Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 193 of 313
Found at i:59243480 original size:21 final size:20
Alignment explanation
Indices: 59243423--59243480 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
59243413 ATCATGTTCA
59243423 TATTTTTA-ACATAATTTAAT
1 TATTTTTACA-ATAATTTAAT
*
59243443 TA-TTTTATAAT-ATTTAAT
1 TATTTTTACAATAATTTAAT
59243461 TATTTTTGACAATAATTTAA
1 TATTTTT-ACAATAATTTAA
59243481 CCGTAATAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 9 0.27
19 11 0.33
20 7 0.21
21 6 0.18
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTTTACAATAATTTAAT
Found at i:59252271 original size:29 final size:29
Alignment explanation
Indices: 59252217--59252274 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
59252207 ATTATAAGGC
* *
59252217 TGGATCAAATTAATATCTTTATTATTAAA
1 TGGATCAAATTAATACCTTTAATATTAAA
*
59252246 TGGATCAATTTAAT-CCTTATAATATTAAA
1 TGGATCAAATTAATACCTT-TAATATTAAA
59252275 AATAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (29 bp):
TGGATCAAATTAATACCTTTAATATTAAA
Found at i:59257580 original size:19 final size:19
Alignment explanation
Indices: 59257534--59257640 Score: 69
Period size: 19 Copynumber: 5.5 Consensus size: 19
59257524 ATTTTTTTTC
* *
59257534 AATTTTTAATATTGTTTACT
1 AATTTTT-ATATTTTTTAAT
59257554 -ATTTTTATATTTTTTAAT
1 AATTTTTATATTTTTTAAT
**
59257572 AATTTTTATA-AATTTAATT
1 AATTTTTATATTTTTTAA-T
*
59257591 AATTTCTAGT-TTTTTTAAT
1 AATTTTTA-TATTTTTTAAT
*
59257610 ATCATTTTTATAACTTTTTAA-
1 A--ATTTTTAT-ATTTTTTAAT
59257631 AGATTTTTAT
1 A-ATTTTTAT
59257641 GATGTCATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
18 15 0.22
19 25 0.36
20 15 0.22
21 7 0.10
22 7 0.10
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (19 bp):
AATTTTTATATTTTTTAAT
Found at i:59259417 original size:29 final size:27
Alignment explanation
Indices: 59259359--59259418 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
59259349 AATTGAAAAT
* * *
59259359 TTTTAAAAATTTAAAAAATGATTTAAA
1 TTTTAAAAATTAAAAAAAAGACTTAAA
*
59259386 TTTTAGAAAATTAAAAAAGAAGACTTATA
1 TTTTA-AAAATTAAAAAA-AAGACTTAAA
59259415 TTTT
1 TTTT
59259419 CAAATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (27 bp):
TTTTAAAAATTAAAAAAAAGACTTAAA
Found at i:59260754 original size:6 final size:6
Alignment explanation
Indices: 59260743--59260767 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59260733 CATTTCCAAG
59260743 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
59260768 GAAAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:59271080 original size:21 final size:21
Alignment explanation
Indices: 59271054--59271094 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59271044 AGACGAGCAA
* *
59271054 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
59271075 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
59271095 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:59282105 original size:17 final size:18
Alignment explanation
Indices: 59282083--59282120 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
59282073 GGACCAGCAA
59282083 AGAAGATACTT-ATATGG
1 AGAAGATACTTGATATGG
59282100 AGAAGATACTTGATATGG
1 AGAAGATACTTGATATGG
59282118 AGA
1 AGA
59282121 TTCTCAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.26
Consensus pattern (18 bp):
AGAAGATACTTGATATGG
Found at i:59292196 original size:13 final size:15
Alignment explanation
Indices: 59292178--59292214 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
59292168 CATCTATTTG
*
59292178 ATAAAAAAT-ACA-A
1 ATAAAAAATAAAAGA
59292191 ATAAAAAATAAAAGA
1 ATAAAAAATAAAAGA
59292206 ATAAAAAAT
1 ATAAAAAAT
59292215 TAAATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 2 0.10
15 10 0.48
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (15 bp):
ATAAAAAATAAAAGA
Found at i:59296010 original size:18 final size:17
Alignment explanation
Indices: 59295982--59296016 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59295972 ATTATTAAGA
*
59295982 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59295999 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59296017 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59296154 original size:18 final size:17
Alignment explanation
Indices: 59296126--59296160 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59296116 ATTATTAAGA
*
59296126 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
59296143 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
59296161 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:59296371 original size:44 final size:45
Alignment explanation
Indices: 59296322--59296416 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
59296312 TTACACCTCT
* *
59296322 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
59296366 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
59296411 ATTACA
1 ATTACA
59296417 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:59296416 original size:16 final size:16
Alignment explanation
Indices: 59296395--59296427 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59296385 TTGATTTGCT
*
59296395 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
59296411 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
59296427 A
1 A
59296428 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:59296437 original size:21 final size:21
Alignment explanation
Indices: 59296408--59296450 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
59296398 ACACCTCTAT
*
59296408 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
59296429 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
59296450 T
1 T
59296451 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:59296506 original size:16 final size:16
Alignment explanation
