Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 56 of 120
Found at i:16476780 original size:36 final size:36
Alignment explanation
Indices: 16476703--16476803 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
16476693 TGGTAACAGG
*
16476703 CATGACCTTTGAGTCAACAGGGAG-AAACATGAACAT
1 CATGACCTTTGAGTCAACAGGGAGTAAA-ACGAACAT
* * * * *
16476739 AATGACCTTTGGGTCAACAGGGGGTAAAACGAGCGT
1 CATGACCTTTGAGTCAACAGGGAGTAAAACGAACAT
16476775 CATGACCTTT-ATGTCAACAGGGAGTAAAA
1 CATGACCTTTGA-GTCAACAGGGAGTAAAA
16476804 TGAATAACGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 51 0.94
37 3 0.06
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (36 bp):
CATGACCTTTGAGTCAACAGGGAGTAAAACGAACAT
Found at i:16477485 original size:21 final size:21
Alignment explanation
Indices: 16477456--16477507 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
16477446 AGAGTTTTTA
*
16477456 GTATCGGTAGTAGTATGACTT
1 GTATCGGTAGTAGTATCACTT
* * *
16477477 GTATTGGTAGTTGTCTCACTT
1 GTATCGGTAGTAGTATCACTT
16477498 GTATCGGTAG
1 GTATCGGTAG
16477508 AACTGTCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (21 bp):
GTATCGGTAGTAGTATCACTT
Found at i:16479815 original size:18 final size:20
Alignment explanation
Indices: 16479761--16479818 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
16479751 AAAAATTACA
16479761 AAAAAATTCAAAATAAATTT-T
1 AAAAAATTCAAAAT--ATTTAT
16479782 --AAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
16479800 AAAAAATT-AAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
16479818 A
1 A
16479819 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.12
18 8 0.24
19 16 0.47
20 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:16479827 original size:16 final size:19
Alignment explanation
Indices: 16479806--16479855 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
16479796 TTATAAAAAA
16479806 TTAAAAATT-T-ATATTTT
1 TTAAAAATTATAATATTTT
*
16479823 TAAAAAATTATAATATTTT
1 TTAAAAATTATAATATTTT
16479842 TTAAAAATTA-AATA
1 TTAAAAATTATAATA
16479856 ATATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 5 0.17
19 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAAATTATAATATTTT
Found at i:16483310 original size:17 final size:19
Alignment explanation
Indices: 16483275--16483311 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
16483265 CTACAATATC
*
16483275 TTTTTTAGAATGTTTATTT
1 TTTTTTAGAATGTTAATTT
16483294 TTTTTTA-AAT-TTAATTT
1 TTTTTTAGAATGTTAATTT
16483311 T
1 T
16483312 AAATTATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTTTAGAATGTTAATTT
Found at i:16484200 original size:20 final size:20
Alignment explanation
Indices: 16484153--16484200 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
16484143 AAAAATTATA
*
16484153 TTACTGTTTTTTTGTTGTTC
1 TTACTGTTTTTGTGTTGTTC
* ** *
16484173 CTGGTGTTTTTGTGTTGTTT
1 TTACTGTTTTTGTGTTGTTC
16484193 TTACTGTT
1 TTACTGTT
16484201 ATTTTTGCTA
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.04, C:0.08, G:0.21, T:0.67
Consensus pattern (20 bp):
TTACTGTTTTTGTGTTGTTC
Found at i:16484276 original size:23 final size:23
Alignment explanation
Indices: 16484241--16484297 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
16484231 TTTTTATTCG
16484241 TTTTTACTATTGTTTCATTGTCA
1 TTTTTACTATTGTTTCATTGTCA
* * * *
16484264 TTTTTAGTGTTGTTTCGTTGTCG
1 TTTTTACTATTGTTTCATTGTCA
*
16484287 TTTTTAATATT
1 TTTTTACTATT
16484298 ATTTGGATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (23 bp):
TTTTTACTATTGTTTCATTGTCA
Found at i:16484413 original size:12 final size:12
Alignment explanation
Indices: 16484398--16484424 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16484388 CAATTTGTTT
16484398 TTTGTTTTAATA
1 TTTGTTTTAATA
16484410 TTTGTTTTAATA
1 TTTGTTTTAATA
16484422 TTT
1 TTT
16484425 TTAAGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTGTTTTAATA
Found at i:16484522 original size:18 final size:18
Alignment explanation
Indices: 16484499--16484533 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16484489 TCTTCTTTAA
16484499 CCTTAAATCTTTCATCTT
1 CCTTAAATCTTTCATCTT
16484517 CCTTAAATCTTTCATCT
1 CCTTAAATCTTTCATCT
16484534 CGTTCTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
CCTTAAATCTTTCATCTT
Found at i:16488014 original size:16 final size:17
Alignment explanation
Indices: 16487985--16488018 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16487975 AGTTTTAAGT
*
16487985 TACTTTTCTATTAATTA
1 TACTTTTATATTAATTA
16488002 TACTTTTAT-TTAATTA
1 TACTTTTATATTAATTA
16488018 T
1 T
16488019 TCTGTCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
TACTTTTATATTAATTA
Found at i:16502210 original size:30 final size:29
Alignment explanation
Indices: 16502149--16502211 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
16502139 ATAAAATTGT
**
16502149 AATTTAATTCTTATATTTTTATTTTCAAA
1 AATTTAATTCTTATATTTTTAAATTCAAA
*
16502178 AATTTAATCTCTT-TATTTTTTAAATTCTAA
1 AATTTAAT-TCTTATA-TTTTTAAATTCAAA
16502208 AATT
1 AATT
16502212 CAGGTCTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (29 bp):
AATTTAATTCTTATATTTTTAAATTCAAA
Found at i:16517253 original size:25 final size:25
Alignment explanation
Indices: 16517220--16517274 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
16517210 TGTAAAACAT
*
16517220 TCACCGGCTCAAAGCTTGCTAAAAA
1 TCACCGGCTCAAAGCCTGCTAAAAA
* *
16517245 TCACTGGCTCGAAGCCTGCTAAAAA
1 TCACCGGCTCAAAGCCTGCTAAAAA
16517270 TCACC
1 TCACC
16517275 TCACATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (25 bp):
TCACCGGCTCAAAGCCTGCTAAAAA
Found at i:16517499 original size:2 final size:2
Alignment explanation
Indices: 16517492--16517522 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16517482 TTGCTTCTTG
16517492 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 A
16517523 AATTATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16520407 original size:42 final size:43
Alignment explanation
Indices: 16520353--16520448 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
16520343 ACATCCGAGT
* *
16520353 CTTTAA-ATCATAACCTCATGCTC-TTCCGAGTCATGAGTCTTC
1 CTTTAATA-CATAACCTCATGCTCAATCCGAGACATGAGTCTTC
* *
16520395 CTTTAATACATAATCTCATGCTCAATCTGAGACATGAGTCTTC
1 CTTTAATACATAACCTCATGCTCAATCCGAGACATGAGTCTTC
16520438 CGTTT-ATACAT
1 C-TTTAATACAT
16520449 CAAGTGATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 20 0.43
43 24 0.51
44 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (43 bp):
CTTTAATACATAACCTCATGCTCAATCCGAGACATGAGTCTTC
Found at i:16528633 original size:15 final size:15
Alignment explanation
Indices: 16528615--16528663 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
16528605 ATGTTTAGAA
16528615 TTTAATTTTTATATT
1 TTTAATTTTTATATT
* *
16528630 TTTAA-TTTTAGAAT
1 TTTAATTTTTATATT
* *
16528644 TTTAGTTTCTATATT
1 TTTAATTTTTATATT
16528659 TTTAA
1 TTTAA
16528664 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTAATTTTTATATT
Found at i:16528656 original size:29 final size:29
Alignment explanation
Indices: 16528598--16528663 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
16528588 GTACAAAAAC
*
16528598 TTTTTATATGTTTAGAATTTAATTTTTATA
1 TTTTTA-ATGTTTAGAATTTAATTTCTATA
*
16528628 TTTTTAAT-TTTAGAATTTTAGTTTCTATA
1 TTTTTAATGTTTAGAA-TTTAATTTCTATA
16528657 TTTTTAA
1 TTTTTAA
16528664 AATTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 7 0.21
29 20 0.61
30 6 0.18
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTTTAATGTTTAGAATTTAATTTCTATA
Found at i:16530374 original size:23 final size:24
Alignment explanation
Indices: 16530348--16530392 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
16530338 AATATGTTCT
* *
16530348 AAATTATATAATATA-TATAAATA
1 AAATAATATAAAATATTATAAATA
16530371 AAATAATATAAAATATTATAAA
1 AAATAATATAAAATATTATAAA
16530393 CTTAAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATATAAAATATTATAAATA
Found at i:16541930 original size:24 final size:24
Alignment explanation
Indices: 16541894--16541948 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
16541884 GTTAGGAGTA
*
16541894 AAAACTGTTAGTGTAAATGTAATAC
1 AAAA-TGTCAGTGTAAATGTAATAC
* *
16541919 AAAATGTCAGTGTAACTGTAATAT
1 AAAATGTCAGTGTAAATGTAATAC
16541943 AAAATG
1 AAAATG
16541949 AATTGAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.31
Consensus pattern (24 bp):
AAAATGTCAGTGTAAATGTAATAC
Found at i:16546394 original size:24 final size:25
Alignment explanation
Indices: 16546344--16546395 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
16546334 TTCCTACATA
* *
16546344 AAACTAAAGAAAATAAATTAAAAAT
1 AAACAAAAGAAAATAAAGTAAAAAT
* *
16546369 AAACAAAAGACAA-AAAGTAAATAT
1 AAACAAAAGAAAATAAAGTAAAAAT
16546393 AAA
1 AAA
16546396 AAATTGTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (25 bp):
AAACAAAAGAAAATAAAGTAAAAAT
Found at i:16552654 original size:15 final size:15
Alignment explanation
Indices: 16552630--16552664 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16552620 GCATAAAATT
*
16552630 TAAAAATGAAACAAG
1 TAAAAATGAAACAAA
*
16552645 TAAAACTGAAACAAA
1 TAAAAATGAAACAAA
16552660 TAAAA
1 TAAAA
16552665 GAAAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (15 bp):
TAAAAATGAAACAAA
Found at i:16561646 original size:24 final size:24
Alignment explanation
Indices: 16561613--16561666 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16561603 GTTAAGAGTA
*
16561613 AAAATTGTCAGTGTAAATGTAATAC
1 AAAA-TGTCAGTGCAAATGTAATAC
* *
16561638 AAAATGTCAGTGCAACTGTAATAT
1 AAAATGTCAGTGCAAATGTAATAC
16561662 AAAAT
1 AAAAT
16561667 AAATTGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (24 bp):
AAAATGTCAGTGCAAATGTAATAC
Found at i:16566427 original size:13 final size:13
Alignment explanation
Indices: 16566395--16566433 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
16566385 TATCATTAAC
*
16566395 TTAGATTAATTTAGT
1 TTAGATTAA--TACT
16566410 TTAGATTAATACT
1 TTAGATTAATACT
16566423 TTAGATTAATA
1 TTAGATTAATA
16566434 TCCTTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
15 9 0.39
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (13 bp):
TTAGATTAATACT
Found at i:16568011 original size:36 final size:36
Alignment explanation
Indices: 16567897--16568003 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
16567887 GCTGTGAATG
* * *
16567897 TAAATATGTGAGTATGTTATTCATGCAATGAGACAA
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAA
*
16567933 TAAATATGTGGGTATGTTATTCATGCCATGTGACAT
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAA
16567969 TAAATATGTGGGTATGTTATTCATGCCATGTGACA
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACA
16568004 GTGAATATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.36
Consensus pattern (36 bp):
TAAATATGTGGGTATGTTATTCATGCCATGTGACAA
Found at i:16568637 original size:23 final size:23
Alignment explanation
Indices: 16568422--16568627 Score: 297
Period size: 23 Copynumber: 9.0 Consensus size: 23
16568412 TAATGCATTA
*
16568422 TATG-TTAAATGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
16568444 TATGCTTAAAAGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
* * * *
16568467 CATGGTTAGATGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
* *
16568490 TATGCTTAAATGTTAATGTGGTT
1 TATGCTTAAAAGTTAATGTGATT
16568513 TATGCTTAAAAGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
* *
16568536 TATGCTTAAAAGATAACGTGATT
1 TATGCTTAAAAGTTAATGTGATT
16568559 TATGCTTAAAAGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
*
16568582 TATGTTTAAAAGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
* *
16568605 TAGGCTTAATAGTTAATGTGATT
