Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 68 of 103
Found at i:25616681 original size:45 final size:45
Alignment explanation
Indices: 25616630--25616719 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
25616620 CATTTACTAA
*
25616630 GACGAAAGTTTTTGTTTACCCAATAAAAGAGAATTACATCAAAGT
1 GACGAAAGTTTTTCTTTACCCAATAAAAGAGAATTACATCAAAGT
25616675 GACGAAAGTTTTTCTTTACCCAATAAAAGAGAATTACATCAAAGT
1 GACGAAAGTTTTTCTTTACCCAATAAAAGAGAATTACATCAAAGT
25616720 ATCCATTACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (45 bp):
GACGAAAGTTTTTCTTTACCCAATAAAAGAGAATTACATCAAAGT
Found at i:25621406 original size:26 final size:26
Alignment explanation
Indices: 25621346--25621407 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
25621336 ACCATATACC
*
25621346 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
25621372 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
25621398 CATCATCATC
1 CATCATCATC
25621408 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:25621612 original size:83 final size:84
Alignment explanation
Indices: 25621466--25621630 Score: 280
Period size: 83 Copynumber: 2.0 Consensus size: 84
25621456 AAGCATCCCC
* *
25621466 CCCCCCCATTCACTAGGCAAGAGGTGCACTTCACTTCGGATCACGAAGCAACGAAGCATTCCCTT
1 CCCCCCCATTCACTAGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGAAGCAGTCCCTT
25621531 CCCTCATCTTCCAAGCTTT
66 CCCTCATCTTCCAAGCTTT
*
25621550 CCCCCCC-TTCACTCA-GCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGTCCCT
1 CCCCCCCATTCACT-AGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGAAGCAGTCCCT
25621613 TCCCTCATCTTCCAAGCT
65 TCCCTCATCTTCCAAGCT
25621631 CTTGGGCGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
83 69 0.90
84 8 0.10
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.22
Consensus pattern (84 bp):
CCCCCCCATTCACTAGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGAAGCAGTCCCTT
CCCTCATCTTCCAAGCTTT
Found at i:25621791 original size:42 final size:42
Alignment explanation
Indices: 25621730--25621894 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 42
25621720 ACGGAGGCAA
* * * * *
25621730 CAACGGCTTATGTGTACTCCCACTCACACATAGCTGGGTCAG
1 CAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
25621772 CAACGACTTATGTGCACTCCTACTCGCACATAGTCAGGTCAG
1 CAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* * *
25621814 CAACGACTTATGTGCACTCCTACTCGTATATAACCGGGTCAG
1 CAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
25621856 CAACGGCTTATGTGCATTCCTACTCGCACATAGCCGGGT
1 CAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGT
25621895 TCAAATCAAC
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (42 bp):
CAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:25629577 original size:2 final size:2
Alignment explanation
Indices: 25629527--25629569 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
25629517 ACACATTTAC
*
25629527 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25629569 A
1 A
25629570 CGTATATACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25629639 original size:20 final size:20
Alignment explanation
Indices: 25629582--25629644 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
25629572 TATATACCCA
*
25629582 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
25629601 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
25629621 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
25629641 TCAT
1 TCAT
25629645 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:25629691 original size:43 final size:43
Alignment explanation
Indices: 25629643--25629761 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
25629633 TCACCAGCTC
** * *
25629643 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
25629686 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
25629729 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
25629762 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:25631501 original size:42 final size:42
Alignment explanation
Indices: 25631443--25631523 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
25631433 ACGGAGGCAA
25631443 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
* *
25631485 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGT
25631524 TCAAATCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
Found at i:25633240 original size:42 final size:42
Alignment explanation
Indices: 25633182--25633304 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
25633172 ACGGAGGCAA
25633182 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
*
25633224 CAACGGCTTATGTGCACTCTCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
* * *
25633266 CAACGGCTTATGTGCACTCCTACTCGCACGTAGCCGGGT
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGT
25633305 TCAAATCAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
Found at i:25637785 original size:38 final size:38
Alignment explanation
Indices: 25637730--25637805 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
25637720 AATTCAACAC
* *
25637730 CATCAGATTTTCCTTACAGATTTTAGGGAA-AGGAAAAG
1 CATCAGATTTTCCTTACAAATTCTAGGGAAGA-GAAAAG
25637768 CATCAGA-TTTCCTTTACAAATTCTAGGGAAGAGAAAAG
1 CATCAGATTTTCC-TTACAAATTCTAGGGAAGAGAAAAG
25637806 AAGGATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 5 0.15
38 28 0.82
39 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (38 bp):
CATCAGATTTTCCTTACAAATTCTAGGGAAGAGAAAAG
Found at i:25641058 original size:18 final size:18
Alignment explanation
Indices: 25641028--25641072 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
25641018 TAATTTATGA
25641028 ATTTTAA-TA-TATTTATT
1 ATTTTAATTATTA-TTATT
25641045 -TTTTAATTATTATTATT
1 ATTTTAATTATTATTATT
25641062 ATTTTAATTAT
1 ATTTTAATTAT
25641073 AACACCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTAATTATTATTATT
Found at i:25642275 original size:2 final size:2
Alignment explanation
Indices: 25642219--25642256 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25642209 TTACTAATGA
25642219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25642257 TAAATTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25650165 original size:12 final size:12
Alignment explanation
Indices: 25650148--25650209 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 12
25650138 ATTAATTTTA
25650148 TTTTATTATATT
1 TTTTATTATATT
25650160 TTTTATTATCATAT
1 TTTTATTAT-AT-T
*
25650174 TTTCTATTCTTATT
1 TTT-TATT-ATATT
*
25650188 TCTTATTATTATT
1 TTTTATTA-TATT
25650201 TTTT-TTATA
1 TTTTATTATA
25650210 CTTTACATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 2 0.05
12 12 0.29
13 13 0.32
14 7 0.17
15 6 0.15
16 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:25650187 original size:13 final size:14
Alignment explanation
Indices: 25650135--25650202 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
25650125 TTATTAATTA
*
25650135 ATTATTAATTTTATT
1 ATTATT-ATTTTCTT
*
25650150 -TTATTATATTTTTT
1 ATTATTAT-TTTCTT
25650164 ATTATCATATTTTC-T
1 ATTAT--TATTTTCTT
*
25650179 ATTCTTA-TTTCTT
1 ATTATTATTTTCTT
25650192 ATTATTATTTT
1 ATTATTATTTT
25650203 TTTTATACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
12 4 0.09
13 11 0.26
14 13 0.30
15 9 0.21
16 3 0.07
17 3 0.07
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTATTATTTTCTT
Found at i:25650330 original size:14 final size:13
Alignment explanation
Indices: 25650298--25650369 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 13
25650288 TGAACAAAAA
25650298 ATTTTATATTAT-T
1 ATTTT-TATTATAT
25650311 -TTTTTATTATACT
1 ATTTTTATTATA-T
*
25650324 ATTTTTATTTTAT
1 ATTTTTATTATAT
*
25650337 ATATTT-TTATAT
1 ATTTTTATTATAT
* *
25650349 TTTTATTATTGTTAT
1 ATTT-TTATT-ATAT
25650364 ATTTTT
1 ATTTTT
25650370 CATAAGCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
11 6 0.13
12 11 0.24
13 9 0.20
14 14 0.30
15 6 0.13
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (13 bp):
ATTTTTATTATAT
Found at i:25650349 original size:8 final size:8
Alignment explanation
Indices: 25650323--25650369 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
25650313 TTTATTATAC
25650323 TATTTTTA
1 TATTTTTA
*
25650331 T-TTTATA
1 TATTTTTA
25650338 TATTTTTA
1 TATTTTTA
25650346 TATTTTTA
1 TATTTTTA
*
25650354 TTATTGTTA
1 -TATTTTTA
25650363 TATTTTT