Indices: 59296481--59296518 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
59296471 TTGATTTGCT
59296481 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
59296497 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
59296513 AATACA
1 ATTACA
59296519 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:59296795 original size:28 final size:28
Alignment explanation
Indices: 59296730--59296796 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
59296720 AATATATAAT
*
59296730 AAATATATTTTTTTATTTTTTATTTTTA
1 AAATAAATTTTTTTATTTTTTATTTTTA
*
59296758 AAAT-ACTTTTTTTATTTTTTATTTTTA
1 AAATAAATTTTTTTATTTTTTATTTTTA
59296785 AAATAAATTTTT
1 AAATAAATTTTT
59296797 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (28 bp):
AAATAAATTTTTTTATTTTTTATTTTTA
Found at i:59296804 original size:26 final size:27
Alignment explanation
Indices: 59296739--59296806 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 27
59296729 TAAATATATT
* * **
59296739 TTTTTATTTTTTATTTTTAAAATACTT
1 TTTTTAGTGTTTATTTTTAAAATACAA
* *
59296766 TTTTTATTTTTTATTTTTAAAATA-AA
1 TTTTTAGTGTTTATTTTTAAAATACAA
*
59296792 TTTTTGGTGTTTATT
1 TTTTTAGTGTTTATT
59296807 AAAAAATGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTTAGTGTTTATTTTTAAAATACAA
Found at i:59308133 original size:15 final size:14
Alignment explanation
Indices: 59308112--59308154 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
59308102 TTGAGTTCAG
59308112 AAAATTATTTAATT
1 AAAATTATTTAATT
* *
59308126 GGAAATTAATTAATT
1 -AAAATTATTTAATT
59308141 AAAATTAATTTAAT
1 AAAATT-ATTTAAT
59308155 AATATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
AAAATTATTTAATT
Found at i:59316978 original size:10 final size:10
Alignment explanation
Indices: 59316963--59317048 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
59316953 TTTGAAATAT
59316963 TTTAATATAA
1 TTTAATATAA
59316973 TTTAATATAA
1 TTTAATATAA
** *
59316983 AAT-ATTTAA
1 TTTAATATAA
59316992 TTTCAAAATATAA
1 TTT---AATATAA
59317005 TTTAATATAA
1 TTTAATATAA
59317015 ---AATAT--
1 TTTAATATAA
*
59317020 TTTAA-ATAT
1 TTTAATATAA
59317029 TTTAATATAA
1 TTTAATATAA
*
59317039 TTTACTATAA
1 TTTAATATAA
59317049 AAATAATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
7 7 0.12
8 2 0.03
9 11 0.19
10 30 0.52
13 8 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTAATATAA
Found at i:59316985 original size:34 final size:33
Alignment explanation
Indices: 59316945--59317050 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 33
59316935 AAATATAAAA
59316945 ATAAAATATTTGAAATATTTTAATATAATTTAAT
1 ATAAAATATTT-AAATATTTTAATATAATTTAAT
**
59316979 ATAAAATATTT-AAT-TTCAAAATATAATTTAAT
1 ATAAAATATTTAAATATT-TTAATATAATTTAAT
*
59317011 ATAAAATATTTTAAATATTTTAATATAATTTACT
1 ATAAAATA-TTTAAATATTTTAATATAATTTAAT
59317045 ATAAAA
1 ATAAAA
59317051 ATAATTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
31 2 0.03
32 24 0.38
33 3 0.05
34 32 0.51
35 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAAAATATTTAAATATTTTAATATAATTTAAT
Found at i:59317001 original size:15 final size:14
Alignment explanation
Indices: 59316972--59317021 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
59316962 TTTTAATATA
59316972 ATTTAATATAAAAT
1 ATTTAATATAAAAT
*
59316986 ATTTAATTTCAAAATAT
1 ATTTAATAT--AAA-AT
59317003 AATTTAATATAAAAT
1 -ATTTAATATAAAAT
59317018 ATTT
1 ATTT
59317022 TAAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.40
15 2 0.07
16 6 0.20
17 2 0.07
18 8 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTAATATAAAAT
Found at i:59317165 original size:11 final size:11
Alignment explanation
Indices: 59317117--59317171 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
59317107 ATCTAATAAT
59317117 AATTA-TATTA
1 AATTATTATTA
* *
59317127 AAATATGATTA
1 AATTATTATTA
59317138 AATTATTTATT-
1 AATTA-TTATTA
*
59317149 ATTTATTATTA
1 AATTATTATTA
*
59317160 AATTATTTTTA
1 AATTATTATTA
59317171 A
1 A
59317172 TAATAATTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
10 9 0.26
11 22 0.63
12 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTATTATTA
Found at i:59317165 original size:59 final size:61
Alignment explanation
Indices: 59317050--59317189 Score: 185
Period size: 59 Copynumber: 2.3 Consensus size: 61
59317040 TTACTATAAA
* *
59317050 AATAATTATATTAAAAATATTATTAAATTATATATTTTTTCATTTTTATTAAATTATATCTAAT
1 AATAATTATATT-AAAATATGATTAAATTATATATTATTTCA--TTTATTAAATTATATCTAAT
* * *
59317114 AATAATTATATTAAAATATGATTAAATTATTTATTATTT-A-TTATTAAATTATTTTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATATTATTTCATTTATTAAATTATATCTAAT
*
59317173 AATAATTCTATTAAAAT
1 AATAATTATATTAAAAT
59317190 TTAATAACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
59 33 0.47
62 1 0.01
63 24 0.34
64 12 0.17
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (61 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATTTCATTTATTAAATTATATCTAAT
Found at i:59322601 original size:41 final size:41
Alignment explanation
Indices: 59322544--59322649 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
59322534 AATGAGATAA
* *
59322544 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
59322585 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
59322626 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
59322650 AATTGCCAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:59326685 original size:40 final size:41
Alignment explanation
Indices: 59326627--59326733 Score: 153
Period size: 40 Copynumber: 2.6 Consensus size: 41
59326617 TTAATTTTAA
* *
59326627 AATACTTTTTTTAATTTTAAATTTTTTTTAAAATACTTTTTT
1 AATA-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
*
59326669 TA-ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 AATATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
