Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 14 of 128
Found at i:4096353 original size:14 final size:14
Alignment explanation
Indices: 4096336--4096365 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4096326 AAAACATAAA
4096336 CCTTAAACCCTAAC
1 CCTTAAACCCTAAC
*
4096350 CCTTAACCCCTAAC
1 CCTTAAACCCTAAC
4096364 CC
1 CC
4096366 CTCTTTCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTTAAACCCTAAC
Found at i:4096503 original size:7 final size:7
Alignment explanation
Indices: 4096493--4096545 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
4096483 CCTCTAACAT
4096493 CTAACCC
1 CTAACCC
4096500 CTAACCC
1 CTAACCC
*
4096507 CTAA-TC
1 CTAACCC
*
4096513 CTAAACC
1 CTAACCC
4096520 CTAAACCC
1 CT-AACCC
*
4096528 TTAACCC
1 CTAACCC
*
4096535 TTAACCC
1 CTAACCC
4096542 CTAA
1 CTAA
4096546 ACCTTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 5 0.13
7 29 0.74
8 5 0.13
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAACCC
Found at i:4096550 original size:21 final size:21
Alignment explanation
Indices: 4096494--4096551 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4096484 CTCTAACATC
* *
4096494 TAACCCCTAACCCCTAATCC-
1 TAACCCCTAACCCTTAACCCT
*
4096514 TAAACCCTAAACCCTTAACCCT
1 TAACCCCT-AACCCTTAACCCT
*
4096536 TAACCCCTAAACCTTA
1 TAACCCCTAACCCTTA
4096552 TTTAATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.22
Consensus pattern (21 bp):
TAACCCCTAACCCTTAACCCT
Found at i:4096678 original size:13 final size:13
Alignment explanation
Indices: 4096660--4096684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4096650 TAATTAATTT
4096660 AACCCCTAACCCC
1 AACCCCTAACCCC
4096673 AACCCCTAACCC
1 AACCCCTAACCC
4096685 ATAAATCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.60, G:0.00, T:0.08
Consensus pattern (13 bp):
AACCCCTAACCCC
Found at i:4096681 original size:74 final size:76
Alignment explanation
Indices: 4096516--4096684 Score: 252
Period size: 74 Copynumber: 2.2 Consensus size: 76
4096506 CCTAATCCTA
*
4096516 AACCCTAAACCCTTAACCCTTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
1 AACCC-AAACCCCTAACCCTTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
4096581 AATCTAAACCCT
65 AATCTAAACCCT
** *
4096593 AACCCAAATTCCTAACCCTTAACCCCTAAACCTTATTT-A-ATATAAATTAAAACACACTAATTA
1 AACCCAAACCCCTAACCCTTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTA
* *
4096656 ATTTAACCCCT
66 ATCTAAACCCT
*
4096667 AACCCCAACCCCTAACCC
1 AACCCAAACCCCTAACCC
4096685 ATAAATCACA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
74 47 0.57
75 1 0.01
76 30 0.36
77 5 0.06
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (76 bp):
AACCCAAACCCCTAACCCTTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTA
ATCTAAACCCT
Found at i:4097193 original size:41 final size:40
Alignment explanation
Indices: 4097136--4097282 Score: 163
Period size: 41 Copynumber: 3.6 Consensus size: 40
4097126 AGATAAAATG
* *
4097136 TTTTTGAAAAGCGCCGCTAAAGCTCTGAGC-TATAGCGACGC
1 TTTTTCAAAAACGCCGCTAAAGC-CTGAGCAT-TAGCGACGC
*
4097177 TTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC
1 TTTTTCAAAAACGCCGCTAAAG-CCTGAGCATTAGCGACGC
* ** *
4097218 TTCTTGGAAAACGCCGTTAAAAGCCTGAGCATTAGC-AGCGC
1 TTTTTCAAAAACGCCGCT-AAAGCCTGAGCATTAGCGA-CGC
*
4097259 TTTTTCAAAAACGTCGCTAAAGCC
1 TTTTTCAAAAACGCCGCTAAAGCC
4097283 CCAAAATGTC
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
40 6 0.07
41 77 0.87
42 6 0.07
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
TTTTTCAAAAACGCCGCTAAAGCCTGAGCATTAGCGACGC
Found at i:4097362 original size:40 final size:39
Alignment explanation
Indices: 4097307--4097403 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 39
4097297 TGGGCTTAGG
*
4097307 TTTTTTGCGGTGTTTTTCCAAAAAACGCCACTAATGCTC-A
1 TTTTTTGCGGCGTTTTT--AAAAAACGCCACTAATGCTCGA
* ** * *
4097347 TTTTTAGCGGCGTTTTATGTAAAGCGTCACTAATGCTCGA
1 TTTTTTGCGGCGTTTT-TAAAAAACGCCACTAATGCTCGA
4097387 TTTTTTGCGGCGTTTTT
1 TTTTTTGCGGCGTTTTT
4097404 TGTCCAAACG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 17 0.35
40 30 0.62
41 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42
Consensus pattern (39 bp):
TTTTTTGCGGCGTTTTTAAAAAACGCCACTAATGCTCGA
Found at i:4097419 original size:41 final size:38
Alignment explanation
Indices: 4097329--4097420 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 38
4097319 TTTTTCCAAA
4097329 AAACGCCACTAATGCTCATTTTTAGCGGCGTTTTATGT
1 AAACGCCACTAATGCTCATTTTTAGCGGCGTTTTATGT
* * *
4097367 AAAGCGTCACTAATGCTCGATTTTTTGCGGCGTTTTTTGT
1 AAA-CGCCACTAATGCTC-ATTTTTAGCGGCGTTTTATGT
4097407 CCAAACGCCACTAA
1 --AAACGCCACTAA
4097421 AAATGCCGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.07
39 13 0.28
40 19 0.41
41 8 0.17
42 3 0.07
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (38 bp):
AAACGCCACTAATGCTCATTTTTAGCGGCGTTTTATGT
Found at i:4109999 original size:63 final size:62
Alignment explanation
Indices: 4109806--4110026 Score: 228
Period size: 63 Copynumber: 3.5 Consensus size: 62
4109796 CTAAAAAAGA
* * * * *
4109806 TGTTGATGCAAGGAATGATTGCGCGTGCTGTAGCGCTTGTGTAAAATAAATCGGTGCTGAATG
1 TGTTGATGCAGGGAATGATTGTGCGTGCTGTGGTGCTTGTGTAAAATAAATCAGTGCTG-ATG
* * * * * * * *
4109869 TATTGATGTAGGCAATGATTGTGTGTGCTGTGGTACTTGTGTAAAATAAACCAGTGCTTAATA
1 TGTTGATGCAGGGAATGATTGTGCGTGCTGTGGTGCTTGTGTAAAATAAATCAGTGC-TGATG
* * *
4109932 TGTTGATGCAGGGAATGATTATGCGTGTTGTGGTGCTTGTGTAAAATAAATCAGAGCTGATGG
1 TGTTGATGCAGGGAATGATTGTGCGTGCTGTGGTGCTTGTGTAAAATAAATCAGTGCTGAT-G
** *
4109995 TGTTGATGGGGGGAATGAGTT-TGCGTGTTGTG
1 TGTTGATGCAGGGAATGA-TTGTGCGTGCTGTG
4110027 ATTCTTGTAA
Statistics
Matches: 129, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
62 3 0.02
63 123 0.95
64 3 0.02
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.34
Consensus pattern (62 bp):
TGTTGATGCAGGGAATGATTGTGCGTGCTGTGGTGCTTGTGTAAAATAAATCAGTGCTGATG
Found at i:4110034 original size:126 final size:126
Alignment explanation
Indices: 4109805--4110034 Score: 284
Period size: 126 Copynumber: 1.8 Consensus size: 126
4109795 CCTAAAAAAG
* * *
4109805 ATGTTGATGCAAGGAATGATTGCGCGTGCTGTAGCGCTTGTGTAAAATAAATCGGTGCTGAATGT
1 ATGTTGATGCAAGGAATGATTACGCGTGCTGTAGCGCTTGTGTAAAATAAATCAGAGCTGAATGT
* * *
4109870 ATTGATGTAGGCAATGATTGTGTGTGCTGTGGTACTTGTGTAAAATAAACCAGTGCTTAAT
66 ATTGATGGAGGCAATGATTGTGCGTGCTGTGATACTTGTGTAAAATAAACCAGTGCTTAAT
* * * * *
4109931 ATGTTGATGCAGGGAATGATTATGCGTGTTGTGGTGCTTGTGTAAAATAAATCAGAGCTG-ATGG
1 ATGTTGATGCAAGGAATGATTACGCGTGCTGTAGCGCTTGTGTAAAATAAATCAGAGCTGAAT-G
* * * * *
4109995 TGTTGATGGGGGGAATGAGTT-TGCGTGTTGTGATTCTTGT
65 TATTGATGGAGGCAATGA-TTGTGCGTGCTGTGATACTTGT
4110035 AACAAAAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
125 2 0.02
126 82 0.95
127 2 0.02
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (126 bp):
ATGTTGATGCAAGGAATGATTACGCGTGCTGTAGCGCTTGTGTAAAATAAATCAGAGCTGAATGT
ATTGATGGAGGCAATGATTGTGCGTGCTGTGATACTTGTGTAAAATAAACCAGTGCTTAAT
Found at i:4110712 original size:41 final size:41
Alignment explanation
Indices: 4110650--4110797 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
4110640 GAGCGTAAAT
* *
4110650 AGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAAC
1 AGGGACACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
* ** *
4110691 AGCGACACGTACCTGCAATTCAAGGGTACTGAAGTACAAAC
1 AGGGACACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
* * *
4110732 AGGGACACATATGTGTAATTCAGGGGTACTGAAATACAAAC
1 AGGGACACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
* *
4110773 AGGGGCATGTATGTGCAATTCAGGG
1 AGGGACACGTATGTGCAATTCAGGG
4110798 AATAATTAAG
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (41 bp):
AGGGACACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
Found at i:4145052 original size:16 final size:17
Alignment explanation
Indices: 4145016--4145056 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
4145006 CCTACTCCCT
4145016 CCCAATTTAAAACCTAG
1 CCCAATTTAAAACCTAG
*
4145033 CCCAATTTAAATCC-AG
1 CCCAATTTAAAACCTAG
4145049 CCCAATTT
1 CCCAATTT
4145057 TGTCTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.27
Consensus pattern (17 bp):
CCCAATTTAAAACCTAG
Found at i:4145183 original size:16 final size:16
Alignment explanation
Indices: 4145164--4145209 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
4145154 TTTTCATTTT
* *
4145164 TCACTTTCACTTTCAC
1 TCACTCTCACTCTCAC
4145180 TCACTCTCACTCTCA-
1 TCACTCTCACTCTCAC
*
4145195 -CAGTCTCACTCTCAC
1 TCACTCTCACTCTCAC
4145210 GACTCACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.20, C:0.43, G:0.02, T:0.35
Consensus pattern (16 bp):
TCACTCTCACTCTCAC
Found at i:4145993 original size:16 final size:16
Alignment explanation
Indices: 4145972--4146005 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4145962 AATTATTGAA
4145972 TATATTGTAATTAATG
1 TATATTGTAATTAATG
4145988 TATATTGTAATTAATG
1 TATATTGTAATTAATG
4146004 TA
1 TA
4146006 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATTGTAATTAATG
Found at i:4149337 original size:24 final size:24
Alignment explanation
Indices: 4149282--4149340 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
4149272 GGTTTAATGC
* *
4149282 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
4149306 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
4149330 AAATGGATATA
1 AAATGGATATA
4149341 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:4149412 original size:17 final size:17
Alignment explanation
Indices: 4149390--4149450 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
4149380 AATTCAAGAC
4149390 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ** *