1 TATTTTT
25650370 CATAAGCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.61
9 7 0.21
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (8 bp):
TATTTTTA
Found at i:25650349 original size:23 final size:25
Alignment explanation
Indices: 25650323--25650369 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
25650313 TTTATTATAC
25650323 TATTTTTATT-TT-ATATATTTTTA
1 TATTTTTATTATTGATATATTTTTA
*
25650346 TATTTTTATTATTGTTATATTTTT
1 TATTTTTATTATTGATATATTTTT
25650370 CATAAGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 2 0.10
25 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (25 bp):
TATTTTTATTATTGATATATTTTTA
Found at i:25650351 original size:17 final size:17
Alignment explanation
Indices: 25650298--25650368 Score: 69
Period size: 16 Copynumber: 4.3 Consensus size: 17
25650288 TGAACAAAAA
25650298 ATTTTATATTATTTTTT
1 ATTTTATATTATTTTTT
* *
25650315 -TATTATACTA-TTTTT
1 ATTTTATATTATTTTTT
25650330 ATTTTATA-TATTTTTAT
1 ATTTTATATTATTTTT-T
*
25650347 ATTTT-TATTATTGTTAT
1 ATTTTATATTATT-TTTT
25650364 ATTTT
1 ATTTT
25650369 TCATAAGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.16
16 20 0.44
17 16 0.36
18 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (17 bp):
ATTTTATATTATTTTTT
Found at i:25650369 original size:17 final size:18
Alignment explanation
Indices: 25650331--25650369 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
25650321 ACTATTTTTA
*
25650331 TTTTATATATTTTTATAT
1 TTTTATATATTGTTATAT
25650349 TTTTAT-TATTGTTATAT
1 TTTTATATATTGTTATAT
25650366 TTTT
1 TTTT
25650370 CATAAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATATATTGTTATAT
Found at i:25651028 original size:16 final size:17
Alignment explanation
Indices: 25651009--25651043 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25650999 CCTTTTTTGA
25651009 TTTTATTA-TCATTATT
1 TTTTATTATTCATTATT
*
25651025 TTTTATTATTTATTATT
1 TTTTATTATTCATTATT
25651042 TT
1 TT
25651044 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTATTCATTATT
Found at i:25651201 original size:21 final size:22
Alignment explanation
Indices: 25651175--25651218 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
25651165 TTAATTTTCT
*
25651175 AAATTTAAACTGTCAT-CTAAA
1 AAATTTAAAATGTCATACTAAA
*
25651196 AAATTTAAAATGTTATACTAAA
1 AAATTTAAAATGTCATACTAAA
25651218 A
1 A
25651219 TAAATTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (22 bp):
AAATTTAAAATGTCATACTAAA
Found at i:25652245 original size:35 final size:36
Alignment explanation
Indices: 25652186--25652258 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 36
25652176 TTTATACTCG
*
25652186 GTTCTTGGGCTCTGGAGGGGGCACGCTCCACTACCTT
1 GTTCTTGGGCACT-GAGGGGGCACGCTCCACTACCTT
*
25652223 GTTCTTGGGCACT-AGGGGGCACGTTCCACTACCTT
1 GTTCTTGGGCACTGAGGGGGCACGCTCCACTACCTT
25652258 G
1 G
25652259 CCAGACGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 22 0.65
37 12 0.35
ACGTcount: A:0.12, C:0.29, G:0.32, T:0.27
Consensus pattern (36 bp):
GTTCTTGGGCACTGAGGGGGCACGCTCCACTACCTT
Found at i:25652705 original size:37 final size:37
Alignment explanation
Indices: 25652547--25652990 Score: 466
Period size: 37 Copynumber: 11.8 Consensus size: 37
25652537 ATTTTTTTTT
* * *
25652547 AATGAATTCCTCAAAACTGAGGCAATGCGACTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGAC-TTTAAA
* * *
25652585 AATGAA---CTCAAAATTGAGGCCACGAGACTTTTAGA
1 AATGAACTCCTCAAAACTGAGGCAACGAGAC-TTTAAA
*
25652620 AATGAATTCCTCAAAACTGAGGCAACGAGACTTTTTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGAC-----TTTAAA
* * *
25652662 AATGAACTCTTCAAAACTGAGGCAATGAGATTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
* **
25652699 AATGAACTCCTCAAATCTGAGGCATTGAGACTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
* * *
25652736 AATGAACTCTTCAAAACTGAGGCACCGAGACTCT-AA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
25652772 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
*
25652809 AGTGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
* * * *
25652846 AATGAACTCCTCAAAGCTGATGCACCAAGACTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
* * *
25652883 AATAAACTCCTCAAAACTAAGGCAACGAGAATTTTTTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAG-A-----CTTTAAA
* * *
25652926 AATGAGCTCCTCAAAGCTGAGGCAACGTA-CCTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACG-AGACTTTAAA
* *
25652963 AATGAATTCCTCAAAATTGAGGCAACGA
1 AATGAACTCCTCAAAACTGAGGCAACGA
25652991 AACCTTTTTT
Statistics
Matches: 344, Mismatches: 47, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
35 30 0.09
36 34 0.10
37 190 0.55
38 27 0.08
42 33 0.10
43 29 0.08
44 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (37 bp):
AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
Found at i:25665004 original size:12 final size:12
Alignment explanation
Indices: 25664987--25665048 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 12
25664977 ATTATTTTTA
25664987 TTTTATTATATT
1 TTTTATTATATT
25664999 TTTTATTATCATAT
1 TTTTATTAT-AT-T
*
25665013 TTTCTATTCTTATT
1 TTT-TATT-ATATT
*
25665027 TCTTATTATTATT
1 TTTTATTA-TATT
25665040 TTTT-TTATA
1 TTTTATTATA
25665049 CTTTACATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 2 0.05
12 12 0.29
13 13 0.32
14 7 0.17
15 6 0.15
16 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:25665026 original size:13 final size:14
Alignment explanation
Indices: 25664961--25665041 Score: 55
Period size: 14 Copynumber: 5.9 Consensus size: 14
25664951 TATTTTTTAG
* **
25664961 TTATTATTAATTAA
1 TTATTATTATTTTC
*
25664975 TTATTATT-TTTATT
1 TTATTATTATTT-TC
25664989 TTATTA-TATTTT-
1 TTATTATTATTTTC
25665001 TTATTATCATATTTTC
1 TTATTAT--TATTTTC
*
25665017 -TATTCTTA-TTTC
1 TTATTATTATTTTC
25665029 TTATTATTATTTT
1 TTATTATTATTTT
25665042 TTTTATACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
12 10 0.19
13 13 0.24
14 20 0.37
15 11 0.20
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATTTTC
Found at i:25665185 original size:8 final size:8
Alignment explanation
Indices: 25665136--25665205 Score: 56
Period size: 8 Copynumber: 8.5 Consensus size: 8
25665126 TGAACAAAAA
25665136 TTTTATAT
1 TTTTATAT
25665144 TATTT-T-T
1 T-TTTATAT
25665151 TTATTATACT
1 TT-TTATA-T
25665161 ATTTTAT-T
1 -TTTTATAT
*
25665169 TTATATAT
1 TTTTATAT
25665177 TTTTATAT
1 TTTTATAT
25665185 TTTTATTAT
1 TTTTA-TAT
*
25665194 TGTTATAT
1 TTTTATAT
25665202 TTTT
1 TTTT
25665206 CATAAGCAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
6 1 0.02
7 9 0.18
8 23 0.46
9 10 0.20
10 5 0.10
11 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTATAT
Found at i:25665185 original size:17 final size:17
Alignment explanation
Indices: 25665167--25665205 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
25665157 TACTATTTTA
*
25665167 TTTTATATATTTTTATAT
1 TTTTAT-TATTGTTATAT
25665185 TTTTATTATTGTTATAT
1 TTTTATTATTGTTATAT
25665202 TTTT
1 TTTT
25665206 CATAAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTATTGTTATAT
Found at i:25665370 original size:4 final size:4
Alignment explanation
Indices: 25665350--25665396 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
25665340 TTTAAATTAG
25665350 TTAT TT-T TT-T TTA- TTAT TTAT TTAT TTAT TT-T ATT-T TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT
25665394 TTA
1 TTA
25665397 ATGTCATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.31
4 27 0.69
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:25665390 original size:19 final size:20
Alignment explanation
Indices: 25665358--25665396 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
25665348 AGTTATTTTT
25665358 TTTTATTATTTATTTATTTA
1 TTTTATTATTTATTTATTTA
25665378 TTTTATT-TTTATTTATTTA
1 TTTTATTATTTATTTATTTA
25665397 ATGTCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTATTTATTTATTTA
Found at i:25665396 original size:23 final size:21
Alignment explanation
Indices: 25665350--25665395 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
25665340 TTTAAATTAG
25665350 TTATTTTTTTTTATTATTTAT
1 TTATTTTTTTTTATTATTTAT
*
25665371 TTA-TTTATTTTATT-TTTAT
1 TTATTTTTTTTTATTATTTAT
25665390 TTATTT
1 TTATTT
25665396 AATGTCATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 12 0.52
21 3 0.13
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