59326709 AATATTTATTTTAATTTTTAAAATA
1 AATATTT-TTTTAA-TTTTAAAATA
59326734 AATTTTTGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
40 36 0.62
41 5 0.09
42 7 0.12
43 10 0.17
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (41 bp):
AATATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
Found at i:59326694 original size:17 final size:17
Alignment explanation
Indices: 59326592--59326697 Score: 63
Period size: 17 Copynumber: 6.7 Consensus size: 17
59326582 CCCGAATAAT
* *
59326592 AAATATTTTTATTTTTT
1 AAATATTTTTAATTTTA
*
59326609 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
59326626 AAATACTTTTTTTAATTTT-
1 AAATA---TTTTTAATTTTA
59326645 -AA-A-TTTT--TTTTA
1 AAATATTTTTAATTTTA
*
59326657 AAATA-CTTT--TTTT-
1 AAATATTTTTAATTTTA
*
59326670 -AATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
59326686 AAATATTTTTAA
1 AAATATTTTTAA
59326698 AATACTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
11 4 0.06
12 3 0.04
13 9 0.13
14 8 0.11
15 4 0.06
17 29 0.41
18 2 0.03
20 11 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:59326695 original size:19 final size:18
Alignment explanation
Indices: 59326597--59326657 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
59326587 ATAATAAATA
* *
59326597 TTTTTATTTTTTAA-ATT
1 TTTTTAATTTTAAATATT
59326614 TTTTTAATTTTAAAATACTT
1 TTTTTAATTTT-AAATA-TT
59326634 TTTTTAATTTTAAAT-TT
1 TTTTTAATTTTAAATATT
59326651 TTTTTAA
1 TTTTTAA
59326658 AATACTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 19 0.49
18 2 0.05
19 5 0.13
20 13 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTAATTTTAAATATT
Found at i:59326726 original size:32 final size:32
Alignment explanation
Indices: 59326690--59326751 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
59326680 ATTTTAAAAT
**
59326690 ATTTTTAAAATACTTTTTTAATATTTATTTTA
1 ATTTTTAAAATAAATTTTTAATATTTATTTTA
**
59326722 ATTTTTAAAATAAATTTTTGGTATTTATTT
1 ATTTTTAAAATAAATTTTTAATATTTATTT
59326752 AAAAAACAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (32 bp):
ATTTTTAAAATAAATTTTTAATATTTATTTTA
Found at i:59333360 original size:14 final size:14
Alignment explanation
Indices: 59333341--59333419 Score: 68
Period size: 14 Copynumber: 5.3 Consensus size: 14
59333331 TGAAATTTAC
59333341 ATTTCTGGAAAATG
1 ATTTCTGGAAAATG
59333355 ATTTCTGGAAAATG
1 ATTTCTGGAAAATG
* *
59333369 TTTGTTTGTCAGTAAAATG
1 ATT-TCTG---G-AAAATG
* * *
59333388 TTTTCCGAAAAATG
1 ATTTCTGGAAAATG
59333402 ATTTCTGGAAAATG
1 ATTTCTGGAAAATG
59333416 ATTT
1 ATTT
59333420 ACTTTTTTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
14 37 0.71
15 3 0.06
18 3 0.06
19 9 0.17
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.41
Consensus pattern (14 bp):
ATTTCTGGAAAATG
Found at i:59333432 original size:20 final size:20
Alignment explanation
Indices: 59333407--59333444 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
59333397 AAATGATTTC
59333407 TGGAAAATGATTTACTTTTT
1 TGGAAAATGATTTACTTTTT
59333427 TGGAAAATGATTTACTTT
1 TGGAAAATGATTTACTTT
59333445 CCTGGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (20 bp):
TGGAAAATGATTTACTTTTT
Found at i:59340424 original size:13 final size:15
Alignment explanation
Indices: 59340406--59340451 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
59340396 TCTATATATT
59340406 TATAACA-AA-TTAA
1 TATAACAGAAGTTAA
59340419 TATAACAGTAAGTTAA
1 TATAACAG-AAGTTAA
59340435 TATAACAGCAAGTTAA
1 TATAACAG-AAGTTAA
59340451 T
1 T
59340452 TAAAGAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 7 0.24
15 2 0.07
16 20 0.69
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (15 bp):
TATAACAGAAGTTAA
Found at i:59340436 original size:16 final size:16
Alignment explanation
Indices: 59340415--59340451 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
59340405 TTATAACAAA
*
59340415 TTAATATAACAGTAAG
1 TTAATATAACAGCAAG
59340431 TTAATATAACAGCAAG
1 TTAATATAACAGCAAG
59340447 TTAAT
1 TTAAT
59340452 TAAAGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (16 bp):
TTAATATAACAGCAAG
Found at i:59343701 original size:10 final size:10
Alignment explanation
Indices: 59343686--59343724 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
59343676 TTATTTTTCA
59343686 ATAAAAATTC
1 ATAAAAATTC
* *
59343696 ATAAAATTTT
1 ATAAAAATTC
*
59343706 ATAAAAATAC
1 ATAAAAATTC
59343716 ATAAAAATT
1 ATAAAAATT
59343725 AAAATAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAAAATTC
Found at i:59343813 original size:20 final size:21
Alignment explanation
Indices: 59343790--59343835 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
59343780 ATTTATTTAT
* *
59343790 TAAAATG-ATAATTTTATAAG
1 TAAAATGAATAATATTATAAA
59343810 TAAAA-GAATAATATTATAAA
1 TAAAATGAATAATATTATAAA
59343830 TAAAAT
1 TAAAAT
59343836 AATTTAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
TAAAATGAATAATATTATAAA
Found at i:59344173 original size:19 final size:19
Alignment explanation
Indices: 59344132--59344173 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
59344122 TTACACGGCA
* *
59344132 GTGTGACATAGCCCAAATT
1 GTGTGACATAGACCAAATC
59344151 GTGTGACATA-ACCAAGATC
1 GTGTGACATAGACCAA-ATC
59344170 GTGT
1 GTGT
59344174 AGGCATTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (19 bp):
GTGTGACATAGACCAAATC
Found at i:59344958 original size:18 final size:19
Alignment explanation
Indices: 59344935--59344972 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
59344925 CTTGAGTTGA
*
59344935 TCCAATCGACGT-CAAAAT
1 TCCAATCGACCTACAAAAT
*
59344953 TCCAATGGACCTACAAAAT
1 TCCAATCGACCTACAAAAT
59344972 T
1 T
59344973 AAATCAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (19 bp):
TCCAATCGACCTACAAAAT
Found at i:59345398 original size:41 final size:41
Alignment explanation