4149407 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
4149427 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
4149444 TTATGTA
1 TTATGTA
4149451 GTGATTTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 3 0.09
19 2 0.06
20 10 0.31
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:4149475 original size:9 final size:9
Alignment explanation
Indices: 4149457--4149564 Score: 117
Period size: 9 Copynumber: 11.6 Consensus size: 9
4149447 TGTAGTGATT
*
4149457 TAATTTGGG
1 TAATTCGGG
4149466 TAATTCGGG
1 TAATTCGGG
*
4149475 TAATTTGGG
1 TAATTCGGG
4149484 TAATTTTCGGG
1 TAA--TTCGGG
4149495 TAATTCGGG
1 TAATTCGGG
4149504 TAATTTTCGGG
1 TAA--TTCGGG
4149515 TAATTCGGG
1 TAATTCGGG
*
4149524 TAAGTCGGG
1 TAATTCGGG
*
4149533 TAAGTCGGG
1 TAATTCGGG
*
4149542 TAAGTCGGG
1 TAATTCGGG
**
4149551 TAGGTCGGG
1 TAATTCGGG
4149560 TAATT
1 TAATT
4149565 TTTAACCAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
9 71 0.81
11 17 0.19
ACGTcount: A:0.21, C:0.08, G:0.35, T:0.35
Consensus pattern (9 bp):
TAATTCGGG
Found at i:4149497 original size:11 final size:11
Alignment explanation
Indices: 4149469--4149519 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
4149459 ATTTGGGTAA
4149469 TTCGGGTAA-T
1 TTCGGGTAATT
4149479 TT-GGGTAATT
1 TTCGGGTAATT
4149489 TTCGGGTAA--
1 TTCGGGTAATT
4149498 TTCGGGTAATT
1 TTCGGGTAATT
4149509 TTCGGGTAATT
1 TTCGGGTAATT
4149520 CGGGTAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 15 0.41
10 5 0.14
11 17 0.46
ACGTcount: A:0.20, C:0.08, G:0.29, T:0.43
Consensus pattern (11 bp):
TTCGGGTAATT
Found at i:4152898 original size:18 final size:19
Alignment explanation
Indices: 4152875--4152910 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4152865 AACTACACCT
4152875 AATATATTTA-CTTTTTTA
1 AATATATTTATCTTTTTTA
4152893 AATATATTTATCTTTTTT
1 AATATATTTATCTTTTTT
4152911 TCATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
AATATATTTATCTTTTTTA
Found at i:4156448 original size:21 final size:21
Alignment explanation
Indices: 4156406--4156456 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4156396 TTTTGAATTA
* *
4156406 AAATTAAA-T-TAAAATAATT
1 AAATTAAATTATAAAAAAACT
*
4156425 AAATTAGATTATAAAAAAACT
1 AAATTAAATTATAAAAAAACT
4156446 AAATTAAATTA
1 AAATTAAATTA
4156457 ATATCTAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 18 0.69
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATTAAATTATAAAAAAACT
Found at i:4157533 original size:96 final size:96
Alignment explanation
Indices: 4157419--4157613 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
4157409 TCTCCCAAGT
4157419 ACACAAGGTTAACCCATAACACAAGAGTTTAACATATATCTTATAGCATGTCATCTATACTTAGA
1 ACACAAGGTTAACCCATAACACAAGAGTTTAACATATATCTTATAGCATGTCATCTATACTTAGA
4157484 AGCCATCCAAAATTGTTTAATGGGTCAATTA
66 AGCCATCCAAAATTGTTTAATGGGTCAATTA
*
4157515 ACACAAGGTTAACCCATAACACAAGAGTTTAAGATATATCTTATAGCATGTCATCTATACTTAGA
1 ACACAAGGTTAACCCATAACACAAGAGTTTAACATATATCTTATAGCATGTCATCTATACTTAGA
4157580 AGCCATCCAAAATTGTTTAATGGGTCAATTA
66 AGCCATCCAAAATTGTTTAATGGGTCAATTA
4157611 ACA
1 ACA
4157614 TACCTAACAT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (96 bp):
ACACAAGGTTAACCCATAACACAAGAGTTTAACATATATCTTATAGCATGTCATCTATACTTAGA
AGCCATCCAAAATTGTTTAATGGGTCAATTA
Found at i:4165423 original size:20 final size:20
Alignment explanation
Indices: 4165400--4165465 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
4165390 GTACTGGCAT
4165400 CTTGTCTGCAACACTGGTGG
1 CTTGTCTGCAACACTGGTGG
** ** *
4165420 CTTGTCCACATTATTGGCT-G
1 CTTGTCTGCAACACTGG-TGG
* *
4165440 CTTGTTTGCAGCACTGGTGG
1 CTTGTCTGCAACACTGGTGG
4165460 CTTGTC
1 CTTGTC
4165466 CATAATACTA
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.27, T:0.36
Consensus pattern (20 bp):
CTTGTCTGCAACACTGGTGG
Found at i:4165503 original size:20 final size:20
Alignment explanation
Indices: 4165480--4165585 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
4165470 ATACTAACAA
*
4165480 CTTGTCTGCAATTCTAGTGG
1 CTTGTCTGCAATTCTGGTGG
** * **
4165500 CTTGTCCACAATACTGGTAC
1 CTTGTCTGCAATTCTGGTGG
*
4165520 CTTGTCTGCAATTATGGTGG
1 CTTGTCTGCAATTCTGGTGG
** * *
4165540 CTTGTCCACAATACTGCTGG
1 CTTGTCTGCAATTCTGGTGG
* *
4165560 TTTATCTGCAATAT-TGGTGG
1 CTTGTCTGCAAT-TCTGGTGG
4165580 CTTGTC
1 CTTGTC
4165586 CATAAACTGG
Statistics
Matches: 60, Mismatches: 25, Indels: 2
0.69 0.29 0.02
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.38
Consensus pattern (20 bp):
CTTGTCTGCAATTCTGGTGG
Found at i:4165568 original size:40 final size:40
Alignment explanation
Indices: 4165454--4165587 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 40
4165444 TTTGCAGCAC
* * * * *
4165454 TGGTGGCTTGTCCATAATACTAAC-AACTTGTCTGCAATTC
1 TGGTGGCTTGTCCACAATACT-GCTACCTTATCTGCAATTA
* * *
4165494 TAGTGGCTTGTCCACAATACTGGTACCTTGTCTGCAATTA
1 TGGTGGCTTGTCCACAATACTGCTACCTTATCTGCAATTA
***
4165534 TGGTGGCTTGTCCACAATACTGCTGGTTTATCTGCAA-TA
1 TGGTGGCTTGTCCACAATACTGCTACCTTATCTGCAATTA
4165573 TTGGTGGCTTGTCCA
1 -TGGTGGCTTGTCCA
4165588 TAAACTGGTG
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
39 2 0.03
40 78 0.98
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (40 bp):
TGGTGGCTTGTCCACAATACTGCTACCTTATCTGCAATTA
Found at i:4169981 original size:14 final size:17
Alignment explanation
Indices: 4169961--4170001 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 17
4169951 TGAAATTTCT
4169961 TCTATGAATCCA-CATA
1 TCTATGAATCCACCATA
*
4169977 -C-ATGAGTCCACCATA
1 TCTATGAATCCACCATA
4169992 TCTATGAATC
1 TCTATGAATC
4170002 ATCTTCTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
14 8 0.40
15 5 0.25
16 1 0.05
17 6 0.30
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (17 bp):
TCTATGAATCCACCATA
Found at i:4177893 original size:17 final size:17
Alignment explanation
Indices: 4177871--4177908 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4177861 TTAGTTGTTC
4177871 TAAATCTAGAATAGTCA
1 TAAATCTAGAATAGTCA
4177888 TAAATCTAGAATAGTCA
1 TAAATCTAGAATAGTCA
4177905 TAAA
1 TAAA
4177909 CGAGTACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (17 bp):
TAAATCTAGAATAGTCA
Found at i:4178871 original size:11 final size:10
Alignment explanation
Indices: 4178845--4178869 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4178835 GATCTCTCAA
4178845 TTTTTAAAAC
1 TTTTTAAAAC
4178855 TTTTTAAAAC
1 TTTTTAAAAC
4178865 TTTTT
1 TTTTT
4178870 TAGATAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTTAAAAC
Found at i:4181286 original size:19 final size:19
Alignment explanation
Indices: 4181262--4181298 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4181252 TAGGTAGCAA
*
4181262 TTTTTTAATTGATTTTAAT
1 TTTTTTAATTGAGTTTAAT
4181281 TTTTTTAATTGAGTTTAA
1 TTTTTTAATTGAGTTTAA
4181299 AGAGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTAATTGAGTTTAAT
Found at i:4183365 original size:60 final size:61
Alignment explanation
Indices: 4183217--4183390 Score: 233
Period size: 61 Copynumber: 2.9 Consensus size: 61
4183207 CTAGGAAAGA
* * * *
4183217 GAAAGTCTTTGTGGTGAGTACTGGATATTAAGGAATGCCTTTATGACACAACTCTAGACAG
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGGAATGCCTTTATGGCACAACTCTAGACAG
* * * * *
4183278 GAAAGCCTTTGTGGCGAGTAATAGATACTAAGAAATGCCTTTGTGGCACAACTCTGGACA-
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGGAATGCCTTTATGGCACAACTCTAGACAG
* * *
4183338 TAAAGCCTTTGTGGCAAGTACTGGATACTAAGGAATGCCTTTATGGAACAACT
1 GAAAGCCTTTGTGGCGAGTACTGGATACTAAGGAATGCCTTTATGGCACAACT
4183391 TCAAGATAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 46 0.47
61 51 0.53
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCGAGTACTGGATACTAAGGAATGCCTTTATGGCACAACTCTAGACAG
Found at i:4183684 original size:10 final size:10
Alignment explanation
Indices: 4183665--4183695 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4183655 ATTGTCCTCA
4183665 ATGTATAAAC
1 ATGTATAAAC
*
4183675 ATGTACAAAC
1 ATGTATAAAC
4183685 ATGTATAAAC
1 ATGTATAAAC
4183695 A
1 A
4183696 CAAAATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (10 bp):
ATGTATAAAC
Found at i:4183973 original size:5 final size:6
Alignment explanation
Indices: 4183937--4183979 Score: 50
Period size: 6 Copynumber: 6.5 Consensus size: 6
4183927 GAAGTCTAAG
4183937 AAAATA AAAATA GAACAACTA AAAATAA AAAATA AAAATA AAA
1 AAAATA AAAATA -AA-AA-TA AAAAT-A AAAATA AAAATA AAA
4183980 CCAAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 17 0.52
7 10 0.30
8 4 0.12
9 2 0.06
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:4183986 original size:13 final size:13
Alignment explanation
Indices: 4183937--4183979 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
4183927 GAAGTCTAAG
4183937 AAAATAAAAATAGA
1 AAAATAAAAATA-A
*
4183951 ACAACTAAAAATAA
1 A-AAATAAAAATAA
4183965 AAAATAAAAATAA
1 AAAATAAAAATAA
4183978 AA
1 AA
4183980 CCAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 13 0.50
14 3 0.12
15 10 0.38
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:4185618 original size:26 final size:26
Alignment explanation
Indices: 4185589--4185643 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
4185579 TAAAAGGACT
* * *
4185589 AAAAAT-AGATAACATACAAAATAAA
1 AAAAATAAAATAAAATAAAAAATAAA
*
4185614 GAAAATAAAATAAAATAAAAAATAAA
1 AAAAATAAAATAAAATAAAAAATAAA
4185640 AAAA
1 AAAA
4185644 TCAAAAGGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (26 bp):
AAAAATAAAATAAAATAAAAAATAAA
Found at i:4185642 original size:19 final size:19
Alignment explanation
Indices: 4185606--4185649 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
4185596 GATAACATAC
*