TTATTTTTTTTTATTATTTAT
Found at i:25665464 original size:13 final size:14
Alignment explanation
Indices: 25665448--25665492 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
25665438 TATGTTTGAA
25665448 TTATTATTATTT-T
1 TTATTATTATTTAT
25665461 TTATTATTATTTTAT
1 TTATTATTA-TTTAT
25665476 TTATTTATTATTTAT
1 TTA-TTATTATTTAT
25665491 TT
1 TT
25665493 TTTTTTGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 11 0.38
16 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:25665466 original size:16 final size:16
Alignment explanation
Indices: 25665447--25665495 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
25665437 ATATGTTTGA
25665447 ATTATTATTATTTTTT
1 ATTATTATTATTTTTT
*
25665463 ATTATTATT-TTATTT
1 ATTATTATTATTTTTT
25665478 ATTTATTATTTATTTTTT
1 A-TTATTA-TTATTTTTT
25665496 TTTGGTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 2 0.07
18 5 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTATTATTATTTTTT
Found at i:25665750 original size:16 final size:17
Alignment explanation
Indices: 25665729--25665763 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25665719 TTTTTCGTGA
25665729 TTTTATTA-TCATTATT
1 TTTTATTATTCATTATT
*
25665745 TTTTATTATTTATTATT
1 TTTTATTATTCATTATT
25665762 TT
1 TT
25665764 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTATTCATTATT
Found at i:25665929 original size:21 final size:22
Alignment explanation
Indices: 25665904--25665947 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
25665894 TTAATTTCCT
*
25665904 AAATTTAAACTGTCAT-CTAAA
1 AAATTTAAAATGTCATACTAAA
*
25665925 AAATTTAAAATGTTATACTAAA
1 AAATTTAAAATGTCATACTAAA
25665947 A
1 A
25665948 TAAATTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (22 bp):
AAATTTAAAATGTCATACTAAA
Found at i:25672367 original size:67 final size:67
Alignment explanation
Indices: 25672229--25672373 Score: 202
Period size: 67 Copynumber: 2.2 Consensus size: 67
25672219 CTGGCGCGAG
* ** * *
25672229 GGAAGGAAGAGCTGAGCGGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCTGCCGGCATA
1 GGAA-GAAGAGCTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCAACCGACAGA
*
25672294 AGA
65 AAA
* *
25672297 GGAAGAAGAGCTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGTCGCGGTACCAACCGACGGAA
1 GGAAGAAGAGCTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCAACCGACAGAA
25672362 AA
66 AA
25672364 GGAAG-AGAGC
1 GGAAGAAGAGC
25672374 CAGGTTTGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 5 0.07
67 60 0.87
68 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.43, T:0.06
Consensus pattern (67 bp):
GGAAGAAGAGCTGAGCAGAGGAATAGAGAAGGAGAGAGGCGGAGCCGCGGTACCAACCGACAGAA
AA
Found at i:25672895 original size:2 final size:2
Alignment explanation
Indices: 25672888--25672913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25672878 GTACATTAAA
25672888 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25672914 GTAGTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25677805 original size:27 final size:27
Alignment explanation
Indices: 25677775--25677931 Score: 143
Period size: 27 Copynumber: 5.7 Consensus size: 27
25677765 TAACATAGTT
* *
25677775 TGTAATAACTAAATCTTCAACATGACA
1 TGTAACAACTAAATTTTCAACATGACA
* *
25677802 TGTAACAATTACATTTTTCAACATGACA
1 TGTAACAACTA-AATTTTCAACATGACA
* *
25677830 TGTAACAACTAAATTTTAAACATGACG
1 TGTAACAACTAAATTTTCAACATGACA
* * * * * **
25677857 TATACCAATTATATTTTTCAACATAATG
1 TGTAACAACTA-AATTTTCAACATGACA
* * *
25677885 TGTAACAACTGAATTTTTAACATGACG
1 TGTAACAACTAAATTTTCAACATGACA
*
25677912 TGTAACAACTAAATCTTCAA
1 TGTAACAACTAAATTTTCAA
25677932 TAAGTATTTT
Statistics
Matches: 102, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
27 59 0.58
28 43 0.42
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (27 bp):
TGTAACAACTAAATTTTCAACATGACA
Found at i:25677818 original size:55 final size:55
Alignment explanation
Indices: 25677749--25677919 Score: 200
Period size: 55 Copynumber: 3.1 Consensus size: 55
25677739 TCATGGTGTA
* * * * * *
25677749 TAACAATTATATTTTTTAACATAGTTTGTAATAACTAAATCTTCAACATGACATG
1 TAACAATTATATTTTTCAACATAGTATGTAACAACTAAATTTTAAACATGACGTG
* * *
25677804 TAACAATTACATTTTTCAACAT-GACATGTAACAACTAAATTTTAAACATGACGTA
1 TAACAATTATATTTTTCAACATAG-TATGTAACAACTAAATTTTAAACATGACGTG
* * * * *
25677859 TACCAATTATATTTTTCAACATAATGTGTAACAACTGAATTTTTAACATGACGTG
1 TAACAATTATATTTTTCAACATAGTATGTAACAACTAAATTTTAAACATGACGTG
25677914 TAACAA
1 TAACAA
25677920 CTAAATCTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
54 1 0.01
55 95 0.99
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (55 bp):
TAACAATTATATTTTTCAACATAGTATGTAACAACTAAATTTTAAACATGACGTG
Found at i:25677824 original size:28 final size:27
Alignment explanation
Indices: 25677790--25677919 Score: 136
Period size: 28 Copynumber: 4.7 Consensus size: 27
25677780 TAACTAAATC
*
25677790 TTCAACATGACATGTAACAATTACATTT
1 TTCAACATGACGTGTAACAATTA-ATTT
* * *
25677818 TTCAACATGACATGTAACAACTAAATT
1 TTCAACATGACGTGTAACAATTAATTT
* * *
25677845 TTAAACATGACGTATACCAATTATATTT
1 TTCAACATGACGTGTAACAATTA-ATTT
* * *
25677873 TTCAACATAATGTGTAACAACTGAATTT
1 TTCAACATGACGTGTAACAA-TTAATTT
25677901 TT-AACATGACGTGTAACAA
1 TTCAACATGACGTGTAACAA
25677920 CTAAATCTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
27 36 0.43
28 46 0.55
29 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (27 bp):
TTCAACATGACGTGTAACAATTAATTT
Found at i:25678005 original size:27 final size:27
Alignment explanation
Indices: 25677955--25678024 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
25677945 ACATGATATC
*
25677955 TACCAACTAAATTTTTTAACATGACGAG
1 TACCAACTAAA-TTTTCAACATGACGAG
* *
25677983 TACCAACTACATTTTCAACATGACGTG
1 TACCAACTAAATTTTCAACATGACGAG
*
25678010 TAACAACTAAATTTT
1 TACCAACTAAATTTT
25678025 AGAACATAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 27 0.73
28 10 0.27
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCAACTAAATTTTCAACATGACGAG
Found at i:25678057 original size:27 final size:28
Alignment explanation
Indices: 25677937--25678060 Score: 103
Period size: 28 Copynumber: 4.5 Consensus size: 28
25677927 TTCAATAAGT
* * * * *
25677937 ATTTTTTAACATGATATCTACCAACTAA
1 ATTTTTCAACATGACATGTAACAACTAC
* *
25677965 ATTTTTTAACATGACGA-GTACCAACTAC
1 ATTTTTCAACATGAC-ATGTAACAACTAC
* *
25677993 A-TTTTCAACATGACGTGTAACAACTAA
1 ATTTTTCAACATGACATGTAACAACTAC
**
25678020 ATTTTAGAACAT-AGCATGTAAC-ACTAC
1 ATTTTTCAACATGA-CATGTAACAACTAC
25678047 ATTTTTCAACATGA
1 ATTTTTCAACATGA
25678061 TGTTAACAAC
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
27 37 0.47
28 40 0.51
29 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (28 bp):
ATTTTTCAACATGACATGTAACAACTAC
Found at i:25680175 original size:27 final size:27
Alignment explanation
Indices: 25680131--25680210 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
25680121 CATGGCATGG
* * *
25680131 TGTGTAACAATATGTTTTTGTACATAA
1 TGTGTAGCAAAATTTTTTTGTACATAA
* * * **
25680158 TGTGTAGCAACATTTTTTTGAATATGG
1 TGTGTAGCAAAATTTTTTTGTACATAA
*
25680185 TGTGTAGCAAAATTTTTGTGTACATA
1 TGTGTAGCAAAATTTTTTTGTACATA
25680211 GCTTGTAGGT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (27 bp):
TGTGTAGCAAAATTTTTTTGTACATAA
Found at i:25680341 original size:27 final size:27
Alignment explanation
Indices: 25680240--25680501 Score: 147
Period size: 27 Copynumber: 9.7 Consensus size: 27
25680230 CACTGTAAAC
*
25680240 ATGGCATGTAGCAAAA--TTTTTGAAC
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* * * *
25680265 ATGACCTGTAG-TAATTCTTTTTTGAAA
1 ATGGCATGTAGCAAAAT-TTTTTTGAAA
* * *
25680292 ATAGCATGTAGCAAACTGTTTTTGAAA
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* *
25680319 ATGGCATGTAGCAAAATTATTTTGAAC
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* * * *
25680346 ATGGCGTGTAACAATATTTTTTTCAAA
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* *
25680373 ATGGCGTGTAGTAAAATTTTTTT-AAA
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* * * * *
25680399 CATGACGTGTAACAACAATATTTTTTCAAC
1 -ATGGCATGTAGCAA-AAT-TTTTTTGAAA
* * * * * *
25680429 ATAGCGTGTAAC-AATTTTTTTTTAAC
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* * * * *
25680455 ATGGCGTGTAACAATATTTTTTTCAAC
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* *
25680482 ATGGCATATAGTAAAATTTT