Indices: 59345320--59345398 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
59345310 ACCTGATACA
*
59345320 ATACACCAGCACAAAGCCTGCTAAACTCAAGGCCCAATTCC
1 ATACACCAGCACAAAGCCTGCTAAACTCAAAGCCCAATTCC
* * * *
59345361 ATACACCGGCACAAAGTCTGCTAGACTCAAAGTCCAAT
1 ATACACCAGCACAAAGCCTGCTAAACTCAAAGCCCAAT
59345399 ACGTTATTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.37, C:0.33, G:0.14, T:0.16
Consensus pattern (41 bp):
ATACACCAGCACAAAGCCTGCTAAACTCAAAGCCCAATTCC
Found at i:59348976 original size:36 final size:36
Alignment explanation
Indices: 59348929--59349001 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
59348919 GAATGATGAA
59348929 CGTGTTAAACTGTTAGCATTAACCATTAATTTGGCT
1 CGTGTTAAACTGTTAGCATTAACCATTAATTTGGCT
59348965 CGTGTTAAACTGTTAGCATTAACCATTAATTTGGCT
1 CGTGTTAAACTGTTAGCATTAACCATTAATTTGGCT
59349001 C
1 C
59349002 ATATCGTCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (36 bp):
CGTGTTAAACTGTTAGCATTAACCATTAATTTGGCT
Found at i:59374219 original size:20 final size:21
Alignment explanation
Indices: 59374186--59374226 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
59374176 TGTTGGAATA
*
59374186 TTTTAATAATAAAAGATTTAC
1 TTTTAATAAAAAAAGATTTAC
*
59374207 TTTT-ATAAAAAAATATTTAC
1 TTTTAATAAAAAAAGATTTAC
59374227 GTATACGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAATAAAAAAAGATTTAC
Found at i:59378501 original size:4 final size:4
Alignment explanation
Indices: 59378494--59378518 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
59378484 ACTGCTTGGT
59378494 TGGC TGGC TGGC TGGC TGGC TGGC T
1 TGGC TGGC TGGC TGGC TGGC TGGC T
59378519 CACTTCACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.48, T:0.28
Consensus pattern (4 bp):
TGGC
Found at i:59379159 original size:2 final size:2
Alignment explanation
Indices: 59379152--59379186 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59379142 TTTTGCTAGT
59379152 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
59379187 ATTGCTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:59385751 original size:23 final size:23
Alignment explanation
Indices: 59385725--59385798 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
59385715 ATAAGTGCAA
59385725 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
59385748 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
59385771 CTCTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59385794 CACTG
1 CACTG
59385799 TTACCATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:59386051 original size:23 final size:23
Alignment explanation
Indices: 59386021--59386073 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
59386011 ATAAGTGCCA
59386021 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59386044 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59386067 CACTGAT
1 CACTGAT
59386074 CAATAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:59394046 original size:28 final size:29
Alignment explanation
Indices: 59393992--59394092 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
59393982 GTATTGTTTC
* * *
59393992 ATATAATATATATGTATAGGGGTTTTGTTAT
1 ATATATTATATATGCAT--GGGCTTTGTTAT
* *
59394023 ATATATAATATA-G-GTGTGGCTTTGTTAT
1 ATATATTATATATGCATG-GGCTTTGTTAT
*
59394051 ATATATTATATATGCATGGGCTTTGTTGT
1 ATATATTATATATGCATGGGCTTTGTTAT
59394080 ATATATTATATAT
1 ATATATTATATAT
59394093 ATTCGTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.02
28 21 0.35
29 25 0.42
30 3 0.05
31 10 0.17
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.49
Consensus pattern (29 bp):
ATATATTATATATGCATGGGCTTTGTTAT
Found at i:59394346 original size:17 final size:18
Alignment explanation
Indices: 59394311--59394348 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
59394301 TGCAAGTCAA
* *
59394311 TTATATTTGTGTACTATG
1 TTATATTTGTGAACCATG
59394329 TTATA-TTGTGAACCATG
1 TTATATTTGTGAACCATG
59394346 TTA
1 TTA
59394349 ACTTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATATTTGTGAACCATG
Found at i:59394391 original size:36 final size:36
Alignment explanation
Indices: 59394344--59394413 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
59394334 TTGTGAACCA
*
59394344 TGTTAACTTGGTGAATTATATTATTATGGCGAACTG
1 TGTTAACTTGGTGAATTATATTAATATGGCGAACTG
* * *
59394380 TGTTAATTTGGTGACTTGTATTAATATGGCGAAC
1 TGTTAACTTGGTGAATTATATTAATATGGCGAAC
59394414 AATTATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (36 bp):
TGTTAACTTGGTGAATTATATTAATATGGCGAACTG
Found at i:59394423 original size:36 final size:36
Alignment explanation
Indices: 59394338--59394425 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
59394328 GTTATATTGT
* * *
59394338 GAACCATGTTAACTTGGTGAATTATATTATTATGGC
1 GAACAATGTTAATTTGGTGAATTATATTAATATGGC
** * *
59394374 GAACTGTGTTAATTTGGTGACTTGTATTAATATGGC
1 GAACAATGTTAATTTGGTGAATTATATTAATATGGC
59394410 GAACAAT-TATAATTTG
1 GAACAATGT-TAATTTG
59394426 CCAAACTGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.98
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (36 bp):
GAACAATGTTAATTTGGTGAATTATATTAATATGGC
Found at i:59398632 original size:34 final size:34
Alignment explanation
Indices: 59398589--59398656 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
59398579 CCTGTGAATT
59398589 GCTTTTTATAAAATTTTCTAGAAAATATTTTCTA
1 GCTTTTTATAAAATTTTCTAGAAAATATTTTCTA
59398623 GCTTTTTATAAAATTTTCTAGAAAATATTTTCTA
1 GCTTTTTATAAAATTTTCTAGAAAATATTTTCTA
59398657 AGTAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (34 bp):
GCTTTTTATAAAATTTTCTAGAAAATATTTTCTA
Found at i:59403418 original size:24 final size:24
Alignment explanation
Indices: 59403373--59403424 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
59403363 TCCGAGCTGT
*
59403373 ATAATAGGAAGCTCATAAGAG-CA
1 ATAATAGAAAGCTCATAAGAGCCA
**
59403396 ATAATTAGAAAGCTCATGCGAGCCA