4185606 AAAATAAAGAAAATAAAAT
1 AAAATAAAGAAAAAAAAAT
*
4185625 AAAATAAAAAATAAAAAAAT
1 AAAATAAAGAA-AAAAAAAT
4185645 CAAAA
1 -AAAA
4185650 GGAGGAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAATAAAGAAAAAAAAAT
Found at i:4185649 original size:26 final size:26
Alignment explanation
Indices: 4185597--4185649 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
4185587 CTAAAAATAG
* *
4185597 ATAACATACAAAATAAAGAAAATAAA
1 ATAAAATAAAAAATAAAGAAAATAAA
4185623 ATAAAATAAAAAATAAA-AAAATCAAA
1 ATAAAATAAAAAATAAAGAAAAT-AAA
4185649 A
1 A
4185650 GGAGGAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (26 bp):
ATAAAATAAAAAATAAAGAAAATAAA
Found at i:4189654 original size:14 final size:13
Alignment explanation
Indices: 4189635--4189685 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
4189625 CAAACAAAAG
4189635 AAAAATTAAAATAT
1 AAAAA-TAAAATAT
*
4189649 AAAAATTAAAT-T
1 AAAAATAAAATAT
4189661 AAAACA-AAAATAT
1 AAAA-ATAAAATAT
4189674 AAAAATAAAATA
1 AAAAATAAAATA
4189686 GAAATGACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 10 0.31
13 17 0.53
14 5 0.16
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:4189690 original size:19 final size:19
Alignment explanation
Indices: 4189635--4189690 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
4189625 CAAACAAAAG
4189635 AAAAATTAAAATATAAAA-AT
1 AAAAA-TAAAATA-AAAATAT
* * *
4189655 TAAATTAAAACAAAAATAT
1 AAAAATAAAATAAAAATAT
*
4189674 AAAAATAAAATAGAAAT
1 AAAAATAAAATAAAAAT
4189691 GACTAAATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 4 0.14
19 21 0.75
20 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATAAAATAAAAATAT
Found at i:4194487 original size:29 final size:28
Alignment explanation
Indices: 4194448--4194575 Score: 130
Period size: 29 Copynumber: 4.4 Consensus size: 28
4194438 TTTCCACAAT
* *
4194448 GCATTCTTTTAACATAGATGACCACAAAG
1 GCATCCTTTTAACAGAGATGA-CACAAAG
* *
4194477 GCATCCTTTTAACAGAGATAGCCACAAAT
1 GCATCCTTTTAACAGAGAT-GACACAAAG
* *
4194506 GCATCCTTTTAAAAGAGACAGACACAAAG
1 GCATCCTTTTAACAGAGA-TGACACAAAG
* *
4194535 GCTTCCATTTAACAGAGATCGACACAAAG
1 GCATCCTTTTAACAGAGAT-GACACAAAG
* *
4194564 GCTTCTTTTTAA
1 GCATCCTTTTAA
4194576 AGATATCCAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 81 0.99
30 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (28 bp):
GCATCCTTTTAACAGAGATGACACAAAG
Found at i:4199066 original size:2 final size:2
Alignment explanation
Indices: 4199059--4199091 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4199049 CGATCTTTTA
*
4199059 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4199092 AAAACATTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4209990 original size:12 final size:12
Alignment explanation
Indices: 4209973--4209998 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4209963 AACTTCATGG
4209973 TATAAAAAATTA
1 TATAAAAAATTA
4209985 TATAAAAAATTA
1 TATAAAAAATTA
4209997 TA
1 TA
4209999 GTGTTTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATAAAAAATTA
Found at i:4217666 original size:45 final size:45
Alignment explanation
Indices: 4217599--4217687 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
4217589 NNNNNNTACT
*
4217599 GTTACTGTTATCGATTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTATCGATTCAGCACTTTGTGTGTCGAATACTGTTACC
*
4217644 GTTACTGTTA-CAGATTCAGCACTTTGTGTGTTGAATACTGTTAC
1 GTTACTGTTATC-GATTCAGCACTTTGTGTGTCGAATACTGTTAC
4217688 TGCTACCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (45 bp):
GTTACTGTTATCGATTCAGCACTTTGTGTGTCGAATACTGTTACC
Found at i:4217699 original size:45 final size:45
Alignment explanation
Indices: 4217611--4217704 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
4217601 TACTGTTATC
* * *
4217611 GATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACA
1 GATTCAGCACTTTGTGTGTCGAATACTGTTACCGCTACCGTTACA
* * *
4217656 GATTCAGCACTTTGTGTGTTGAATACTGTTACTGCTACCGTTACT
1 GATTCAGCACTTTGTGTGTCGAATACTGTTACCGCTACCGTTACA
4217701 GATT
1 GATT
4217705 ACTGTATACT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (45 bp):
GATTCAGCACTTTGTGTGTCGAATACTGTTACCGCTACCGTTACA
Found at i:4218877 original size:12 final size:12
Alignment explanation
Indices: 4218860--4218893 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4218850 CGGCCAGTCC
4218860 ATATTAATTTTT
1 ATATTAATTTTT
*
4218872 ATATTATTTTTT
1 ATATTAATTTTT
4218884 ATA-TAATTTT
1 ATATTAATTTT
4218894 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:4220623 original size:14 final size:15
Alignment explanation
Indices: 4220592--4220624 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4220582 ATCATGTTTT
*
4220592 TTTTTATTTAATCTC
1 TTTTGATTTAATCTC
4220607 TTTTGATTTAATC-C
1 TTTTGATTTAATCTC
4220621 TTTT
1 TTTT
4220625 TTTTCTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTGATTTAATCTC
Found at i:4227071 original size:9 final size:8
Alignment explanation
Indices: 4227057--4227099 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
4227047 AAATTTTTCA
4227057 TTTAAATT
1 TTTAAATT
4227065 CTTTAAAATT
1 -TTT-AAATT
4227075 TTTAAAGTT
1 TTTAAA-TT
*
4227084 TTTAAAAT
1 TTTAAATT
4227092 TTTAAATT
1 TTTAAATT
4227100 AGTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 11 0.37
9 14 0.47
10 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (8 bp):
TTTAAATT
Found at i:4227080 original size:18 final size:16
Alignment explanation
Indices: 4227057--4227099 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
4227047 AAATTTTTCA
4227057 TTTAAATTCTTTAAAATT
1 TTTAAATT-TTTAAAA-T
4227075 TTTAAAGTTTTTAAAAT
1 TTTAAA-TTTTTAAAAT
4227092 TTTAAATT
1 TTTAAATT
4227100 AGTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 7 0.29
18 13 0.54
19 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTAAATTTTTAAAAT
Found at i:4228585 original size:126 final size:124
Alignment explanation
Indices: 4228338--4228713 Score: 511
Period size: 126 Copynumber: 3.0 Consensus size: 124
4228328 GGATTGTTTG
* *
4228338 GGTCTTGAAAAAATTATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTA-CTAG
1 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC-AG
* * *
4228402 GATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACACGATTTTGCTACAGTA
65 GATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGATTTTGCTACAGTA
* * * *
4228462 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACACTTCAAGCA
1 GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAG--TATAAAATCGCTTCTAGCA
** * * * ** * *
4228527 GGATGCGATCTGAGAAAAATTTCTGAAATCGCGCCTTCGTGGACGCGGTTTTGCTACAGTT
64 GGATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGATTTTGCTACAGTA
* * *
4228588 GGTCCTGAAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTGGCAA
1 GGTCCTGAAA-AAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAG
*
4228653 GATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
65 GATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGATTTTGCTACAGTA
4228713 G
1 G
4228714 CATGTTTAGG
Statistics
Matches: 215, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
124 42 0.20
125 66 0.31
126 73 0.34
127 34 0.16
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (124 bp):
GGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGG
ATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGATTTTGCTACAGTA
Found at i:4230462 original size:45 final size:45
Alignment explanation
Indices: 4230388--4230564 Score: 212
Period size: 45 Copynumber: 4.0 Consensus size: 45
4230378 AACGGTAGTT
* * * * *
4230388 GTAACAGTAACAATATTCAACACACAAAGTGCTGAACCTGTAACA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
* * * * *
4230433 GTAACGGTAACAGTATTCGACATATAAAGTGCCGAGTCGGTAACA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
*
4230478 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGAAACA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
* * * *
4230523 GTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAATCAGTAA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
4230565 GACGGCAAAT
Statistics
Matches: 112, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 15 0.13
45 97 0.87
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
Found at i:4230533 original size:90 final size:89
Alignment explanation
Indices: 4230388--4230554 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 89
4230378 AACGGTAGTT
* * * * *
4230388 GTAACAGTAACAATATTCAACACACAAAGTGCTGAACCTGTAACAGTAACGGTAACAGTATTCGA
1 GTAACAGTAACAATATTCAACACACAAAGTGCCGAACCAGAAACAGTAACAGTAACAGTAGTCGA
*
4230453 CATATAAAGTGCCGAGTCGGTAACA
66 CACAT-AAGTGCCGAGTCGGTAACA
* * * *
4230478 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGAAACAGTAACAGTAACAGTAGTCGG
1 GTAACAGTAACAATATTCAACACACAAAGTGCCGAACCAGAAACAGTAACAGTAACAGTAGTCGA
4230543 CACATAAGTGCC
66 CACATAAGTGCC
4230555 TAATCAGTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 7 0.10
90 60 0.90
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (89 bp):
GTAACAGTAACAATATTCAACACACAAAGTGCCGAACCAGAAACAGTAACAGTAACAGTAGTCGA
CACATAAGTGCCGAGTCGGTAACA
Found at i:4230866 original size:45 final size:44
Alignment explanation
Indices: 4230814--4230901 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
4230804 CCGAGTCGGT
*
4230814 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGA
1 AACAGTAACAGTAACAGTAGTCGACACA-AAAGTGCCGAATCAGA
* * *
4230859 AACAGTAACAGTAACAGTAGTCGGCACATAAGTGCCTAATCAG
1 AACAGTAACAGTAACAGTAGTCGACACAAAAGTGCCGAATCAG
4230902 TAAGACGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 13 0.33
45 26 0.67
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (44 bp):