1 TATGCTTAAAAGTTAATGTGATT
16568628 AATGTGTAAT
Statistics
Matches: 164, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
22 4 0.02
23 160 0.98
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (23 bp):
TATGCTTAAAAGTTAATGTGATT
Found at i:16573755 original size:90 final size:90
Alignment explanation
Indices: 16573516--16573756 Score: 231
Period size: 90 Copynumber: 2.7 Consensus size: 90
16573506 AAATTCCTAA
* * * * *
16573516 AAGGGTCGTGAGTGTATATTGATGAAGT-ATCAAAACAATACTCTAATTCTTGGAGGGGTAGAGT
1 AAGGGTCGTGAGTGTATATCGATGAAGTAATCAAAACAGTACTCTAATTCCTGGAGAGGTCGAGT
* *
16573580 ACGAATCATTAACTCTGATTCTCGG
66 ACAAATCATTAACTCTGATCCTCGG
* * * ** * * * *
16573605 -GGGGTTGTAAGCATATATCAATGAAGTAATCAAAATAGTACTCTAATTGCTAGA-AGGGTCGAG
1 AAGGGTCGTGAGTGTATATCGATGAAGTAATCAAAACAGTACTCTAATTCCTGGAGA-GGTCGAG
*
16573668 TACAAATCATTAGCTCCATG-TCCT-GG
65 TACAAATCATTAACT-C-TGATCCTCGG
* * * *
16573694 AAGGGTCGTGAGTGTATATCGATGAATTAATTAGAACAGTACTCTAATTCCCGGAGAGGTCGA
1 AAGGGTCGTGAGTGTATATCGATGAAGTAATCAAAACAGTACTCTAATTCCTGGAGAGGTCGA
16573757 CTATGTGTCA
Statistics
Matches: 116, Mismatches: 30, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
88 20 0.17
89 42 0.36
90 51 0.44
91 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (90 bp):
AAGGGTCGTGAGTGTATATCGATGAAGTAATCAAAACAGTACTCTAATTCCTGGAGAGGTCGAGT
ACAAATCATTAACTCTGATCCTCGG
Found at i:16575178 original size:280 final size:280
Alignment explanation
Indices: 16574677--16575236 Score: 1093
Period size: 280 Copynumber: 2.0 Consensus size: 280
16574667 TGTATGTGTG
16574677 GCTCATATAATTTGATATAAATAAAACCCGTGTTCAAATTGATAAGGAACTAAAAGTTGGTGCAT
1 GCTCATATAATTTGATATAAATAAAACCCGTGTTCAAATTGATAAGGAACTAAAAGTTGGTGCAT
16574742 TCAGTATAAGACTTATGCAGTCTGTAGCATCATTCCACAACAGTGGGATTCATATCCCAACTAAA
66 TCAGTATAAGACTTATGCAGTCTGTAGCATCATTCCACAACAGTGGGATTCATATCCCAACTAAA
*
16574807 GGGTAAATGATATCATCTCATTAGCGTTACATGATAAATAAAAAGTAAATATGGTCATGACTCAT
131 GGGTAAATGATATCATCTCATCAGCGTTACATGATAAATAAAAAGTAAATATGGTCATGACTCAT
*
16574872 TTGTCTTTGTGATAGATGATTTAATTACTATTTGATAGTAATTGACTATTCATTGAAGAAGATGT
196 TTGTCTTTGTGATAGATGATTTAATTACCATTTGATAGTAATTGACTATTCATTGAAGAAGATGT
16574937 AATGATTACCATGAGATAAA
261 AATGATTACCATGAGATAAA
16574957 GCTCATATAATTTGATATAAATAAAACCCGTGTTCAAATTGATAAGGAACTAAAAGTTGGTGCAT
1 GCTCATATAATTTGATATAAATAAAACCCGTGTTCAAATTGATAAGGAACTAAAAGTTGGTGCAT
*
16575022 TCAGTATAAGACTTATGTAGTCTGTAGCATCATTCCACAACAGTGGGATTCATATCCCAACTAAA
66 TCAGTATAAGACTTATGCAGTCTGTAGCATCATTCCACAACAGTGGGATTCATATCCCAACTAAA
16575087 GGGTAAATGATATCATCTCATCAGCGTTACATGATAAATAAAAAGTAAATATGGTCATGACTCAT
131 GGGTAAATGATATCATCTCATCAGCGTTACATGATAAATAAAAAGTAAATATGGTCATGACTCAT
16575152 TTGTCTTTGTGATAGATGATTTAATTACCATTTGATAGTAATTGACTATTCATTGAAGAAGATGT
196 TTGTCTTTGTGATAGATGATTTAATTACCATTTGATAGTAATTGACTATTCATTGAAGAAGATGT
16575217 AATGATTACCATGAGATAAA
261 AATGATTACCATGAGATAAA
16575237 ATAGGATCAT
Statistics
Matches: 277, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 277 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (280 bp):
GCTCATATAATTTGATATAAATAAAACCCGTGTTCAAATTGATAAGGAACTAAAAGTTGGTGCAT
TCAGTATAAGACTTATGCAGTCTGTAGCATCATTCCACAACAGTGGGATTCATATCCCAACTAAA
GGGTAAATGATATCATCTCATCAGCGTTACATGATAAATAAAAAGTAAATATGGTCATGACTCAT
TTGTCTTTGTGATAGATGATTTAATTACCATTTGATAGTAATTGACTATTCATTGAAGAAGATGT
AATGATTACCATGAGATAAA
Found at i:16581003 original size:21 final size:21
Alignment explanation
Indices: 16580960--16581008 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
16580950 GTTGTGATGG
* **
16580960 TTCTACCGATACAAGTGGGAC
1 TTCTACCGAAACAAGTCAGAC
*
16580981 TTCTACCGAAACAAGTCATAC
1 TTCTACCGAAACAAGTCAGAC
16581002 TTCTACC
1 TTCTACC
16581009 CTGCAACTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCAGAC
Found at i:16584202 original size:26 final size:26
Alignment explanation
Indices: 16584125--16584211 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
16584115 AGCATTGTAC
* * * *
16584125 CCAGAATTGTCGCTGCAAGAACCT-A
1 CCAGAATTGTCACTGCATGAACATGT
* *
16584150 CTCAGAATTATCACTGCATGAATATGT
1 C-CAGAATTGTCACTGCATGAACATGT
16584177 CCAGAATTGTCACTGCAT-AAGCATGT
1 CCAGAATTGTCACTGCATGAA-CATGT
*
16584203 CCAAAATTG
1 CCAGAATTG
16584212 CACCTAGAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.06
26 46 0.92
27 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (26 bp):
CCAGAATTGTCACTGCATGAACATGT
Found at i:16593024 original size:20 final size:19
Alignment explanation
Indices: 16592986--16593024 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
16592976 CTTTATTTTC
*
16592986 CATCTTTCCCGTTTCCAAT
1 CATCTTTCCCATTTCCAAT
*
16593005 CATCGTTTCCCATTTGCAAT
1 CATC-TTTCCCATTTCCAAT
16593025 AGTTGTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.33, G:0.08, T:0.41
Consensus pattern (19 bp):
CATCTTTCCCATTTCCAAT
Found at i:16599685 original size:102 final size:102
Alignment explanation
Indices: 16599565--16599774 Score: 420
Period size: 102 Copynumber: 2.1 Consensus size: 102
16599555 AAAAAACCAT
16599565 TTTGAACCGAATTTTTTCCAACTTTTACATGCATTTGAGTTTTGATATCGTATATGGCACAAGTG
1 TTTGAACCGAATTTTTTCCAACTTTTACATGCATTTGAGTTTTGATATCGTATATGGCACAAGTG
16599630 TGCAATTCTTGGTTAGTTTGGAGGGACACCTGGTGTG
66 TGCAATTCTTGGTTAGTTTGGAGGGACACCTGGTGTG
16599667 TTTGAACCGAATTTTTTCCAACTTTTACATGCATTTGAGTTTTGATATCGTATATGGCACAAGTG
1 TTTGAACCGAATTTTTTCCAACTTTTACATGCATTTGAGTTTTGATATCGTATATGGCACAAGTG
16599732 TGCAATTCTTGGTTAGTTTGGAGGGACACCTGGTGTG
66 TGCAATTCTTGGTTAGTTTGGAGGGACACCTGGTGTG
16599769 TTTGAA
1 TTTGAA
16599775 ATGTTATCCA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (102 bp):
TTTGAACCGAATTTTTTCCAACTTTTACATGCATTTGAGTTTTGATATCGTATATGGCACAAGTG
TGCAATTCTTGGTTAGTTTGGAGGGACACCTGGTGTG
Found at i:16608066 original size:19 final size:19
Alignment explanation
Indices: 16608029--16608068 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16608019 AATGTTTTAT
* * *
16608029 ATTATGTTATTTTTTATAC
1 ATTATGTAATTTATAATAC
16608048 ATTATGTAATTTATAATAC
1 ATTATGTAATTTATAATAC
16608067 AT
1 AT
16608069 AAAAGTTAAA
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:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTATGTAATTTATAATAC
Found at i:16609418 original size:3 final size:3
Alignment explanation
Indices: 16609405--16609444 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
16609395 AAAACACAAA
16609405 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16609445 GTTAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16614261 original size:38 final size:38
Alignment explanation
Indices: 16614207--16614539 Score: 321
Period size: 38 Copynumber: 8.8 Consensus size: 38
16614197 AGTTGTACAC
*
16614207 GGTGTTTATCGGGCTTAGTGCCTAGCAAGC-TCTATGCT
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTC-ATGCT
** * * *
16614245 GGTGTTTATCAAGCTTAATGCCTAGCAGGATTCGTGCT
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
* * *
16614283 AGTGTTTATCGAGCTTAGTGCCTAGCAGGCTTCATGCC
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
** * *
16614321 AATGTTTTTCGGGCTTAGTGCCTAGAAGGCTTCATG-T
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
* *
16614358 CGATGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCC
1 -GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
** * * * * *
16614397 ATTTTTTATCGGGCTTAATGCCTAGCAAGCTTCGTGCC
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
*
16614435 GGTGTTTATTGGGCTTAGTGCCTAGCAGGCTTCATG-T
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
* ** ** * *
16614472 CGGTGTTCATCGGGCTTAGTGCCTAATAGGCTTTGTACC
1 -GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
* * *
16614511 GGTATTTATCGGGCTTTGTGCCTAACAGG
1 GGTGTTTATCGGGCTTAGTGCCTAGCAGG
16614540 TTTCGTGTCA
Statistics
Matches: 243, Mismatches: 47, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
38 241 0.99
39 2 0.01
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.35
Consensus pattern (38 bp):
GGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCATGCT
Found at i:16614545 original size:114 final size:114
Alignment explanation
Indices: 16614206--16614546 Score: 382
Period size: 114 Copynumber: 3.0 Consensus size: 114
16614196 TAGTTGTACA
* * ** *
16614206 CGGTGTTTATCGGGCTTAGTGCCTAGCAAGC-TCTATG-CTGGTGTTTATCAAGCTTAATGCCTA
1 CGGTGTTTATTGGGCTTAGTGCCTAGCAGGCTTC-ATGTC-GGTGTTTATCGGGCTTAGTGCCTA
* * * * *
16614269 GCAGGATTCGTGCTAGTGTTTATCGAGCTTAGTGCCTAGCAGGCTTCATGC
64 GCAGGCTTCGTGCCAGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGC
** * *
16614320 CAATGTTT-TTCGGGCTTAGTGCCTAGAAGGCTTCATGTCGATGTTTATCGGGCTTAGTGCCTAG
1 CGGTGTTTATT-GGGCTTAGTGCCTAGCAGGCTTCATGTCGGTGTTTATCGGGCTTAGTGCCTAG
* * * * *
16614384 CAGGCTTCATGCCATTTTTTATCGGGCTTAATGCCTAGCAAGCTTCGTGC
65 CAGGCTTCGTGCCAGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGC
* **
16614434 CGGTGTTTATTGGGCTTAGTGCCTAGCAGGCTTCATGTCGGTGTTCATCGGGCTTAGTGCCTAAT
1 CGGTGTTTATTGGGCTTAGTGCCTAGCAGGCTTCATGTCGGTGTTTATCGGGCTTAGTGCCTAGC
* * * * * *
16614499 AGGCTTTGTACCGGTATTTATCGGGCTTTGTGCCTAACAGGTTTCGTG
66 AGGCTTCGTGCCAGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
16614547 TCAGTGTATA
Statistics
Matches: 187, Mismatches: 36, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
113 1 0.01
114 181 0.97
115 5 0.03
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.35
Consensus pattern (114 bp):
CGGTGTTTATTGGGCTTAGTGCCTAGCAGGCTTCATGTCGGTGTTTATCGGGCTTAGTGCCTAGC
AGGCTTCGTGCCAGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGC
Found at i:16616825 original size:8 final size:8
Alignment explanation
Indices: 16616797--16616840 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
16616787 AGCACCTAAA
16616797 AAAAAAAG
1 AAAAAAAG
16616805 AAAGAAAAG
1 AAA-AAAAG
*
16616814 AAAAAGAG
1 AAAAAAAG
* *
16616822 AAAAGAAT
1 AAAAAAAG
16616830 AAAAAAAG
1 AAAAAAAG
16616838 AAA
1 AAA
16616841 TAATTTGCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16616826 original size:18 final size:16
Alignment explanation
Indices: 16616794--16616838 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
16616784 TTTAGCACCT
16616794 AAAAAAAAA-AGAAAG
1 AAAAAAAAAGAGAAAG
16616809 AAAAGAAAAAGAGAAAAG
1 AAAA-AAAAAGAG-AAAG
16616827 AATAAAAAAAGA
1 AA-AAAAAAAGA
16616839 AATAATTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 2 0.08
18 13 0.50
19 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAGAGAAAG
Found at i:16621038 original size:12 final size:13
Alignment explanation
Indices: 16621004--16621036 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16620994 CTTTTATTTA
*
16621004 ATTTTATTTATTT
1 ATTTTATTTATGT
16621017 A-TTTATTTATGT
1 ATTTTATTTATGT
16621029 ATTTTATT
1 ATTTTATT
16621037 ATTTTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (13 bp):
ATTTTATTTATGT
Found at i:16621038 original size:16 final size:17
Alignment explanation
Indices: 16620995--16621049 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
16620985 ACATGCTTGC
*
16620995 TTTTATTTAATTTTATT-
1 TTTTATTT-ATTTTGTTA
16621012 TATTTATTTATTTATG-TA
1 T-TTTATTTATTT-TGTTA
16621030 TTTTA-TTATTTTGTTA
1 TTTTATTTATTTTGTTA
16621046 TTTT
1 TTTT
16621050 TATGCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 2 0.06
16 12 0.36
17 10 0.30
18 9 0.27
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTATTTATTTTGTTA
Found at i:16621295 original size:18 final size:18
Alignment explanation
Indices: 16621272--16621306 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16621262 TACTATGATT
* *
16621272 ATATTGTTATTTTATTTA
1 ATATTGTAATTATATTTA
16621290 ATATTGTAATTATATTT
1 ATATTGTAATTATATTT