1 ATAA-TAGAAAGCTCATAAGAGCCA
59403421 ATAA
1 ATAA
59403425 CGGGTAGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 14 0.58
25 6 0.25
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (24 bp):
ATAATAGAAAGCTCATAAGAGCCA
Found at i:59403503 original size:23 final size:25
Alignment explanation
Indices: 59403438--59403541 Score: 74
Period size: 25 Copynumber: 4.2 Consensus size: 25
59403428 GTAGCTCTGA
**
59403438 AGAGCCATTAA-C-GAGAAGCTCCGG
1 AGAGCCATTAATCAG-GAAGCTCAAG
* *
59403462 ATAGCCA-TATATCAAGAAGCTCAAG
1 AGAGCCATTA-ATCAGGAAGCTCAAG
* * *
59403487 CGAGCCA-T-ATCGGGAAGCTCCAG
1 AGAGCCATTAATCAGGAAGCTCAAG
*
59403510 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCA-AG
59403536 AGAGCC
1 AGAGCC
59403542 CTATAACGGG
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
23 20 0.33
24 8 0.13
25 26 0.43
26 7 0.11
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTCAAG
Found at i:59403530 original size:25 final size:24
Alignment explanation
Indices: 59403452--59403541 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
59403442 CCATTAACGA
* * *
59403452 GAAGCTCCGGATAGCCATATATCAA
1 GAAGCTCCAGAGAGCCATA-ATCAG
* * *
59403477 GAAGCTCAAGCGAGCCAT-ATCGG
1 GAAGCTCCAGAGAGCCATAATCAG
59403500 GAAGCTCCAGAGAGCCATTAATCAG
1 GAAGCTCCAGAGAGCCA-TAATCAG
*
59403525 GAAGCTCACAAAGAGCC
1 GAAGCTC-CAGAGAGCC
59403542 CTATAACGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
23 18 0.35
24 1 0.02
25 25 0.48
26 8 0.15
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (24 bp):
GAAGCTCCAGAGAGCCATAATCAG
Found at i:59406484 original size:23 final size:23
Alignment explanation
Indices: 59406465--59406515 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
59406455 TGATAATGTA
59406465 ATTTTATATATATATGTAATTAT
1 ATTTTATATATATATGTAATTAT
* *
59406488 TTTTTATCTATATATGT-ATATAT
1 ATTTTATATATATATGTAAT-TAT
59406511 ATTTT
1 ATTTT
59406516 GTTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTTATATATATATGTAATTAT
Found at i:59406823 original size:15 final size:15
Alignment explanation
Indices: 59406800--59406833 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
59406790 GTTTATTGAC
* *
59406800 TTATGTTTTTTTCAT
1 TTATATTTTGTTCAT
59406815 TTATATTTTGTTCAT
1 TTATATTTTGTTCAT
59406830 TTAT
1 TTAT
59406834 TTGATATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATATTTTGTTCAT
Found at i:59406955 original size:19 final size:20
Alignment explanation
Indices: 59406914--59406955 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
59406904 ATTTCTATGC
* *
59406914 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
59406934 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
59406953 CAT
1 CAT
59406956 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:59408069 original size:4 final size:4
Alignment explanation
Indices: 59408053--59408107 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
59408043 CTGTTGCATT
*
59408053 AATG AATG TATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
59408101 AATG AAT
1 AATG AAT
59408108 TAATTAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (4 bp):
AATG
Found at i:59417815 original size:36 final size:36
Alignment explanation
Indices: 59417775--59417856 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
59417765 AAAATAAAAG
*
59417775 AGGAGGTCAAGAAAAAGTTTGATGCTGGGTTTTTAC
1 AGGAGGTCAAGAAAAAGTTTGATGCTGGGTTTCTAC
59417811 AGGAGGTCAAGAAAAAGTTTGATGCTGGGTTTCTAC
1 AGGAGGTCAAGAAAAAGTTTGATGCTGGGTTTCTAC
59417847 AGGAGGTCAA
1 AGGAGGTCAA
59417857 ATATTCTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (36 bp):
AGGAGGTCAAGAAAAAGTTTGATGCTGGGTTTCTAC
Found at i:59421522 original size:44 final size:43
Alignment explanation
Indices: 59421464--59422655 Score: 495
Period size: 44 Copynumber: 27.5 Consensus size: 43
59421454 CCGATAATCC
* * * *
59421464 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAGATCT
* * ***
59421508 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
* * *
59421548 TACCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAGATCT
* * * * * *
59421592 TATC-CTCTTGAAGTTGCAGTGGGGCAGACTGAAGATGAC-AAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAAT--CTAGATCT
* ** *
59421637 TATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAGATCT
* * * *
59421681 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAGATCT
* * ***
59421725 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
* * *
59421765 TACCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAGATCT
* * * * * *
59421809 TATC-CTCTTGAAGTTGCAGT-GAGGCAAACTGAAGATGGC-AAACCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAGATCT
* * * *
59421854 TATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAGATCT
* * * * * *
59421898 TATCTCCCTAAAGTTGTAATGGAGCGGATTAAAATCTTGGATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAGATCT
* * * * * *
59421942 TATCTCTCTGAAGTTGTAG-AGACCAGA-TCATATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
** * * *
59421982 TATCTTTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAGATCT
* * * * *
59422026 TATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGC-AAACCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAGATCT
* * *
59422071 TATCTCCCTGAAGTTGCAGTAGAGCAGGTTAAAACCGATA-ATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAGATCT
* * * * * *
59422115 TATCTCTCTAAAGTTGCAATGGAGCGGATTAAAATCTTGAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAG-ATCT
* * * * * *
59422159 TATCTCTCTGAAGTTTCA-TAGACCAGA-TCACATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
* * * * *
59422199 TATCTTCCTGAAGTTGCAGTGAAGCAGACTAAGTAAGCAAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAGATCT
* * * * * *