1 ATGGCATGTAGCAAAATTTT
25680502 AGAACATGAT
Statistics
Matches: 186, Mismatches: 42, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.01
25 9 0.05
26 23 0.12
27 127 0.68
28 7 0.04
29 16 0.09
30 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (27 bp):
ATGGCATGTAGCAAAATTTTTTTGAAA
Found at i:25680383 original size:81 final size:77
Alignment explanation
Indices: 25680240--25680509 Score: 220
Period size: 81 Copynumber: 3.4 Consensus size: 77
25680230 CACTGTAAAC
* * ** * * *
25680240 ATGGCATGTAGCAAAA-TTTTTGAACATGACCTGTAGTAATTCTTTTTTGAAAATAGCATGTAGC
1 ATGGCATGTAGCAAAATTTTTTGAACATGGCGTGTAACAATT-TTTTTTCAAAATGGCGTGTAGC
*
25680304 AAACTGTTTTTGAAA
65 AAA-T-TTTTTCAAA
25680319 ATGGCATGTAGCAAAATTATTTTGAACATGGCGTGTAACAATATTTTTTTCAAAATGGCGTGTAG
1 ATGGCATGTAGCAAAATT-TTTTGAACATGGCGTGTAACAAT-TTTTTTTCAAAATGGCGTGTAG
* *
25680384 TAAAATTTTTTTAAA
64 -CAAATTTTTTCAAA
* * * * * * *
25680399 CATGACGTGTAACAACAATATTTTTTCAACATAGCGTGTAACAATTTTTTTTTAACATGGCGTGT
1 -ATGGCATGTAGC-A-AA-ATTTTTTGAACATGGCGTGTAACAATTTTTTTTCAAAATGGCGTGT
* *
25680464 AACAATATTTTTTTCAAC
62 AGCAA-A-TTTTTTCAAA
* * *
25680482 ATGGCATATAGTAAAA-TTTTAGAACATG
1 ATGGCATGTAGCAAAATTTTTTGAACATG
25680510 ATGTATAGCA
Statistics
Matches: 153, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
78 9 0.06
79 17 0.11
80 11 0.07
81 50 0.33
82 32 0.21
83 31 0.20
84 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (77 bp):
ATGGCATGTAGCAAAATTTTTTGAACATGGCGTGTAACAATTTTTTTTCAAAATGGCGTGTAGCA
AATTTTTTCAAA
Found at i:25695252 original size:26 final size:26
Alignment explanation
Indices: 25695201--25695285 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
25695191 GGCATATAAC
* * *
25695201 AACAACATTTTTTCAAT-GTAGTGTGT
1 AACAACCTTTTTTCAATATTA-CGTGT
25695227 AACAACCTTTTTTCAATATTACGTGT
1 AACAACCTTTTTTCAATATTACGTGT
* * * * **
25695253 AGCAAAACTTTTTTGAACATGGCGTGT
1 AAC-AACCTTTTTTCAATATTACGTGT
25695280 AACAAC
1 AACAAC
25695286 AATAACATTT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (26 bp):
AACAACCTTTTTTCAATATTACGTGT
Found at i:25695303 original size:31 final size:26
Alignment explanation
Indices: 25695223--25695400 Score: 131
Period size: 26 Copynumber: 6.6 Consensus size: 26
25695213 TCAATGTAGT
** * **
25695223 GTGTAACAACCTTTTTTCAATATTAC
1 GTGTAACAAAATTTTTTCAACATGGC
* *
25695249 GTGTAGCAAAACTTTTTTGAACATGGC
1 GTGTAACAAAA-TTTTTTCAACATGGC
25695276 GTGTAACAACAATAACATTTTTCAACATGGC
1 GTGTAACAA-AAT----TTTTTCAACATGGC
* * *
25695307 TTGTTACAAAATTTTTTCAATATGGC
1 GTGTAACAAAATTTTTTCAACATGGC
* * *
25695333 GTGTAAGAATATTTTTTCAACATGGT
1 GTGTAACAAAATTTTTTCAACATGGC
* * *
25695359 ATGTAACAACATTTTTTTCAACATAGC
1 GTGTAACAA-AATTTTTTCAACATGGC
* *
25695386 ATGTAGCAAAATTTT
1 GTGTAACAAAATTTT
25695401 ATAACACATG
Statistics
Matches: 119, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
26 53 0.45
27 41 0.34
28 2 0.02
30 3 0.03
31 20 0.17
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (26 bp):
GTGTAACAAAATTTTTTCAACATGGC
Found at i:25699953 original size:28 final size:29
Alignment explanation
Indices: 25699912--25699971 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
25699902 GTCTATGGGC
* *
25699912 AATTTTTCAGTTTT-TGGGGTAAAAATGT
1 AATTTTTCACTTTTAGGGGGTAAAAATGT
* *
25699940 AATTTTTGACTTTTACGGGGGTAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGTAAAAATGT
25699970 AA
1 AA
25699972 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGTAAAAATGT
Found at i:25724857 original size:13 final size:13
Alignment explanation
Indices: 25724839--25724863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25724829 GGAGAAATTG
25724839 TGATTTTATAAAA
1 TGATTTTATAAAA
25724852 TGATTTTATAAA
1 TGATTTTATAAA
25724864 TTTTTTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:25736641 original size:5 final size:5
Alignment explanation
Indices: 25736628--25736667 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
25736618 TAACTCGATA
* *
25736628 TAACC TAACT TAACT TGACT T-ACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT T
25736668 GGGCCACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:25736722 original size:15 final size:15
Alignment explanation
Indices: 25736702--25736752 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
25736692 TTCTTAAAAC
25736702 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
* *
25736717 AACTTTGAAATCCAA
1 AACTTTAAAATCAAA
*
25736732 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
25736747 ATCTTT
1 AACTTT
25736753 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:25740761 original size:13 final size:13
Alignment explanation
Indices: 25740743--25740767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25740733 GTTGGCTGGA
25740743 TATTTCAAAATGG
1 TATTTCAAAATGG
25740756 TATTTCAAAATG
1 TATTTCAAAATG
25740768 CTTACAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TATTTCAAAATGG
Found at i:25745776 original size:15 final size:15
Alignment explanation
Indices: 25745756--25745809 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
25745746 ACAATGCAAC
*
25745756 GTGATTACAGGTAAT
1 GTGATTACAAGTAAT
*
25745771 GTGATTGCAAGTAAT
1 GTGATTACAAGTAAT
* *
25745786 GTGATTGCAAGCAAT
1 GTGATTACAAGTAAT
25745801 GTGATTACA
1 GTGATTACA
25745810 GGAAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (15 bp):
GTGATTACAAGTAAT
Found at i:25746065 original size:13 final size:13
Alignment explanation
Indices: 25746010--25746075 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
25746000 ATCTCTTAAA
*
25746010 TATATTTTTAATGT
1 TATATTTTTTAT-T
* *
25746024 CATATATTTTATT
1 TATATTTTTTATT
*
25746037 T-TCATTTTTTA-A
1 TAT-ATTTTTTATT
25746049 TATATTTTTTATT
1 TATATTTTTTATT
*
25746062 TATATATTTTATT
1 TATATTTTTTATT
25746075 T
1 T
25746076 TAATTTCTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
12 10 0.24
13 22 0.54
14 9 0.22
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (13 bp):
TATATTTTTTATT
Found at i:25746071 original size:25 final size:25
Alignment explanation
Indices: 25746025--25746072 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
25746015 TTTTAATGTC
*
25746025 ATATATTTTATTTTCATTTTTTAAT
1 ATATATTTTATTTTCATATTTTAAT
*
25746050 ATATTTTTTATTTAT-ATATTTTA
1 ATATATTTTATTT-TCATATTTTA
25746073 TTTTAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
ATATATTTTATTTTCATATTTTAAT
Found at i:25746073 original size:38 final size:39
Alignment explanation
Indices: 25746008--25746081 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
25745998 TCATCTCTTA
*
25746008 AATATATTTTTAATGTCATATATTTTATTTTCATTTTTT
1 AATATATTTTTAATGTCATATATTTTATTTTAATTTTTT
* *
25746047 AATATATTTTTTAT-TTATATATTTTATTTTAATTT
1 AATATATTTTTAATGTCATATATTTTATTTTAATTT
25746082 CTTTTACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 19 0.59
39 13 0.41
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (39 bp):
AATATATTTTTAATGTCATATATTTTATTTTAATTTTTT
Found at i:25746081 original size:26 final size:26
Alignment explanation
Indices: 25746052--25746172 Score: 79
Period size: 28 Copynumber: 4.4 Consensus size: 26
25746042 TTTTTAATAT
*
25746052 ATTTTTTATTTATATATTTTATTTTA
1 ATTTTTTATTTATATATTTAATTTTA
* *
25746078 ATTTCTTTTACTTATATTATATAAATTTTA
1 A-TT-TTTTATTTATA-TAT-TTAATTTTA
25746108 ATTTCTTATATTT-TAT-TTTAATTTTTA
1 ATTT-TT-TATTTATATATTTAA-TTTTA
* *
25746135 A-TTCTTATATTATATATTT-GTTTTAA
1 ATTTTTTAT-TTATATATTTAATTTT-A
25746161 TATTTTTTATTT
1 -ATTTTTTATTT
25746173 TAATTATAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
24 3 0.04
25 7 0.09
26 10 0.14
27 15 0.20
28 18 0.24
29 9 0.12
30 12 0.16
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (26 bp):
ATTTTTTATTTATATATTTAATTTTA
Found at i:25746097 original size:24 final size:22
Alignment explanation
Indices: 25746070--25746147 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 22
25746060 TTTATATATT
25746070 TTATTTTAATTTCTTTTACTTATA
1 TTATTTTAATTT-TTTT-CTTATA
* *
25746094 TTATATAAATTTTAATTTCTTATA
1 TTATTTTAATTTT--TTTCTTATA
25746118 TTTTATTTTAATTTTTAATTCTTATA
1 --TTATTTTAATTTTT--TTCTTATA
25746144 TTAT
1 TTAT
25746148 ATATTTGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
23 1 0.02
24 21 0.48
25 3 0.07
26 19 0.43
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTTAATTTTTTTCTTATA
Found at i:25760264 original size:19 final size:19
Alignment explanation
Indices: 25760242--25760279 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25760232 GCATTTGACT
25760242 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25760261 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
25760280 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:25760382 original size:28 final size:28
Alignment explanation
Indices: 25760329--25760382 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
25760319 GTATAAGGTT
* *
25760329 AAAATGGTAATTTTGCCACTCTAGGAGC
1 AAAATGGTAATTTTGCCACACCAGGAGC
*
25760357 AAAATTGTAATTTT-CCACCACCAGGA
1 AAAATGGTAATTTTGCCA-CACCAGGA
25760383 CAATTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAATGGTAATTTTGCCACACCAGGAGC
Found at i:25766713 original size:60 final size:60
Alignment explanation
Indices: 25766636--25766762 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 60
25766626 AAAAAGGACG
* *
25766636 AAAA-GAAGAAGAACCCATCACTAGAGTGCAAGGAGGAATGAGAGAAAAAAAA-AGAAAAA
1 AAAAGGAAGAAGAACCCATCACTAGAGAGCAAGAAGGAATGAGAGAAAAAAAAGA-AAAAA
* * * *
25766695 AAAAGGAAGAAGAGCCCATCACTAGAGAGTAATAAGGAATGAGAGAAGAAAAAGAAAAAA
1 AAAAGGAAGAAGAACCCATCACTAGAGAGCAAGAAGGAATGAGAGAAAAAAAAGAAAAAA
25766755 AAAAGGAA
1 AAAAGGAA
25766763 AAGTCCATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 4 0.07
60 55 0.92
61 1 0.02
ACGTcount: A:0.60, C:0.09, G:0.24, T:0.07
Consensus pattern (60 bp):
AAAAGGAAGAAGAACCCATCACTAGAGAGCAAGAAGGAATGAGAGAAAAAAAAGAAAAAA
Found at i:25766832 original size:15 final size:16
Alignment explanation
Indices: 25766793--25766835 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
25766783 TGGGTGCAAG
*
25766793 AAGAAATAAGAGAAAAA
1 AAGAAAGAA-AGAAAAA
25766810 AATGAAAGAAAGAAAAA
1 AA-GAAAGAAAGAAAAA
25766827 AA-AAAGAAA
1 AAGAAAGAAA
25766836 AGGGTGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
17 11 0.46
18 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAGAAAGAAAGAAAAA
Found at i:25772735 original size:26 final size:24
Alignment explanation
Indices: 25772704--25772770 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 24
25772694 ATAATAGATC
25772704 ATTTAAATATTAATATTTTATTAATA
1 ATTTAAATATTAATATTTTATT--TA
25772730 ATTT-AATCATTAATATTTTATTTA
1 ATTTAAAT-ATTAATATTTTATTTA
* *
25772754 ATTTAAATGTTATTATT
1 ATTTAAATATTAATATT
25772771 AATTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 13 0.35
25 6 0.16
26 18 0.49
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (24 bp):
ATTTAAATATTAATATTTTATTTA
Found at i:25772830 original size:27 final size:27
Alignment explanation
Indices: 25772788--25772848 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
25772778 ATTTTATTTT
* *
25772788 ATTT-TTT-AAATATTAATAGTTGGTA
1 ATTTATTTAAAATATTAATAATTGATA
* *
25772813 ATTTATTTAAAATTTTAATAATTGATT
1 ATTTATTTAAAATATTAATAATTGATA
25772840 ATTTATTTA
1 ATTTATTTA
25772849 TTAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 23 0.77
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
ATTTATTTAAAATATTAATAATTGATA
Found at i:25772892 original size:140 final size:139
Alignment explanation
Indices: 25772599--25772870 Score: 367
Period size: 136 Copynumber: 2.0 Consensus size: 139
25772589 TTTTAAAATG
25772599 TTAATATTTTATTTAATTAAAATATTATTATGATCAATTATTTTATTTTATTTTATTTTTAAGAA
1 TTAATATTTTATTTAATTAAAATATTATTAT-ATCAATTATTTTATTTTATTTTATTTTTAAGAA
*
25772664 TCAATAATTGATTATTTATTTAAAATATTAATAATAGATCATTTAAATATTAATATTTTATTAAT
65 TCAATAATTGATAATTTATTTAAAATATTAATAATAGATCATTTAAATATTAATATTTTATTAAT
25772729 AATTTAATCA
130 AATTTAATCA
* *
25772739 TTAATATTTTATTTAATTTAAATGTTATTAT-T-AA-T-TTTTATTTTATTTTATTTTTTAA-AT
1 TTAATATTTTATTTAATTAAAATATTATTATATCAATTATTTTATTTTATTTTA-TTTTTAAGA-
* * * * * * ** *
25772799 ATTAATAGTTGGTAATTTATTTAAAATTTTAATAATTGATTATTTATTTATTAATATTTT-TTTA
64 ATCAATAATTGATAATTTATTTAAAATATTAATAATAGATCATTTAAATATTAATATTTTATTAA
25772863 TAATTTAA
129 TAATTTAA
25772871 ATGATATTAT
Statistics
Matches: 118, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
135 27 0.23
136 59 0.50
137 2 0.02
138 1 0.01
140 29 0.25
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (139 bp):
TTAATATTTTATTTAATTAAAATATTATTATATCAATTATTTTATTTTATTTTATTTTTAAGAAT
CAATAATTGATAATTTATTTAAAATATTAATAATAGATCATTTAAATATTAATATTTTATTAATA
ATTTAATCA
Found at i:25772963 original size:112 final size:108
Alignment explanation
Indices: 25772727--25772983 Score: 279
Period size: 112 Copynumber: 2.3 Consensus size: 108
25772717 TATTTTATTA
25772727 ATAATTT-AATCATTAATATTTTATT-TAATTTAAATGTTATTATTAATTTTTATTTTATTTTAT
1 ATAATTTAAAT-ATTAATATTTTATTATAATTTAAATGTTATTATTAATTTTTATTTTATTTTAT
** * * *
25772790 TTTTTAAATATTAATAGTTGGTAATTTATTTAAAATTTTAATAATTG
65 TTTTTAAATAAGAATAATTGATAATTTATTT---ATATTAATAATTG
* ** * *
25772837 ATTATTTATTTATTAATATTTTTTTATAATTTAAATGATATTATGCTTATTTATTTTTATTTTAT
1 ATAATTTAAATATTAATATTTTATTATAATTTAAATG---TTA---TTATTAATTTTTATTTTAT
*
25772902 TTTA-TTTTTAAATAAGAATAATTTATAATTTATTT-TATTAATAATTG
60 TTTATTTTTTAAATAAGAATAATTGATAATTTATTTATATTAATAATTG
*
25772949 ATAATTTAAATATTAATATTTAACTTATAATTTAA
1 ATAATTTAAATATTAATATTTTA-TTATAATTTAA
25772984 TATTAATATT
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
110 19 0.16
111 12 0.10
112 29 0.24
113 11 0.09
114 3 0.02
116 26 0.21
117 22 0.18
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (108 bp):
ATAATTTAAATATTAATATTTTATTATAATTTAAATGTTATTATTAATTTTTATTTTATTTTATT
TTTTAAATAAGAATAATTGATAATTTATTTATATTAATAATTG
Found at i:25773459 original size:35 final size:33
Alignment explanation
Indices: 25773414--25773539 Score: 103
Period size: 35 Copynumber: 3.7 Consensus size: 33
25773404 TTAGTTGTTG
* *
25773414 GGTTTTGGTTGATCTCGTGAAAAACCATTATTGTA
1 GGTTGTGGTTGAGC-CGTGAAAAACCATT-TTGTA
* * *
25773449 GGTTGTGGTTGAGCCTTTGAAAAATCA-CTT-TA
1 GGTTGTGGTTGAGCC-GTGAAAAACCATTTTGTA
* * *
25773481 GGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAA
1 GGTTGTGGTTGAG-CCGTGAAAAACCATTTTG-TA
*
25773516 GGTTGTGGTTGAGCCTTTGAAAAA
1 GGTTGTGGTTGAGCC-GTGAAAAA
25773540 TCACTTTGGG
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
32 23 0.32
33 5 0.07
34 3 0.04
35 41 0.57
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (33 bp):
GGTTGTGGTTGAGCCGTGAAAAACCATTTTGTA
Found at i:25773490 original size:32 final size:32
Alignment explanation
Indices: 25773447--25773559 Score: 129
Period size: 32 Copynumber: 3.4 Consensus size: 32
25773437 ACCATTATTG
25773447 TAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
1 TAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
* ** *
25773479 TAGGTTTTGGTTGAGCCCGTGAAAAACCA-TT
1 TAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
25773510 GTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
1 -T---AGGTTGTGGTTGAGCCTTTGAAAAATCACTT
* *
25773546 TGGGTTTTGGTTGA
1 TAGGTTGTGGTTGA
25773560 TCCCGGTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
31 2 0.03
32 37 0.56
35 25 0.38
36 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (32 bp):
TAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
Found at i:25773492 original size:67 final size:67
Alignment explanation
Indices: 25773414--25773586 Score: 269
Period size: 67 Copynumber: 2.6 Consensus size: 67
25773404 TTAGTTGTTG
* * *
25773414 GGTTTTGGTTGATCTCGTGAAAAACCATTATTG-TAGGTTGTGGTTGAGCCTTTGAAAAATCACT
1 GGTTTTGGTTGATCCCGTGAAAAACCATT-GTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACT
25773478 TTA
65 TTA
*
25773481 GGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
1 GGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
*
25773546 TG
66 TA
25773548 GGTTTTGGTTGATCCCG-GTAAAAACCATTGTGAAAGGTT
1 GGTTTTGGTTGATCCCGTG-AAAAACCATTGTGAAAGGTT
25773587 TTTGCTAAGC
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
66 3 0.03
67 95 0.97
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (67 bp):
GGTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
TA
Found at i:25774489 original size:21 final size:21
Alignment explanation
Indices: 25774454--25774510 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
25774444 TTGTGAACTT
25774454 AATT-CAT-ATGCTTTTGATG
1 AATTGCATGATGCTTTTGATG
*
25774473 AATTGCATGATGTTTTTGATG
1 AATTGCATGATGCTTTTGATG
25774494 AATTGCATGATGCTTTT