16621307 TTATTGTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATATTGTAATTATATTTA
Found at i:16624926 original size:16 final size:17
Alignment explanation
Indices: 16624901--16624938 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
16624891 ATTAAATTTC
*
16624901 ATAAAAAAATCATAA-A
1 ATAAAAAAATAATAATA
*
16624917 ATAAATAAATAATAATA
1 ATAAAAAAATAATAATA
16624934 ATAAA
1 ATAAA
16624939 GATCCTTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAAAAATAATAATA
Found at i:16652181 original size:17 final size:16
Alignment explanation
Indices: 16652158--16652210 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
16652148 TCAAACTTGC
16652158 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
16652174 AGAAAAG-AAAAAGAAA
1 A-AAAAGAAAAAAGAAA
*
16652190 AAGAGAGAAAAAAGAAA
1 AA-AAAGAAAAAAGAAA
16652207 AAAA
1 AAAA
16652211 GGAGGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 15 0.47
17 16 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:16652188 original size:23 final size:23
Alignment explanation
Indices: 16652158--16652208 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
16652148 TCAAACTTGC
16652158 AAAAAGAAAAA-AGAAAAGAAAAG
1 AAAAAGAAAAAGAGAAAA-AAAAG
*
16652181 AAAAAGAAAAAGAGAGAAAAAAG
1 AAAAAGAAAAAGAGAAAAAAAAG
16652204 AAAAA
1 AAAAA
16652209 AAGGAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAGAGAAAAAAAAG
Found at i:16653405 original size:49 final size:49
Alignment explanation
Indices: 16653264--16653971 Score: 429
Period size: 49 Copynumber: 14.4 Consensus size: 49
16653254 TAGAGTTGAT
* * ** * * *
16653264 GAGGGATAGGTTGAAGCCGTAATGGCAGACCTAACACCCTAAAATCAAA
1 GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * ** * * * *
16653313 GA-TGAAAAGATTGAAGTTGCAACGATGGATCTTACACCTTAAAATTGAA
1 GAGGGATAAG-TTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * * * * *
16653362 GAGGGATAAGTTAAAGTCGTAATAACAGACCTAACACCCTAAAATCGAA
1 GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* ** ** *
16653411 GAGGGATAAATTGAAGCCATAAAAACAGATCTAACACCTTAAAATCGATA
1 GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGA-A
* * * *
16653461 -AGGGA-AAGATTGAAGCAGCAATGACAGATCTCACACCTTAAAATTGAA
1 GAGGGATAAG-TTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * * * * *
16653509 TAGGGATAGGTTGAAGTCACAATGATGGACCTAACACCCTAAAATCGAA
1 GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * * *
16653558 GAGGGATAAATTAAAGCCGTAAT-AGTGGATCTAACACCCTAAAATCGAA
1 GAGGGATAAGTTGAAGCCGCAATGA-TAGATCTAACACCTTAAAATCGAA
* * *
16653607 GAGGGA-AAGATTGAAGCCGCAAT-AGTGGATCTTACACCTTAAAATTGAA
1 GAGGGATAAG-TTGAAGCCGCAATGA-TAGATCTAACACCTTAAAATCGAA
* * *
16653656 GAGGGAT-CGATTGAAGCCGCAACGATAGATCTAACACCCTAAAATCG-A
1 GAGGGATAAG-TTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * *** * *
16653704 GAAGGGA-AAGATTGAAGTCACAACGGCGGATCTTACACCTTAAAATTGAA
1 G-AGGGATAAG-TTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * *
16653754 GAGGGGTAGGTTGAAGCCGCAATGA-CGAACCTAACACC-TAAAATCGAA
1 GAGGGATAAGTTGAAGCCGCAATGATAG-ATCTAACACCTTAAAATCGAA
* * ** * * * *
16653802 GAGGGA-AAGATTGAAGTCGTAACAATAAATCTTACACCTTAAAACCAAA
1 GAGGGATAAG-TTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* * * * * *
16653851 GAGGGATAGGTTAAAGTCGTAACGATAGACCTAACACCTTAAAATCGAA
1 GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
* ** * *
16653900 GAGGGATATA-TTAAAGCCATAA-CAGTGGATCTAACACCTTAAAA-CTGAA
1 GAGGGATA-AGTTGAAGCCGCAATGA-TAGATCTAACACCTTAAAATC-GAA
* *
16653949 GAGGGAACAAATTGAAGCCGCAA
1 GAGGG-ATAAGTTGAAGCCGCAA
16653972 CGGTGAATCT
Statistics
Matches: 513, Mismatches: 122, Indels: 47
0.75 0.18 0.07
Matches are distributed among these distances:
47 2 0.00
48 48 0.09
49 437 0.85
50 26 0.05
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (49 bp):
GAGGGATAAGTTGAAGCCGCAATGATAGATCTAACACCTTAAAATCGAA
Found at i:16653442 original size:98 final size:98
Alignment explanation
Indices: 16653259--16653954 Score: 571
Period size: 98 Copynumber: 7.1 Consensus size: 98
16653249 AATCCTAGAG
* * * * * * * *
16653259 TTGATGAGGGATAGGTTGAAGCCGTAATGGCAGACCTAACACCCTAAAATCAAAGATGAAAAGAT
1 TTGAAGAGGGATAAGTTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAGAGGGAAAGAT
*** *
16653324 TGAAGTTGCAACGATGGATCTTACACCTTAAAA
66 TGAAGCCACAACAATGGATCTTACACCTTAAAA
* * *
16653357 TTGAAGAGGGATAAGTTAAAGTCGTAATAACAGACCTAACACCCTAAAATCGAAGAGGGATAA-A
1 TTGAAGAGGGATAAGTTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAGAGGGA-AAGA
* * ** *
16653421 TTGAAGCCATAAAAACAGATCTAACACCTTAAAA
65 TTGAAGCCACAACAATGGATCTTACACCTTAAAA
* * * * * * * * *
16653455 TCGATA-AGGGA-AAGATTGAAGCAGCAATGACAGATCTCACACCTTAAAATTGAATAGGGATAG
1 TTGA-AGAGGGATAAG-TTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAGAGGGAAAG
* * ** * * *
16653518 GTTGAAGTCACAATGATGGACCTAACACCCTAAAA
64 ATTGAAGCCACAACAATGGATCTTACACCTTAAAA
* * * ** *
16653553 TCGAAGAGGGATAAATTAAAGCCGTAAT-AGTGGATCTAACACCCTAAAATCGAAGAGGGAAAGA
1 TTGAAGAGGGATAAGTTAAAGCCGCAATGA-CAGACCTAACACCCTAAAATCGAAGAGGGAAAGA
* * *
16653617 TTGAAGCCGCAATAGTGGATCTTACACCTTAAAA
65 TTGAAGCCACAACAATGGATCTTACACCTTAAAA
* * * * *
16653651 TTGAAGAGGGAT-CGATTGAAGCCGCAACGATAGATCTAACACCCTAAAATCG-AGAAGGGAAAG
1 TTGAAGAGGGATAAG-TTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAG-AGGGAAAG
* ***
16653714 ATTGAAGTCACAACGGCGGATCTTACACCTTAAAA
64 ATTGAAGCCACAACAATGGATCTTACACCTTAAAA
* * *
16653749 TTGAAGAGGGGTAGGTTGAAGCCGCAATGAC-GAACCTAACA-CCTAAAATCGAAGAGGGAAAGA
1 TTGAAGAGGGATAAGTTAAAGCCGCAATGACAG-ACCTAACACCCTAAAATCGAAGAGGGAAAGA
* ** **
16653812 TTGAAGTCGTAACAATAAATCTTACACCTTAAAA
65 TTGAAGCCACAACAATGGATCTTACACCTTAAAA
*** * * * * * * * *
16653846 CCAAAGAGGGATAGGTTAAAGTCGTAACGATAGACCTAACACCTTAAAATCGAAGAGGGATATAT
1 TTGAAGAGGGATAAGTTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAGAGGGAAAGAT
* * * *
16653911 TAAAGCCATAACAGTGGATCTAACACCTTAAAA
66 TGAAGCCACAACAATGGATCTTACACCTTAAAA
*
16653944 CTGAAGAGGGA
1 TTGAAGAGGGA
16653955 ACAAATTGAA
Statistics
Matches: 480, Mismatches: 103, Indels: 30
0.78 0.17 0.05
Matches are distributed among these distances:
97 85 0.18
98 388 0.81
99 7 0.01
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (98 bp):
TTGAAGAGGGATAAGTTAAAGCCGCAATGACAGACCTAACACCCTAAAATCGAAGAGGGAAAGAT
TGAAGCCACAACAATGGATCTTACACCTTAAAA
Found at i:16653735 original size:147 final size:147
Alignment explanation
Indices: 16653289--16653973 Score: 574
Period size: 147 Copynumber: 4.7 Consensus size: 147
16653279 GCCGTAATGG
* * * * * ** * *
16653289 CAGACCTAACACCCTAAAATCAAAGATGAAAAGATTGAAGTTGCAACGATGGATCTTACACCTTA
1 CAGATCTAACACCTTAAAATCGAAGAGGGAAAGATTGAAGCCGCAATGATGGATCTAACACCTTA
* * ** *
16653354 AAATTGAAGAGGGATA-AGTTAAAGTCGTAATAACAGACCTAACACCCTAAAATCGAAGAGGGAT
66 AAATTGAAGAGGGATAGA-TTGAAGTCGCAACGATAGACCTAACACCCTAAAATCGAAGAGGGAT
* *
16653418 AAATTGAAGCCATAAAAA
130 AAATTAAAGCCATAACAA
* ** *
16653436 CAGATCTAACACCTTAAAATCGATA-AGGGAAAGATTGAAGCAGCAATGACAGATCTCACACCTT
1 CAGATCTAACACCTTAAAATCGA-AGAGGGAAAGATTGAAGCCGCAATGATGGATCTAACACCTT
* * * * *
16653500 AAAATTGAATAGGGATAGGTTGAAGTCACAATGATGGACCTAACACCCTAAAATCGAAGAGGGAT
65 AAAATTGAAGAGGGATAGATTGAAGTCGCAACGATAGACCTAACACCCTAAAATCGAAGAGGGAT
* * *
16653565 AAATTAAAGCCGTAATAG
130 AAATTAAAGCCATAACAA
** * *
16653583 TGGATCTAACACCCTAAAATCGAAGAGGGAAAGATTGAAGCCGCAAT-AGTGGATCTTACACCTT
1 CAGATCTAACACCTTAAAATCGAAGAGGGAAAGATTGAAGCCGCAATGA-TGGATCTAACACCTT
* * *
16653647 AAAATTGAAGAGGGATCGATTGAAGCCGCAACGATAGATCTAACACCCTAAAATCG-AGAAGGGA
65 AAAATTGAAGAGGGATAGATTGAAGTCGCAACGATAGACCTAACACCCTAAAATCGAAG-AGGGA
* * * **
16653711 -AAGATTGAAGTCACAACGG
129 TAA-ATTAAAGCCATAACAA
* * * ** * * * *
16653730 CGGATCTTACACCTTAAAATTGAAGAGGGGTAGGTTGAAGCCGCAATGACGAACCTAACACC-TA
1 CAGATCTAACACCTTAAAATCGAAGAGGGAAAGATTGAAGCCGCAATGATGGATCTAACACCTTA
* * * * * * * * * *
16653794 AAATCGAAGAGGGAAAGATTGAAGTCGTAACAATAAATCTTACACCTTAAAACCAAAGAGGGATA
66 AAATTGAAGAGGGATAGATTGAAGTCGCAACGATAGACCTAACACCCTAAAATCGAAGAGGGATA
** * * *
16653859 GGTTAAAGTCGTAACGA
131 AATTAAAGCCATAACAA
* * * * * ** *
16653876 TAGACCTAACACCTTAAAATCGAAGAGGGATATATTAAAGCCATAA-CAGTGGATCTAACACCTT
1 CAGATCTAACACCTTAAAATCGAAGAGGGAAAGATTGAAGCCGCAATGA-TGGATCTAACACCTT
* * * *
16653940 AAAACTGAAGAGGGAACAAATTGAAGCCGCAACG
65 AAAATTGAAGAGGG-ATAGATTGAAGTCGCAACG
16653974 GTGAATCTTA
Statistics
Matches: 432, Mismatches: 94, Indels: 23
0.79 0.17 0.04
Matches are distributed among these distances:
145 1 0.00
146 113 0.26
147 302 0.70
148 16 0.04
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (147 bp):
CAGATCTAACACCTTAAAATCGAAGAGGGAAAGATTGAAGCCGCAATGATGGATCTAACACCTTA
AAATTGAAGAGGGATAGATTGAAGTCGCAACGATAGACCTAACACCCTAAAATCGAAGAGGGATA
AATTAAAGCCATAACAA
Found at i:16654374 original size:81 final size:81
Alignment explanation
Indices: 16654222--16654809 Score: 714
Period size: 81 Copynumber: 7.2 Consensus size: 81
16654212 TTACATCATC
* * * * *
16654222 CCATCCAATCTCTTACCCCGACCATGGGACAAATTAAAGAACATCCAATCTTTTA-CCTAGCCAG
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAG-CCATCCAATCTTTTACCCTAACCAG
*
16654286 AGTGCAGATTGAAGACA
65 AGGGCAGATTGAAGACA
* ** * *
16654303 CCATCCAATCTCTTACCCCGACCATTGGGCAGATTGAAGATATCCAATCTTTTACCTTAACTAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
*
16654368 GGGCAGATTAAAGACA
66 GGGCAGATTGAAGACA
*
16654384 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTATCCTAACCAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
16654449 GGGCAGATTGAAGACA
66 GGGCAGATTGAAGACA
* *
16654465 CCATCCAATTTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATATTTTACCCTAACCAG-
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
* *
16654529 GAGGCAAATTAAAGACA
66 G-GGCAGATTGAAGACA
* * * *
16654546 CCATCCAATCTCTTACCCTGACCATAGGGCAGATAGAAGCCATCCAATCTTTTACCCTAACTAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
*
16654611 GGGTAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * * * *
16654627 CCATCCAATCTCTTACCACAACCATAGGGCAGATTGAAGCCATCCAATCTTTCACCCTAACCAAA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
* *
16654692 AGGCAAATTGAAGACA
66 GGGCAGATTGAAGACA
** * * * * ** * *
16654708 TAATCGAATCTCTTACCCTGACCATGGGGAAAATTGAAATCATCCAGTCTTTTACCCCTTATCCA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTA-CCC-TAACCA
* *
16654773 AAGGGGCATATTGAAG-CAA
64 GA-GGGCAGATTGAAGAC-A
* *
16654792 CCATCAAATCTTTTACCC
1 CCATCCAATCTCTTACCC
16654810 ATAATCAAGA
Statistics
Matches: 439, Mismatches: 61, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
80 15 0.03
81 386 0.88
82 4 0.01
83 8 0.02
84 26 0.06
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
GGGCAGATTGAAGACA
Found at i:16654805 original size:45 final size:44
Alignment explanation
Indices: 16654755--16654879 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 44
16654745 AATCATCCAG
* *
16654755 TCTTTTACCCCTTATCCAAAGGGGCATATTGAAGCAACCATCAAA
1 TCTTTTACCCCTAAT-CAAAGGGGCAGATTGAAGCAACCATCAAA
* * * *
16654800 TCTTTTACCCATAATCAAGAGGGGCAGATTGAAGCCACCATTAAG
1 TCTTTTACCCCTAATCAA-AGGGGCAGATTGAAGCAACCATCAAA
*
16654845 TCCTTTACCCCTAAT-ATAGAGGGGCAGATTGAAGC
1 TCTTTTACCCCTAATCA-A-AGGGGCAGATTGAAGC
16654880 CTGATCGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 4 0.06
45 66 0.94
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (44 bp):
TCTTTTACCCCTAATCAAAGGGGCAGATTGAAGCAACCATCAAA
Found at i:16666836 original size:45 final size:46
Alignment explanation
Indices: 16666785--16666904 Score: 145
Period size: 45 Copynumber: 2.6 Consensus size: 46
16666775 AAGCCACCAT
* *
16666785 CCCTAATCCAGAAGGGCAGATTGAAG-CAACC-ATTCAATCATTTAC
1 CCCTAATCCAGAGGGGCAGATTGAAGTC-ACCAATCCAATCATTTAC
