size:27
Alignment explanation
Indices: 16243687--16244050 Score: 373
Period size: 27 Copynumber: 13.5 Consensus size: 27
16243677 CTTTCGATTT
*
16243687 GAAGGGTAAAATGATTGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* * * *
16243714 GAAAGGTAAAATAATTGAAATACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16243741 GAAGGGTAAAATGATTGAAATACCCTT
1 GAAGGGTAAAATGATCGAAATACCCTC
* * *
16243768 AAAGGGTAAAATGACCGAAATACGCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16243795 AAAGAGTAAAATGA-CAGAAATACCCTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * *
16243822 AAAGGGTAAAATGA-CTAAAATACCCAC
1 GAAGGGTAAAATGATC-GAAATACCCTC
*
16243849 GAAGGGTAAAATGATCGAAATACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
16243876 GAAGGGTAAAATGA-CGAAAATACCCTC
1 GAAGGGTAAAATGATCG-AAATACCCTC
* * * *
16243903 GAAGGGTAAAATGACCAAAACACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16243930 GAAGGGTAAAATGATCAAAATACCCTA
1 GAAGGGTAAAATGATCGAAATACCCTC
16243957 GAAGGGTAAAATGATCGAAATACCC-C
1 GAAGGGTAAAATGATCGAAATACCCTC
* ** *
16243983 TGAAGGGTAAACTGGCCAAAATACCC-C
1 -GAAGGGTAAAATGATCGAAATACCCTC
* *
16244010 -ACAGGGTAAAATGATTGAAATACCTTC
1 GA-AGGGTAAAATGATCGAAATACCCTC
16244037 -ATAGGGTAAAATGA
1 GA-AGGGTAAAATGA
16244051 CCATTATACC
Statistics
Matches: 288, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 20 0.07
27 265 0.92
28 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (27 bp):
GAAGGGTAAAATGATCGAAATACCCTC
Found at i:16250242 original size:11 final size:11
Alignment explanation
Indices: 16250226--16250250 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16250216 ACAGTTGTGG
16250226 GGATTTTGAAT
1 GGATTTTGAAT
16250237 GGATTTTGAAT
1 GGATTTTGAAT
16250248 GGA
1 GGA
16250251 GTTGTTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (11 bp):
GGATTTTGAAT
Found at i:16251295 original size:27 final size:27
Alignment explanation
Indices: 16251262--16251711 Score: 457
Period size: 27 Copynumber: 16.7 Consensus size: 27
16251252 AACTTTTGAT
* *
16251262 TCGAAGGGTAAAATGATCGAAATATCC
1 TCGAAGGGTAAAATGACCGAAATACCC
*
16251289 TTGAAGGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16251316 CCAAAGGGTAAAATGATCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16251343 TCGAAGGGTAAAATAATCGAAATATCCC
1 TCGAAGGGTAAAATGACCGAAATA-CCC
* * *
16251371 T-AAATGGTAAAAT-AGCTGAAATACCC
1 TCGAAGGGTAAAATGA-CCGAAATACCC
** *
16251397 TTAAAGGGTAAAAT-AGCTGAAATACCC
1 TCGAAGGGTAAAATGA-CCGAAATACCC
*
16251424 TTGAAGGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16251451 TAGAATGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16251478 CCGAAAGGTAAAATGACCGAAATAACCA
1 TCGAAGGGTAAAATGACCGAAAT-ACCC
* *
16251506 T-GAAGGGTAAAATAATCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16251532 TCGAAGGGTAAAATGATCGAAATACTC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16251559 TCAAAGGGTAAAATGATCGAAACACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* **
16251586 CCTGAAGGGTAAAATGACTAAAATACCC
1 TC-GAAGGGTAAAATGACCGAAATACCC
* * *
16251614 TCGAAAGGTAATATGACCAAAATACCAC
1 TCGAAGGGTAAAATGACCGAAATACC-C
*
16251642 -CGAAGGGTAAAATGACCAAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
16251668 -C-ACAGGGTAAAATGACCGAAATACCC
1 TCGA-AGGGTAAAATGACCGAAATACCC
*
16251694 T-TATAGGGTAAAATGACC
1 TCGA-AGGGTAAAATGACC
16251712 ATTATACCCC
Statistics
Matches: 365, Mismatches: 47, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.00
26 33 0.09
27 301 0.82
28 30 0.08
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (27 bp):
TCGAAGGGTAAAATGACCGAAATACCC
Found at i:16252041 original size:28 final size:28
Alignment explanation
Indices: 16252000--16252091 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
16251990 GTTGCATTAT
* * *
16252000 CACACTGTTACTGTAATAGGCTAAGGTC
1 CACACTGTTTCTGTATTAGGCTAAGGCC
*
16252028 CACACTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTAGGCTAAGGCC
*
16252056 CACATTGTTAT-TGTATTAGGCTAAGGCC
1 CACACTGTT-TCTGTATTAGGCTAAGGCC
16252084 CACACTGT
1 CACACTGT
16252092 ACTATTATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 55 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (28 bp):
CACACTGTTTCTGTATTAGGCTAAGGCC
Found at i:16252100 original size:28 final size:27
Alignment explanation
Indices: 16252016--16252100 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
16252006 GTTACTGTAA
* * *
16252016 TAGGCTAAGGTCCACACTGTTTCTGTAT
1 TAGGCTAAGGCCCACACTGTCTAT-TAT
* *
16252044 TGGGCTAAGGCCCACATTGT-TATTGTAT
1 TAGGCTAAGGCCCACACTGTCTA-T-TAT
16252072 TAGGCTAAGGCCCACACTGTACTATTAT
1 TAGGCTAAGGCCCACACTGT-CTATTAT
16252100 T
1 T
16252101 GCGTTGGGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 44 0.92
29 1 0.02
30 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
TAGGCTAAGGCCCACACTGTCTATTAT
Found at i:16260447 original size:75 final size:75
Alignment explanation
Indices: 16260320--16260475 Score: 296
Period size: 75 Copynumber: 2.1 Consensus size: 75
16260310 TTTAGGTAAA
16260320 TTTG-ATTGTGGAAGTTGAGGTGTCATTTTGGCAAAATGGTTGTATGGATAGTTTTAGGTTGTTT
1 TTTGCATTGTGGAAGTTGAGGTGTCATTTTGGCAAAATGGTTGTATGGATAGTTTTAGGTTGTTT
*
16260384 AAGTTTGATT
66 AAGTTTGAAT
16260394 TTTGCATTGTGGAAGTTGAGGTGTCATTTTGGCAAAATGGTTGTATGGATAGTTTTAGGTTGTTT
1 TTTGCATTGTGGAAGTTGAGGTGTCATTTTGGCAAAATGGTTGTATGGATAGTTTTAGGTTGTTT
16260459 AAGTTTGAAT
66 AAGTTTGAAT
16260469 TTTGCAT
1 TTTGCAT
16260476 ATGTTAAGTG
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
74 4 0.05
75 76 0.95
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.46
Consensus pattern (75 bp):
TTTGCATTGTGGAAGTTGAGGTGTCATTTTGGCAAAATGGTTGTATGGATAGTTTTAGGTTGTTT
AAGTTTGAAT
Found at i:16262004 original size:16 final size:16
Alignment explanation
Indices: 16261983--16262056 Score: 96
Period size: 16 Copynumber: 4.6 Consensus size: 16
16261973 CGTTTGGTTC
16261983 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
*
16261999 GCTGTAATTGAATAGA
1 GCTGTAATAGAATAGA
*
16262015 GCTGTAATAGAATAAA
1 GCTGTAATAGAATAGA
16262031 GCTGTAAT-GTAATAGA
1 GCTGTAATAG-AATAGA
**
16262047 ATTGTAATAG
1 GCTGTAATAG
16262057 TAATTCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.02
16 48 0.96
17 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:16262126 original size:44 final size:45