AACAGTAACAGTAACAGTAGTCGACACAAAAGTGCCGAATCAGA
Found at i:4234816 original size:21 final size:21
Alignment explanation
Indices: 4234770--4235217 Score: 430
Period size: 21 Copynumber: 21.3 Consensus size: 21
4234760 ATTAAGTTAA
4234770 GGGTTTTTAGGTTAAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
*
4234791 AGGGTTTTTAGGTTGAGGGTTT
1 -GGGTTTTTAGGTTAAGGGTTT
4234813 GGGTTTTTAGGTTAAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
* * *
4234834 AAGGTTTTTAGGTTGAGGGTTA
1 -GGGTTTTTAGGTTAAGGGTTT
* *
4234856 GGGTTTTTAGGTTTAGGGTTA
1 GGGTTTTTAGGTTAAGGGTTT
* * * *
4234877 AGGTTTTTATGTTGAGGGTTA
1 GGGTTTTTAGGTTAAGGGTTT
* *
4234898 GGGGTTTTAAGTTAAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
* *
4234919 AGGGTTTTTAGGTTTATGGTTT
1 -GGGTTTTTAGGTTAAGGGTTT
4234941 AGGG--TTTAGGGTTAA------
1 -GGGTTTTTA-GGTTAAGGGTTT
* *
4234956 -GGTTTCTAGGTTAAGGGTTA
1 GGGTTTTTAGGTTAAGGGTTT
* *
4234976 GGGTTTTTAGGTTGAGGGTTA
1 GGGTTTTTAGGTTAAGGGTTT
* *
4234997 AGGTTTTTAGGTTGAGGGTTAT
1 GGGTTTTTAGGTTAAGGGTT-T
4235019 -GGTTTTTAGGTTAAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
* *
4235039 AGCGTTTTTAGGTTAAGGGTTA
1 -GGGTTTTTAGGTTAAGGGTTT
* * *
4235061 GGGTATTTAGGTTGAGGGTTA
1 GGGTTTTTAGGTTAAGGGTTT
4235082 GGGTTTTTAGGTTAAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
**
4235103 CTAGTTTTTAGGTTAAGGGTTT
1 -GGGTTTTTAGGTTAAGGGTTT
* * *
4235125 AGGGTTTTGAGGTTAAAGGTTA
1 -GGGTTTTTAGGTTAAGGGTTT
*
4235147 GGGTTTTTAGGTTAAGAGTTT
1 GGGTTTTTAGGTTAAGGGTTT
*
4235168 AGGGTTTTTAGGTTAAGGGTTA
1 -GGGTTTTTAGGTTAAGGGTTT
*
4235190 GGGTTTTTAGGTTGAGGGTTT
1 GGGTTTTTAGGTTAAGGGTTT
4235211 AGGGTTT
1 -GGGTTT
4235218 AGGGTTTAAG
Statistics
Matches: 358, Mismatches: 50, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.01
14 6 0.02
15 3 0.01
20 5 0.01
21 205 0.57
22 137 0.38
ACGTcount: A:0.18, C:0.01, G:0.37, T:0.45
Consensus pattern (21 bp):
GGGTTTTTAGGTTAAGGGTTT
Found at i:4234818 original size:43 final size:43
Alignment explanation
Indices: 4234769--4235352 Score: 605
Period size: 43 Copynumber: 14.1 Consensus size: 43
4234759 AATTAAGTTA
*
4234769 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* * *
4234812 TGGGTTTTTAGGTTAAGGGTTTAAGGTTTTTAGGTTGAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* * * *
4234855 AGGGTTTTTAGGTTTAGGG-TTAAGGTTTTTATGTTGAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* *
4234897 AGGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAGG-T-----TT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* * * *
4234934 ATGG--TTTAGGGTTTAGGG-TTAAGGTTTCTAGGTTAAGGGTT
1 AGGGTTTTTA-GGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* * *
4234975 AGGGTTTTTAGGTTGAGGG-TTAAGGTTTTTAGGTTGAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* *
4235017 ATGGTTTTTAGGTTAAGGGTTTAGCGTTTTTAGGTTAAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* *
4235060 AGGGTATTTAGGTTGAGGG-TTAGGGTTTTTAGGTTAAGGGTTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGG-TT
*** * *
4235103 CTAGTTTTTAGGTTAAGGGTTTAGGGTTTTGAGGTTAAAGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
*
4235146 AGGGTTTTTAGGTTAAGAGTTTAGGGTTTTTAGGTTAAGGGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* *
4235189 AGGGTTTTTAGGTTGAGGGTTTAGGG--TTTA-G----GGTTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
* * * *
4235225 A-AGTTTTTAGGTTTAGGGTTTATGG---TT--GTTAAGTGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
*
4235262 AGGGTTTTTAGGTTAAGGG-TTAGGGTTTTTAGGTTGAA-TGTT
1 AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTT-AAGGGTT
*
4235304 AGGGTTCTTT-GGTTAAGGGTTTA-GGTTTTTAGGTTTAGGGTTT
1 AGGGTT-TTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGG-TT
4235347 AGGGTT
1 AGGGTT
4235353 AGGGTTTTTA
Statistics
Matches: 459, Mismatches: 54, Indels: 56
0.81 0.09 0.10
Matches are distributed among these distances:
33 1 0.00
34 2 0.00
35 37 0.08
36 13 0.03
37 14 0.03
38 15 0.03
40 3 0.01
41 10 0.02
42 140 0.31
43 205 0.45
44 19 0.04
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (43 bp):
AGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTT
Found at i:4234874 original size:64 final size:64
Alignment explanation
Indices: 4234765--4235352 Score: 557
Period size: 64 Copynumber: 9.5 Consensus size: 64
4234755 TTATAATTAA
* *
4234765 GTTAAGGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTGAGGGTTTGGGTTTTTAGGTTAAGG
1 GTTAA-GGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
* * * * *
4234830 GTTTAAGGTTTTTAGGTTGAGGG-TTAGGGTTTTTAGGTTTAGGGTTAAGGTTTTTATGTTGAGG
1 G-TTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
* * * * *
4234894 GTTAGGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAGG-T-----TTATGG--TTTAGGGTTTAGG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTA-GGTTAAGG
* * * *
4234951 GTTAAGGTTTCTAGGTTAAGGG-TTAGGGTTTTTAGGTTGAGGGTTAAGGTTTTTAGGTTGAGG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
* * * *
4235014 GTTATGGTTTTTAGGTTAAGGGTTTAGCGTTTTTAGGTTAAGGGTTAGGGTATTTAGGTTGAGG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
* *** * *
4235078 GTTAGGGTTTTTAGGTTAAGGGTTTCTAGTTTTTAGGTTAAGGGTTTAGGGTTTTGAGGTTAAAG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGG-TTAGGGTTTTTAGGTTAAGG
* * *
4235143 GTTAGGGTTTTTAGGTTAAGAGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTGAGG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
* * * * * *
4235207 GTTTA-G------GGTTTAGGGTTTA-AGTTTTTAGGTTTAGGGTTTATGGTTGTTAAGTGTT-A
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGG-TTAGGGTT-TTTAG-GTTAA
4235263 --
63 GG
*
4235263 G----GGTTTTTAGGTTAAGGG-TTAGGGTTTTTAGGTTGAA-TGTTAGGGTTCTTT-GGTTAAG
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTT-AAGGGTTAGGGTT-TTTAGGTTAAG
4235321 G
64 G
* *
4235322 GTTTAGGTTTTTAGGTTTAGGGTTTAGGGTT
1 GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTT
4235353 AGGGTTTTTA
Statistics
Matches: 434, Mismatches: 56, Indels: 67
0.78 0.10 0.12
Matches are distributed among these distances:
53 1 0.00
56 37 0.09
57 45 0.10
58 22 0.05
59 24 0.06
60 1 0.00
62 5 0.01
63 62 0.14
64 160 0.37
65 73 0.17
66 4 0.01
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (64 bp):
GTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAGGTTAAGG
Found at i:4234943 original size:13 final size:13
Alignment explanation
Indices: 4234914--4235230 Score: 63
Period size: 15 Copynumber: 22.4 Consensus size: 13
4234904 TTAAGTTAAG
4234914 GGTTTAGGGTTTTTA
1 GGTTTAGGG--TTTA
*
4234929 GGTTTATGGTTTA
1 GGTTTAGGGTTTA
*
4234942 GGGTTTAGGGTTAA
1 -GGTTTAGGGTTTA
*
4234956 GGTTTCTA-GGTTAA
1 GG-TT-TAGGGTTTA
*
4234970 GGGTTAGGGTTTTTA
1 GGTTTAGGG--TTTA
* *
4234985 GGTTGAGGGTTAA
1 GGTTTAGGGTTTA
*
4234998 GGTTTTTA-GGTTGA
1 GG--TTTAGGGTTTA
* *
4235012 GGGTTATGGTTTTTA
1 GGTTTA-GG-GTTTA
*
4235027 GGTTAAGGGTTTA
1 GGTTTAGGGTTTA
*
4235040 GCGTTTTTA-GGTTAA
1 G-G--TTTAGGGTTTA
*
4235055 GGGTTAGGGTATTTA
1 GGTTTAGGG--TTTA
*
4235070 GGTTGAGGG-TTA
1 GGTTTAGGGTTTA
*
4235082 GGGTTTTTA-GGTTAA
1 -GG--TTTAGGGTTTA
**
4235097 GGGTTTCTAGTTTTTA
1 -GG-TT-TAGGGTTTA
*
4235113 GGTTAAGGGTTTA
1 GGTTTAGGGTTTA
* *
4235126 GGGTTTTGAGGTTAAA
1 -GGTTTAG-GGTT-TA
4235142 GG-TTAGGGTTTTTA
1 GGTTTAGGG--TTTA
* *
4235156 GGTTAAGAGTTTA
1 GGTTTAGGGTTTA
*
4235169 GGGTTTTTA-GGTTAA
1 -GG--TTTAGGGTTTA
*
4235184 GGGTTAGGGTTTTTA
1 GGTTTAGGG--TTTA
*
4235199 GGTTGAGGGTTTA
1 GGTTTAGGGTTTA
4235212 GGGTTTAGGGTTTA
1 -GGTTTAGGGTTTA
*
4235226 AGTTT
1 GGTTT
4235231 TTAGGTTTAG
Statistics
Matches: 220, Mismatches: 46, Indels: 74
0.65 0.14 0.22
Matches are distributed among these distances:
12 14 0.06
13 45 0.20
14 67 0.30
15 84 0.38
16 10 0.05
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.44
Consensus pattern (13 bp):
GGTTTAGGGTTTA
Found at i:4235223 original size:21 final size:21
Alignment explanation
Indices: 4234775--4235359 Score: 99
Period size: 21 Copynumber: 27.5 Consensus size: 21
4234765 GTTAAGGGTT
*
4234775 TTTA-GGTTAAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
*
4234795 TTTTTA-GGTTGAGGGTTT-GGG
1 --TTTAGGGTTTAGGGTTTAGGG
* *
4234816 TTTTTA-GGTTAAGGGTTTAAGGTT
1 --TTTAGGGTTTAGGGTTT-AGG-G
*
4234840 TTTA-GGTTGAGGG-TTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
* *
4234859 TTTTTA-GGTTTAGGGTTAAGGTT
1 --TTTAGGGTTTAGGGTTTAGG-G
* *
4234882 TTTA-TGTTGAGGG-TTAGGGG
1 TTTAGGGTTTAGGGTTTA-GGG
* *
4234902 TTTTA-AGTTAAGGGTTTAGGG
1 -TTTAGGGTTTAGGGTTTAGGG
*
4234923 TTTTTA-GGTTTATGGTTTAGGG
1 --TTTAGGGTTTAGGGTTTAGGG
* *
4234945 TTTAGGGTTAAGGTTTCTA-GG
1 TTTAGGGTTTAGGGTT-TAGGG
*
4234966 TTAAGGG-TTAGGGTTTTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
* * *
4234987 TTGAGGGTTAAGGTTTTTA-GG
1 TTTAGGGTTTAGG-GTTTAGGG
* *
4235008 TTGAGGG-TTATGGTTTTTA-GG
1 TTTAGGGTTTA-GG-GTTTAGGG
* *
4235029 TTAAGGGTTTAGCGTTTTTA-GG
1 TTTAGGGTTTAG-G-GTTTAGGG
*
4235051 TTAAGGG-TTAGGGTATTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
*
4235072 TTGAGGG-TTAGGGTTTTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
* **
4235093 TTAAGGGTTTCTAGTTTTTA-GG
1 TTTAGGG-TT-TAGGGTTTAGGG
* *
4235115 TTAAGGGTTTAGGGTTTTGAGG
1 TTTAGGGTTTAGGGTTTAG-GG
* *
4235137 TTAAAGG-TTAGGGTTTTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
* *
4235158 TTAAGAGTTTAGGGTTTTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
*
4235180 TTAAGGG-TTAGGGTTTTTA-GG
1 TTTAGGGTTTAGGG--TTTAGGG
*
4235201 TTGAGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
**
4235222 TTTAAGTTTTTA-GGTTTAGGG
1 TTT-AGGGTTTAGGGTTTAGGG
* *
4235243 TTTATGGTTGTTA-AGTGTTAGGG
1 TTTA-GGGT-TTAGGGT-TTAGGG
*
4235266 TTTTTA-GGTTAAGGG-TTAGGG