* * *
16666830 CCCTAATCCAGAGGGGCAGATTAAAGTCACCAAATCCAATCTTTTAT
1 CCCTAATCCAGAGGGGCAGATTGAAGTCACC-AATCCAATCATTTAC
*
16666877 CCCTAAATCCATAGGGGCAGATTGAAGT
1 CCCT-AATCCAGAGGGGCAGATTGAAGT
16666905 TACAACACCA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 27 0.42
46 1 0.02
47 15 0.23
48 21 0.33
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (46 bp):
CCCTAATCCAGAGGGGCAGATTGAAGTCACCAATCCAATCATTTAC
Found at i:16667340 original size:24 final size:24
Alignment explanation
Indices: 16667309--16667365 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
16667299 ACTGAGGGAT
16667309 TTTTTTATTT-TTTCAGAGACGAAA
1 TTTTTTATTTGTTT-AGAGACGAAA
*
16667333 TTTTTTATTTGTTTAGAGA-GGAA
1 TTTTTTATTTGTTTAGAGACGAAA
16667356 TTTTTT-TTTG
1 TTTTTTATTTG
16667366 GAATAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.13
23 9 0.29
24 15 0.48
25 3 0.10
ACGTcount: A:0.23, C:0.04, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTTTTATTTGTTTAGAGACGAAA
Found at i:16667718 original size:20 final size:22
Alignment explanation
Indices: 16667679--16667719 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
16667669 TACTTGTTTA
16667679 TATATTTATTTATCATTAAATTT
1 TATATTTATTTA-CATTAAATTT
16667702 TATATTT-TTTA-ATTAAAT
1 TATATTTATTTACATTAAAT
16667720 GTTGTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATTTATTTACATTAAATTT
Found at i:16667858 original size:16 final size:16
Alignment explanation
Indices: 16667832--16667872 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16667822 TGCTTTTATT
*
16667832 TTATTTATTTATTTATG
1 TTATTTTTTTATTT-TG
16667849 -TATTTTTTTATTTTG
1 TTATTTTTTTATTTTG
16667864 TTATTTTTT
1 TTATTTTTT
16667873 ATACTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (16 bp):
TTATTTTTTTATTTTG
Found at i:16668186 original size:36 final size:40
Alignment explanation
Indices: 16668137--16668209 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 40
16668127 TTTATTGTGT
16668137 TATTAATTGTATTTGATT-GTTTT-CATT-TAATTATTTA
1 TATTAATTGTATTTGATTAGTTTTCCATTATAATTATTTA
* *
16668174 TATTAA-TGTATTTTATTATTTTTCCATTATAATTAT
1 TATTAATTGTATTTGATTAGTTTTCCATTATAATTAT
16668210 AAATTATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 10 0.32
37 10 0.32
38 4 0.13
39 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (40 bp):
TATTAATTGTATTTGATTAGTTTTCCATTATAATTATTTA
Found at i:16673310 original size:21 final size:21
Alignment explanation
Indices: 16673266--16673310 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16673256 TAAAAGGATG
* *
16673266 ACTTGTTTCGGTAGAAGTCAC
1 ACTTGTATCGGTAGAAGCCAC
16673287 ACTTGTATCGGTAGAA-CCATC
1 ACTTGTATCGGTAGAAGCCA-C
16673308 ACT
1 ACT
16673311 ACTATCAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGCCAC
Found at i:16678083 original size:14 final size:13
Alignment explanation
Indices: 16678060--16678089 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
16678050 TTGGTTGAAC
16678060 TTTTATTTAATAA
1 TTTTATTTAATAA
16678073 TTTTAATTTAATAA
1 TTTT-ATTTAATAA
16678087 TTT
1 TTT
16678090 AATCCAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTATTTAATAA
Found at i:16682786 original size:20 final size:20
Alignment explanation
Indices: 16682761--16682801 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
16682751 ACTTATTTGG
16682761 GTTAGAAATTAAATTATAAA
1 GTTAGAAATTAAATTATAAA
16682781 GTTAGAAATTAAATTATAAA
1 GTTAGAAATTAAATTATAAA
16682801 G
1 G
16682802 CCAGAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (20 bp):
GTTAGAAATTAAATTATAAA
Found at i:16682807 original size:20 final size:20
Alignment explanation
Indices: 16682764--16682812 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
16682754 TATTTGGGTT
**
16682764 AGAAATTAAATTATAAAGTT
1 AGAAATTAAATTATAAAGCC
16682784 AGAAATTAAATTATAAAGCC
1 AGAAATTAAATTATAAAGCC
*
16682804 AGAAGTTAA
1 AGAAATTAA
16682813 GTGGCACGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (20 bp):
AGAAATTAAATTATAAAGCC
Found at i:16701172 original size:18 final size:18
Alignment explanation
Indices: 16701149--16701199 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
16701139 TGATTCAAGT
*
16701149 GAAGATCCTGAAGAAGAG
1 GAAGATCCTGAAGAAGAA
*
16701167 GAAGATCTTGAAGAAGAA
1 GAAGATCCTGAAGAAGAA
*
16701185 GAAGATCCTAAAGAA
1 GAAGATCCTGAAGAA
16701200 ACAAAGCCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.27, T:0.14
Consensus pattern (18 bp):
GAAGATCCTGAAGAAGAA
Found at i:16705211 original size:35 final size:35
Alignment explanation
Indices: 16705161--16705306 Score: 132
Period size: 35 Copynumber: 4.1 Consensus size: 35
16705151 CTTCTTAATA
*
16705161 TTAAATGAAAAAAGTA-CTGGTGTTGTGGCGGGACG
1 TTAAATGAAAGAAGTATC-GGTGTTGTGGCGGGACG
* * *
16705196 TTAAATGAATGAAGTATCGGTGTTTTGGCGGGATG
1 TTAAATGAAAGAAGTATCGGTGTTGTGGCGGGACG
* * * * *
16705231 TTAATTGAAAGAAGTATCAGTGTTGTGACTGGATG
1 TTAAATGAAAGAAGTATCGGTGTTGTGGCGGGACG
* * ** *
16705266 TTAATTGAAAGAGAAGTTTCAATGTTGTGGCGGGATG
1 TTAAATG-AA-AGAAGTATCGGTGTTGTGGCGGGACG
16705303 TTAA
1 TTAA
16705307 TTAAAAGAGG
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 65 0.69
36 3 0.03
37 26 0.28
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (35 bp):
TTAAATGAAAGAAGTATCGGTGTTGTGGCGGGACG
Found at i:16705894 original size:28 final size:28
Alignment explanation
Indices: 16705860--16705916 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
16705850 CAGGTATGAA
* *
16705860 TCCGCAAACCTGAGTCCACA-GCTATGTG
1 TCCGCAAACATGAATCCACAGGC-ATGTG
16705888 TCCGCAAACATGAATCCACAGGCATGTG
1 TCCGCAAACATGAATCCACAGGCATGTG
16705916 T
1 T
16705917 TTGGTGTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (28 bp):
TCCGCAAACATGAATCCACAGGCATGTG
Found at i:16711028 original size:16 final size:17
Alignment explanation
Indices: 16711007--16711049 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
16710997 AAATAGCATG
*
16711007 AAATAAAGATATAAA-A
1 AAATAAAGAGATAAATA
16711023 AAATAAATGAGATAAATA
1 AAATAAA-GAGATAAATA
16711041 AAATGAAAG
1 AAAT-AAAG
16711050 TAAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 6 0.26
19 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AAATAAAGAGATAAATA
Found at i:16711032 original size:25 final size:23
Alignment explanation
Indices: 16710968--16711038 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
16710958 ATCCGCAATC
* *
16710968 ATAAAAAAAGAAAATAAAATAAAA
1 ATAAAAAAA-TAAATGAAATAAAA
*
16710992 AT-AAAAAATAGCATGAAATAAAGA
1 ATAAAAAAATA-AATGAAATAAA-A
*
16711016 TATAAAAAAATAAATGAGATAAA
1 -ATAAAAAAATAAATGAAATAAA
16711039 TAAAATGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 15 0.39
24 3 0.08
25 11 0.29
26 8 0.21
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (23 bp):
ATAAAAAAATAAATGAAATAAAA
Found at i:16713247 original size:93 final size:93
Alignment explanation
Indices: 16713078--16713297 Score: 221
Period size: 93 Copynumber: 2.4 Consensus size: 93
16713068 AACTTCAATT
* * * * *
16713078 CATTCCACTATAACCTTAGGGACATTGAGATTTGTTACTCATTTTGATCCGATCTACTGCAACTT
1 CATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTCATTTTGATCCCATCTACTACAACCT
* * **
16713143 CAGGAATATAGGATCTGGTGCATCACTC
66 CAAGAAGATAGGATCTGAAGCATCACTC
* * *
16713171 CATTCCACTATAACCTCAAGGACATTGAGATCTGTTAC-CTATTTTGA-CCCA-CTTCATTATAA
1 CATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTC-ATTTTGATCCCATC-T-ACTACAA
* * **
16713233 CCTCAAGAAGATAGGTTTTGAAGTTTCACTC
63 CCTCAAGAAGATAGGATCTGAAGCATCACTC
* * *
16713264 CACTCCACTGTAACCTCAGGGACGTTGAGATCTG
1 CATTCCACTATAACCTCAGGGACATTGAGATCTG
16713298 CTTCATCGTT
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
91 1 0.01
92 5 0.05
93 98 0.94
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (93 bp):
CATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTCATTTTGATCCCATCTACTACAACCT
CAAGAAGATAGGATCTGAAGCATCACTC
Found at i:16713541 original size:42 final size:42
Alignment explanation
Indices: 16713461--16713578 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
16713451 TTTAGGGACG
* *
16713461 TAAGATTCGCCTTTGT-AGCTTCAATCTAGC-CCTTTACAG-CTT
1 TAAGATTCGCCTTTGTGA-CTTCAATCT-GCTTCTCTACAGTC-T
* *
16713503 TGAGATTCGCCTATGTGACTTCAATCTGCTTCTCTACAGTCT
1 TAAGATTCGCCTTTGTGACTTCAATCTGCTTCTCTACAGTCT
* *
16713545 TAAGATTCGCCTTTGTGGCATCAATCTGCTTCTC
1 TAAGATTCGCCTTTGTGACTTCAATCTGCTTCTC
16713579 CTCATCTTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (42 bp):
TAAGATTCGCCTTTGTGACTTCAATCTGCTTCTCTACAGTCT
Found at i:16713697 original size:49 final size:49
Alignment explanation
Indices: 16713588--16714131 Score: 485
Period size: 49 Copynumber: 11.2 Consensus size: 49
16713578 CCTCATCTTC
* * * * * **
16713588 AGGGTATAAGATTCGTTGTTGCGTCCTCAATCTTT-CCTTTACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* * * * * *
16713636 AGAGTATTAGGTTCGTTGTTACGACTTCAACCTTTCCTTCCACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* * * *
16713685 AGAGTATAAGGTTCGTTGTTGCGGCTTCAGCCTTTCCCTCCATATCT-T
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* ** * *
16713733 -GGGTATAAGATTCACCGTTGCGGCTTCAATCTTTTCCAT-CACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAA-CCTTTCCCTCCACATCTCT
* *** * * *
16713781 AAGGTATAAGGTTTACCGTTGCAGCTTTAAACCTTTCCCTCCATATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGC-TTCAACCTTTCCCTCCACATCTCT
* * *
16713831 AGGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCAT-CACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCC-TCCACATCTCT
* * *
16713880 A---AATAAGGTTTGTCGTTACGGCTTCAACCTTTCCCTCCACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* * * *
16713926 AGGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCAT-CACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCC-TCCACATCTCT
* * * **
16713975 AAGGTATAGGGTTCGTCGTTGCGGCTTCAACCTTTTCCTTAACATCTCT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* ** * ** *
16714024 AGGGTATCAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCGTATCTTT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
* * * * *
16714073 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTCAACATCTTT
1 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
16714122 AGGGTATAAG
1 AGGGTATAAG
16714132 ATTCAACTTT
Statistics
Matches: 397, Mismatches: 86, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
45 1 0.00
46 38 0.10
47 29 0.07
48 38 0.10
49 259 0.65
50 32 0.08
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (49 bp):
AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTCCACATCTCT
Found at i:16714044 original size:243 final size:241
Alignment explanation
Indices: 16713588--16714119 Score: 690
Period size: 243 Copynumber: 2.2 Consensus size: 241
16713578 CCTCATCTTC
* * * * * *
16713588 AGGGTATAAGATTCGTTGTTGCGTCCTCAATCTTTCCTTTACATCTCTAGAGTATTAGGTTCGTT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTCACATCTCTAGAG-ATAAGGTTCGTC
* * *** *
16713653 GTTACGACTTCAACCTTTCCTTCCACATCTCTAGAGTATAAGGTTCGTTGTTGCGGCTTCAGCCT
65 GTTACGACTTCAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGCCATTGCGGCTTCAACCT
** * *
16713718 TTCCCTCCATATCTTGGGTATAAGATTCACCGTTGCGGCTTCAATCTTTTCCATCACATCTCTAA
130 TTCCCTCCATATCTAAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTTCCATAACATCTCTAA
*
16713783 GGTATAAGGTTTACCGTTGCAGCTTTAAACCTTTCCCTCCATATCTCT
195 GGTATAAGGTTCACCGTTGCAGC-TTAAACCTTTCCCTCCATATCTCT
* * *
16713831 AGGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCATCACATCTCTA-A-ATAAGGTTTGTC
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCC-TCACATCTCTAGAGATAAGGTTCGTC
* * *