59422243 TATC-CTCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGC-AAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAAT--CTAGATCT
* * * * *
59422288 TATCTCTCTGAAGTTGCAGTAGAGCAGGTTAAAACCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC--TAGATCT
* * * *
59422332 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAGATCT
* * ***
59422376 TATCTCTCTGAAGTTGCAGAGG-GCAGA-TCGCATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
* * *
59422416 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCTAGATCT
* * * *
59422460 TATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCGA-ATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CTAGATCT
* * * * *
59422505 TATCTTCTTGAAGTTGCAGTAGAGCAGATTAAAGA-CGATGATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATCTA-GATCT
* * * *
59422549 TATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-TAGATCT
* * * **
59422593 TATCTCTCTGAAGTTGCAG-AGAGCAAATT-GCATCTAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
**
59422633 TATCTCCCTGGTGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
59422656 ATGGATCGAA
Statistics
Matches: 844, Mismatches: 224, Indels: 163
0.69 0.18 0.13
Matches are distributed among these distances:
40 118 0.14
41 43 0.05
42 41 0.05
43 60 0.07
44 429 0.51
45 142 0.17
46 11 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTAGATCT
Found at i:59421828 original size:217 final size:217
Alignment explanation
Indices: 59421453--59422655 Score: 1868
Period size: 217 Copynumber: 5.5 Consensus size: 217
59421443 CGGATCGGTG
59421453 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
*
59421518 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* * *
59421583 AGCAGATCTTATCCTCTTGAAGTTGCAGTGGGGCAGACTGAAGATGACAAACCTTATCTCCCTGA
131 AGCAGATCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGA
*
59421648 AGTTGCAGTGGAGCAGGTTAAA
196 AGTTGCAGTAGAGCAGGTTAAA
59421670 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
*
59421735 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTACCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* *
59421800 AGCAGATCTTATCCTCTTGAAGTTGCAGTGAGGCAAACTGAAGATGGCAAACCTTATCTCCCTGA
131 AGCAGATCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGA
* *
59421865 AGTTACAGTGGAGCAGGTTAAA
196 AGTTGCAGTAGAGCAGGTTAAA
* * *
59421887 GTCGATAATCCTATCTCCCTAAAGTTGTAATGGAGCGGATTAAAATCTTGGATCCTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
* * ** **
59421952 AAGTTGTAGAGACCAGATCATATCTAGTCTTATCTTTCTGAAGTTGCAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* *
59422017 AGCAGGTCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAACCTTATCTCCCTGA
131 AGCAGATCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGA
59422082 AGTTGCAGTAGAGCAGGTTAAA
196 AGTTGCAGTAGAGCAGGTTAAA
* * * * * * *
59422104 ACCGATAATCTTATCTCTCTAAAGTTGCAATGGAGCGGATTAAAATCTTGAATCCTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
* * * * * *
59422169 AAGTTTCATAGACCAGATCACATCTAGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* * *
59422234 AGCA-AGTCTTATCCTCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCTCTG
131 AGCAGA-TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTG
59422298 AAGTTGCAGTAGAGCAGGTTAAA
195 AAGTTGCAGTAGAGCAGGTTAAA
*
59422321 ACCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
*
59422386 AAGTTGCAGAGGGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* * * * * *
59422451 AGCAGGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCGAATCTTATCTTCTTGA
131 AGCAGATCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGA
*
59422516 AGTTGCAGTAGAGCAGATTAAA
196 AGTTGCAGTAGAGCAGGTTAAA
* * * * * ***
59422538 GACGATGATCCTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAACCACAGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
* * **
59422603 AAGTTGCAGAGAGCAAATTGCATCTAGTCTTATCTCCCTGGTGTTGCAGTGGA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA
59422656 ATGGATCGAA
Statistics
Matches: 910, Mismatches: 74, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
217 910 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (217 bp):
GCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCTCTG
AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
AGCAGATCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGA
AGTTGCAGTAGAGCAGGTTAAA
Found at i:59424187 original size:18 final size:18
Alignment explanation
Indices: 59424164--59424207 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
59424154 TGTTTTTTTA
*
59424164 ATGAATATTTTTCTATAT
1 ATGAATATTTATCTATAT
59424182 ATGAATATTTATCTATAT
1 ATGAATATTTATCTATAT
*
59424200 ATGTATAT
1 ATGAATAT
59424208 ATATTATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (18 bp):
ATGAATATTTATCTATAT
Found at i:59424410 original size:15 final size:15
Alignment explanation
Indices: 59424387--59424420 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
59424377 GTTTATTGAC
* *
59424387 TTATGTTTTTTTCAT
1 TTATATTTTGTTCAT
59424402 TTATATTTTGTTCAT
1 TTATATTTTGTTCAT
59424417 TTAT
1 TTAT
59424421 TTGATATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATATTTTGTTCAT
Found at i:59424542 original size:19 final size:20
Alignment explanation
Indices: 59424501--59424542 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
59424491 ATTTCTATGC
* *
59424501 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
59424521 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
59424540 CAT
1 CAT
59424543 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:59425649 original size:4 final size:4
Alignment explanation
Indices: 59425640--59425670 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
59425630 CTGTTGCATT
59425640 AATG AATG AATG AATG AATG AATG AATG AAT
1 AATG AATG AATG AATG AATG AATG AATG AAT