1 AATTGCATGATGCTTTT
25774511 AAAGATTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 27 0.79
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (21 bp):
AATTGCATGATGCTTTTGATG
Found at i:25776982 original size:8 final size:7
Alignment explanation
Indices: 25776954--25776983 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
25776944 AAAAGAAATG
25776954 AATGAAA
1 AATGAAA
25776961 AATGAAA
1 AATGAAA
25776968 AATGAAA
1 AATGAAA
25776975 AATAGAAA
1 AAT-GAAA
25776983 A
1 A
25776984 GATAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AATGAAA
Found at i:25779202 original size:19 final size:20
Alignment explanation
Indices: 25779178--25779215 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25779168 CTATAAATAC
25779178 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
25779197 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
25779216 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:25780116 original size:2 final size:2
Alignment explanation
Indices: 25780101--25780134 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
25780091 TGATGATGGG
* *
25780101 TA TA TA TG TG 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
25780135 GTNATTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25783384 original size:28 final size:29
Alignment explanation
Indices: 25783343--25783402 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
25783333 GTCTATGGGC
*
25783343 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
25783371 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
25783401 AA
1 AA
25783403 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:25791564 original size:28 final size:29
Alignment explanation
Indices: 25791523--25791582 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
25791513 GTCTATGGGC
*
25791523 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
25791551 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
25791581 AA
1 AA
25791583 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:25793764 original size:11 final size:11
Alignment explanation
Indices: 25793730--25793768 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
25793720 GAAAATAGAA
25793730 TATTTTCCTTAT
1 TATTTT-CTTAT
25793742 TA-TTTCTT-T
1 TATTTTCTTAT
25793751 TATTTTCTTAT
1 TATTTTCTTAT
25793762 TATTTTC
1 TATTTTC
25793769 AAATAACCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.12
10 9 0.36
11 11 0.44
12 2 0.08
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTCTTAT
Found at i:25794900 original size:66 final size:67
Alignment explanation
Indices: 25794753--25794909 Score: 158
Period size: 66 Copynumber: 2.4 Consensus size: 67
25794743 CGATTGTTGT
* * * * *
25794753 AGGTTGTGGTTGAGTCTTGGAAAAACCACTTTGGGTTTTAGTTTAGCCCGTGAAAGACTAGTGTA
1 AGGTTGTGGTTGAGCCTTCGAAAAACCACTTTGGGTTTTAGTTGAGCCCGCGAAAAACTAGTGTA
25794818 AA
66 AA
* * * ** *
25794820 AGGTTATGGTTGAGCCTT-GAAAAACCACTTTGGGTTTTGGTTGATCTTGCGAAAAA-TCATTGC
1 AGGTTGTGGTTGAGCCTTCGAAAAACCACTTTGGGTTTTAGTTGAGCCCGCGAAAAACT-AGTG-
25794883 TAAA
64 TAAA
* *
25794887 A-GTTGTGGCTGAGCTTTCGAAAA
1 AGGTTGTGGTTGAGCCTTCGAAAA
25794910 GTCATTGTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
65 1 0.01
66 47 0.64
67 26 0.35
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTCGAAAAACCACTTTGGGTTTTAGTTGAGCCCGCGAAAAACTAGTGTA
AA
Found at i:25802563 original size:66 final size:67
Alignment explanation
Indices: 25802463--25802642 Score: 188
Period size: 66 Copynumber: 2.7 Consensus size: 67
25802453 GGTTGATCCT
* * ** * * *
25802463 GTGAAAAACCATTGTTGTAGGTTGTGGTTAAGCCTTGGAAAAACCATTTTGGGTTTTAGTTTAGC
1 GTGAAAAACCAGTGCTAAAGGTTGTGGTTGAGCCTTGGAAAAACCATTTTGAGTTTTAGTTGAGC
25802528 TC
66 TC
* * * * *
25802530 GTG-AAAACTAGTG-TAAAAGGTTGTGGTTGAGCCTT-GAAAAACTACTTTGAGTTTTGGTTGAT
1 GTGAAAAACCAGTGCT-AAAGGTTGTGGTTGAGCCTTGGAAAAACCATTTTGAGTTTTAGTTGAG
25802592 CTC
65 CTC
* *
25802595 GTGAAAAACCATTGCTAAAGGTTGTGGCTGAGCC-TGTGAAAAACCATT
1 GTGAAAAACCAGTGCTAAAGGTTGTGGTTGAGCCTTG-GAAAAACCATT
25802643 GTAAAGCATG
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
65 29 0.32
66 50 0.54
67 13 0.14
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (67 bp):
GTGAAAAACCAGTGCTAAAGGTTGTGGTTGAGCCTTGGAAAAACCATTTTGAGTTTTAGTTGAGC
TC
Found at i:25804157 original size:20 final size:20
Alignment explanation
Indices: 25804132--25804170 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25804122 TATTGAATGT
* *
25804132 TTGATGATGATTGATAATAC
1 TTGATGATAATTGAGAATAC
25804152 TTGATGATAATTGAGAATA
1 TTGATGATAATTGAGAATA
25804171 GTGCTTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGATGATAATTGAGAATAC
Found at i:25805538 original size:26 final size:26
Alignment explanation
Indices: 25805508--25805560 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
25805498 GATTAAAAGA
*
25805508 AAATCTTGATTCACTCATTAAGGAGG
1 AAATCTTGATGCACTCATTAAGGAGG
25805534 AAATCTTGATGCACTCATTAAGGAGG
1 AAATCTTGATGCACTCATTAAGGAGG
25805560 A
1 A
25805561 GTTTTGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (26 bp):
AAATCTTGATGCACTCATTAAGGAGG
Found at i:25806741 original size:61 final size:61
Alignment explanation
Indices: 25806646--25806764 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
25806636 TTTGGTTGAT
* *
25806646 CCCGTGAAAAACCATTGTTGTAGGTTGTAGTTGAGCCTTTGAAAAACCACTTTGGGTTAAG
1 CCCGTGAAAAACCATTGATGAAGGTTGTAGTTGAGCCTTTGAAAAACCACTTTGGGTTAAG
*
25806707 CCCGTGAAAAACCATT-ATGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTT
1 CCCGTGAAAAACCATTGATG-AAGGTTGTAGTTGAGCCTTTGAAAAACCACTTTGGGTT
25806765 TTGGTTGATC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 2 0.04
61 52 0.96
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (61 bp):
CCCGTGAAAAACCATTGATGAAGGTTGTAGTTGAGCCTTTGAAAAACCACTTTGGGTTAAG
Found at i:25812784 original size:17 final size:17
Alignment explanation
Indices: 25812759--25812809 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
25812749 AGTAAATAAA
*
25812759 CACACACTAAGAGGGAG
1 CACATACTAAGAGGGAG
*
25812776 CACATACTAAGGGGGAG
1 CACATACTAAGAGGGAG
*
25812793 CAC-TCACTTAGAGGGAG
1 CACAT-ACTAAGAGGGAG
25812810 AAATCCTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 1 0.03
17 28 0.97
ACGTcount: A:0.35, C:0.22, G:0.31, T:0.12
Consensus pattern (17 bp):
CACATACTAAGAGGGAG
Found at i:25813218 original size:56 final size:56
Alignment explanation
Indices: 25813127--25813240 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
25813117 TCAGAAGTTG
25813127 GTGGGCTCAAGAGTATTGAGAAATAGAAAAAACTTAGTTGACCAAGAAATAGGTTA
1 GTGGGCTCAAGAGTATTGAGAAATAGAAAAAACTTAGTTGACCAAGAAATAGGTTA
*
25813183 GTGGGCTCAAGAGTATTGAGAAATAGAAAAGACTTAGTTGACCAAGAAATAGGTTA
1 GTGGGCTCAAGAGTATTGAGAAATAGAAAAAACTTAGTTGACCAAGAAATAGGTTA
25813239 GT
1 GT
25813241 CGACTAAGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (56 bp):
GTGGGCTCAAGAGTATTGAGAAATAGAAAAAACTTAGTTGACCAAGAAATAGGTTA
Found at i:25814557 original size:100 final size:101
Alignment explanation
Indices: 25814362--25814659 Score: 415
Period size: 100 Copynumber: 3.0 Consensus size: 101
25814352 AATGTTAGGA
* * *
25814362 ATTTCAAAATT-TGTGAGTTAAAGGGTTTAGTACAATTATTT-GATTTGGAGAGAAAAAAATTGT
1 ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTATTTGGATTT-GAGAGAAAAAAATTGT
* *
25814425 TTGATTTACTCATCAAAAAAGAGAATAGGAGAAAGGG
65 TTGATTTACTCATCAAAAAAGAGAATAAGAGAAAGAG
*
25814462 ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTATTTGGCTTTGAGAG-AAAAAATTGTT
1 ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTATTTGGATTTGAGAGAAAAAAATTGTT
* ** *
25814526 TGATTTATTCATGGAAAAAGGGAATAAGAGAAAGAG
66 TGATTTACTCATCAAAAAAGAGAATAAGAGAAAGAG
* *
25814562 ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTGTTTGGTTTTGAGAGAAAAAAATTGTT
1 ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTATTTGGATTTGAGAGAAAAAAATTGTT
* * *
25814627 TGATTGACTTA-CAAAAAAGGAGAATAGGAGAAA
66 TGATTTACTCATCAAAAAA-GAGAATAAGAGAAA
25814660 TGGTGAGAAC
Statistics
Matches: 175, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
100 107 0.61
101 64 0.37
102 4 0.02
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (101 bp):
ATTTCAAATTTGTGTGAGTTAAAGGGTTTAGTATAGTTATTTGGATTTGAGAGAAAAAAATTGTT
TGATTTACTCATCAAAAAAGAGAATAAGAGAAAGAG
Found at i:25828535 original size:2 final size:2