Alignment explanation
Indices: 16262036--16262128 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
16262026 ATAAAGCTGT
* *
16262036 AATGTAATAGAATTGTAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
*
16262081 AATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
16262125 AATG
1 AATG
16262129 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (45 bp):
AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
Found at i:16268139 original size:22 final size:22
Alignment explanation
Indices: 16268109--16268151 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16268099 ACAACAAAAC
*
16268109 AGGCTTTTAGCGGCACTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
*
16268131 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCACTTTTT
16268152 AGCGCCACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:16268296 original size:43 final size:43
Alignment explanation
Indices: 16268243--16268557 Score: 350
Period size: 43 Copynumber: 7.3 Consensus size: 43
16268233 GTTTCTAGGA
*
16268243 ACAAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
16268286 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* *
16268329 ACAAACGCCGCTAAATACCAAGACCTTTAGCGGCGCTTCAAGC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* *
16268372 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCAT-ATTAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCA-AAC
* * * * ***
16268415 ATAAACGCCGCTAAATACTAAGATCTTTAGCGGCGCTTCTCTC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* * * ****
16268458 GCAAACGCCGCTAAATG-CTAAGTCCTTTAGCGGCGCTTTTCTC
1 ACAAACGCCGCTAAA-GACCAAGACCTTTAGCGGCGCTTCAAAC
* ****
16268501 ACAAACGCCGCTAAATG-CTAAGTA-CTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAA-GACCAAG-ACCTTTAGCGGCGCTTCAAAC
16268544 ACAAACGCCGCTAA
1 ACAAACGCCGCTAA
16268558 TTTTGGCAGA
Statistics
Matches: 244, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.00
43 243 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
Found at i:16275029 original size:22 final size:21
Alignment explanation
Indices: 16275004--16275136 Score: 84
Period size: 22 Copynumber: 6.4 Consensus size: 21
16274994 GTTACATATC
16275004 ATATTAATGTAAGTTATGTATT
1 ATATTAATGTAAGTTATGTA-T
* *
16275026 ATATAAGTTATTTAAGTTATGTA-
1 ATAT---TAATGTAAGTTATGTAT
* *
16275049 A-GTT-GTGTAAGTTATGTAT
1 ATATTAATGTAAGTTATGTAT
**
16275068 AATATTACGGTAAGTTATG---
1 -ATATTAATGTAAGTTATGTAT
16275087 -TATT-ATGTAAGTTATGTAT
1 ATATTAATGTAAGTTATGTAT
16275106 AATATTAATGTAAGTTATGTATT
1 -ATATTAATGTAAGTTATGTA-T
*
16275129 ATGTTAAT
1 ATATTAAT
16275137 ATTTAGAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
16 10 0.12
17 4 0.05
18 12 0.14
19 1 0.01
20 1 0.01
21 6 0.07
22 36 0.42
23 2 0.02
25 14 0.16
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (21 bp):
ATATTAATGTAAGTTATGTAT
Found at i:16275036 original size:9 final size:9
Alignment explanation
Indices: 16275010--16275104 Score: 81
Period size: 9 Copynumber: 10.6 Consensus size: 9
16275000 TATCATATTA
16275010 ATGTAAGTT
1 ATGTAAGTT
16275019 ATGT-A-TT
1 ATGTAAGTT
*
16275026 ATATAAGTT
1 ATGTAAGTT
*
16275035 ATTTAAGTT
1 ATGTAAGTT
16275044 ATGTAAGTT
1 ATGTAAGTT
*
16275053 GTGTAAGTT
1 ATGTAAGTT
*
16275062 ATGTATAATATT
1 ATG--TAA-GTT
*
16275074 ACGGTAAGTT
1 A-TGTAAGTT
16275084 ATGT-A-TT
1 ATGTAAGTT
16275091 ATGTAAGTT
1 ATGTAAGTT
16275100 ATGTA
1 ATGTA
16275105 TAATATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.16
8 4 0.06
9 41 0.59
10 3 0.04
11 6 0.09
12 3 0.04
13 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:16275050 original size:18 final size:18
Alignment explanation
Indices: 16275010--16275104 Score: 81
Period size: 16 Copynumber: 5.3 Consensus size: 18
16275000 TATCATATTA
16275010 ATGTAAGTTATGT-A-TT
1 ATGTAAGTTATGTAAGTT
* *
16275026 ATATAAGTTATTTAAGTT
1 ATGTAAGTTATGTAAGTT
*
16275044 ATGTAAGTTGTGTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
16275062 ATGTATAATATTACGGTAAGTT
1 ATG--TAA-GTTA-TGTAAGTT
16275084 ATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
16275100 ATGTA
1 ATGTA
16275105 TAATATTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 22 0.35
17 4 0.06
18 20 0.32
19 1 0.02
20 4 0.06
21 2 0.03
22 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:16275096 original size:38 final size:38
Alignment explanation
Indices: 16275038--16275132 Score: 145
Period size: 38 Copynumber: 2.4 Consensus size: 38
16275028 ATAAGTTATT
* *
16275038 TAAGTTATGTAAGTTGTGTAAGTTATGTATAATATTACGG
1 TAAGTTATGT-A-TTATGTAAGTTATGTATAATATTAAGG
*
16275078 TAAGTTATGTATTATGTAAGTTATGTATAATATTAATG
1 TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
16275116 TAAGTTATGTATTATGT
1 TAAGTTATGTATTATGT
16275133 TAATATTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 41 0.79
39 1 0.02
40 10 0.19
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (38 bp):
TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
Found at i:16275259 original size:21 final size:21
Alignment explanation
Indices: 16275226--16275265 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16275216 TAACATTTAC
*
16275226 AATTATTTCTGAAATTATAAA
1 AATTATTTCTGAAAATATAAA
16275247 AATTATTAT-TGAAAATATA
1 AATTATT-TCTGAAAATATA
16275266 GGTTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
AATTATTTCTGAAAATATAAA
Found at i:16275288 original size:69 final size:69
Alignment explanation
Indices: 16275129--16275323 Score: 220
Period size: 69 Copynumber: 2.8 Consensus size: 69
16275119 GTTATGTATT
* * *
16275129 ATGTTAATATTTAG-AAAATAGCAATTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAA
1 ATGTTAATCTTT-GCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAA
16275193 TATAG
65 TATAG
* * *
16275198 ATGTTAATCTTTGGAAAATAACATTTACAATTATTTCTGAAATTATAAAAATTATTATTGAAAAT
1 ATGTTAATCTTTGCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
16275263 ATAG
66 ATAG
* *** *
16275267 GT-TTAAT-TGTTGTCTTCATAACATTTATC-ATTATTTTTAAAATTA-AAAATTTATTAT
1 ATGTTAATCT-TTG-CAAAATAACATTTA-CAATTATTTCTAAAATTATAAAATTTATTAT
16275324 CAATAAAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
67 1 0.01
68 20 0.18
69 87 0.80
70 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (69 bp):
ATGTTAATCTTTGCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
ATAG
Found at i:16276938 original size:24 final size:22
Alignment explanation
Indices: 16276900--16276945 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
16276890 CTAGGGTTCT
16276900 AAATTTGGGGGATTTTTGGGGA
1 AAATTTGGGGGATTTTTGGGGA
16276922 AAATTTGGGGGGAATTTTTGGGGA
1 AAATTT-GGGGG-ATTTTTGGGGA
16276946 GAAAACTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (22 bp):
AAATTTGGGGGATTTTTGGGGA
Found at i:16279009 original size:42 final size:40
Alignment explanation
Indices: 16278953--16279108 Score: 127
Period size: 41 Copynumber: 3.8 Consensus size: 40
16278943 GCTAAAACTC
*
16278953 CAACATTAGTGGCGCTTTATAAACAAACGCCACTAAAAACCT
1 CAACATTAGCGGCGC-TTATAAA-AAACGCCACTAAAAACCT
* * * * *
16278995 CAACTTTAGCGGCGCATTATCAAAAATGCCGCTAAAAGCC-
1 CAACATTAGCGGCGC-TTATAAAAAACGCCACTAAAAACCT
* * *
16279035 CTAAAATTAGCGGCGCTCAGGAAAAAACGCCACTAAAAACCAT
1 C-AACATTAGCGGCGCTTA-TAAAAAACGCCACTAAAAACC-T
* * *
16279078 -AACATTAGCGGCGTTTGTTTAAAAACGCCAC
1 CAACATTAGCGGCGCTT-ATAAAAAACGCCAC
16279109 GAAAGCCCTC
Statistics
Matches: 88, Mismatches: 21, Indels: 11
0.73 0.17 0.09
Matches are distributed among these distances:
40 3 0.03
41 66 0.75
42 19 0.22
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (40 bp):
CAACATTAGCGGCGCTTATAAAAAACGCCACTAAAAACCT
Found at i:16279030 original size:41 final size:42
Alignment explanation
Indices: 16278936--16279050 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 42
16278926 GTTTCCATCG
* *
16278936 AAATGCCGCT-AAAACTCCAACATTAGTGGCGCTTTATAAAC
1 AAATGCCGCTAAAAACTCCAACATTAGCGGCGCATTATAAAC
* * * *
16278977 AAACGCCACTAAAAAC-CTCAACTTTAGCGGCGCATTATCAA-
1 AAATGCCGCTAAAAACTC-CAACATTAGCGGCGCATTATAAAC
* *
16279018 AAATGCCGCTAAAAGC-CCTAAAATTAGCGGCGC
1 AAATGCCGCTAAAAACTCC-AACATTAGCGGCGC
16279051 TCAGGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.02
41 35 0.58
42 24 0.40
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (42 bp):
AAATGCCGCTAAAAACTCCAACATTAGCGGCGCATTATAAAC
Found at i:16281934 original size:17 final size:18
Alignment explanation
Indices: 16281912--16281945 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16281902 TTATTTATAA
16281912 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
16281929 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
16281946 AATTAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:16295528 original size:16 final size:16
Alignment explanation
Indices: 16295507--16295544 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16295497 TAAAATACTT
16295507 TTTTTAATTGTTTTAA
1 TTTTTAATTGTTTTAA
* *
16295523 TTTTTACTTTTTTTAA
1 TTTTTAATTGTTTTAA
16295539 TTTTTA
1 TTTTTA
16295545 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTAATTGTTTTAA
Found at i:16295549 original size:28 final size:25
Alignment explanation
Indices: 16295502--16295556 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 25
16295492 ATTTTTAAAA
*
16295502 TACTTTTTTTAATTGTTTTAATTTT
1 TACTTTTTTTAATTATTTTAATTTT
16295527 TACTTTTTTTAATTTTTATTTTAATTTT
1 TACTTTTTTTAA---TTATTTTAATTTT
16295555 TA
1 TA
16295557 AAATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
28 14 0.54
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (25 bp):
TACTTTTTTTAATTATTTTAATTTT
Found at i:16296232 original size:14 final size:14
Alignment explanation
Indices: 16296213--16296298 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
16296203 TTCCTTCTAG
16296213 TTTATTTTATTATT
1 TTTATTTTATTATT
16296227 TTTATTATTA-TATT
1 TTTATT-TTATTATT
* *
16296241 AGTTT-TATTATTAGT
1 --TTTATTTTATTATT
* *
16296256 TTTATTATATTGTT
1 TTTATTTTATTATT
*
16296270 TTTATATTATT-TAT
1 TTTATTTTATTAT-T
*
16296284 CTTATTTTCATTATT
1 TTTATTTT-ATTATT
16296299 AGGATTAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
13 4 0.07
14 35 0.65
15 11 0.20
16 4 0.07
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTTTATTATT
Found at i:16296236 original size:12 final size:12
Alignment explanation
Indices: 16296217--16296322 Score: 53
Period size: 12 Copynumber: 8.8 Consensus size: 12
16296207 TTCTAGTTTA
16296217 TTTTATTATT-T
1 TTTTATTATTAT
*
16296228 TTATTATTATATTAG
1 TT-TTA-T-TATTAT
*
16296243 TTTTATTATTAG
1 TTTTATTATTAT
16296255 TTTTATTA-TAT
1 TTTTATTATTAT
16296266 TGTTT-TTA-TAT
1 T-TTTATTATTAT
*
16296277 TATTTA-TCTTAT
1 T-TTTATTATTAT
* *
16296289 TTTCATTATTAG
1 TTTTATTATTAT
**
16296301 GATTAGTT-TTAT
1 TTTTA-TTATTAT
16296313 TTTTATTATT
1 TTTTATTATT
16296323 GCTATAGTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 19
0.69 0.12 0.18
Matches are distributed among these distances:
11 21 0.29
12 38 0.53
13 4 0.06
14 7 0.10
15 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:16296260 original size:26 final size:25
Alignment explanation
Indices: 16296217--16296271 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
16296207 TTCTAGTTTA
*
16296217 TTTTATTATTTTTATTATTATATTAG
1 TTTTATTATTGTTATTATTATATT-G
16296243 TTTTATTATTAGTT-TTATTATATTG
1 TTTTATTATT-GTTATTATTATATTG
16296268 TTTT
1 TTTT
16296272 TATATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 20 0.74
27 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (25 bp):
TTTTATTATTGTTATTATTATATTG
Found at i:16296262 original size:9 final size:8
Alignment explanation
Indices: 16296214--16296252 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
16296204 TCCTTCTAGT
16296214 TTATTTTA
1 TTATTTTA
16296222 TTATTTTTA
1 TTA-TTTTA
*
16296231 TTATTATA
1 TTATTTTA
16296239 TTAGTTTTA
1 TTA-TTTTA
16296248 TTATT
1 TTATT
16296253 AGTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (8 bp):
TTATTTTA
Found at i:16296479 original size:16 final size:16
Alignment explanation
Indices: 16296443--16296482 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16296433 ATTACGTGCC
*
16296443 GATTTGTTTTATTTGTT
1 GATTTG-TTTATTTATT
*
16296460 GATTTGTTTCTTTATT
1 GATTTGTTTATTTATT
16296476 GATTTGT
1 GATTTGT
16296483 ACTGATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.12, C:0.03, G:0.17, T:0.68
Consensus pattern (16 bp):
GATTTGTTTATTTATT
Found at i:16298006 original size:35 final size:35
Alignment explanation