1 --TTTAGGGTTTAGGGTTTAGGG
* **
4235287 TTTTTA-GGTTGAATG-TTAGGG
1 --TTTAGGGTTTAGGGTTTAGGG
** * *
4235308 TTCTTTGGTTAAGGGTTTAGGTT
1 TT-TAGGGTTTAGGGTTTAGG-G
4235331 TTTA-GGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
4235351 -TTAGGGTTT
1 TTTAGGGTTT
4235360 TTACCTTAAG
Statistics
Matches: 457, Mismatches: 62, Indels: 90
0.75 0.10 0.15
Matches are distributed among these distances:
19 5 0.01
20 33 0.07
21 250 0.55
22 145 0.32
23 17 0.04
24 3 0.01
25 4 0.01
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAGGG
Found at i:4235340 original size:14 final size:14
Alignment explanation
Indices: 4235321--4235362 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
4235311 TTTGGTTAAG
4235321 GGTTTAGGTTTTTA
1 GGTTTAGGTTTTTA
*
4235335 GGTTTAGG-GTTTA
1 GGTTTAGGTTTTTA
*
4235348 GGGTTAGGGTTTTTA
1 GGTTTA-GGTTTTTA
4235363 CCTTAAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (14 bp):
GGTTTAGGTTTTTA
Found at i:4235350 original size:28 final size:27
Alignment explanation
Indices: 4235314--4235398 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 27
4235304 AGGGTTCTTT
*
4235314 GGTTAAGGGTTTAGGTTTTTAGGTTTAG
1 GGTTTAGGG-TTAGGTTTTTAGGTTTAG
** *
4235342 GGTTTAGGGTTAGGGTTTTTACCTTAAG
1 GGTTTAGGGTTA-GGTTTTTAGGTTTAG
4235370 GGTTTA----TA-GTTTTTAGGTTTAG
1 GGTTTAGGGTTAGGTTTTTAGGTTTAG
4235392 GGTTTAG
1 GGTTTAG
4235399 CAATTTTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
22 17 0.35
24 2 0.04
27 3 0.06
28 26 0.54
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (27 bp):
GGTTTAGGGTTAGGTTTTTAGGTTTAG
Found at i:4235426 original size:21 final size:21
Alignment explanation
Indices: 4235402--4235441 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4235392 GGTTTAGCAA
*
4235402 TTTTAATTTAA-AAGTTAGGGT
1 TTTTAAGTTAAGAA-TTAGGGT
4235423 TTTTAAGTTAAGAATTAGG
1 TTTTAAGTTAAGAATTAGG
4235442 ATTAAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTTAAGTTAAGAATTAGGGT
Found at i:4236038 original size:18 final size:18
Alignment explanation
Indices: 4236015--4236054 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4236005 GACTCGGAAA
* *
4236015 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
4236033 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
4236051 AGGA
1 AGGA
4236055 AACACACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:4237986 original size:23 final size:23
Alignment explanation
Indices: 4237960--4238015 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
4237950 ATTAAATATG
*
4237960 AATTTGAGAGAAATTTG-GAAGGA
1 AATTTGAGAGAAACTTGAG-AGGA
*
4237983 AA-TTGAGAGGAACTTGAGAGGA
1 AATTTGAGAGAAACTTGAGAGGA
*
4238005 AATTTGGGAGA
1 AATTTGAGAGA
4238016 GGATTTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.23
Consensus pattern (23 bp):
AATTTGAGAGAAACTTGAGAGGA
Found at i:4239521 original size:58 final size:58
Alignment explanation
Indices: 4239447--4239573 Score: 200
Period size: 58 Copynumber: 2.2 Consensus size: 58
4239437 TAGGACCCCC
* *
4239447 CACACGGTCTTGTCTTCCCTGCAGGTTGATTTTGCAATTTTCACACGGTCAAAGTCTCT
1 CACACGG-CCTGTCTTCCCTGCAGGTTGATTTTGCAATTTTCACACGGCCAAAGTCTCT
* * *
4239506 TACACGGCCTGTCTTCCCTGTAGGTTGATTTTGCAATTTTCACACGGCCACAGTCTCT
1 CACACGGCCTGTCTTCCCTGCAGGTTGATTTTGCAATTTTCACACGGCCAAAGTCTCT
4239564 CACACGGCCT
1 CACACGGCCT
4239574 AGCCACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 56 0.90
59 6 0.10
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.33
Consensus pattern (58 bp):
CACACGGCCTGTCTTCCCTGCAGGTTGATTTTGCAATTTTCACACGGCCAAAGTCTCT
Found at i:4243828 original size:45 final size:45
Alignment explanation
Indices: 4243764--4243887 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 45
4243754 ACTTGATGCG
* * * *
4243764 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATCTTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTATCGAATTCA
* * *
4243809 ATCTGCTCCACTACAACTTCAGAGAGATAGGA-TTATCGAATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATCGAATTCA
* *
4243853 ATCTGCTCCACTGCAACCTCAGGGAGAGAAGATTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
4243888 GCTTCTTCAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 4 0.06
44 31 0.48
45 30 0.46
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATCGAATTCA
Found at i:4243909 original size:44 final size:44
Alignment explanation
Indices: 4243860--4243973 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
4243850 TCAATCTGCT
* * *
4243860 CCACTGCAACCTCAGGGAGAGAAGATTTGCTTCT-TCAGTCTACC
1 CCACTGCAACTTCAGGGAGATAAGACTTG-TTCTCTCAGTCTACC
** * * * *
4243904 CCACTGTGACTTCAGGGTGATAAGACTTGTTTTCTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTTCTCTCAGTCTACC
*
4243948 CCGCTGCAACTTCAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
4243974 CCGATGCGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 3 0.05
44 53 0.95
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGTTCTCTCAGTCTACC
Found at i:4244226 original size:86 final size:86
Alignment explanation
Indices: 4244069--4244363 Score: 473
Period size: 86 Copynumber: 3.4 Consensus size: 86
4244059 TGTAATCTTT
* ** * * *
4244069 GATCTGCTTCACTGTCGACGCAGGAGGGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCG
*
4244134 ATGGAGGTAAGGCTTTGTTTTC
65 ATGGAGGCAAGGCTTTGTTTTC
*
4244156 GATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
4244221 TGGAGGCAAGGCTTTGTTTTC
66 TGGAGGCAAGGCTTTGTTTTC
4244242 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
4244307 TGGAGGCAAGGCTTTGTTTTC
66 TGGAGGCAAGGCTTTGTTTTC
* * * *
4244328 GATCTACTTTGCTGTCAATGCAGGAAGGAAAGATCT
1 GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
4244364 ACTATCTTCA
Statistics
Matches: 195, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
86 162 0.83
87 33 0.17
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (86 bp):
GATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGA
TGGAGGCAAGGCTTTGTTTTC
Found at i:4244229 original size:43 final size:43
Alignment explanation
Indices: 4244095--4244316 Score: 127
Period size: 43 Copynumber: 5.1 Consensus size: 43
4244085 GACGCAGGAG
4244095 GGCAAGATCTGCTATCTTCAACCAGCTCCACTGCAACCGATGGA
1 GGCAAGATCTGCT-TCTTCAACCAGCTCCACTGCAACCGATGGA
* * * * * * * * *
4244139 GGTAAGGCTTTG-TT-TTCGATCTGCTCCGCTGTTAA-TGCA-GGAA
1 GGCAA-GATCTGCTTCTTCAACCAGCTCCACTG-CAACCG-ATGG-A
*
4244182 GGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGA
1 GGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAACCGATGGA
* * * * * * * * *
4244225 GGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAA-TGCA-GGAA
1 GGCAA-GATCTGCTTCTTCAACCAGCTCCACTG-CAACCG-ATGG-A
*
4244268 GGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGA
1 GGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAACCGATGGA
4244311 GGCAAG
1 GGCAAG
4244317 GCTTTGTTTT
Statistics
Matches: 123, Mismatches: 39, Indels: 33
0.63 0.20 0.17
Matches are distributed among these distances:
42 38 0.31
43 43 0.35
44 38 0.31
45 4 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (43 bp):
GGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAACCGATGGA
Found at i:4246031 original size:21 final size:19
Alignment explanation
Indices: 4246000--4246048 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
4245990 TCATGTTTTA
4246000 TTTTGACTTTGATTGATTTCTC
1 TTTTG-CTTTGATT--TTTCTC
4246022 TTTTGCTTTGATTTTTCTC
1 TTTTGCTTTGATTTTTCTC
4246041 TTTT-CTTT
1 TTTTGCTTT
4246049 CTTTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
21 8 0.30
22 5 0.19
ACGTcount: A:0.08, C:0.14, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTGCTTTGATTTTTCTC
Found at i:4246069 original size:6 final size:6
Alignment explanation
Indices: 4246050--4246098 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
4246040 CTTTTCTTTC
*
4246050 TTTG-T TTT-AT TTTGAT TTTGAT TTTGAT TGTGAT TTTGAT TTTGAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
4246096 TTT
1 TTT
4246099 TTTTTGAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
5 7 0.17
6 33 0.82
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.69
Consensus pattern (6 bp):
TTTGAT
Found at i:4252892 original size:16 final size:16
Alignment explanation
Indices: 4252855--4252897 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
4252845 ATACACGGGA
4252855 AATTTT-AAATAAAAT
1 AATTTTAAAATAAAAT
* *
4252870 AA-ATTAAAATAAACT
1 AATTTTAAAATAAAAT
4252885 AATTTTAAAATAA
1 AATTTTAAAATAA
4252898 CATATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 9 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTTTAAAATAAAAT
Found at i:4260162 original size:22 final size:24
Alignment explanation
Indices: 4260137--4260189 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
4260127 TCAAATTATT
*
4260137 ATTTTTTAGAA-TTTATTTTTA-A
1 ATTTTTTAGAATTTTATTTTCATA
**
4260159 ATTTTAAAGAATTTTATTTTCATA
1 ATTTTTTAGAATTTTATTTTCATA
4260183 ATTTTTT
1 ATTTTTT
4260190 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTTTTAGAATTTTATTTTCATA
Found at i:4260178 original size:23 final size:23
Alignment explanation
Indices: 4260144--4260187 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4260134 ATTATTTTTT
*
4260144 AGAATTTATTTTTA-AATTTTAA
1 AGAATTTATTTTCATAATTTTAA
4260166 AGAATTTTATTTTCATAATTTT
1 AGAA-TTTATTTTCATAATTTT
4260188 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
AGAATTTATTTTCATAATTTTAA
Found at i:4260200 original size:16 final size:17
Alignment explanation
Indices: 4260170--4260207 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
4260160 TTTTAAAGAA
4260170 TTTTATTTTCATAATTTT
1 TTTTATTTT-ATAATTTT