Alignment explanation
Indices: 25828530--25828564 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25828520 ACACACACAC
25828530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25828565 CTANNNNACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25828597 original size:2 final size:2
Alignment explanation
Indices: 25828592--25828625 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25828582 ACACACACAC
25828592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25828626 CCATTGCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25843814 original size:20 final size:20
Alignment explanation
Indices: 25843789--25843834 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
25843779 TTTTGGCCCC
*
25843789 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
25843809 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
25843829 ATTTGA
1 ATTTGA
25843835 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:25843910 original size:28 final size:27
Alignment explanation
Indices: 25843879--25843931 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
25843869 TTTGGAGTAT
*
25843879 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
25843907 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
25843932 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:25843937 original size:28 final size:28
Alignment explanation
Indices: 25843879--25843937 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
25843869 TTTGGAGTAT
* *
25843879 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
25843907 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
25843935 AGG
1 AGG
25843938 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:25851849 original size:20 final size:20
Alignment explanation
Indices: 25851824--25851869 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
25851814 TTTTGACCCC
25851824 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
25851844 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
25851864 ATTTGA
1 ATTTGA
25851870 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:25851945 original size:28 final size:27
Alignment explanation
Indices: 25851914--25851966 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
25851904 TTTGGAGTAT
*
25851914 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
25851942 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
25851967 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:25851972 original size:28 final size:28
Alignment explanation
Indices: 25851914--25851972 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
25851904 TTTGGAGTAT
* *
25851914 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
25851942 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
25851970 AGG
1 AGG
25851973 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:25854856 original size:20 final size:20
Alignment explanation
Indices: 25854831--25854871 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25854821 ATAAGCCTTG
25854831 TTGATTTTTACGAAATGAAA
1 TTGATTTTTACGAAATGAAA
*
25854851 TTGATTTTTATGAAATGAAA
1 TTGATTTTTACGAAATGAAA
25854871 T
1 T
25854872 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTTTACGAAATGAAA
Found at i:25854877 original size:21 final size:20
Alignment explanation
Indices: 25854833--25854878 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
25854823 AAGCCTTGTT
*
25854833 GATTTTTACGAAATGAAATT
1 GATTTTTACGAAATGAAATA
*
25854853 GATTTTTATGAAATGAAATGA
1 GATTTTTACGAAATGAAAT-A
25854874 GATTT
1 GATTT
25854879 GATGTTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (20 bp):
GATTTTTACGAAATGAAATA
Found at i:25866183 original size:21 final size:21
Alignment explanation
Indices: 25866153--25866220 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
25866143 AGATATGTTC
25866153 ATGCAATTCATGACAAAGACTG
1 ATGC-ATTCATGACAAAGACTG
*
25866175 ATGCATTCATAACAAAGACTG
1 ATGCATTCATGACAAAGACTG
* * *
25866196 ATGCATTTATGATAAGGACTG
1 ATGCATTCATGACAAAGACTG
25866217 ATGC
1 ATGC
25866221 CTCCATTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:25867818 original size:20 final size:18
Alignment explanation
Indices: 25867793--25867829 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
25867783 GCTCCACGAA
25867793 AAAAAAATTTCACAAAAAAT
1 AAAAAAA-TTCA-AAAAAAT
25867813 AAAAAAATTCAAAAAAA
1 AAAAAAATTCAAAAAAA
25867830 AAAGGTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAAAATTCAAAAAAAT
Found at i:25867831 original size:20 final size:20
Alignment explanation
Indices: 25867793--25867830 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25867783 GCTCCACGAA
*
25867793 AAAAAAATTTCACAAAAAAT
1 AAAAAAATTTCAAAAAAAAT
25867813 AAAAAAA-TTCAAAAAAAA
1 AAAAAAATTTCAAAAAAAA
25867831 AAGGTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAATTTCAAAAAAAAT
Found at i:25870001 original size:19 final size:20
Alignment explanation
Indices: 25869974--25870019 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
25869964 AGGAGACAAG
*
25869974 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
25869993 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
25870012 ATAATATT
1 ATAATATT
25870020 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:25876978 original size:18 final size:18
Alignment explanation
Indices: 25876955--25876997 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
25876945 AAATTATGTG
25876955 CTTCAGGTAACTTAAATC
1 CTTCAGGTAACTTAAATC
25876973 CTTCAGGTAACTTAAATC
1 CTTCAGGTAACTTAAATC
25876991 CTTCAGG
1 CTTCAGG
25876998 AATTTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
CTTCAGGTAACTTAAATC
Found at i:25878459 original size:19 final size:20
Alignment explanation
Indices: 25878434--25878474 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
25878424 ATTGTTATTA
*
25878434 TTATTATTATTATTTATTTATC
1 TTATTAATA-TATTT-TTTATC
25878456 TTATTAATATATTTTTTAT
1 TTATTAATATATTTTTTAT
25878475 TAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTAATATATTTTTTATC
Found at i:25878480 original size:19 final size:20
Alignment explanation
Indices: 25878431--25878482 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
25878421 AGTATTGTTA
*
25878431 TTATTATTATTATTATTTAT
1 TTATTATTAATATTATTTAT
25878451 TTATCTTATTAATA-TATTT-T
1 TTA--TTATTAATATTATTTAT
25878471 TTATTAATTAAT
1 TTATT-ATTAAT
25878483 TTAAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.07
19 6 0.21
20 7 0.25
21 5 0.18
22 8 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTAATATTATTTAT
Found at i:25883502 original size:29 final size:29
Alignment explanation
Indices: 25883462--25883521 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
25883452 TAATAAGAGT
*
25883462 TTTTGCAGCTGGTATATGAGATTTAGTTA
1 TTTTGCAACTGGTATATGAGATTTAGTTA
25883491 TTTTGCAACTGGTATATGAGATTTAGTTA
1 TTTTGCAACTGGTATATGAGATTTAGTTA
25883520 TT
1 TT
25883522 CTCTTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47
Consensus pattern (29 bp):
TTTTGCAACTGGTATATGAGATTTAGTTA
Found at i:25889416 original size:69 final size:69
Alignment explanation
Indices: 25889343--25889511 Score: 185
Period size: 69 Copynumber: 2.4 Consensus size: 69
25889333 ACATTGGCCA
* * * * * **
25889343 AACTTAACCCTGCGGTATTCTTACCCCCTCACCCATACTGGTAAAAAGGAAAAAAGTGGTACAAT
1 AACTTAACCCTGTGGTATTATTACCCCCACACCAAGACTCATAAAAAGGAAAAAAGTGGTACAAT
25889408 ACCC
66 ACCC
* * ** **
25889412 AACTTAACCCTGTAGTATTATTACCCCCACACCAAGACTCATAAATAGGGGAAAAGTGGTATGAT
1 AACTTAACCCTGTGGTATTATTACCCCCACACCAAGACTCATAAAAAGGAAAAAAGTGGTACAAT
*
25889477 GCCC
66 ACCC
* * *
25889481 AACCTAACCTTGTGGTATTGTTACCCCCACA
1 AACTTAACCCTGTGGTATTATTACCCCCACA
25889512 TCAGAACTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 82 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (69 bp):
AACTTAACCCTGTGGTATTATTACCCCCACACCAAGACTCATAAAAAGGAAAAAAGTGGTACAAT
ACCC
Found at i:25891041 original size:27 final size:27
Alignment explanation
Indices: 25891003--25891055 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
25890993 TCTCTTCGTT
25891003 ATTCATCCACTCTAGGTGGTTAAAAGA
1 ATTCATCCACTCTAGGTGGTTAAAAGA
*
25891030 ATTCATCCACTCTTGGTGGTTAAAAG
1 ATTCATCCACTCTAGGTGGTTAAAAG
25891056 TATAATTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (27 bp):