Indices: 16297967--16298033 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
16297957 GCACTATTTT
* *
16297967 TTTAT-TTTTTCAGTTTTTTTCTAGTTTT-TTATCTC
1 TTTATATTATTCA-TTTTTGTCTA-TTTTCTTATCTC
16298002 TTTATATTATTCATTTTTGTCTATTTTCTTAT
1 TTTATATTATTCATTTTTGTCTATTTTCTTAT
16298034 TAGTTTGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 18 0.64
36 6 0.21
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.70
Consensus pattern (35 bp):
TTTATATTATTCATTTTTGTCTATTTTCTTATCTC
Found at i:16298750 original size:35 final size:35
Alignment explanation
Indices: 16298704--16298773 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
16298694 GTTGTATTAA
16298704 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
*
16298739 CCCCTAGTAAACATTGTTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
16298774 TTTTCTCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (35 bp):
CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
Found at i:16305041 original size:18 final size:18
Alignment explanation
Indices: 16305014--16305099 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
16305004 CACATTTTTC
16305014 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
* **
16305033 TTCAGTCATATATACTCAT
1 TTCATTCATAT-TTTTCAT
* **
16305052 TCCAATTCCCATTTTTC-T
1 TTC-ATTCATATTTTTCAT
16305070 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
16305089 TTCATTCATAT
1 TTCATTCATAT
16305100 ATCCTTATTC
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.02
18 26 0.51
19 19 0.37
20 5 0.10
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (18 bp):
TTCATTCATATTTTTCAT
Found at i:16305086 original size:56 final size:56
Alignment explanation
Indices: 16305006--16305128 Score: 194
Period size: 56 Copynumber: 2.2 Consensus size: 56
16304996 TTCCATGTCA
16305006 CATTTTTC-TTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
1 CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
* * * *
16305061 CATTTTTCTTTCATTTCATATTTTTCATTTCATTCATATATCCTTATTCCAATTCT
1 CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
*
16305117 CATTTTTATTTC
1 CATTTTTCTTTC
16305129 CCTATTAACG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
55 8 0.13
56 54 0.87
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.55
Consensus pattern (56 bp):
CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
Found at i:16313339 original size:11 final size:11
Alignment explanation
Indices: 16313323--16313349 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16313313 CGTCCCTAGA
16313323 AAGTTAGAATT
1 AAGTTAGAATT
16313334 AAGTTAGAATT
1 AAGTTAGAATT
16313345 AAGTT
1 AAGTT
16313350 TTCTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (11 bp):
AAGTTAGAATT
Found at i:16317359 original size:18 final size:18
Alignment explanation
Indices: 16317336--16317399 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
16317326 TTCCAAGCCC
16317336 CGTTTTTAATGTTCTTTA
1 CGTTTTTAATGTTCTTTA
* * *
16317354 CGTTTTTGGA-GTTCCGGTAA
1 CGTTTTT-AATGTT-C-TTTA
*
16317374 CTTTTTTAATGTTCTTTA
1 CGTTTTTAATGTTCTTTA
16317392 CGTTTTTA
1 CGTTTTTA
16317400 GAGTCTTGGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 19 0.56
19 4 0.12
20 11 0.32
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (18 bp):
CGTTTTTAATGTTCTTTA
Found at i:16318114 original size:101 final size:102
Alignment explanation
Indices: 16317999--16318183 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
16317989 AAAGTGATGG
*
16317999 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGAT-GGTCGCATGTGTAGT
*
16318062 ACTATGTGTAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
16318100 TCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTATCGGATAGTGATGGTCTCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCGCATGTGTAGTA
16318165 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
16318184 TGAACCGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCGCATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:16318119 original size:51 final size:49
Alignment explanation
Indices: 16317996--16318190 Score: 212
Period size: 51 Copynumber: 3.9 Consensus size: 49
16317986 GTGAAAGTGA
* * *
16317996 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-G-T
* * * *
16318046 AGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-T
* * * *
16318096 TCGATCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
* *
16318146 GATGGTCTCATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
16318191 ATATCATTAA
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 41 0.34
51 77 0.65
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
Found at i:16318430 original size:16 final size:16
Alignment explanation
Indices: 16318409--16318440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16318399 TGATTGAAAG
*
16318409 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
16318425 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
16318441 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:16322264 original size:20 final size:21
Alignment explanation
Indices: 16322219--16322266 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
16322209 ATAGGTAAAT
*
16322219 TCATC-CACAGTATAAGTAGA
1 TCATCTCACAGTATAAGTACA
*
16322239 T-TTCTCACA-TATAAGTACA
1 TCATCTCACAGTATAAGTACA
16322258 TCATCTCAC
1 TCATCTCAC
16322267 CAATCCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (21 bp):
TCATCTCACAGTATAAGTACA
Found at i:16336753 original size:3 final size:3
Alignment explanation
Indices: 16336674--16336738 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
16336664 TTAGGACACC
* * * *
16336674 TTA TCTA TT- TTA TTA TTA TTA TGA TGTGA TTA TTA ATA TTA ATA TTG
1 TTA T-TA TTA TTA TTA TTA TTA TTA T-T-A TTA TTA TTA TTA TTA TTA
16336721 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
16336739 CATTACTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 4 0.08
5 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:16337983 original size:23 final size:23
Alignment explanation
Indices: 16337953--16338005 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
16337943 ATGTACATCT
16337953 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16337976 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16337999 TTATTTT