59425671 TAATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:59425675 original size:4 final size:4
Alignment explanation
Indices: 59425668--59425700 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
59425658 TGAATGAATG
59425668 AATT AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT A
59425701 TTTTGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:59440053 original size:6 final size:6
Alignment explanation
Indices: 59440038--59440074 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
59440028 ATATATATTA
* *
59440038 TTTTAT TTTTAG TTTTAG TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
59440075 AGTTTTCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:59441193 original size:29 final size:29
Alignment explanation
Indices: 59441151--59441209 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
59441141 AAATTATAGA
59441151 TTAAAATCATCCCTTGAGTTCTCTTTAGC
1 TTAAAATCATCCCTTGAGTTCTCTTTAGC
59441180 TTAAAATCATCCCTTGAGTTCTCTTTAGC
1 TTAAAATCATCCCTTGAGTTCTCTTTAGC
59441209 T
1 T
59441210 GAAAGCTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (29 bp):
TTAAAATCATCCCTTGAGTTCTCTTTAGC
Found at i:59441363 original size:17 final size:17
Alignment explanation
Indices: 59441337--59441370 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59441327 TTTCACATAT
*
59441337 AATAACATGAATTTCAA
1 AATAAAATGAATTTCAA
*
59441354 AATAAAATGATTTTCAA
1 AATAAAATGAATTTCAA
59441371 TATTTTTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (17 bp):
AATAAAATGAATTTCAA
Found at i:59442237 original size:14 final size:14
Alignment explanation
Indices: 59442190--59442238 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
59442180 CAAAATCTTG
59442190 AACCTTAAA-CTCA
1 AACCTTAAACCTCA
* * *
59442203 AACCCTAACCCTTA
1 AACCTTAAACCTCA
59442217 AACCTTAAACCTCA
1 AACCTTAAACCTCA
*
59442231 AATCTTAA
1 AACCTTAA
59442239 GGTTTAGGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCTTAAACCTCA
Found at i:59442252 original size:14 final size:14
Alignment explanation
Indices: 59442235--59442285 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
59442225 ACCTCAAATC
*
59442235 TTAAGGTTTAGGGT
1 TTAAGATTTAGGGT
* *
59442249 TTAAAATTTAAGGT
1 TTAAGATTTAGGGT
*
59442263 TTAATATTT-GGGT
1 TTAAGATTTAGGGT
59442276 TTAAGATTTA
1 TTAAGATTTA
59442286 AAGGTTCGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTAAGATTTAGGGT
Found at i:59442344 original size:20 final size:19
Alignment explanation
Indices: 59442321--59442378 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
59442311 TTGGGATTTA
59442321 GGGTTTATGTTTAAGGTTAT
1 GGGTTTATGTTTAAGGTT-T
59442341 GGGTTTGA-GTTTAAGGTTT
1 GGGTTT-ATGTTTAAGGTTT
* *
59442360 GGGCTTATGATTTAGGGTT
1 GGGTTTATG-TTTAAGGTT
59442379 CAAGGTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 24 0.73
21 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.34, T:0.47
Consensus pattern (19 bp):
GGGTTTATGTTTAAGGTTT
Found at i:59442472 original size:89 final size:89
Alignment explanation
Indices: 59442324--59442499 Score: 248
Period size: 89 Copynumber: 2.0 Consensus size: 89
59442314 GGATTTAGGG
* *
59442324 TTTATGTTTAAGGTTATGGGTTTGAGTTTAAGGTTTGGGCTTATGATTTAGGGTTCAAGGTTTGA
1 TTTAGGTTTAAGGTTATGGGTTTGAGTTTAAGGTTTGGGCTTATAATTTAGGGTTCAAGGTTTGA
59442389 GATTCTAAATTTATG-GTTTAGGAT
66 GATTCTAAATTTA-GAGTTTAGGAT
* * * *
59442413 TTTAGGTTTATGGTTATGGG-TTGAGTTTAGGGTTTGGGCTTCTAAGTTTTGGGTTCAAGGTTTG
1 TTTAGGTTTAAGGTTATGGGTTTGAGTTTAAGGTTTGGGCTTATAA-TTTAGGGTTCAAGGTTTG
* *
59442477 AGATTTTAGATTTAGAGTTTAGG
65 AGATTCTAAATTTAGAGTTTAGG
59442500 GTTTAAGATT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 23 0.30
89 54 0.70
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.46
Consensus pattern (89 bp):
TTTAGGTTTAAGGTTATGGGTTTGAGTTTAAGGTTTGGGCTTATAATTTAGGGTTCAAGGTTTGA
GATTCTAAATTTAGAGTTTAGGAT
Found at i:59442512 original size:35 final size:35
Alignment explanation
Indices: 59442456--59442545 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 35
59442446 TTGGGCTTCT
* * * *
59442456 AAGTTTTGGGTTCAAGGTTTGAGATTTTAGATTTA
1 AAGTTTAGGGTTTAAGATTTGAGATTCTAGATTTA
*
59442491 GAGTTTAGGGTTTAAGATTTGAGATTCTAGATTTA
1 AAGTTTAGGGTTTAAGATTTGAGATTCTAGATTTA
*
59442526 AAGTTTATGGTTTAAGATTT
1 AAGTTTAGGGTTTAAGATTT
59442546 AGGGTTTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (35 bp):
AAGTTTAGGGTTTAAGATTTGAGATTCTAGATTTA
Found at i:59442578 original size:14 final size:13
Alignment explanation
Indices: 59442529--59442585 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
59442519 AGATTTAAAG
*
59442529 TTTATGGTTTAAGA
1 TTTA-GGTTTAGGA
* *
59442543 TTTAGGGTTTGGGT
1 TTTA-GGTTTAGGA
*
59442557 TTTAGGTTTTGGA
1 TTTAGGTTTAGGA
59442570 TTTACGGTTTAGGA
1 TTTA-GGTTTAGGA
59442584 TT
1 TT
59442586 CATGATTCGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
13 11 0.31
14 24 0.69
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.51
Consensus pattern (13 bp):
TTTAGGTTTAGGA
Found at i:59443391 original size:12 final size:12
Alignment explanation
Indices: 59443374--59443398 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59443364 ATGAACATGA
59443374 ATTTAACAAAAT
1 ATTTAACAAAAT
59443386 ATTTAACAAAAT
1 ATTTAACAAAAT
59443398 A
1 A
59443399 CTGGTTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTTAACAAAAT
Found at i:59444565 original size:9 final size:9
Alignment explanation
Indices: 59444551--59444578 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
59444541 TTTTGTTACA
59444551 ACAATTAAT
1 ACAATTAAT
59444560 ACAATTAAT
1 ACAATTAAT
59444569 ACAATTAAT
1 ACAATTAAT
59444578 A
1 A
59444579 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:59444600 original size:68 final size:66
Alignment explanation
Indices: 59444521--59444662 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