16713894 GTTACGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGATTCGCCATTGCGGCTTCAATCT
65 GTTACGACTTCAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGCCATTGCGGCTTCAACCT
* * * ** *
16713959 TTCCCATCACATCTCTAAGGTATAGGGTTCGTCGTTGCGGCTTCAACCTTTTCCTTAACATCTCT
130 TTCCC-TC-CATATCTAAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTTCCATAACATCTCT
* * * * *
16714024 AGGGTATCAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCGTATCTTT
193 AAGGTATAAGGTTCACCGTTGCAGCTTAAACCTTTCCCTCCATATCTCT
16714073 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTCAACATCT
1 AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTC-ACATCT
16714120 TTAGGGTATA
Statistics
Matches: 249, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
241 72 0.29
242 65 0.26
243 102 0.41
244 10 0.04
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (241 bp):
AGGGTATAAGATTCGTCGTTGCGGCCTCAATCTTTCCCTCACATCTCTAGAGATAAGGTTCGTCG
TTACGACTTCAACCTTTCCCTCCACATCTCTAGAGTATAAGATTCGCCATTGCGGCTTCAACCTT
TCCCTCCATATCTAAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTTCCATAACATCTCTAAG
GTATAAGGTTCACCGTTGCAGCTTAAACCTTTCCCTCCATATCTCT
Found at i:16715008 original size:9 final size:8
Alignment explanation
Indices: 16714986--16715019 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
16714976 CAACCTCTCC
16714986 TTTTTCTT
1 TTTTTCTT
16714994 TTTTTCTT
1 TTTTTCTT
16715002 TTCTTTC-T
1 TT-TTTCTT
16715010 TTTTTCTT
1 TTTTTCTT
16715018 TT
1 TT
16715020 ATTGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 4 0.17
8 16 0.67
9 4 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:16717255 original size:49 final size:48
Alignment explanation
Indices: 16717122--16717592 Score: 335
Period size: 49 Copynumber: 9.6 Consensus size: 48
16717112 TCTTTCCCAT
* *
16717122 CACATCTCTAAGGAATAAGGTTCG-CTGTTGCGGCTTTAACCTTTCCCTC
1 CACATCTCTAAGGTATAAGGTTCGAC-GTTGCGGCTTCAACCTTT-CCTC
* * * * * * * * *
16717171 TATA-CTGTAGGGTACAAGATTC-ATTGTTGAGGCTTCAATCTTTCGCAT-
1 CACATCTCTAAGGTATAAGGTTCGA-CGTTGCGGCTTCAACCTTTC-C-TC
* *
16717219 CACATCTCTAAGGTATAAGGTTCGACATTGTGGCTTCAACCTTTCTCTC
1 CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACCTTTC-CTC
* * * * * * *
16717268 CATATCTCTAGGGTATAAGATTCGTCGTTGAGGCTTCAATCTTTCCTAT
1 CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACCTTTCCT-C
* * *
16717317 CACATCTCTAAGGTATAAGGTTCGCCGTTGCAGCTTTAACCTTTTCCTC
1 CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACC-TTTCCTC
** * * *
16717366 CACATCTCTTGGGTGTAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTC
1 CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACCTTT-CCTC
* * * * ** *
16717415 CATATCTCTAGGGTACAAGATTC-ATCGTTATGGCTTCAATCTTT-CTC
1 CACATCTCTAAGGTATAAGGTTCGA-CGTTGCGGCTTCAACCTTTCCTC
* * *
16717462 ATCACATCTCTAACGTATAAGGTTCGTCGTTGCGGCTTAAACCTTTTCCTC
1 --CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACC-TTTCCTC
* * * ** *
16717513 AACATCTCTAGGGTATAAGGTTC-ATCATTGTAGCTTCAACTTTTCCTTC
1 CACATCTCTAAGGTATAAGGTTCGA-CGTTGCGGCTTCAACCTTTCC-TC
* * *
16717562 CATATCTCTAAGGTATAAGATTCGTCGTTGC
1 CACATCTCTAAGGTATAAGGTTCGACGTTGC
16717593 AACCTCAATC
Statistics
Matches: 322, Mismatches: 81, Indels: 38
0.73 0.18 0.09
Matches are distributed among these distances:
47 4 0.01
48 42 0.13
49 263 0.82
50 10 0.03
51 3 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (48 bp):
CACATCTCTAAGGTATAAGGTTCGACGTTGCGGCTTCAACCTTTCCTC
Found at i:16717320 original size:98 final size:97
Alignment explanation
Indices: 16717111--16717617 Score: 429
Period size: 98 Copynumber: 5.2 Consensus size: 97
16717101 TGTGGTTTTG
* * * * *
16717111 ATCTTTCCCATCACATCTCTAAGGAATAAGGTTCG-CTGTTGCGGCTTTAACCTTTCCCTCTATA
1 ATCTTT-CCATCACATCTCTAAGGTATAAGGTTCGAC-GTTGTGGCTTCAACCTTTCTCTCCATA
* * * *
16717175 -CTGTAGGGTACAAGATTCATTGTTGAGGCTTCA
64 TCTCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
*
16717208 ATCTTTCGCATCACATCTCTAAGGTATAAGGTTCGACATTGTGGCTTCAACCTTTCTCTCCATAT
1 ATCTTTC-CATCACATCTCTAAGGTATAAGGTTCGACGTTGTGGCTTCAACCTTTCTCTCCATAT
16717273 CTCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
65 CTCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
* ** * *
16717306 ATCTTTCCTATCACATCTCTAAGGTATAAGGTTCGCCGTTGCAGCTTTAACCTTT-TCCTCCACA
1 ATCTTTCC-ATCACATCTCTAAGGTATAAGGTTCGACGTTGTGGCTTCAACCTTTCT-CTCCATA
* * * * * *
16717370 TCTCTTGGGTGTAAGGTTCGCCATTGCGGCTTCA
64 TCTCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
* * * * * * * * *
16717404 ACCTTTCCCTCCATATCTCTAGGGTACAAGATTC-ATCGTTATGGCTTCAATCTTTCTCAT-CAC
1 ATCTTTCCAT-CACATCTCTAAGGTATAAGGTTCGA-CGTTGTGGCTTCAACCTTTCTC-TCCAT
** * * *
16717467 ATCTCTAACGTATAAGGTTCGTCGTTGCGGCTTAA
63 ATCTCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
* * * * *
16717502 ACCTTTTCC-TCAACATCTCTAGGGTATAAGGTTC-ATCATTGTAGCTTCAACTTTTC-CTTCCA
1 ATC-TTTCCATC-ACATCTCTAAGGTATAAGGTTCGA-CGTTGTGGCTTCAACCTTTCTC-TCCA
* * *
16717564 TATCTCTAAGGTATAAGATTCGTCGTTGCA-ACCTCA
62 TATCTCTAGGGTATAAGATTCGTCGTTG-AGGCTTCA
*
16717600 ATCTTTCCCTCAACATCT
1 ATCTTTCCATC-ACATCT
16717618 TTAGGATATA
Statistics
Matches: 338, Mismatches: 58, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
96 1 0.00
97 65 0.19
98 265 0.78
99 7 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (97 bp):
ATCTTTCCATCACATCTCTAAGGTATAAGGTTCGACGTTGTGGCTTCAACCTTTCTCTCCATATC
TCTAGGGTATAAGATTCGTCGTTGAGGCTTCA
Found at i:16717401 original size:147 final size:147
Alignment explanation
Indices: 16717219--16717591 Score: 538
Period size: 147 Copynumber: 2.5 Consensus size: 147
16717209 TCTTTCGCAT
*
16717219 CACATCTCTAAGGTATAAGGTTCGACATTGTGGCTTCAACCTTTCTCTCCATATCTCTAGGGTAT
1 CACATCTCTAGGGTATAAGGTTCGACATTGTGGCTTCAACCTTTC-CTCCATATCTCTAGGGTAT
*
16717284 AAGATTCGTCGTTGA-GGCTTCAATCTTTC-CTATCACATCTCTAAGGTATAAGGTTCGCCGTTG
65 AAGATTCGTCGTTGATGGCTTCAATCTTTCTC-ATCACATCTCTAACGTATAAGGTTCGCCGTTG
*
16717347 CAGCTTTAACCTTTTCCTC
129 CAGCTTAAACCTTTTCCTC
* * * * *
16717366 CACATCTCTTGGGTGTAAGGTTCGCCATTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTAC
1 CACATCTCTAGGGTATAAGGTTCGACATTGTGGCTTCAACCTTT-CCTCCATATCTCTAGGGTAT
* *
16717431 AAGATTCATCGTT-ATGGCTTCAATCTTTCTCATCACATCTCTAACGTATAAGGTTCGTCGTTGC
65 AAGATTCGTCGTTGATGGCTTCAATCTTTCTCATCACATCTCTAACGTATAAGGTTCGCCGTTGC
*
16717495 GGCTTAAACCTTTTCCTC
130 AGCTTAAACCTTTTCCTC
* * * *
16717513 AACATCTCTAGGGTATAAGGTTC-ATCATTGTAGCTTCAACTTTTCCTTCCATATCTCTAAGGTA
1 CACATCTCTAGGGTATAAGGTTCGA-CATTGTGGCTTCAACCTTTCC-TCCATATCTCTAGGGTA
16717577 TAAGATTCGTCGTTG
64 TAAGATTCGTCGTTG
16717592 CAACCTCAAT
Statistics
Matches: 199, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
146 3 0.02
147 194 0.97
148 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (147 bp):
CACATCTCTAGGGTATAAGGTTCGACATTGTGGCTTCAACCTTTCCTCCATATCTCTAGGGTATA
AGATTCGTCGTTGATGGCTTCAATCTTTCTCATCACATCTCTAACGTATAAGGTTCGCCGTTGCA
GCTTAAACCTTTTCCTC
Found at i:16717607 original size:49 final size:49
Alignment explanation
Indices: 16717008--16717617 Score: 330
Period size: 49 Copynumber: 12.5 Consensus size: 49
16716998 AGGTTGTTAT
* * * *
16717008 AGCTTCAACCTTTCCTTCTACATCTCTAAAGTATAAGCTTCGTTGTTGC
1 AGCTTCAACCTTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * * ** ** * *
16717057 AGCTTCAACCTTTTCC-ACCACA--ACTAGGGTACAAGACTCACCATTGT
1 AGCTTCAACC-TTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * ** * * *
16717104 GGTTTTGATCTTTCCCAT-CACATCTCTAAGGAATAAGGTTCG-CTGTTGC
1 AGCTTCAACCTTT-CCTTCCACATCTCTAAGGTATAAGGTTCGTC-GTTGC
* * * * * * * * * * *
16717153 GGCTTTAACCTTTCCCTCTATA-CTGTAGGGTACAAGATTCATTGTTG-
1 AGCTTCAACCTTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * * *
16717200 AGGCTTCAATCTTTCGCAT-CACATCTCTAAGGTATAAGGTTCGACATTGT
1 A-GCTTCAACCTTTC-CTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * *
16717250 GGCTTCAACCTTT-CTCTCCATATCTCTAGGGTATAAGATTCGTCGTTG-
1 AGCTTCAACCTTTCCT-TCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* *
16717298 AGGCTTCAATCTTTCCTAT-CACATCTCTAAGGTATAAGGTTCGCCGTTGC
1 A-GCTTCAACCTTTCCT-TCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* ** * * *
16717348 AGCTTTAACCTTTTCC-TCCACATCTCTTGGGTGTAAGGTTCGCCATTGC
1 AGCTTCAACC-TTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * * * * * **
16717397 GGCTTCAACCTTTCCCTCCATATCTCTAGGGTACAAGATTCATCGTTAT
1 AGCTTCAACCTTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * *
16717446 GGCTTCAATCTTTCTCAT-CACATCTCTAACGTATAAGGTTCGTCGTTGC
1 AGCTTCAACCTTTC-CTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * * * * *
16717495 GGCTTAAACCTTTTCC-TCAACATCTCTAGGGTATAAGGTTCATCATTGT
1 AGCTTCAACC-TTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * *
16717544 AGCTTCAACTTTTCCTTCCATATCTCTAAGGTATAAGATTCGTCGTTGC
1 AGCTTCAACCTTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
* * * * *
16717593 AACCTCAATCTTTCCCTCAACATCT
1 AGCTTCAACCTTTCCTTCCACATCT
16717618 TTAGGATATA
Statistics
Matches: 414, Mismatches: 123, Indels: 48
0.71 0.21 0.08
Matches are distributed among these distances:
46 3 0.01
47 26 0.06
48 47 0.11
49 318 0.77
50 20 0.05
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (49 bp):
AGCTTCAACCTTTCCTTCCACATCTCTAAGGTATAAGGTTCGTCGTTGC
Found at i:16721958 original size:21 final size:21
Alignment explanation
Indices: 16721934--16721974 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16721924 TGAGTTAGAA
*
16721934 AACATAAAAGCTAAGTATGAT
1 AACATAAAAACTAAGTATGAT
16721955 AACATAAAAACTAAGTATGA
1 AACATAAAAACTAAGTATGA
16721975 AATGCCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (21 bp):
AACATAAAAACTAAGTATGAT
Found at i:16722757 original size:14 final size:14
Alignment explanation
Indices: 16722738--16722774 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
16722728 ATTTTTCCTT
16722738 TGACCACATATGCA
1 TGACCACATATGCA
16722752 TGACCACATATGCA
1 TGACCACATATGCA
16722766 TGACCACAT
1 TGACCACAT
16722775 TGTCTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (14 bp):
TGACCACATATGCA
Found at i:16733958 original size:109 final size:109
Alignment explanation
Indices: 16733834--16734048 Score: 290
Period size: 109 Copynumber: 2.0 Consensus size: 109
16733824 AACAAAAAAT
* * *
16733834 ATTTATTGATTTTAAATAGAATA-TCCAATTACTTAGTTTTAAAGAAAAATCATACCCAACACGT
1 ATTTATCGATTTTAAATAGAATACT-CAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGT
* ** *
16733898 TAGGGCACAATTTTTTGAGTCCCCTAAAATAACAA-AACATTGAGA
65 TAGCGCACAATTTTTCAAATCCCCTAAAATAA-AAGAACATTGAGA
* * * *
16733943 ATTTATCGGTTTTAAATAGGATACTCAATTATTTAGGTTCAAAGAAAAATCATACCTAACACGTT
1 ATTTATCGATTTTAAATAGAATACTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTT
*
16734008 AGCGCACAATTTTTCAAATTCCCTAAAATAAAAGAACATTG
66 AGCGCACAATTTTTCAAATCCCCTAAAATAAAAGAACATTG
16734049 CATTGATTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
108 2 0.02
109 89 0.97
110 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (109 bp):
ATTTATCGATTTTAAATAGAATACTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTT
AGCGCACAATTTTTCAAATCCCCTAAAATAAAAGAACATTGAGA
Found at i:16734230 original size:3 final size:3
Alignment explanation
Indices: 16734222--16734268 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
16734212 TAAATAAAAT
16734222 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16734269 CAAAGTTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16734423 original size:38 final size:38
Alignment explanation
Indices: 16734340--16734426 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
16734330 AAATAATAAT
* * *
16734340 AATAAATAGAATGAAATAAAGATATAAAAAATAAATGA
1 AATAAATAAAATGAAATAAAGATAGAAAAAATAAATCA
* *