1 TTATTTT
16338006 AAGAGACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (23 bp):
TTATTTTGATCATTTTAGGAAGA
Found at i:16352926 original size:27 final size:22
Alignment explanation
Indices: 16352873--16352918 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16352863 ATGAGTTAAG
16352873 AAAGGAAATTAGGATTGGAACA
1 AAAGGAAATTAGGATTGGAACA
16352895 AAAGGAAATTAGGATTGGAACA
1 AAAGGAAATTAGGATTGGAACA
16352917 AA
1 AA
16352919 TCTCAAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.26, T:0.17
Consensus pattern (22 bp):
AAAGGAAATTAGGATTGGAACA
Found at i:16357799 original size:42 final size:42
Alignment explanation
Indices: 16357736--16357907 Score: 231
Period size: 42 Copynumber: 4.1 Consensus size: 42
16357726 GAAAGCATTT
*
16357736 ATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
* *
16357778 ATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACCTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
* *
16357820 ATTGCATTTAGAGGCCCAGGGGTGGCA-GACCATTTACTTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGG-AGGTCCATTTACTTTTC
* ** *
16357862 ATTGCATTTAGAGGCTCAGGAATGGAGGTTCATTTA-TTTATC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTT-TC
16357904 ATTG
1 ATTG
16357908 TATATGAAAG
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.03
42 110 0.96
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.36
Consensus pattern (42 bp):
ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
Found at i:16364421 original size:30 final size:30
Alignment explanation
Indices: 16364385--16364472 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
16364375 CTGGGCACTT
*
16364385 CCACACGAGCTGGCCACACACCCATGTGAG
1 CCACACGAGCTGGCCACACGCCCATGTGAG
* * *
16364415 CCACACGAGATGGCCACATGCCCCTGTGAG
1 CCACACGAGCTGGCCACACGCCCATGTGAG
*
16364445 CCACACGGGCTGGCCACACGCCCATGTG
1 CCACACGAGCTGGCCACACGCCCATGTG
16364473 CCAGCCTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (30 bp):
CCACACGAGCTGGCCACACGCCCATGTGAG
Found at i:16371895 original size:6 final size:5
Alignment explanation
Indices: 16371889--16371961 Score: 51
Period size: 6 Copynumber: 13.6 Consensus size: 5
16371879 ATTGAGTTTA
*
16371889 TTATT ATTATT ATTATT TTCGTT TTATTT TTATT TTATT TTATT TT-TAT
1 TTATT -TTATT -TTATT TT-ATT TTA-TT TTATT TTATT TTATT TTAT-T
*
16371938 TTATCT TT-TT TTAATT TTGTT TTA
1 TTAT-T TTATT TT-ATT TTATT TTA
16371962 GTTGCTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
4 4 0.07
5 24 0.43
6 28 0.50
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:16371940 original size:20 final size:21
Alignment explanation
Indices: 16371917--16371955 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
16371907 TCGTTTTATT
16371917 TTTATTTTATTTT-ATTTTTA
1 TTTATTTTATTTTAATTTTTA
16371937 TTTATCTTT-TTTTAATTTT
1 TTTAT-TTTATTTTAATTTT
16371956 GTTTTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTATTTTATTTTAATTTTTA
Found at i:16371940 original size:26 final size:27
Alignment explanation
Indices: 16371889--16371960 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 27
16371879 ATTGAGTTTA
16371889 TTATTATTATTATTATTTTCGTTTTAT-TT
1 TTATT-TTATT-TTATTTTC-TTTTATCTT
16371918 TTATTTTATTTTATTTT-TATTTATCTT
1 TTATTTTATTTTATTTTCT-TTTATCTT
* *
16371945 TT-TTTAATTTTGTTTT
1 TTATTTTATTTTATTTT
16371961 AGTTGCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.03
26 17 0.44
27 11 0.28
28 5 0.13
29 5 0.13
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (27 bp):
TTATTTTATTTTATTTTCTTTTATCTT
Found at i:16371946 original size:17 final size:16
Alignment explanation
Indices: 16371895--16371946 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
16371885 TTTATTATTA
*
16371895 TTATTATTATTTTCGTT
1 TTATTTTTATTTTC-TT
*
16371912 TTATTTTTATTTTATT
1 TTATTTTTATTTTCTT
16371928 TTATTTTTATTTATCTT
1 TTATTTTTATTT-TCTT
16371945 TT
1 TT
16371947 TTTAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (16 bp):
TTATTTTTATTTTCTT
Found at i:16373823 original size:30 final size:30
Alignment explanation
Indices: 16373789--16373846 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16373779 CTGGGCACTT
* *
16373789 CCACACGGGCTGGCCACATGCCCGTGTGAG
1 CCACACGAGCTGGCCACATGCCCATGTGAG
*
16373819 CCACACGAGCTGGGCACATGCCCATGTG
1 CCACACGAGCTGGCCACATGCCCATGTG
16373847 CCAGCCCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACATGCCCATGTGAG
Found at i:16385210 original size:50 final size:50
Alignment explanation
Indices: 16385095--16385294 Score: 197
Period size: 50 Copynumber: 3.9 Consensus size: 50
16385085 ACATTAAGAG
* *
16385095 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGAATCGTTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* * * *
16385146 GATTATGAGTGGTCCCATGTGAGACCATGTTTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * *
16385199 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCTCCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * *
16385249 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16385295 GTACAAGAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
50 78 0.64
51 1 0.01
53 3 0.02
54 5 0.04
55 1 0.01
56 33 0.27
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:16391944 original size:16 final size:16
Alignment explanation
Indices: 16391923--16391966 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
16391913 AAAATTAACT
16391923 AAGTAATAAAAATAAA
1 AAGTAATAAAAATAAA
16391939 AAGTAATAAAAATAAA
1 AAGTAATAAAAATAAA
16391955 AAGTAA-AAAAAT
1 AAGTAATAAAAAT
16391967 TCCAATGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAGTAATAAAAATAAA
Found at i:16398386 original size:21 final size:20
Alignment explanation
Indices: 16398344--16398382 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16398334 GATATTTATA
16398344 TTATTTTTAATTTAATAAAT
1 TTATTTTTAATTTAATAAAT
*
16398364 TTATTCTTT-ATTTATTAAA
1 TTATT-TTTAATTTAATAAA
16398383 ATTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTTAATTTAATAAAT
Found at i:16402519 original size:24 final size:25
Alignment explanation
Indices: 16402469--16402523 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16402459 TCGGTTTATT
*
16402469 TTTAATTATATTTAAAATATTTTAA
1 TTTATTTATATTTAAAATATTTTAA
**
16402494 TTTATTTATATTTTCAA-ATTTTAA