4260188 TTTTATTTT-TAATTTT
1 TTTTATTTTATAATTTT
4260204 TTTT
1 TTTT
4260208 TTACTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.55
18 9 0.45
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATAATTTT
Found at i:4260215 original size:19 final size:19
Alignment explanation
Indices: 4260184--4260235 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
4260174 ATTTTCATAA
4260184 TTTTTTTTA-TTTTTAATT-
1 TTTTTTTTACTTTTT-ATTC
4260202 TTTTTTTTACTTTTTATTC
1 TTTTTTTTACTTTTTATTC
**
4260221 TTTTTGATACTTTTT
1 TTTTTTTTACTTTTT
4260236 TGGGTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTTACTTTTTATTC
Found at i:4260216 original size:12 final size:13
Alignment explanation
Indices: 4260187--4260219 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4260177 TTCATAATTT
4260187 TTTTTATTTTTAA
1 TTTTTATTTTTAA
*
4260200 TTTTT-TTTTTAC
1 TTTTTATTTTTAA
4260212 TTTTTATT
1 TTTTTATT
4260220 CTTTTTGATA
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:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTATTTTTAA
Found at i:4260224 original size:18 final size:19
Alignment explanation
Indices: 4260185--4260235 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
4260175 TTTTCATAAT
*
4260185 TTTTTTTA-TTTTTAATTT
1 TTTTTTTACTTTTTAATTC
4260203 TTTTTTTACTTTTT-ATTC
1 TTTTTTTACTTTTTAATTC
*
4260221 TTTTTGATACTTTTT
1 TTTTT-TTACTTTTT
4260236 TGGGTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTTACTTTTTAATTC
Found at i:4260381 original size:30 final size:30
Alignment explanation
Indices: 4260345--4260405 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4260335 AATTATTTTT
*
4260345 TAAAAAAACTTGCCAGTCGATTAATTTGTA
1 TAAAAAAACTTGCCAGTCAATTAATTTGTA
* * * *
4260375 TAAAAAACCTTGTCGGTTAATTAATTTGTA
1 TAAAAAAACTTGCCAGTCAATTAATTTGTA
4260405 T
1 T
4260406 GCTCATCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (30 bp):
TAAAAAAACTTGCCAGTCAATTAATTTGTA
Found at i:4260785 original size:14 final size:14
Alignment explanation
Indices: 4260766--4260792 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4260756 AAATAAAATT
4260766 ACAAAATTATATAA
1 ACAAAATTATATAA
4260780 ACAAAATTATATA
1 ACAAAATTATATA
4260793 TATACTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAAATTATATAA
Found at i:4260869 original size:29 final size:29
Alignment explanation
Indices: 4260837--4260904 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
4260827 CTTTTCAAAT
* *
4260837 ATGATAAAAAATTATTAAAA-ATAATAAAA
1 ATGATAAAAAATT-GTAAAATATAAAAAAA
* *
4260866 ATGATTAGAAATTGTAAAATATAAAAAAA
1 ATGATAAAAAATTGTAAAATATAAAAAAA
4260895 AT-ATAAAAAA
1 ATGATAAAAAA
4260905 AATATTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (29 bp):
ATGATAAAAAATTGTAAAATATAAAAAAA
Found at i:4260897 original size:11 final size:11
Alignment explanation
Indices: 4260881--4260909 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
4260871 TAGAAATTGT
4260881 AAAATATAAAA
1 AAAATATAAAA
4260892 AAAATATAAAA
1 AAAATATAAAA
4260903 AAAATAT
1 AAAATAT
4260910 TATAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATATAAAA
Found at i:4260925 original size:19 final size:18
Alignment explanation
Indices: 4260901--4260945 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
4260891 AAAAATATAA
4260901 AAAAAATATTATAAATTGT
1 AAAAAATATTA-AAATTGT
*
4260920 AAAAAATTATTAAAATTTT
1 AAAAAA-TATTAAAATTGT
4260939 AAAAAAT
1 AAAAAAT
4260946 GGTCAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 18 0.75
20 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAAATATTAAAATTGT
Found at i:4260935 original size:39 final size:40
Alignment explanation
Indices: 4260841--4260944 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 40
4260831 TCAAATATGA
*
4260841 TAAAAAATTATTAAAA-ATAATAAAAATGATTAGAAATTG
1 TAAAAAATTATTAAAATATAAAAAAAATGATTAGAAATTG
* * ** *
4260880 TAAAATATAAAAAAAATATAAAAAAAAT-ATTATAAATTG
1 TAAAAAATTATTAAAATATAAAAAAAATGATTAGAAATTG
* *
4260919 TAAAAAATTATTAAAATTTTAAAAAA
1 TAAAAAATTATTAAAATATAAAAAAA
4260945 TGGTCAAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 42 0.81
40 10 0.19
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (40 bp):
TAAAAAATTATTAAAATATAAAAAAAATGATTAGAAATTG
Found at i:4260943 original size:20 final size:21
Alignment explanation
Indices: 4260898--4260944 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4260888 AAAAAAAATA
4260898 TAAAAAAAATATTATAAATTG
1 TAAAAAAAATATTATAAATTG
* *
4260919 T-AAAAAATTATTA-AAATTT
1 TAAAAAAAATATTATAAATTG
4260938 TAAAAAA
1 TAAAAAA
4260945 TGGTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAAAAATATTATAAATTG
Found at i:4261058 original size:11 final size:11
Alignment explanation
Indices: 4261044--4261156 Score: 58
Period size: 11 Copynumber: 10.4 Consensus size: 11
4261034 TATACCAAAA
4261044 AATATTTTAAT
1 AATATTTTAAT
*
4261055 AATAATTTAAT
1 AATATTTTAAT
*
4261066 ACACT-TTTAAAT
1 A-A-TATTTTAAT
*
4261078 TATATTTTTAAT
1 AATA-TTTTAAT
*** *
4261090 AATA-CCAAAA
1 AATATTTTAAT
4261100 AATATTTTAAT
1 AATATTTTAAT
*
4261111 AATAATTTAAT
1 AATATTTTAAT
4261122 ACAT-TTTTAAAT
1 A-ATATTTT-AAT
*
4261134 TATATTTT--T
1 AATATTTTAAT
4261143 AATATTTTAA-
1 AATATTTTAAT
4261153 AATA
1 AATA
4261157 CATAAATTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
9 8 0.11
10 11 0.15
11 30 0.41
12 24 0.32
13 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (11 bp):
AATATTTTAAT
Found at i:4261100 original size:56 final size:56
Alignment explanation
Indices: 4261035--4261146 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
4261025 CAAAAAAAAT
4261035 ATACCAAAAAATATTTTAATAATAATTTAATACACTTTTAAATTATATTTTTAATA
1 ATACCAAAAAATATTTTAATAATAATTTAATACACTTTTAAATTATATTTTTAATA
*
4261091 ATACCAAAAAATATTTTAATAATAATTTAATACATTTTTAAATTATATTTTTAATA
1 ATACCAAAAAATATTTTAATAATAATTTAATACACTTTTAAATTATATTTTTAATA
4261147 TTTTAAAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (56 bp):
ATACCAAAAAATATTTTAATAATAATTTAATACACTTTTAAATTATATTTTTAATA
Found at i:4262627 original size:21 final size:21
Alignment explanation
Indices: 4262603--4262643 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4262593 CTTTCTATTC
4262603 AGCTCTTACGAGCTTTTGTTT
1 AGCTCTTACGAGCTTTTGTTT
4262624 AGCTCTTACGAGCTTTTGTT
1 AGCTCTTACGAGCTTTTGTT
4262644 GGCGTATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (21 bp):
AGCTCTTACGAGCTTTTGTTT
Found at i:4262830 original size:10 final size:10
Alignment explanation
Indices: 4262815--4262852 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4262805 AATAGAAGTT
4262815 GTGAATGACA
1 GTGAATGACA
4262825 GTGAATGACA
1 GTGAATGACA
*
4262835 GGGAATTGACA
1 GTGAA-TGACA
4262846 -TGAATGA
1 GTGAATGA
4262853 TTTTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 3 0.12
10 17 0.68
11 5 0.20
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (10 bp):
GTGAATGACA
Found at i:4264258 original size:21 final size:21
Alignment explanation
Indices: 4264225--4264278 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
4264215 ATTTTCTATT
*
4264225 TTTTAATA-ATTTTTT-AAAA
1 TTTTAATATTTTTTTTGAAAA
*
4264244 TTTTAAATATTTTTTTTGTAAA
1 TTTT-AATATTTTTTTTGAAAA
4264266 TTTTAATATTTTT
1 TTTTAATATTTTT
4264279 ATTTTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 15 0.50
22 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTAATATTTTTTTTGAAAA
Found at i:4264265 original size:23 final size:25
Alignment explanation
Indices: 4264233--4264297 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 25
4264223 TTTTTTAATA
4264233 ATTTTT-TAAAATTTTAA-ATATTT
1 ATTTTTGTAAAATTTTAATATATTT
*
4264256 -TTTTTGT-AAATTTTAATATTTTT
1 ATTTTTGTAAAATTTTAATATATTT
*
4264279 ATTTTTGAAAAGATTTTAA
1 ATTTTTGTAAA-ATTTTAA
4264298 GGTTTTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 14 0.40
23 6 0.17
24 6 0.17
25 2 0.06
26 7 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (25 bp):
ATTTTTGTAAAATTTTAATATATTT
Found at i:4265156 original size:19 final size:20
Alignment explanation
Indices: 4265118--4265156 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4265108 AATTTCTTTG
4265118 GATCTTGCCAAATCCTTGAT
1 GATCTTGCCAAATCCTTGAT
4265138 GATCTTGCCAAAT-CTTGAT
1 GATCTTGCCAAATCCTTGAT
4265157 ACCAATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
GATCTTGCCAAATCCTTGAT
Found at i:4265981 original size:21 final size:21
Alignment explanation
Indices: 4265957--4266003 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4265947 AATTTTTTTT
* *
4265957 ATGAGCAGTTTATCTTCAATG
1 ATGAGCAGTTTATCTCCAACG
**
4265978 ATGAGTGGTTTATCTCCAACG
1 ATGAGCAGTTTATCTCCAACG
4265999 ATGAG
1 ATGAG
4266004 TGGTTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (21 bp):
ATGAGCAGTTTATCTCCAACG
Found at i:4266020 original size:22 final size:21
Alignment explanation
Indices: 4265964--4266009 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4265954 TTTATGAGCA
* *
4265964 GTTTATCTTCAATGATGAGTG
1 GTTTATCTCCAACGATGAGTG
4265985 GTTTATCTCCAACGATGAGTG
1 GTTTATCTCCAACGATGAGTG
4266006 GTTT
1 GTTT
4266010 TATCCACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (21 bp):
GTTTATCTCCAACGATGAGTG
Found at i:4267522 original size:48 final size:48
Alignment explanation
Indices: 4267451--4267545 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
4267441 TTCTTTGCTC
*
4267451 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATAATAAAGGATTCAACAGT
* *
4267499 AAAAACGCCTAAGTCATCTTAACTTGCAATAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTTGCAATAATAAAGGATTCAACAG
4267546 AATTCCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTTGCAATAATAAAGGATTCAACAGT