16734378 GACAAATAAAATGAAAGTAAA-A-AGAAAAGAATAAATCA
1 AATAAATAAAATGAAA-TAAAGATAGAAAA-AATAAATCA
16734416 AATAAATAAAA
1 AATAAATAAAA
16734427 GGGTAAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
37 5 0.12
38 31 0.77
39 4 0.10
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.17
Consensus pattern (38 bp):
AATAAATAAAATGAAATAAAGATAGAAAAAATAAATCA
Found at i:16736517 original size:93 final size:93
Alignment explanation
Indices: 16736352--16736586 Score: 226
Period size: 93 Copynumber: 2.5 Consensus size: 93
16736342 ATGTAACTTC
* * *
16736352 ACTCCATTCCACTGTAACCTCAGGGAAATTGAGAT-TCGTTACTCATTTTGATCCAATCCATTGC
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCT-GCTACTCATTTTGATCCAATCCACTGC
* * * *
16736416 AACTTCAGGGATATAAGATCTGGTGCTTA
65 AACCTCAGGAAGATAAGATCTGATGCTTA
* * *
16736445 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTAC-CTGTTTTGA-CCTACTTCACTG
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTACTC-ATTTTGATCC-AATCCACTG
* * * * * *
16736508 TAACCTCAGGAAGATAGGTTTTGATGTTTC
64 CAACCTCAGGAAGATAAGATCTGATGCTTA
* * * *
16736538 ACTCCACTCTACTGTAACCTCA-GGACGTTGAGATCTGCTTCATCATTTT
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTAC-TCATTTT
16736587 AATCTGCCTA
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
92 20 0.17
93 94 0.81
94 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (93 bp):
ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTACTCATTTTGATCCAATCCACTGCA
ACCTCAGGAAGATAAGATCTGATGCTTA
Found at i:16737166 original size:37 final size:37
Alignment explanation
Indices: 16737116--16737193 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
16737106 TTAATACTAA
* * ** *
16737116 TGTCGCTGCATGAGCACTTCTAGATTGTGCCTAAAAC
1 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
16737153 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
1 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
16737190 TGTC
1 TGTC
16737194 ACCACAGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
Found at i:16738179 original size:16 final size:16
Alignment explanation
Indices: 16738158--16738188 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16738148 TTGTGGATCC
16738158 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
16738174 CATTTTATCTTTATT
1 CATTTTACCTTTATT
16738189 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:16740503 original size:17 final size:17
Alignment explanation
Indices: 16740483--16740541 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
16740473 ATAATTGTTC
16740483 CTGCATTTTTATTGTCA
1 CTGCATTTTTATTGTCA
* * *
16740500 CTGCCTTTTTATTTTTA
1 CTGCATTTTTATTGTCA
* **
16740517 CTGCATCTACATTGTCA
1 CTGCATTTTTATTGTCA
*
16740534 TTGCATTT
1 CTGCATTT
16740542 CCATATACAT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.53
Consensus pattern (17 bp):
CTGCATTTTTATTGTCA
Found at i:16741637 original size:37 final size:37
Alignment explanation
Indices: 16741581--16741683 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
16741571 ACTGCATTAG
* *
16741581 CACTTCTAGATTG-AGCCCAAAACTGTCGCCGCATGAA
1 CACTTCCAGATTGCA-CCCAAAACTGTCGCCGCAGGAA
*
16741618 CACTTCCAGATTGCACCCAAAACTGTCGTCGCAGGAA
1 CACTTCCAGATTGCACCCAAAACTGTCGCCGCAGGAA
* * * * * *
16741655 TATTTCCGGAATGCACCCAAGACTATCGC
1 CACTTCCAGATTGCACCCAAAACTGTCGC
16741684 TACATAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 54 0.98
38 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (37 bp):
CACTTCCAGATTGCACCCAAAACTGTCGCCGCAGGAA
Found at i:16742901 original size:49 final size:48
Alignment explanation
Indices: 16742829--16743480 Score: 621
Period size: 49 Copynumber: 13.3 Consensus size: 48
16742819 CCTTTTCTTC
* *
16742829 CACATCTCTAAAGTATAAGGTTCGCCGTTACGGCTTCAATCTTTCCCAT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCC-T
* * *
16742878 CACATCTCTAAGGTATAAGGTTCGTCGTTGTGGCTTCAACCTTTCCCT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCCT
* * * * * * *
16742926 C-TATACTCTAGGGTACAAGATTCACCGTTGCGGCCTCAGTCTTTCCCGT
1 CACAT-CTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCC-T
* * * *
16742975 CACATCTCTAAGGGATAAGGTTCGCCATTGAGGCTTCAACCTTTCCCT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCCT
* *
16743023 CTACATCTCTAAGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCAT
1 C-ACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCC-T
* * * * * *
16743073 CACATCTCTAAAGTATAAGCTTCGTCATTGCGGCTTCAACCTTTTCCT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCCT
* * *
16743121 CCACATATCTAGGGTATAAGGTTCGCCGTTGTGGCTTCAA-CTTTTCCCT
1 -CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATC-TTTCCCT
* * * * * *
16743170 CCATATCTCTAGGGTACAAGATTTGCCGTTGCGGCTTCAATTTTTCCCAT
1 -CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCC-T
*
16743220 CACATCTCTAAGGTATAAGGTTCACCGTTGCGGCTTCAA-CATTTCCCTT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATC-TTTCCC-T
* * * * *
16743269 CACATCTTTAGGGTAAAAGATTCGCCGTTGCGACTTCAATCTTTCCCAT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCC-T
* * * *
16743318 CACATCTCTAAGGTATAAGGTTCGCCATTACGGCTTCAAATTTTTCCTT
1 CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTC-AATCTTTCCCT
* * * * *
16743367 AACATCTCT-AGTGTATAAGGTTCACCATTGTGGCTTCAACCTTTCCCT
1 CACATCTCTAAG-GTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCCT
* * * * *
16743415 CCATATCTCTAGGGTATAAGATTCGTCATTGCGGCCTT-AATCTTTCCCT
1 -CACATCTCTAAGGTATAAGGTTCGCCGTTGCGG-CTTCAATCTTTCCCT
* *
16743464 CAACATCTTTAGGGTAT
1 C-ACATCTCTAAGGTAT
16743481 TGGATTTAAC
Statistics
Matches: 493, Mismatches: 93, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.00
48 50 0.10
49 423 0.86
50 18 0.04
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (48 bp):
CACATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAATCTTTCCCT
Found at i:16744357 original size:16 final size:16
Alignment explanation
Indices: 16744336--16744368 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16744326 CGACCTCTCC
16744336 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTCTTT
16744352 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTCTTT
16744368 T
1 T
16744369 ATTGAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTTTCTTT
Found at i:16746284 original size:153 final size:149
Alignment explanation
Indices: 16745927--16746313 Score: 564
Period size: 150 Copynumber: 2.6 Consensus size: 149
16745917 TGTCTTTTAG
*
16745927 AAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTAACTATTTCGAAATAAAAGTTTCGATTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTT
* * *
16745991 TTAAGTAAAGTAGTTATTTTCATTAAAAAAGAAAAAAAAGTATATTTTTTAAAATAAAAATCTAT
66 TTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAAAAAAGTATAATTTTTAAAATAAAAATATAT
*
16746056 TTTTTAGTTATTTTAAAGA
131 TTTTTAGTGATTTTAAAGA
* *
16746075 AAATGTTTAAATATTTAAATAAAGTTTTGATTTTTTTCAACTATTTCGAAATAAAAGTTTTGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTTGATT
* * * *
16746140 TTTAATTAGAGTAGTGATTTTCATTAAAATAAG-AAAGAAAGTTTAGATTTTTAAAA-AATAAAT
65 TTTAAGTAAAGTAGTGATTTTCATTAAAA-AAGAAAAAAAAGTATA-ATTTTTAAAATAA-AAAT
16746203 ATATGTTTTTTAGTGATTTTAAAGAA
127 ATA--TTTTTTAGTGATTTTAAAG-A
* *
16746229 AAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTT
*
16746294 TGAAGTAAAGTAGTGATTTT
66 TTAAGTAAAGTAGTGATTTT
16746314 GTTTTAATCA
Statistics
Matches: 213, Mismatches: 18, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
148 28 0.13
149 6 0.03
150 64 0.30
151 18 0.08
153 63 0.30
154 34 0.16
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (149 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTT
TTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAAAAAAGTATAATTTTTAAAATAAAAATATAT
TTTTTAGTGATTTTAAAGA
Found at i:16746375 original size:153 final size:149
Alignment explanation
Indices: 16745815--16746358 Score: 511
Period size: 153 Copynumber: 3.7 Consensus size: 149
16745805 TTGGGAAAAT
* * * * *
16745815 TTTTGGTTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAATAGTGATTTTCTT
1 TTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTTTT
* *
16745880 TAA-AAAAGAAAA---AG-TTTATATTTTAAAAAAAAAAT-TG---T-GT-CTTTT--AG-AAAA
65 TAATAAAAGAAAATTTAGATTTTTATTTTAAAAAAAAAATATGTTTTAGTAATTTTAAAGAAAAA
16745931 GTTTAAATTTTTAAATAAAG
130 GTTTAAATTTTTAAATAAAG
* * **
16745951 TTTTGA-TTTTTTAACTATTTCGAAATAAAAGTTTCGATTTTTAAGTAAAGTAGTTATTTTCATT
1 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTTTTT
*** * * * *
16746015 AA-AAAAGAAAAAAAAG-TATATT-TTTTAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
66 AATAAAAGAAAATTTAGAT-TTTTATTTTAAAA-AAAAA-ATATGTTTTAGTAATTTTAAAGAAA
* *
16746077 ATGTTTAAATATTTAAATAAAG
128 AAGTTTAAATTTTTAAATAAAG
* *
16746099 TTTTGATTTTTTTCAACTATTTCGAAATAAAAGTTTTGATTTTTAATTAGAGTAGTGATTTTCAT
1 TTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTT--T
** * * *
16746164 TAAAATAAGAAAGAAAGTTTAGATTTTTA----AAAAATAAATATATGTTTTTTAGTGATTTTAA
63 TTTAAT-A-AAAGAAAATTTAGATTTTTATTTTAAAAA-AAAAATATG--TTTTAGTAATTTTAA
* *
16746225 AGAAAAAAGTTTAAATTTTTAAACAAAA
123 AG-AAAAAGTTTAAATTTTTAAATAAAG
*
16746253 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTTGTTT
1 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTT-TTT
*
16746318 TAATCAAAAGAAAACTTTTGATTTTTATTTTAAAAAAAAAA
65 TAAT-AAAAGAAAA-TTTAGATTTTTATTTTAAAAAAAAAA
16746359 GAAGAAAAAG
Statistics
Matches: 330, Mismatches: 45, Indels: 47
0.78 0.11 0.11
Matches are distributed among these distances:
134 57 0.17
135 6 0.02
136 5 0.02
137 11 0.03
138 7 0.02
139 1 0.00
140 1 0.00
143 1 0.00
144 2 0.01
145 4 0.01
147 2 0.01
148 28 0.08
149 6 0.02
150 44 0.13
151 11 0.03
152 26 0.08
153 61 0.18
154 35 0.11
155 16 0.05
156 6 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (149 bp):
TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTTTTT
AATAAAAGAAAATTTAGATTTTTATTTTAAAAAAAAAATATGTTTTAGTAATTTTAAAGAAAAAG
TTTAAATTTTTAAATAAAG
Found at i:16747115 original size:17 final size:17
Alignment explanation
Indices: 16747080--16747121 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
16747070 CTCCCTTGAC
*
16747080 CTTTAACCTTCTATCTT
1 CTTTAACCTTCTATATT
16747097 CTTTAACCATTC-ATATT
1 CTTTAACC-TTCTATATT
16747114 CTTGTAAC
1 CTT-TAAC
16747122 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCTATATT
Found at i:16752477 original size:17 final size:17
Alignment explanation
Indices: 16752457--16752498 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16752447 CTCCATTGAC
*
16752457 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
16752474 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
16752491 CTTGTAAC
1 CTT-TAAC
16752499 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:16752482 original size:24 final size:24
Alignment explanation
Indices: 16752437--16752484 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16752427 ATGGATGTTC
* *
16752437 AACCTTTCATCTCCATTGACCTTT
1 AACCTTCCATCTCCATTAACCTTT
* *
16752461 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCATTAACCTTT
16752485 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.33, G:0.02, T:0.44
Consensus pattern (24 bp):
AACCTTCCATCTCCATTAACCTTT
Found at i:16756179 original size:4 final size:4
Alignment explanation
Indices: 16756170--16756203 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
16756160 GTGTCCCAGT
* *
16756170 TTCA TTCA TTCA TTCA TTCA TTTA TCCA TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
16756204 TACTCATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (4 bp):
TTCA
Found at i:16760008 original size:7 final size:7
Alignment explanation