1 TTTATTTATATTTAAAATATTTTAA
16402518 TTTATT
1 TTTATT
16402524 AACATTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTTATATTTAAAATATTTTAA
Found at i:16403336 original size:17 final size:18
Alignment explanation
Indices: 16403297--16403339 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16403287 TTTAATTAAA
*
16403297 AAATATAATTTTATATAT
1 AAATATGATTTTATATAT
*
16403315 AAATATGATTTTAT-TTT
1 AAATATGATTTTATATAT
16403332 AAATATGA
1 AAATATGA
16403340 AAATAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AAATATGATTTTATATAT
Found at i:16405327 original size:62 final size:62
Alignment explanation
Indices: 16405230--16405379 Score: 264
Period size: 62 Copynumber: 2.4 Consensus size: 62
16405220 TCATGTTTCC
* *
16405230 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAGGGGCACGAGCGTGTGCTT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
*
16405292 AGGCCGTGTAACTCACTGTTTGTGAAATAGTGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
*
16405354 AGGCCGTGTAACTCACTGTTCGTGAA
1 AGGCCGTGTAACTCACTGTTTGTGAA
16405380 TTAAAGTCAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (62 bp):
AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAAGGGCACGAGCGTGTGCCT
Found at i:16410240 original size:47 final size:47
Alignment explanation
Indices: 16410186--16410302 Score: 141
Period size: 47 Copynumber: 2.5 Consensus size: 47
16410176 ACCGGATAGG
* *
16410186 TGATGCTTAAATGCTG-CCTAATTTGTTGCATATATGTTGTCCAATTT
1 TGATGCTTAAATGCTGTCC-AATTTGTTGCATATATGCTGCCCAATTT
* *
16410233 TGATGCTTAAATGCTGTCCAATTTTTTGTATATATGCTGCCCAA-TT
1 TGATGCTTAAATGCTGTCCAATTTGTTGCATATATGCTGCCCAATTT
* *
16410279 TGTTG-TATATATGCTGTCCAATTT
1 TGATGCT-TAAATGCTGTCCAATTT
16410303 TGGTGTACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 1 0.02
46 22 0.35
47 37 0.60
48 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (47 bp):
TGATGCTTAAATGCTGTCCAATTTGTTGCATATATGCTGCCCAATTT
Found at i:16410276 original size:23 final size:23
Alignment explanation
Indices: 16410196--16410303 Score: 112
Period size: 23 Copynumber: 4.7 Consensus size: 23
16410186 TGATGCTTAA
* *
16410196 ATGCTG-CCTAATTTGTTGCATAT
1 ATGCTGTCC-AATTTTTTGTATAT
* * *
16410219 ATGTTGTCCAATTTTGATGCT-TAA
1 ATGCTGTCCAATTTT-TTG-TATAT
16410243 ATGCTGTCCAATTTTTTGTATAT
1 ATGCTGTCCAATTTTTTGTATAT
* *
16410266 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTTTTGTATAT
16410289 ATGCTGTCCAATTTT
1 ATGCTGTCCAATTTT
16410304 GGTGTACAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 48 0.70
24 20 0.29
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (23 bp):
ATGCTGTCCAATTTTTTGTATAT
Found at i:16410315 original size:13 final size:13
Alignment explanation
Indices: 16410297--16410322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16410287 ATATGCTGTC
16410297 CAATTTTGGTGTA
1 CAATTTTGGTGTA
16410310 CAATTTTGGTGTA
1 CAATTTTGGTGTA
16410323 AAAATGCTGC
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
CAATTTTGGTGTA
Found at i:16410427 original size:70 final size:70
Alignment explanation
Indices: 16410310--16410488 Score: 281
Period size: 70 Copynumber: 2.6 Consensus size: 70
16410300 TTTTGGTGTA
16410310 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
1 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
16410375 CTGTC
66 CTGTC
* *
16410380 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGTTGCCCAAATTGTTGTATTTATG
1 CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
16410445 CTGTC
66 CTGTC
* * * *
16410450 CAATTTTTGGTGTGAGAATGCTG-TCTAATT-TGGTATATA
1 CAA-TTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATA
16410489 AATGCTGTCC
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
69 8 0.08
70 77 0.75
71 17 0.17
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (70 bp):
CAATTTTGGTGTAAAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTGAATTTATG
CTGTC
Found at i:16410452 original size:23 final size:22
Alignment explanation
Indices: 16410326--16410452 Score: 119
Period size: 23 Copynumber: 5.5 Consensus size: 22
16410316 TGGTGTAAAA
16410326 ATGCTGCTCAAATTGTTGTATAT
1 ATGCTGC-CAAATTGTTGTATAT
* *
16410349 ATGCTGCCCAAATTGTTGAATTT
1 ATGCTG-CCAAATTGTTGTATAT
* * * *
16410372 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTG-CCAA-ATTGTTGTATAT
16410396 ATGCTGCTCAAATTGTTGTATAT
1 ATGCTGC-CAAATTGTTGTATAT
* *
16410419 ATGTTGCCCAAATTGTTGTATTT
1 ATGCTG-CCAAATTGTTGTATAT
16410442 ATGCTGTCCAA
1 ATGCTG-CCAA
16410453 TTTTTGGTGT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
23 66 0.80
24 17 0.20
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (22 bp):
ATGCTGCCAAATTGTTGTATAT
Found at i:16415162 original size:126 final size:126
Alignment explanation
Indices: 16414937--16415165 Score: 323
Period size: 126 Copynumber: 1.8 Consensus size: 126
16414927 GTGTCAAGCT
* * * *
16414937 GTGTGTCCAAGTCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGGCATGGGCGT
1 GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
*
16415002 GTGTCTAAGCCATGTAAGTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
66 GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
* * * *
16415063 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATGGGCTAGGGACACGGGCAT
1 GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
* * * * * *
16415128 GTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAG
66 GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAG
16415166 TCACGCGGAC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
126 88 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (126 bp):
GTGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAAGGTCACACGAGCTAGGGACACGGGCAT
GTGTCTAAGCCATGTAACTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGGA
Found at i:16415163 original size:63 final size:63
Alignment explanation
Indices: 16414938--16415169 Score: 261
Period size: 63 Copynumber: 3.7 Consensus size: 63
16414928 TGTCAAGCTG
* * * * *
16414938 TGTGTCCAAGTCGTGTAACTCACTATTTGTGAATTA-AGGTCACACGAGCTAGGGGCATGGGCG
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGA-GTCACATGGGCTAGGGACATGGGCA
* * * * * *
16415001 TGTGTCTAAGCCATGTAAGTCACTATTTGTAAATTAGAGCCACATGGGTTAGGGACATGGG-A
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