Found at i:4267884 original size:35 final size:36
Alignment explanation
Indices: 4267844--4267915 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
4267834 TCTAGGATCA
4267844 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* * *
4267879 CATATCTTCAAAAGATTACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
4267915 C
1 C
4267916 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.33
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:4274140 original size:35 final size:35
Alignment explanation
Indices: 4274100--4274171 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 35
4274090 TCTAGGATCA
4274100 CATATC-TCAAAAGATCTCACCTTCC-ATTTGCCAAG
1 CATATCTTCAAAAGAT-T-ACCTTCCTATTTGCCAAG
*
4274135 CATATCTTCAAAAGATTACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATTACCTTCC-TATTTGCCAAG
4274171 C
1 C
4274172 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 6 0.18
35 7 0.21
36 20 0.61
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (35 bp):
CATATCTTCAAAAGATTACCTTCCTATTTGCCAAG
Found at i:4274996 original size:24 final size:23
Alignment explanation
Indices: 4274965--4275009 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
4274955 TATTCACACA
4274965 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
4274988 TATTACTTACCTTAATTTAAAT
1 TATT-CTTACCTTAATTTAAAT
4275010 ATCCCATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:4275302 original size:22 final size:24
Alignment explanation
Indices: 4275259--4275302 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
4275249 TAACTAAGCT
4275259 TACTTACTTTTCTAGCTTAATTCA
1 TACTTACTTTTCTAGCTTAATTCA
4275283 TACTT-CTTTTCTA-CTTAATT
1 TACTTACTTTTCTAGCTTAATT
4275303 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAGCTTAATTCA
Found at i:4278164 original size:72 final size:72
Alignment explanation
Indices: 4278018--4278252 Score: 253
Period size: 72 Copynumber: 3.3 Consensus size: 72
4278008 CCCTAGCCAC
* * *
4278018 TAAAACCGACAAATGAGTGTG-TCAGCACTGGTCGGTATAACCGAAAAATAAAT-ATGCCCTGTG
1 TAAAACTGACAAATGAGTGTGCCCAGCACTGGTCGGTATAACCGAAAAATAAATGA-GCCCTGCG
*
4278081 CTAGTTAG
65 CTAGTCAG
* * * *
4278089 TAAAACTGAAAAATGAGTGTGCCCAGAACTGGTCGGTATAACC-AAAAAGTAAATGCGCCTTGCG
1 TAAAACTGACAAATGAGTGTGCCCAGCACTGGTCGGTATAACCGAAAAA-TAAATGAGCCCTGCG
* * *
4278153 TTGGTCGG
65 CTAGTCAG
* *
4278161 TAAAACAT-ACAAATGAGTGTGCCTAGCACTGGCCGGTATAACCGAAAAATAAATGAGCCCTGCG
1 TAAAAC-TGACAAATGAGTGTGCCCAGCACTGGTCGGTATAACCGAAAAATAAATGAGCCCTGCG
* *
4278225 CTGGCCAG
65 CTAGTCAG
* **
4278233 TGAAACCAACAAATGAGTGT
1 TAAAACTGACAAATGAGTGT
4278253 TCATTCATTT
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
71 24 0.18
72 106 0.78
73 6 0.04
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (72 bp):
TAAAACTGACAAATGAGTGTGCCCAGCACTGGTCGGTATAACCGAAAAATAAATGAGCCCTGCGC
TAGTCAG
Found at i:4279692 original size:22 final size:23
Alignment explanation
Indices: 4279613--4279705 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
4279603 AAATGTCTAC
* *
4279613 TTGGACAACACTTAAAACATGCT
1 TTGGACAACATTTAAAACATACT
* *
4279636 TTGGATGAA-ATTTAAAACATATT
1 TTGGA-CAACATTTAAAACATACT
*
4279659 TTGGACAACATTTAAAACTTACT
1 TTGGACAACATTTAAAACATACT
* *
4279682 TT-GACAGCATTTGAAACATACT
1 TTGGACAACATTTAAAACATACT
4279704 TT
1 TT
4279706 TGCTGGCACT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
22 21 0.36
23 35 0.60
24 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (23 bp):
TTGGACAACATTTAAAACATACT
Found at i:4285386 original size:3 final size:3
Alignment explanation
Indices: 4285378--4285406 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4285368 TATTGCACCC
4285378 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4285407 TTGTTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4285527 original size:7 final size:6
Alignment explanation
Indices: 4285492--4285526 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
4285482 TGTGTACATA
4285492 TTTTAT TTTTAT TTTTAT TTTTATT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTT
4285527 TTTGTGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:4285672 original size:22 final size:21
Alignment explanation
Indices: 4285639--4285682 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4285629 ATTCTATACC
*
4285639 TTTTATATATACATATATTTA
1 TTTTATAAATACATATATTTA
*
4285660 TTTTCATAAATACATATTTTTA
1 TTTT-ATAAATACATATATTTA
4285682 T
1 T
4285683 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATAAATACATATATTTA
Found at i:4290230 original size:6 final size:6
Alignment explanation
Indices: 4290222--4290270 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
4290212 AATACACCCT
* * *
4290222 TCACCT TCACCT TCACCT TCACCA TCACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA TCACCA
4290270 T
1 T
4290271 GACTTTACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.27, C:0.49, G:0.00, T:0.24
Consensus pattern (6 bp):
TCACCA
Found at i:4293275 original size:753 final size:753
Alignment explanation
Indices: 4291829--4293334 Score: 2886
Period size: 753 Copynumber: 2.0 Consensus size: 753
4291819 TTTATCAAAC
* *
4291829 TTTCGTTTCCCCCTTCAATCGGCACCGCTTTCTGCCTCCTCAGTTTTATCAAACTTTCTTTTCTA
1 TTTCGTTTCACCCATCAATCGGCACCGCTTTCTGCCTCCTCAGTTTTATCAAACTTTCTTTTCTA
* *
4291894 AACATAGTCTTGGAAGAATTTCAACTACCGCTTTTCGAAACGGGGAATTTCATATGAAGATGATG
66 AACATAGTCTTGGAAGAATTTCAACTACCGATTTTCGAAACGGGGAATTTCATATGAAGATCATG
4291959 ACAGTGAAGGACAGAAGGGAGGGCCGGCTGGTTATCTTGCTTGGAAGATATCTTAGTGTCAAGAA
131 ACAGTGAAGGACAGAAGGGAGGGCCGGCTGGTTATCTTGCTTGGAAGATATCTTAGTGTCAAGAA
4292024 GAAAATCTAAATTGATTTCATAACTTAAAATTTATGGCAAACTACTTAGAAATAGAAATTTAAGA
196 GAAAATCTAAATTGATTTCATAACTTAAAATTTATGGCAAACTACTTAGAAATAGAAATTTAAGA
4292089 CGCTATCATCATTCATATAGCAAATATGATTTCCTCGTTTGGGTTCTTAAATATATATATATATA
261 CGCTATCATCATTCATATAGCAAATATGATTTCCTCGTTTGGGTTCTTAAATATATATATATATA
4292154 TATATATGCTAAATTAGCAATGGTTATACCAATAATAACTAAATTGATATAAAGGTTAAATATTA
326 TATATATGCTAAATTAGCAATGGTTATACCAATAATAACTAAATTGATATAAAGGTTAAATATTA
4292219 TATCCTTTATGTCTAGCTAGGGTAGCATTTTTTAGACATATTATGATATCAAACTTATCAAATAT
391 TATCCTTTATGTCTAGCTAGGGTAGCATTTTTTAGACATATTATGATATCAAACTTATCAAATAT
* * *
4292284 CAATTTGTAAGTGATTGTATAAATTAATGGAGTTATGTTTTGTGTGTTTTGTATGTATATGTTAC
456 CAATTTGTAAGTGATTCTATAAATTAATAGAGTTATGTTTTGTATGTTTTGTATGTATATGTTAC
4292349 TCTAAGTTGTTGCCTGCTTTTAATACAACCACAATTGTATTAGTTGACAAAATAATATTGTGATA
521 TCTAAGTTGTTGCCTGCTTTTAATACAACCACAATTGTATTAGTTGACAAAATAATATTGTGATA
4292414 ATTATTTTAATACTAGTTGATTTTAATTTGATTTCTGAATTTAAATTCTTTTGTATATTAGCACC
586 ATTATTTTAATACTAGTTGATTTTAATTTGATTTCTGAATTTAAATTCTTTTGTATATTAGCACC
4292479 CTTGTTAAATTTCTTGCTGCTGGTGTATCTGACCACTGTTGTTCCAGTAAATTGATGTTTAATGT
651 CTTGTTAAATTTCTTGCTGCTGGTGTATCTGACCACTGTTGTTCCAGTAAATTGATGTTTAATGT
4292544 GAACTTTTGTAGGTATTGGACTGTTAGCTACCGATTTG
716 GAACTTTTGTAGGTATTGGACTGTTAGCTACCGATTTG
*
4292582 TTTCGTTTCACCCATCAATCGGCACCGCTTTCTGCCTCTTCAGTTTTATCAAACTTTCTTTTCTA
1 TTTCGTTTCACCCATCAATCGGCACCGCTTTCTGCCTCCTCAGTTTTATCAAACTTTCTTTTCTA
* * *
4292647 AACATAGTCTTGGAAGAATTTCAACTACCTATTTTTGAAACTGGGAATTTCATATGAAGATCATG
66 AACATAGTCTTGGAAGAATTTCAACTACCGATTTTCGAAACGGGGAATTTCATATGAAGATCATG
**
4292712 ATGGTGAAGGACAGAAGGGAGGGCCGGCTGGTTATCTTGCTTGGAAGATATCTTAGTGTCAAGAA
131 ACAGTGAAGGACAGAAGGGAGGGCCGGCTGGTTATCTTGCTTGGAAGATATCTTAGTGTCAAGAA
*
4292777 GAAAATCTAAATTGATTTCATAGCTTAAAATTTATGGCAAACTACTTAGAAATAGAAATTTAAGA
196 GAAAATCTAAATTGATTTCATAACTTAAAATTTATGGCAAACTACTTAGAAATAGAAATTTAAGA
4292842 CGCTATCATCATTCATATAGCAAATATGATTTCCTCGTTTGGGTTCTTAAATATATATATATATA
261 CGCTATCATCATTCATATAGCAAATATGATTTCCTCGTTTGGGTTCTTAAATATATATATATATA
4292907 TATATATGCTAAATTAGCAATGGTTATACCAATAATAACTAAATTGATATAAAGGTTAAATATTA
326 TATATATGCTAAATTAGCAATGGTTATACCAATAATAACTAAATTGATATAAAGGTTAAATATTA
4292972 TATCCTTTATGTCTAGCTAGGGTAGCATTTTTTAGACATATTATGATATCAAACTTATCAAATAT
391 TATCCTTTATGTCTAGCTAGGGTAGCATTTTTTAGACATATTATGATATCAAACTTATCAAATAT
4293037 CAATTTGTAAGTGATTCTATAAATTAATAGAGTTATGTTTTGTATGTTTTGTATGTATATGTTAC
456 CAATTTGTAAGTGATTCTATAAATTAATAGAGTTATGTTTTGTATGTTTTGTATGTATATGTTAC
4293102 TCTAAGTTGTTGCCTGCTTTTAATACAACCACAATTGTATTAGTTGACAAAATAATATTGTGATA
521 TCTAAGTTGTTGCCTGCTTTTAATACAACCACAATTGTATTAGTTGACAAAATAATATTGTGATA
4293167 ATTATTTTAATACTAGTTGATTTTAATTTGATTTCTGAATTTAAATTCTTTTGTATATTAGCACC
586 ATTATTTTAATACTAGTTGATTTTAATTTGATTTCTGAATTTAAATTCTTTTGTATATTAGCACC
4293232 CTTGTTAAATTTCTTGCTGCTGGTGTATCTGACCACTGTTGTTCCAGTAAATTGATGTTTAATGT
651 CTTGTTAAATTTCTTGCTGCTGGTGTATCTGACCACTGTTGTTCCAGTAAATTGATGTTTAATGT
4293297 GAACTTTTGTAGGTATTGGACTGTTAGCTACCGATTTG
716 GAACTTTTGTAGGTATTGGACTGTTAGCTACCGATTTG
4293335 NNNNNNNNNN
Statistics
Matches: 739, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
753 739 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (753 bp):
TTTCGTTTCACCCATCAATCGGCACCGCTTTCTGCCTCCTCAGTTTTATCAAACTTTCTTTTCTA
AACATAGTCTTGGAAGAATTTCAACTACCGATTTTCGAAACGGGGAATTTCATATGAAGATCATG
ACAGTGAAGGACAGAAGGGAGGGCCGGCTGGTTATCTTGCTTGGAAGATATCTTAGTGTCAAGAA
GAAAATCTAAATTGATTTCATAACTTAAAATTTATGGCAAACTACTTAGAAATAGAAATTTAAGA
CGCTATCATCATTCATATAGCAAATATGATTTCCTCGTTTGGGTTCTTAAATATATATATATATA
TATATATGCTAAATTAGCAATGGTTATACCAATAATAACTAAATTGATATAAAGGTTAAATATTA
TATCCTTTATGTCTAGCTAGGGTAGCATTTTTTAGACATATTATGATATCAAACTTATCAAATAT
CAATTTGTAAGTGATTCTATAAATTAATAGAGTTATGTTTTGTATGTTTTGTATGTATATGTTAC
TCTAAGTTGTTGCCTGCTTTTAATACAACCACAATTGTATTAGTTGACAAAATAATATTGTGATA
ATTATTTTAATACTAGTTGATTTTAATTTGATTTCTGAATTTAAATTCTTTTGTATATTAGCACC
CTTGTTAAATTTCTTGCTGCTGGTGTATCTGACCACTGTTGTTCCAGTAAATTGATGTTTAATGT
GAACTTTTGTAGGTATTGGACTGTTAGCTACCGATTTG