Indices: 16759983--16760047 Score: 87
Period size: 7 Copynumber: 9.3 Consensus size: 7
16759973 TGTTTAAATC
16759983 AAGAAAA
1 AAGAAAA
*
16759990 AA-AAAG
1 AAGAAAA
16759996 AAGAAAA
1 AAGAAAA
16760003 AAGAAAA
1 AAGAAAA
*
16760010 TAGAAAA
1 AAGAAAA
*
16760017 TAGAAAA
1 AAGAAAA
16760024 AAGAAAA
1 AAGAAAA
16760031 AAGAAAAA
1 AAG-AAAA
16760039 AAGAAAA
1 AAGAAAA
16760046 AA
1 AA
16760048 AATAGAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.10
7 40 0.77
8 7 0.13
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:16760014 original size:14 final size:13
Alignment explanation
Indices: 16759983--16760055 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
16759973 TGTTTAAATC
16759983 AAGAAAAAA-AAA
1 AAGAAAAAAGAAA
16759995 GAAGAAAAAAGAAA
1 -AAGAAAAAAGAAA
*
16760009 ATAGAAAATAGAAAA
1 A-AGAAAAAAG-AAA
16760024 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
16760037 AA-AAGAAAA-AAA
1 AAGAA-AAAAGAAA
16760049 ATAGAAA
1 A-AGAAA
16760056 GAGGGAGCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.12
13 21 0.40
14 21 0.40
15 4 0.08
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:16760023 original size:21 final size:20
Alignment explanation
Indices: 16759983--16760055 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
16759973 TGTTTAAATC
*
16759983 AAGAAAA-AAAAAGAAGAAAA
1 AAGAAAATAGAAA-AAGAAAA
16760003 AAGAAAATAGAAAATAGAAAA
1 AAGAAAATAGAAAA-AGAAAA
*
16760024 AAGAAAAAAGAAAAA-AAGAA
1 AAGAAAATAGAAAAAGAA-AA
16760044 AA-AAAATAGAAA
1 AAGAAAATAGAAA
16760056 GAGGGAGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 11 0.23
20 13 0.28
21 23 0.49
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (20 bp):
AAGAAAATAGAAAAAGAAAA
Found at i:16761086 original size:42 final size:42
Alignment explanation
Indices: 16760456--16761083 Score: 830
Period size: 42 Copynumber: 14.9 Consensus size: 42
16760446 AAGGAAAGCA
*
16760456 TTCATTGCGTTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * **
16760498 TTTATCGCATTCAGAGGCCCATGTGTGGAGGCCCATAAACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16760540 TTCATTTCATTTAAAGGCCCAGGTGTGGAGGTCCATTTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCA-TTTACTT
*
16760583 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16760625 TTCATTACATTTAGAAGCCCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
16760667 TTCATTGCATTTAGAGGCCCAGGCGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
16760709 TTCATTGCATTTAAAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
16760751 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTAAATCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT-T
* *
16760794 TT-ATTGCATTTAGAGGCCGAGGTGAGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
* *
16760835 TTCATTGCATTTAGAGGCCCAGGTGTGGTGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
16760877 TTCATTGCATTTAGAGGCCTAGGTGTTAAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
16760919 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * *
16760961 TTCATTACATTTAAAGGTCGAGGTGTGGAGGCCCATTTACTC
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
16761003 TTCATTGCATTTGGAGGCCCAAGTGTGGAGGCCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
16761045 TTCATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA
16761084 TTTATATTTT
Statistics
Matches: 505, Mismatches: 74, Indels: 14
0.85 0.12 0.02
Matches are distributed among these distances:
41 4 0.01
42 460 0.91
43 41 0.08
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:16762225 original size:99 final size:99
Alignment explanation
Indices: 16762083--16762265 Score: 210
Period size: 99 Copynumber: 1.8 Consensus size: 99
16762073 TTTGTTTAGA
* * * * *
16762083 AAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAA-TAAAAGTTTGAATTT
1 AAAGTTTAAATTTTTAAATAAAATTCTGATTTTTTTAACTATTT-GAAAGAAAAAGTGTAAATTT
*
16762147 TTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAG
65 TTAAATAAAGTAGTGATTTTCATTAAAAAAGAAAG
* ** *
16762182 AAAGTTTATATTTTTAAATATAAATATCT-A-TTTTTTAGTTATTTTAAAGAAAAAGTGTAAATT
1 AAAGTTTAAATTTTTAAATA-AAAT-TCTGATTTTTTTAACTATTTGAAAGAAAAAGTGTAAATT
**
16762245 TTTAAATAAAGTTTTGATTTT
64 TTTAAATAAAGTAGTGATTTT
16762266 TTTCAACTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
98 3 0.04
99 60 0.87
100 4 0.06
101 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (99 bp):
AAAGTTTAAATTTTTAAATAAAATTCTGATTTTTTTAACTATTTGAAAGAAAAAGTGTAAATTTT
TAAATAAAGTAGTGATTTTCATTAAAAAAGAAAG
Found at i:16762438 original size:154 final size:149
Alignment explanation
Indices: 16762082--16762471 Score: 582
Period size: 154 Copynumber: 2.6 Consensus size: 149
16762072 GTTTGTTTAG
*
16762082 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGAATTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAATTTG-ATTT
* * * * *
16762147 TTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTTATATTTTTAAATATAAATATCTA
65 TTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTCAGATTTTAAAAAATAAAAATCTA
*
16762212 TTTTTTAGTTATTTTAAAGA
130 TTTTTTAGTGATTTTAAAGA
*
16762232 AAAAGTGTAAATTTTTAAATAAAGTTTTGATTTTTTTCAACTATTTCGAAATAAAAATTTTGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAA-TTTGATT
*
16762297 TTTAAATAAAGTAGTGATTTTCATTAAAAAAAGAAAGAAAGTTCAGATTTTAAAAAAATAAAAAT
64 TTTAAGTAAAGTAGTGATTTTCATT-AAAAAAGAAAGAAAGTTCAGATTTT-AAAAAATAAAAAT
*
16762362 CTGTTTTTTAGTGATTTTAAAGAA
127 CTATTTTTTAGTGATTTTAAAG-A
* *
16762386 AAAAGTTTAAATTTTTAAACAAATTTTTGATTTTTTTAAACTATTTCGAAATAAAAGATTTGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAA-ATTTGATT
* *
16762451 TTGAAGTAAAGTTGTGATTTT
64 TTTAAGTAAAGTAGTGATTTT
16762472 GTTTTAATCA
Statistics
Matches: 217, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
150 36 0.17
151 45 0.21
152 27 0.12
153 30 0.14
154 78 0.36
155 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (149 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAATTTGATTTT
TAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTCAGATTTTAAAAAATAAAAATCTAT
TTTTTAGTGATTTTAAAGA
Found at i:16766611 original size:109 final size:109
Alignment explanation
Indices: 16766412--16766625 Score: 288
Period size: 109 Copynumber: 2.0 Consensus size: 109
16766402 AACAAAGAAT
* ** * *
16766412 ATTTATCGATTTTAAATAGAATATCCAATTACTTAGTTTCAAAGAAAAATCATACCCAACATGTT
1 ATTTAACGATTTTAAATAGAATATCCAATTACTTAGGGTCAAAGAAAAACCATACCCAACACGTT
* * *
16766477 AGGGCACAATTTTTCGAGTCCTCTAAAATAACATAACATTGAGC
66 AGGGCACAATTTTTCGAATCCTCTAAAATAAAAAAACATTGAGC
* *
16766521 ATTTAACGATTTTAAATAGGATA-CTCAATTATTTAGGGTCAAAGAAAAACCATACCCAACACGT
1 ATTTAACGATTTTAAATAGAATATC-CAATTACTTAGGGTCAAAGAAAAACCATACCCAACACGT
**
16766585 TAGGGCACAATTTCTT-GAATTGTCTAAAATAAAAAAACATT
65 TAGGGCACAATTT-TTCGAATCCTCTAAAATAAAAAAACATT
16766626 ACCTTGATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
108 1 0.01
109 88 0.97
110 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (109 bp):
ATTTAACGATTTTAAATAGAATATCCAATTACTTAGGGTCAAAGAAAAACCATACCCAACACGTT
AGGGCACAATTTTTCGAATCCTCTAAAATAAAAAAACATTGAGC
Found at i:16781316 original size:13 final size:14
Alignment explanation
Indices: 16781286--16781316 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16781276 TTTCAGTACA
16781286 TTGACATTTAACCT
1 TTGACATTTAACCT
16781300 TTGACATTTAA-CT
1 TTGACATTTAACCT
16781313 TTGA
1 TTGA
16781317 TTAAGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (14 bp):
TTGACATTTAACCT
Found at i:16784368 original size:49 final size:49
Alignment explanation
Indices: 16784262--16784493 Score: 168
Period size: 49 Copynumber: 4.8 Consensus size: 49
16784252 ACCATTGTGT
* * * * * * * *
16784262 CTTCAATCTTTCTCT-TCACATCTTTAGGGTATAAAGTCCGCCGTTTCGG
1 CTTCAACCTTTC-CTATCATATCTCTAGAGTATAAGGTTCGTCGTTGCGG
* * * *
16784311 CTTTAACCTTTCCTTTAATATCTCTAGAGTATTAGGTTCGTCGTTGCGG
1 CTTCAACCTTTCCTATCATATCTCTAGAGTATAAGGTTCGTCGTTGCGG
* * * * * ** *
16784360 CTTCAACCTTTCC-CTC-TATATCTAGGGTACAAGATTTTTTGTTGCGG
1 CTTCAACCTTTCCTATCATATCTCTAGAGTATAAGGTTCGTCGTTGCGG
* * * *
16784407 CTTCAATCTTTCCTATCACATCTCTA-AGGTATAAGGTTCGTTGTTGTGG
1 CTTCAACCTTTCCTATCATATCTCTAGA-GTATAAGGTTCGTCGTTGCGG
**
16784456 CTTCAATATTTCCTATCATATCTCTA-AGGTATAAGGTT
1 CTTCAACCTTTCCTATCATATCTCTAGA-GTATAAGGTT
16784494 TGCCATTACG
Statistics
Matches: 145, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
47 35 0.24
48 5 0.03
49 105 0.72
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (49 bp):
CTTCAACCTTTCCTATCATATCTCTAGAGTATAAGGTTCGTCGTTGCGG
Found at i:16784509 original size:49 final size:49
Alignment explanation
Indices: 16784407--16784510 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 49
16784397 TTTGTTGCGG
* *** ** *
16784407 CTTCAATCTTTCCTATCACATCTCTAAGGTATAAGGTTCGTTGTTGTGG
1 CTTCAATATTTCCTATCACATCTCTAAGGTATAAGGTTCGCCATTACGA
* *
16784456 CTTCAATATTTCCTATCATATCTCTAAGGTATAAGGTTTGCCATTACGA
1 CTTCAATATTTCCTATCACATCTCTAAGGTATAAGGTTCGCCATTACGA
16784505 CTTCAA
1 CTTCAA
16784511 CCTTTTTCGC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (49 bp):
CTTCAATATTTCCTATCACATCTCTAAGGTATAAGGTTCGCCATTACGA
Found at i:16786234 original size:49 final size:49
Alignment explanation
Indices: 16786082--16786510 Score: 348
Period size: 49 Copynumber: 8.8 Consensus size: 49
16786072 TGTGCTATCA
* * * * *
16786082 CGGCTTCAATCTTTCCCAT-CACATCTCTAAGGTATTAGGTTCACCGTTG
1 CGGCTTCAACCTTTCCC-TCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * *
16786131 CGGCTTCAACATTT-CCTCCACATCTCTAGGATATAAGGTTCGTCGTTG
1 CGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * * * *
16786179 CAGCTTCAACCTTTCCCTCCATATCTCTAGGGTACAAGATTTGCCATTA
1 CGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * *
16786228 CGGCTTCAATCTTTCCCAT-CACATCTCTAAGGTATAAGGTTTGCCATTG
1 CGGCTTCAACCTTTCCC-TCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * *
16786277 TGGCTTCAACCTTTCCCACCACATCTCTAGGGTATAAGATTCGCCATTG
1 CGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * *
16786326 CGGCTTCAATCTTTCCCAT-CACATCTCTAAGGTATAAGGTTCGCTATTC
1 CGGCTTCAACCTTTCCC-TCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * * ** ** *
16786375 CAGCTTCAACAGTTT-CCTCAACATCTTTAGGGTATAAGGTTTACTGTTA
1 CGGCTTCAAC-CTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * * * * * *
16786424 CAGCTTCAACCTTTCCCTCCATATCTATAAGCTATAAGATTCACCGTT-
1 CGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
* * * **
16786472 CCGATGTCAATCTTTCCCTTAACATCTCTAGGGTATAAG
1 CGGCT-TCAACCTTTCCCTCCACATCTCTAGGGTATAAG
16786511 ATTCAATGTT
Statistics
Matches: 306, Mismatches: 65, Indels: 18
0.79 0.17 0.05
Matches are distributed among these distances:
47 1 0.00
48 46 0.15
49 255 0.83
50 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (49 bp):
CGGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCGCCATTG
Found at i:16786415 original size:147 final size:145
Alignment explanation
Indices: 16786084--16786514 Score: 429
Period size: 147 Copynumber: 2.9 Consensus size: 145
16786074 TGCTATCACG
* * * * *
16786084 GCTTCAATCTTTCCCATCACATCTCTAAGGTATTAGGTTCACCGTTGCGGCTTCAACATTT-CCT
1 GCTTCAATCTTTCCCA-CACATCTCTAAGGTATAAGGTTTACCATTACGGCTTCAACCTTTCCCT
* * * *
16786148 CCACATCTCTAGGATATAAGGTTCGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTCTAGGGTA
65 CCACATCTCTAGGATATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCT-CACATCTCTAGGGTA
* * *
16786213 CAAGATTTGCCATTACG
129 TAAGATTCGCCATTACA
* ** *
16786230 GCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTTGCCATTGTGGCTTCAACCTTTCCCA
1 GCTTCAATCTTTCCCA-CACATCTCTAAGGTATAAGGTTTACCATTACGGCTTCAACCTTTCCCT
* * * *