* * *
16415063 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATGGGCTAGGGACACGGGCA
1 -TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
* * * * *
16415127 TGTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAGTCAC
1 TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCAC
16415170 GCGGACGTGT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
63 139 0.99
64 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (63 bp):
TGTGTCCAAGCCGTGTAACTCACTATTTGTGAATTAGAGTCACATGGGCTAGGGACATGGGCA
Found at i:16416619 original size:37 final size:37
Alignment explanation
Indices: 16416518--16416623 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 37
16416508 AAATCTTATT
* * *
16416518 ATTATACTGAATGAATCTCAATCAAGCAAATTATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
* *
16416555 GTTATATTGAATGAAGCTCAATCGAGCAAATCATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
*
16416592 ATTATACTGAATGGAGCTCAA-CTGAGCAAATC
1 ATTATACTGAATGAAGCTCAATC-GAGCAAATC
16416624 TTACTGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (37 bp):
ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
Found at i:16416634 original size:37 final size:37
Alignment explanation
Indices: 16416507--16416636 Score: 138
Period size: 37 Copynumber: 3.5 Consensus size: 37
16416497 TCTATCAAGC
** * *
16416507 CAAATCTTATTATTATACTGAATGAATCTCAATCAAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
* *
16416544 CAAAT-TATACCGTTATATTGAATGAAGCTCAATCGAG
1 CAAATCT-TACCATTATACTGAATGAAGCTCAATCGAG
* *
16416581 CAAATCATACCATTATACTGAATGGAGCTCAA-CTGAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATC-GAG
**
16416618 CAAATCTTACTGTTATACT
1 CAAATCTTACCATTATACT
16416637 AACTGATGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 2 0.03
37 75 0.97
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (37 bp):
CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
Found at i:16418263 original size:25 final size:25
Alignment explanation
Indices: 16418226--16418280 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16418216 TGAGCATCTT
*
16418226 GATA-TTGGCTCTCTTGAGCTACCC
1 GATAGTTGGCTCTCTCGAGCTACCC
*
16418250 GATAGTTGGCTCTCTCGAGCTTCCC
1 GATAGTTGGCTCTCTCGAGCTACCC
*
16418275 GTTAGT
1 GATAGT
16418281 AGCTCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.35
Consensus pattern (25 bp):
GATAGTTGGCTCTCTCGAGCTACCC
Found at i:16420887 original size:33 final size:33
Alignment explanation
Indices: 16420845--16420915 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
16420835 GCAAACTCTG
16420845 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
1 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
16420878 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
1 TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
16420911 TGTGA
1 TGTGA
16420916 ATTTTGGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (33 bp):
TGTGAGAAACAACTGTATGCTAAATTTAGCAAA
Found at i:16424398 original size:24 final size:24
Alignment explanation
Indices: 16424336--16424392 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
16424326 CAACTTGAAA
* *
16424336 GAGCATCATGTTATT-AGCTCTCAT
1 GAGCATCCTGATATTGA-CTCTCAT
*
16424360 GAGCATCCTGATATTGACTCTCTT
1 GAGCATCCTGATATTGACTCTCAT
16424384 GAGCTATCC
1 GAGC-ATCC
16424393 GGTATTTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (24 bp):
GAGCATCCTGATATTGACTCTCAT
Found at i:16424405 original size:25 final size:24
Alignment explanation
Indices: 16424347--16424412 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
16424337 AGCATCATGT
* *
16424347 TATTAGCTCTCATGAGCATCCTGA
1 TATTGGCTCTCATGAGCATCCGGA
* *
16424371 TATTGACTCTCTTGAGCTATCCGG-
1 TATTGGCTCTCATGAGC-ATCCGGA
*
16424395 TATTTGGCTCTCAAGAGC
1 TA-TTGGCTCTCATGAGC
16424413 TTCATGTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (24 bp):
TATTGGCTCTCATGAGCATCCGGA
Found at i:16426080 original size:10 final size:10
Alignment explanation
Indices: 16426065--16426095 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
16426055 TATAAGGGAC
16426065 AATATGATTG
1 AATATGATTG
16426075 AATATGATTG
1 AATATGATTG
16426085 AATATGATTG
1 AATATGATTG
16426095 A
1 A
16426096 TTTCTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (10 bp):
AATATGATTG
Found at i:16426363 original size:32 final size:32
Alignment explanation
Indices: 16426322--16426385 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
16426312 TGTTTTGACT
16426322 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
1 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
*
16426354 TGTTGTGCACTTTATCAACTTGTGATTTCCTA
1 TGTTGTGCACTTGATCAACTTGTGATTTCCTA
16426386 CTTGTTACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (32 bp):
TGTTGTGCACTTGATCAACTTGTGATTTCCTA
Found at i:16426703 original size:43 final size:43
Alignment explanation
Indices: 16426654--16426735 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
16426644 GAGACACTGG
*
16426654 CGTGTGACTCGACCATGCGAGGCACACGGCCTTGCAACATGGC
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACATGGC
* *
16426697 CGTGTGACTCGACCGTGTGAGGCACACGGCCTTACAACA
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACA
16426736 CTTCCATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (43 bp):
CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACATGGC
Found at i:16430310 original size:5 final size:5
Alignment explanation
Indices: 16430300--16430325 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16430290 TATAAAATCA
16430300 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
16430326 AAAAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:16435504 original size:58 final size:57
Alignment explanation
Indices: 16435325--16435504 Score: 152
Period size: 57 Copynumber: 3.2 Consensus size: 57
16435315 TGTAAAATCA
* * * * ** * *
16435325 CGAGCTATTTTGAACTTAAG--TATATTTAAAATAATCAGCTGGGGATGTAAATCCGT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCC-T
* * *
16435381 -GAGCTATTTTTAACTTAGGCATATTTTTTATATAATCAAATGAGAATGTAAATCCT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCCT
* * * * * *
16435437 CGAGTTGTTTTGAACTTAGGCATATTTTTTGAAATACTTAATTGGGAATGTAAAT-TT
1 CGAGCTGTTTTGAACTTAGGCATATTTTTT-AAATAATCAAATGAGAATGTAAATCCT