Found at i:4295029 original size:26 final size:26
Alignment explanation
Indices: 4294969--4295020 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4294959 TTTCTACCTA
4294969 CAGGTTTTTGTCATTGATATTAGCTG
1 CAGGTTTTTGTCATTGATATTAGCTG
4294995 CAGGTTTTTGTCATTGATATTAGCTG
1 CAGGTTTTTGTCATTGATATTAGCTG
4295021 TAGTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (26 bp):
CAGGTTTTTGTCATTGATATTAGCTG
Found at i:4295121 original size:12 final size:12
Alignment explanation
Indices: 4295104--4295137 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
4295094 GTTCGTTCTT
4295104 TTCTTTTGCTCG
1 TTCTTTTGCTCG
4295116 TTCTTTTGCTCG
1 TTCTTTTGCTCG
4295128 TTCTTTTGCT
1 TTCTTTTGCT
4295138 TAAAATGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.15, T:0.62
Consensus pattern (12 bp):
TTCTTTTGCTCG
Found at i:4295293 original size:25 final size:25
Alignment explanation
Indices: 4295265--4295326 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
4295255 GCTGAAGCTC
*
4295265 TAGTTGCAATTCAAGAGGTGTTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
4295290 TAGTTGCAATTCAAGAGGTATTTTA
1 TAGTTGCAATTCAAGAGGTATTTTA
4295315 TAGTTGCAATTC
1 TAGTTGCAATTC
4295327 CAGTAAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (25 bp):
TAGTTGCAATTCAAGAGGTATTTTA
Found at i:4295494 original size:18 final size:19
Alignment explanation
Indices: 4295471--4295511 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
4295461 TAATGGACTT
4295471 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
4295489 TATAGGATAATTTTTATTGG
1 TATAGGATAA-TTTTATTGG
4295509 TAT
1 TAT
4295512 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:4300246 original size:39 final size:41
Alignment explanation
Indices: 4300201--4300306 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
4300191 TTTCCTTATG
* *
4300201 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
4300241 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
4300286 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
4300307 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:4300281 original size:44 final size:46
Alignment explanation
Indices: 4300218--4300308 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
4300208 ACCTCTATTC
*
4300218 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
4300262 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
4300308 C
1 C
4300309 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:4300309 original size:16 final size:16
Alignment explanation
Indices: 4300288--4300324 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
4300278 AGAATTACCT
4300288 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
4300304 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
4300320 ATTAC
1 ATTAC
4300325 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:4301001 original size:18 final size:18
Alignment explanation
Indices: 4300980--4301015 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4300970 CTATTTTTAA
4300980 TTATAAAAATACAAAAAC
1 TTATAAAAATACAAAAAC
* *
4300998 TTATAAAATTTCAAAAAC
1 TTATAAAAATACAAAAAC
4301016 AATACAAAAG
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:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
TTATAAAAATACAAAAAC
Found at i:4306524 original size:21 final size:22
Alignment explanation
Indices: 4306500--4306542 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4306490 TCATTTCAAT
*
4306500 ACCTT-ATAAAGCATATCAAAA
1 ACCTTGATAAACCATATCAAAA
*
4306521 ACCTTGTTAAACCATATCAAAA
1 ACCTTGATAAACCATATCAAAA
4306543 TCTTACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
ACCTTGATAAACCATATCAAAA
Found at i:4307317 original size:23 final size:23
Alignment explanation
Indices: 4307273--4307375 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
4307263 AAACTCCTCC
*
4307273 TGAGCTGATAAACAGTAGGCTCTAT
1 TGAGCTG--AAACAGTAAGCTCTAT
*
4307298 TGAGCTGAAACGGTAAGCTCTGA-
1 TGAGCTGAAACAGTAAGCTCT-AT
*
4307321 CGAGCTG-AACAGTAAGCTC-AT
1 TGAGCTGAAACAGTAAGCTCTAT
** * *
4307342 ACAAGCTAAAACAGTAAGCTCTAA
1 -TGAGCTGAAACAGTAAGCTCTAT
4307366 TGAGCTGAAA
1 TGAGCTGAAA
4307376 ATAGTAGGCT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
22 16 0.25
23 37 0.59
24 2 0.03
25 7 0.11
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAT
Found at i:4307684 original size:67 final size:67
Alignment explanation
Indices: 4307600--4307972 Score: 557
Period size: 67 Copynumber: 5.6 Consensus size: 67
4307590 ATATATATAT
* * * *
4307600 ATATAATCTATTCAATTAAATACATACATTTAAATACTCAATCCGCATACCTTCTCAAATCACAT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
*
4307665 AT
66 AC
* *
4307667 ATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATAT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
4307732 AC
66 AC
** * *
4307734 ATACCATCAATTTAATTAAATACATACATTTAATTACTCAATTCGCATACTTTCTCAAATTACAT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
4307799 AC
66 AC
* *
4307801 ATATAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATAT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
4307866 AC
66 AC
** * *
4307868 ATACCATCAATTTAATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACAT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
*
4307933 TC
66 AC
* * *
4307935 ATATAATCAATTCAATTAAACATATACATTTAAATACT
1 ATATAATCAATTTAATTAAATACATACATTTAAATACT
4307973 ATTGCAATTG
Statistics
Matches: 275, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 275 1.00
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (67 bp):
ATATAATCAATTTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCACAT
AC
Found at i:4307834 original size:134 final size:134
Alignment explanation
Indices: 4307613--4307972 Score: 630
Period size: 134 Copynumber: 2.7 Consensus size: 134
4307603 TAATCTATTC
* * *
4307613 AATTAAATACATACATTTAAATACTCAATCCGCATACCTTCTCAAATCACATATATATAATCGAT
1 AATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACATACATATAATCGAT
4307678 TTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATATACATACCATCA
66 TTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATATACATACCATCA
4307743 ATTT
131 ATTT
* *
4307747 AATTAAATACATACATTTAATTACTCAATTCGCATACTTTCTCAAATTACATACATATAATCGAT
1 AATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACATACATATAATCGAT
4307812 TTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATATACATACCATCA
66 TTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATATACATACCATCA
4307877 ATTT
131 ATTT
* *
4307881 AATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACATTCATATAATCAAT
1 AATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACATACATATAATCGAT
* * *
4307946 TCAATTAAACATATACATTTAAATACT
66 TTAATTAAATACATACATTTAAATACT
4307973 ATTGCAATTG
Statistics
Matches: 214, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 214 1.00
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (134 bp):
AATTAAATACATACATTTAATTACTCAATTCGCATACCTTCTCAAATCACATACATATAATCGAT
TTAATTAAATACATACATTTAAATACTCAATTCGCATACTTTCTCAAATCATATACATACCATCA
ATTT
Found at i:4313003 original size:2 final size:2
Alignment explanation
Indices: 4312991--4313027 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4312981 ATTTAAAGGA
*
4312991 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4313028 GTAAAAAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4313697 original size:18 final size:18
Alignment explanation
Indices: 4313669--4313703 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4313659 CAGTAACAGG
4313669 AGAAGTGAAG-AAGAAAA
1 AGAAGTGAAGAAAGAAAA
4313686 AGAAGATGAAGAAAGAAA
1 AGAAG-TGAAGAAAGAAA
4313704 GGGAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (18 bp):
AGAAGTGAAGAAAGAAAA
Found at i:4314945 original size:20 final size:20
Alignment explanation
Indices: 4314920--4314962 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4314910 CAATGTGGCA
4314920 AGTTAAC-AGCCCACATCAGC
1 AGTTAACTAG-CCACATCAGC
*
4314940 AGTTAACTTGCCACATCAGC
1 AGTTAACTAGCCACATCAGC
4314960 AGT
1 AGT
4314963 CCCATTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (20 bp):
AGTTAACTAGCCACATCAGC
Found at i:4317481 original size:23 final size:23
Alignment explanation
Indices: 4317437--4317481 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4317427 AATTTGAAAA
* * * *
4317437 TCGAATAATTCATTTGAGTTAAT
1 TCGAATAACTCAATTCAATTAAT
4317460 TCGAATAACTCAATTCAATTAA
1 TCGAATAACTCAATTCAATTAA
4317482 CTCAAATTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
TCGAATAACTCAATTCAATTAAT
Found at i:4319264 original size:2 final size:2
Alignment explanation
Indices: 4319257--4319294 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4319247 ATAATTAAGT
4319257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4319295 GTAGGGCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4319339 original size:64 final size:64
Alignment explanation
Indices: 4319257--4319383 Score: 227
Period size: 64 Copynumber: 2.0 Consensus size: 64
4319247 ATAATTAAGT
4319257 TATATATATATATATATATATATATATATATATATATAGTAGGGCAATGTTGGGAAGGAGAATGT
1 TATATATATATATATAT-TA-ATATATATATATATATAGTAGGGCAATGTTGGGAAGGAGAATGT
4319322 G
64 G
*
4319323 TATATATATATATATATTAATATATATATGTATATAGTAGGGCAATGTTGGGAAGGAGAAT
1 TATATATATATATATATTAATATATATATATATATAGTAGGGCAATGTTGGGAAGGAGAAT
4319384 TTGATTCTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 41 0.68
65 2 0.03
66 17 0.28
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (64 bp):
TATATATATATATATATTAATATATATATATATATAGTAGGGCAATGTTGGGAAGGAGAATGTG
Done.