16786295 CCACATCTCTAGGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTA
65 CCACATCTCTAGGATATAAGATTCGCCGTTGCAGCTTCAATCTTTCCC-TCACATCTCTAGGGTA
* * *
16786360 TAAGGTTCGCTATTCCA
129 TAAGATTCGCCATTACA
* * ** *
16786377 GCTTCAA-CAGTTTCCTCA-ACATCTTTAGGGTATAAGGTTTACTGTTACAGCTTCAACCTTTCC
1 GCTTCAATC--TTTCC-CACACATCTCTAAGGTATAAGGTTTACCATTACGGCTTCAACCTTTCC
* * * * * * * *
16786440 CTCCATATCTATAAGCTATAAGATTCACCGTT-CCGATGTCAATCTTTCCCTTAACATCTCTAGG
63 CTCCACATCTCTAGGATATAAGATTCGCCGTTGCAGCT-TCAATCTTTCCC-TCACATCTCTAGG
16786504 GTATAAGATTC
126 GTATAAGATTC
16786515 AATGTTTCCT
Statistics
Matches: 237, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
146 59 0.25
147 170 0.72
148 6 0.03
149 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (145 bp):
GCTTCAATCTTTCCCACACATCTCTAAGGTATAAGGTTTACCATTACGGCTTCAACCTTTCCCTC
CACATCTCTAGGATATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTCACATCTCTAGGGTATA
AGATTCGCCATTACA
Found at i:16790194 original size:17 final size:17
Alignment explanation
Indices: 16790174--16790213 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
16790164 TAGATACAAC
*
16790174 GACAATAAAAATGCAGT
1 GACAATAAAAATGCAGG
16790191 GACAATAAAAATGCAGG
1 GACAATAAAAATGCAGG
16790208 GACAAT
1 GACAAT
16790214 TATACTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (17 bp):
GACAATAAAAATGCAGG
Found at i:16797763 original size:80 final size:81
Alignment explanation
Indices: 16797624--16797785 Score: 272
Period size: 80 Copynumber: 2.0 Consensus size: 81
16797614 CACCCCAAAC
* *
16797624 TTAATACATTGCTCATCCCGAGTAATGCACAAATTACAAAAGAGTTGATCATTCTTCCTCATACT
1 TTAATACATTGCTCATCCCGAGTAATGCACAAATCACAAAAGAGTTGATCATTCCTCCTCATACT
16797689 TATGAATTTAAAATAA
66 TATGAATTTAAAATAA
* * *
16797705 TTAAT-CATTGGTCATCCCGAGTAATGCACAAATCATAAAAGAGTTTATCATTCCTCCTCATACT
1 TTAATACATTGCTCATCCCGAGTAATGCACAAATCACAAAAGAGTTGATCATTCCTCCTCATACT
16797769 TATGAATTTAAAATAA
66 TATGAATTTAAAATAA
16797785 T
1 T
16797786 AAAGCATAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 71 0.93
81 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.34
Consensus pattern (81 bp):
TTAATACATTGCTCATCCCGAGTAATGCACAAATCACAAAAGAGTTGATCATTCCTCCTCATACT
TATGAATTTAAAATAA
Found at i:16813577 original size:18 final size:18
Alignment explanation
Indices: 16813554--16813590 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16813544 ATCATCGGAA
16813554 GGTGTGGTTAATGTGCAT
1 GGTGTGGTTAATGTGCAT
*
16813572 GGTGTGGTTAATGTTCAT
1 GGTGTGGTTAATGTGCAT
16813590 G
1 G
16813591 TTTAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.05, G:0.38, T:0.41
Consensus pattern (18 bp):
GGTGTGGTTAATGTGCAT
Found at i:16827218 original size:24 final size:24
Alignment explanation
Indices: 16827182--16827228 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16827172 AAGCAAACAA
* *
16827182 AAAAAAATGAAGCGATAAAATAAG
1 AAAAAAATAAAGCAATAAAATAAG
*
16827206 AAAAAGATAAAGCAATAAAATAA
1 AAAAAAATAAAGCAATAAAATAA
16827229 ACAAAGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAAAATAAAGCAATAAAATAAG
Found at i:16833331 original size:18 final size:18
Alignment explanation
Indices: 16833308--16833346 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
16833298 GGGCAAGTGT
16833308 TTTCTTTTCTTTTTTTTA
1 TTTCTTTTCTTTTTTTTA
16833326 TTTCTTTTCTTTTTTTTA
1 TTTCTTTTCTTTTTTTTA
16833344 TTT
1 TTT
16833347 TTTAAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTCTTTTCTTTTTTTTA
Found at i:16833347 original size:9 final size:9
Alignment explanation
Indices: 16833307--16833349 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
16833297 GGGGCAAGTG
*
16833307 TTTTCTTTTC
1 TTTT-TTTTA
16833317 TTTTTTTTA
1 TTTTTTTTA
* *
16833326 TTTCTTTTC
1 TTTTTTTTA
16833335 TTTTTTTTA
1 TTTTTTTTA
16833344 TTTTTT
1 TTTTTT
16833350 AAGTTTTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:16847730 original size:22 final size:22
Alignment explanation
Indices: 16847703--16847751 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
16847693 ATTTAAGCAG
16847703 TCTTAATGACTCACCTCTCTTT
1 TCTTAATGACTCACCTCTCTTT
16847725 TCTTAATGACTCACCTCTCTTT
1 TCTTAATGACTCACCTCTCTTT
16847747 TCTTA
1 TCTTA
16847752 CAACCCTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.31, G:0.04, T:0.47
Consensus pattern (22 bp):
TCTTAATGACTCACCTCTCTTT
Found at i:16851644 original size:38 final size:37
Alignment explanation
Indices: 16851536--16851658 Score: 174
Period size: 37 Copynumber: 3.3 Consensus size: 37
16851526 ACAATTTTAA
* *
16851536 TCCAGAATTGTGCCCAAACATGTCGCTGCATGAGCACT
1 TCCAG-ATTGCGCCCAAACATGTCGCCGCATGAGCACT
* *
16851574 TCTAGATTGCGCCCAAACATGTCGCCGCATGAGCACC
1 TCCAGATTGCGCCCAAACATGTCGCCGCATGAGCACT
* *
16851611 TCCAGATTGCGCCCAAAAACTGTCGCCACATGAGCACT
1 TCCAGATTGCGCCCAAACA-TGTCGCCGCATGAGCACT
16851649 TCCAGATTGC
1 TCCAGATTGC
16851659 ACCAAAACTA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
37 46 0.61
38 30 0.39
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (37 bp):
TCCAGATTGCGCCCAAACATGTCGCCGCATGAGCACT
Found at i:16857915 original size:15 final size:15
Alignment explanation
Indices: 16857895--16857925 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16857885 TTGGAAGCTC
16857895 AATGAGAACGAGAGG
1 AATGAGAACGAGAGG
*
16857910 AATGAGATCGAGAGG
1 AATGAGAACGAGAGG
16857925 A
1 A
16857926 GATACACGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.39, T:0.10
Consensus pattern (15 bp):
AATGAGAACGAGAGG
Found at i:16859127 original size:23 final size:23
Alignment explanation
Indices: 16859101--16859146 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
16859091 TCCCACTCTA
16859101 TCTCACCTT-TTGATTTCTCCTTC
1 TCTCACCTTCTT-ATTTCTCCTTC
*
16859124 TCTCGCCTTCCTTATTTCTCCTT
1 TCTCACCTT-CTTATTTCTCCTT
16859147 TTAGGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 10 0.50
25 2 0.10
ACGTcount: A:0.07, C:0.37, G:0.04, T:0.52
Consensus pattern (23 bp):
TCTCACCTTCTTATTTCTCCTTC
Found at i:16863033 original size:9 final size:8
Alignment explanation
Indices: 16863019--16863063 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
16863009 TCATAAATTA
16863019 TTTTCTTCT
1 TTTTCTT-T
16863028 TTTTCTTT
1 TTTTCTTT
16863036 TTCTTCTTT
1 TT-TTCTTT
*
16863045 TTTTCTCAT
1 TTTTCT-TT
16863054 TTTTCTTT
1 TTTTCTTT
16863062 TT
1 TT
16863064 CAAGTGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 10 0.31
9 22 0.69
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCTTT
Found at i:16865226 original size:47 final size:48
Alignment explanation
Indices: 16865157--16865250 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 48
16865147 GTACCATCAA
16865157 TGCAAAGGTCCCTCATGATATGAGCAATTACTTTATCATCC-AATCGC
1 TGCAAAGGTCCCTCATGATATGAGCAATTACTTTATCATCCGAATCGC
16865204 TGCAAAGGTCCCTCATGATATGAGCAATTACTTTATCATCCGAATCG
1 TGCAAAGGTCCCTCATGATATGAGCAATTACTTTATCATCCGAATCG
16865251 ACAAGGTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 41 0.89
48 5 0.11
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (48 bp):
TGCAAAGGTCCCTCATGATATGAGCAATTACTTTATCATCCGAATCGC
Found at i:16871513 original size:2 final size:2
Alignment explanation
Indices: 16871506--16871537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16871496 AGGTATATTA
16871506 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
16871538 GTTTATCTAA
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:16872368 original size:30 final size:29
Alignment explanation
Indices: 16872335--16872520 Score: 151
Period size: 30 Copynumber: 6.3 Consensus size: 29
16872325 CGAACTTTTA
* *
16872335 AAAAATTT-GAATTAACCCCCAAACTTCAC
1 AAAAATTTAGATTTAACCCCTAAACTTC-C
* *
16872364 AAAAATTT-GAATTTAACCTCAAAACTTTCC
1 AAAAATTTAG-ATTTAACCCCTAAAC-TTCC
* *
16872394 AAAAATTTAGATTTAAGCCTTAAACTTCC
1 AAAAATTTAGATTTAACCCCTAAACTTCC
* * *
16872423 TAAAAATTTGGATTTGACCCCGAAACTTTCC
1 -AAAAATTTAGATTTAACCCCTAAAC-TTCC
* *
16872454 AAAAATTTAGATTTGACCCCTAAACTTCTT
1 AAAAATTTAGATTTAACCCCTAAACTTC-C
* * * * *
16872484 AAAAATTCAAATTTAGCCCCAAAACTTTC
1 AAAAATTTAGATTTAACCCCTAAACTTCC
*
16872513 TAAAATTT
1 AAAAATTT
16872521 CATTTTTGAC
Statistics
Matches: 127, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
29 22 0.17
30 97 0.76
31 8 0.06
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAATTTAGATTTAACCCCTAAACTTCC
Found at i:16872430 original size:60 final size:60
Alignment explanation
Indices: 16872335--16872517 Score: 217
Period size: 60 Copynumber: 3.1 Consensus size: 60
16872325 CGAACTTTTA
* * *
16872335 AAAAATTT-GAATTAACCCCCAAACTTCAC-AAAAATTTGAATTTAACCTCAAAACTTTCC
1 AAAAATTTAGATTTAACCCCTAAACTTC-CTAAAAATTTGAATTTAACCCCAAAACTTTCC
* * * * *
16872394 AAAAATTTAGATTTAAGCCTTAAACTTCCTAAAAATTTGGATTTGACCCCGAAACTTTCC
1 AAAAATTTAGATTTAACCCCTAAACTTCCTAAAAATTTGAATTTAACCCCAAAACTTTCC
* * ** * *
16872454 AAAAATTTAGATTTGACCCCTAAACTTCTTAAAAATTCAAATTTAGCCCCAAAACTTTCT
1 AAAAATTTAGATTTAACCCCTAAACTTCCTAAAAATTTGAATTTAACCCCAAAACTTTCC
16872514 AAAA
1 AAAA
16872518 TTTCATTTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
59 9 0.09
60 94 0.91
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (60 bp):
AAAAATTTAGATTTAACCCCTAAACTTCCTAAAAATTTGAATTTAACCCCAAAACTTTCC
Found at i:16872498 original size:90 final size:89
Alignment explanation
Indices: 16872335--16872498 Score: 190
Period size: 90 Copynumber: 1.8 Consensus size: 89
16872325 CGAACTTTTA
*
16872335 AAAAATTTGAATTAACCCCCAAACTTCACAAAAATTTGAATTTAACCTCAAAACTTTCCAAAAAT
1 AAAAATTTGAATTAACCCCCAAACTTCACAAAAATTTGAATTTAACCCCAAAACTTTCCAAAAAT
* *
16872400 TTAGATTTAAGCCTTAAACTTCCT
66 TCAAATTTAAGCCTTAAACTTCCT
* * * * * *
16872424 AAAAATTTGGATTTGACCCCGAAACTTTC-CAAAAATTT-AGATTTGACCCCTAAAC-TTCTTAA
1 AAAAATTT-GAATTAACCCCCAAAC-TTCACAAAAATTTGA-ATTTAACCCCAAAACTTTC-CAA
16872486 AAATTCAAATTTA
62 AAATTCAAATTTA
16872499 GCCCCAAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
89 12 0.19
90 47 0.76
91 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.32
Consensus pattern (89 bp):
AAAAATTTGAATTAACCCCCAAACTTCACAAAAATTTGAATTTAACCCCAAAACTTTCCAAAAAT
TCAAATTTAAGCCTTAAACTTCCT
Found at i:16878122 original size:13 final size:14
Alignment explanation
Indices: 16878096--16878124 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16878086 ATACTTAGAA
16878096 AATTAAATTTAACT
1 AATTAAATTTAACT
16878110 AATTAAA-TTAACT
1 AATTAAATTTAACT
16878123 AA
1 AA
16878125 AGAACACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAATTTAACT
Found at i:16890228 original size:18 final size:18
Alignment explanation
Indices: 16890207--16890242 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16890197 TATAACAAAT
16890207 ATAAAAATAATAATAATA
1 ATAAAAATAATAATAATA
* *
16890225 ATAAATATTATAATAATA
1 ATAAAAATAATAATAATA
16890243 CTGTAACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATAATAATAATA
Found at i:16894430 original size:23 final size:23
Alignment explanation
Indices: 16894404--16894447 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
16894394 ATTATCACAT
16894404 TTTAAATATGATTCATTAATGTG
1 TTTAAATATGATTCATTAATGTG
*
16894427 TTTAAGTATGATTCATTAATG
1 TTTAAATATGATTCATTAATG
16894448 GTACTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TTTAAATATGATTCATTAATGTG
Found at i:16895149 original size:17 final size:17
Alignment explanation
Indices: 16895127--16895160 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16895117 AAAAAAATTC
*
16895127 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
16895144 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
16895161 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Done.