16435494 ACGAGCTGTTT
1 -CGAGCTGTTT
16435505 GGAGGTTGCG
Statistics
Matches: 100, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
55 17 0.17
56 1 0.01
57 54 0.54
58 28 0.28
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (57 bp):
CGAGCTGTTTTGAACTTAGGCATATTTTTTAAATAATCAAATGAGAATGTAAATCCT
Found at i:16435763 original size:71 final size:71
Alignment explanation
Indices: 16435502--16436233 Score: 594
Period size: 71 Copynumber: 10.4 Consensus size: 71
16435492 TTACGAGCTG
* * * * ** ** * * *
16435502 TTTGGAGGTTGCGGTGTTAAA-CTGCGAGCCTTAAAATGACAGTTAAGCGCTTTTAACTATTGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16435566 AA-T-T
66 AACTAT
* * ** * * **
16435570 GTTTGGAGGTTGCAGTATTAAACCTGTGAGCCTTAAAACGACAGTTGGGAGCTTTTAACTCTCGC
1 -TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGC
*
16435635 TAACT-G
65 TAACTAT
* * * * ** * *
16435641 TTTGGAGGCAGCGATATTACACTTGTGAGCCTTAGAATGACAAATGGGAGCTTTCAACTCTCGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16435706 AACTAT
66 AACTAT
* * * * * *
16435712 TTGGGAGGCTACGGTTTTAAACCTACAAGCCTTAGAATGACAGCTGAGAGCTTTTAACTCTCGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16435777 AACTAT
66 AACTAT
* * * * * * * **
16435783 TTGGGAGGCTGCGGTTTTAAACCTGCAATG-CTTAAAATGATAGCTAGGAGCTTTTTACTCTCTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAA-GCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGC
16435847 TAACTAT
65 TAACTAT
* ** * * ** * * ** *
16435854 TTTTGATACTGCGATATTAAACTTGGGAGCCTTACAATGAGAACTGGGAGCTTTTAGGTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16435919 AACTAT
66 AACTAT
* * ** * *
16435925 TTTGGAGTCTGCAGTGCTAAACATGCAAGCCTTAGAATGA-AACCTGGGAGCTTTTAACTCTCAC
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAA-CTGGGAGCTTTTAACTCTCGC
*
16435989 TAGCTAT
65 TAACTAT
* * * * ** * *
16435996 ATTAGAGGCTGTGGTATTAAACTTGTGAGCCTTAGAATGACAACTGAGAGCTTTTAACTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
*
16436061 AACTGT
66 AACTAT
* ** * ** * * * *
16436067 TTTGAAGGCTGCAATATTAAATCTGTGAGCCTTGGAATGACAACTAGGAGCTTTTAACTTTTGCT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16436132 AACTAT
66 AACTAT
* * * * ** *
16436138 TTTGGAGGCTGCGATATTAAACCTACAAGCCTTCGAATGATAGTTGGGAGCTTTTAACTCTCGTT
1 TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
16436203 AACTAT
66 AACTAT
*
16436209 TTTTGAGGCTGCGGTATTAAACCTG
1 TTTGGAGGCTGCGGTATTAAACCTG
16436234 TGAGACTTGC
Statistics
Matches: 531, Mismatches: 125, Indels: 12
0.79 0.19 0.02
Matches are distributed among these distances:
69 19 0.04
70 99 0.19
71 410 0.77
72 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (71 bp):
TTTGGAGGCTGCGGTATTAAACCTGCAAGCCTTAGAATGACAACTGGGAGCTTTTAACTCTCGCT
AACTAT
Found at i:16436262 original size:213 final size:210
Alignment explanation
Indices: 16435550--16436305 Score: 693
Period size: 213 Copynumber: 3.6 Consensus size: 210
16435540 ACAGTTAAGC
* * * * * * * *
16435550 GCTTTTAACTATTGCTAA-T-TGTTTGGAGGTTGCAGTATTAAACCTGTGAGCCTTAAAACGACA
1 GCTTTTAACTCTCGCTAACTAT-TTTAGAGGCTGCGGTATTAAACCTGTGAG-CTT-GAATGATA
* * *
16435613 GTTGGGAGCTTTTAACTCTCGCTAACTG-TTTGGAGGCAGCGATATTACACTTGTGAGCCTTAGA
63 GTT-GGAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACTTGTGAGCCTTAGA
* * * * * *
16435677 ATGACAAATGGGAGCTTTCAACTCTCGCTAACTATTTGGGAGGCTACGGTTTTAAACCTACAAGC
127 ATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
* *
16435742 CTTAGAATGACAGCTGAGA
192 CTTAGAATGAAAGCTGGGA
** * ** *
16435761 GCTTTTAACTCTCGCTAACTATTTGGGAGGCTGCGGTTTTAAACCTGCAATGCTTAAAATGATAG
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGA-GCTT-GAATGATAG
* * ** * * *
16435826 CTAGGAGCTTTTTACTCTCTTTAACTATTTTTGATA--CTGCGATATTAAACTTGGGAGCCTTAC
64 -TTGGAGCTTTTAACTCTCGCTAACT-GTTTTGA-AGGCTGCGATATTAAACTTGTGAGCCTTAG
* ** * * ** * *
16435889 AATGAGAACTGGGAGCTTTTAGGTCTCGTTAACTATTTTGGAGTCTGC-AGTGCTAAACATGCAA
126 AATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGA-TATTAAACCTACAA
*
16435953 GCCTTAGAATGAAACCTGGGA
190 GCCTTAGAATGAAAGCTGGGA
* * * * * * *
16435974 GCTTTTAACTCTCACTAGCTATATTAGAGGCTGTGGTATTAAACTTGTGAGCCTTAGAATGACAA
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAG-CTT-GAATGATAG
* * * *
16436039 CTGAGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAATATTAAA-TCTGTGAGCCTTGGA
64 TTG-GAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACT-TGTGAGCCTTAGA
* * *
16436103 ATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
127 ATGACAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGC
* * *
16436168 CTTCGAATGATAGTTGGGA
192 CTTAGAATGAAAGCTGGGA
* *
16436187 GCTTTTAACTCTCGTTAACTATTTTTGAGGCTGCGGTATTAAACCTGTGAGACTTGCAAT-AGTA
1 GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAG-CTTG-AATGA-TA
* * * *
16436251 GTTGTGAGCTTTTCACTTTTGCTAACTGTTTTGAAGG-TCGTGATATTAAACTTGT
63 GTTG-GAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCT-GCGATATTAAACTTGT
16436306 ATTGGAATTG
Statistics
Matches: 434, Mismatches: 93, Indels: 34
0.77 0.17 0.06
Matches are distributed among these distances:
211 17 0.04
212 66 0.15
213 344 0.79
214 6 0.01
215 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (210 bp):
GCTTTTAACTCTCGCTAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAGCTTGAATGATAGTT
GGAGCTTTTAACTCTCGCTAACTGTTTTGAAGGCTGCGATATTAAACTTGTGAGCCTTAGAATGA
CAACTGGGAGCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACCTACAAGCCTTA
GAATGAAAGCTGGGA
Found at i:16445209 original size:27 final size:29
Alignment explanation
Indices: 16445179--16445232 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
16445169 ATTTTCTTAC
*
16445179 TATT-CAATA-ATTTGATTATAAAAAATG
1 TATTGCAATAGATTAGATTATAAAAAATG
*
16445206 TATTGCATTAGATTAGATTATAAAAAA
1 TATTGCAATAGATTAGATTATAAAAAA
16445233 ATATTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 15 0.65
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (29 bp):
TATTGCAATAGATTAGATTATAAAAAATG
Found at i:16453338 original size:5 final size:5
Alignment explanation
Indices: 16453328--16453353 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16453318 AATTATTTAT
16453328 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
16453354 AATTTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Done.