ATTCATCCACTCTAGGTGGTTAAAAGA
Found at i:25894563 original size:2 final size:2
Alignment explanation
Indices: 25894556--25894584 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25894546 GATTAACCTT
25894556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25894585 TTCATTACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25894678 original size:2 final size:2
Alignment explanation
Indices: 25894671--25894702 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25894661 TTTCCGCTAA
25894671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25894703 GTTGTTCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25898054 original size:29 final size:29
Alignment explanation
Indices: 25898021--25898081 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
25898011 CATTAAAGTG
* * *
25898021 CAATAAAAATTTTTGAACATGGTGTGTAA
1 CAATAAAAATTTTTCAACACGGAGTGTAA
* *
25898050 CAATAATATTTTTTCAACACGGAGTGTAA
1 CAATAAAAATTTTTCAACACGGAGTGTAA
25898079 CAA
1 CAA
25898082 CAATATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (29 bp):
CAATAAAAATTTTTCAACACGGAGTGTAA
Found at i:25898097 original size:31 final size:29
Alignment explanation
Indices: 25898030--25898092 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
25898020 GCAATAAAAA
* * * *
25898030 TTTTTGAACATGGTGTGTAACAATAATAT
1 TTTTTCAACACGGAGTGTAACAACAATAT
25898059 TTTTTCAACACGGAGTGTAACAACAATAT
1 TTTTTCAACACGGAGTGTAACAACAATAT
25898088 TTTTT
1 TTTTT
25898093 TTCAATATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTTTCAACACGGAGTGTAACAACAATAT
Found at i:25898151 original size:24 final size:26
Alignment explanation
Indices: 25898114--25898161 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
25898104 ATATGACAAC
*
25898114 TTTTTTTAACCATGGCATGTAACATA
1 TTTTTTTAACCATGACATGTAACATA
*
25898140 TTTTTTT-A-CATGACGTGTAACA
1 TTTTTTTAACCATGACATGTAACA
25898162 ATAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 1 0.05
26 7 0.35
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (26 bp):
TTTTTTTAACCATGACATGTAACATA
Found at i:25900150 original size:21 final size:22
Alignment explanation
Indices: 25900120--25900160 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
25900110 GGATATGTTC
25900120 ATGCAATTCATGACAAAGACCG
1 ATGCAATTCATGACAAAGACCG
25900142 ATGC-ATTCATGACAAAGAC
1 ATGCAATTCATGACAAAGAC
25900161 TAATACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (22 bp):
ATGCAATTCATGACAAAGACCG
Found at i:25904640 original size:4 final size:4
Alignment explanation
Indices: 25904631--25904679 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
25904621 TTTTATGTTT
* *
25904631 AATA AATA AATA AATA AATA TAATA TAATA AATA ACAAA AAAA AATA AA
1 AATA AATA AATA AATA AATA -AATA -AATA AATA A-ATA AATA AATA AA
25904680 AAAAAAAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 29 0.71
5 12 0.29
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:25904660 original size:18 final size:16
Alignment explanation
Indices: 25904631--25904679 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
25904621 TTTTATGTTT
25904631 AATAAATAAATAAATA
1 AATAAATAAATAAATA
25904647 AATATAATATAATAAATA
1 AATA-AATA-AATAAATA
* *
25904665 ACAAAAAAAAATAAA
1 A-ATAAATAAATAAA
25904680 AAAAAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 12 0.43
19 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAATAAATAAATA
Found at i:25904677 original size:22 final size:21
Alignment explanation
Indices: 25904631--25904679 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
25904621 TTTTATGTTT
* *
25904631 AATAAATAAATAAATAAATAT
1 AATAAATAAATAAATAAAAAA
25904652 AATATAATAAATAACA-AAAAAA
1 AATA-AATAAATAA-ATAAAAAA
25904674 AATAAA
1 AATAAA
25904680 AAAAAAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAAATAAATAAATAAAAAA
Found at i:25906389 original size:3 final size:3
Alignment explanation
Indices: 25906381--25906415 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
25906371 AAATCTTCAA
* *
25906381 AAT AAT AAT AAT AGT AAT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25906416 ATAGACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:25906416 original size:9 final size:9
Alignment explanation
Indices: 25906379--25906454 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
25906369 CAAAATCTTC
25906379 AAAATAATA
1 AAAATAATA
* *
25906388 ATAATAGTA
1 AAAATAATA
*
25906397 ATAATAATA
1 AAAATAATA
25906406 AAAATAAT-
1 AAAATAATA
*
25906414 -AAATAGACA
1 AAAATA-ATA
25906423 AAAATAA-A
1 AAAATAATA
25906431 AAAAT-ATCA
1 AAAATAAT-A
25906440 AAGAATAAATA
1 AA-AAT-AATA
25906451 AAAA
1 AAAA
25906455 ATAAAATGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
7 6 0.11
8 7 0.13
9 26 0.48
10 10 0.19
11 3 0.06
12 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:25906954 original size:28 final size:27
Alignment explanation
Indices: 25906895--25907014 Score: 82
Period size: 28 Copynumber: 4.1 Consensus size: 27
25906885 AGTAACTTAG
*
25906895 AATAAAAAATGTAAAGTATGAAAAAATAAT
1 AATAAAAAA--TAAAATA-GAAAAAATAAT
* * *
25906925 AATTAGAAATAAAATAGAAAAATATGAT
1 AATAAAAAATAAAATAGAAAAA-ATAAT
*
25906953 AATAAAAAATAAAATA-AAATGAA-AAT
1 AATAAAAAATAAAATAGAAA-AAATAAT
25906979 AATAAAATAATAATAATAAATGAAAAAATAGAT
1 AATAAAA-AATAA-AAT--A-GAAAAAATA-AT
25907012 AAT
1 AAT
25907015 TGCATTAGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 9 0.13
27 15 0.21
28 28 0.39
30 8 0.11
31 2 0.03
32 4 0.06
33 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.23
Consensus pattern (27 bp):
AATAAAAAATAAAATAGAAAAAATAAT
Found at i:25906961 original size:23 final size:24
Alignment explanation
Indices: 25906932--25907008 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 24
25906922 AATAATTAGA
* *
25906932 AATAAAATAGAAA-AATATGATAAT
1 AATAAAATA-AAATAAAATGAAAAT
25906956 AA-AAAATAAAATAAAATGAAAAT
1 AATAAAATAAAATAAAATGAAAAT
25906979 AATAAAATAATAATAATAAATGAAAA-
1 AATAAAATAA-AAT-A-AAATGAAAAT
25907005 AATA
1 AATA
25907009 GATAATTGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.07
23 17 0.37
24 9 0.20
25 3 0.07
26 5 0.11
27 9 0.20
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (24 bp):
AATAAAATAAAATAAAATGAAAAT
Found at i:25906984 original size:14 final size:14
Alignment explanation
Indices: 25906965--25907008 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
25906955 TAAAAAATAA
25906965 AATAAAATGAAAAT
1 AATAAAATGAAAAT
25906979 AATAAAAT-AATAAT
1 AATAAAATGAA-AAT
25906993 AAT-AAATGAAAA-
1 AATAAAATGAAAAT
25907005 AATA
1 AATA
25907009 GATAATTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 16 0.59
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AATAAAATGAAAAT
Found at i:25907004 original size:19 final size:18
Alignment explanation
Indices: 25906951--25907013 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
25906941 GAAAAATATG
25906951 ATAATAAAAAATAAAATA
1 ATAATAAAAAATAAAATA
25906969 A-AATGAAAATAATAAAATA
1 ATAAT-AAAA-AATAAAATA
*
25906988 ATAATAATAAATGAAAA-A
1 ATAATAAAAAAT-AAAATA
25907006 ATAGATAA
1 ATA-ATAA
25907014 TTGCATTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 3 0.08
18 12 0.31
19 21 0.54
20 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
ATAATAAAAAATAAAATA
Found at i:25907008 original size:40 final size:38
Alignment explanation
Indices: 25906915--25906998 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 38
25906905 GTAAAGTATG
*
25906915 AAAAAATAATAATTAGAAATAAAATAGAAAAATATGATAAT
1 AAAAAATAA-AA-TA-AAATAAAATAGAAAAATATAATAAT
25906956 AAAAAATAAAATAAAATGAAAATA-ATAAAATAATAATAAT
1 AAAAAATAAAATAAAAT-AAAATAGA-AAAAT-ATAATAAT
25906996 AAA
1 AAA
25906999 TGAAAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
38 5 0.13
39 13 0.33
40 12 0.31
41 9 0.23
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (38 bp):
AAAAAATAAAATAAAATAAAATAGAAAAATATAATAAT
Found at i:25908434 original size:18 final size:18
Alignment explanation
Indices: 25908411--25908452 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25908401 TTATCTCTAG
* *
25908411 TAGTAATGGTAGTTGTAC
1 TAGTAATAGTAGTAGTAC
*
25908429 TAGTAATAGTAGTAGTAG
1 TAGTAATAGTAGTAGTAC
25908447 TAGTAA
1 TAGTAA
25908453 CTTAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (18 bp):
TAGTAATAGTAGTAGTAC
Done.