59444511 TCAAGTTTGT
*
59444521 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAAT--AATTAATAATTTGAT
59444586 AAA
64 AAA
59444589 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
*
59444654 T
66 A
59444655 TTTACTAA
1 TTTACTAA
59444663 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 25 0.35
68 47 0.65
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
A
Found at i:59444672 original size:16 final size:16
Alignment explanation
Indices: 59444651--59444692 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
59444641 AATAATTTGA
*
59444651 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
59444667 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
59444683 TAGTTTTAAT
1 TAATTTTAAT
59444693 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:59444676 original size:22 final size:22
Alignment explanation
Indices: 59444672--59444726 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
59444662 ACAATTAATT
* * *
59444672 TTAATAACAATTAGTTTTAATT
1 TTAATAAAAAATAATTTTAATT
*
59444694 TTATTAAAAAATAATTTTAATT
1 TTAATAAAAAATAATTTTAATT
*
59444716 TTAATTAAAAA
1 TTAATAAAAAA
59444727 CGGGCCGGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATAAAAAATAATTTTAATT
Found at i:59444681 original size:59 final size:65
Alignment explanation
Indices: 59444521--59444684 Score: 214
Period size: 68 Copynumber: 2.5 Consensus size: 65
59444511 TCAAGTTTGT
*
59444521 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATA-AATTAATAATTTGAT
59444586 AAA
63 AAA
59444589 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAAT-AATTAATAATTTGATA
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATAAATTAATAATTTGATA
*
59444653 AT
64 AA
*
59444655 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
59444685 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 25 0.27
68 46 0.50
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (65 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATAAATTAATAATTTGATAAA
Found at i:59447028 original size:23 final size:23
Alignment explanation
Indices: 59446999--59447043 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
59446989 AATTGAATTT
*
59446999 TTTTATTTCATCATTTTTTATTA
1 TTTTATTTCATCACTTTTTATTA
59447022 TTTTATTTCATCACTTTTTATT
1 TTTTATTTCATCACTTTTTATT
59447044 GTACTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTTCATCACTTTTTATTA
Found at i:59451816 original size:31 final size:31
Alignment explanation
Indices: 59451781--59451842 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
59451771 AAAAAATGAT
59451781 AGACGTGGGTTTGATCATTCAAAATTCAGAG
1 AGACGTGGGTTTGATCATTCAAAATTCAGAG
59451812 AGACGTGGGTTTGATCATTCAAAATTCAGAG
1 AGACGTGGGTTTGATCATTCAAAATTCAGAG
59451843 GAGGTGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (31 bp):
AGACGTGGGTTTGATCATTCAAAATTCAGAG
Found at i:59456549 original size:50 final size:50
Alignment explanation
Indices: 59456474--59456589 Score: 187
Period size: 50 Copynumber: 2.3 Consensus size: 50
59456464 TCCCATATCG
59456474 CTGAAGATGCAGTGGATCGGATCAAAGTTATAATGGAAAATTTTATCTCC
1 CTGAAGATGCAGTGGATCGGATCAAAGTTATAATGGAAAATTTTATCTCC
* **
59456524 CTGAAGATGAAGTGGATCGGATCAAAGTTATAATGGCGAATTTTATCTCC
1 CTGAAGATGCAGTGGATCGGATCAAAGTTATAATGGAAAATTTTATCTCC
* *
59456574 CTAAAGTTGCAGTGGA
1 CTGAAGATGCAGTGGA
59456590 GTAAGATGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (50 bp):
CTGAAGATGCAGTGGATCGGATCAAAGTTATAATGGAAAATTTTATCTCC
Found at i:59456629 original size:44 final size:44
Alignment explanation
Indices: 59456566--59456910 Score: 144
Period size: 44 Copynumber: 7.5 Consensus size: 44
59456556 ATGGCGAATT
* *
59456566 TTATCTCCCTAAAGTTGCAGTGGAGTAAGATGAAACTACAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
* * *
59456610 TTATCTCCTTAAAGTTGCAGTGTAGCAAGATAAAACTATAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
* * * * *
59456654 ATT-TATCCCTAAAGATGCAATGGATC-AGATCAAAATTATAATATCAAATC
1 -TTATCTCCCTAAAGTTGCAGTGGAGCAAGAT---AA--A-ACTA-CAAATC
* * * *
59456704 TTATCTCCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAAT-
1 TTATCT-CCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
* * * * * * * *
59456748 TCTATATCCTTGAA-TATGTAGTGGATC-AGACCAAAGTTACAATGGCGAATC
1 T-TATCTCCCTAAAGT-TGCAGTGGAGCAAGA-TAAA---AC--T-ACAAATC
* * * * * *
59456799 TTATCTCCCTGAGGCTGCAGTGGAGCAAGATGAAGCTACAAGTC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
* * * * * * *
59456843 TTATATCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTATAAATC
1 TTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
* *
59456887 CTATATCCCTAAA-TATGCAGTGGA
1 TTATCTCCCTAAAGT-TGCAGTGGA
59456911 TCGGATCAAA
Statistics
Matches: 222, Mismatches: 55, Indels: 48
0.68 0.17 0.15
Matches are distributed among these distances:
43 9 0.04
44 132 0.59
45 12 0.05
46 4 0.02
47 3 0.01
48 1 0.00
49 7 0.03
50 31 0.14
51 19 0.09
52 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAACTACAAATC
Found at i:59456773 original size:95 final size:93
Alignment explanation
Indices: 59456604--59456849 Score: 251
Period size: 95 Copynumber: 2.6 Consensus size: 93
59456594 GATGAAACTA
* * * * * *
59456604 CAAATCTTATCTCCTTAAAGTTGCAGTGTAGCAAGATAAAACTATAAATCATTTATCCCTAAAGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTG-AGCAAGATGAAGCTACAAATCATATATCCCTAAAGA
* * *
59456669 TGCAATGGATCAGATCAAAATTATAATAT
65 TGCAATGGATCAGACCAAAATTACAATAG
* *
59456698 CAAATCTTATCTCCCCTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATTC-TATATCCTTGAA
1 CAAATCTTATCT-CCCTGAAGTTGCAGT-GAGCAAGATGAAGCTACAAA-TCATATATCCCTAAA
* * * * *
59456762 TATGTAGTGGATCAGACCAAAGTTACAATGG
63 GATGCAATGGATCAGACCAAAATTACAATAG
* * * * *
59456793 CGAATCTTATCTCCCTGAGGCTGCAGTGGAGCAAGATGAAGCTACAAGTCTTATATC
1 CAAATCTTATCTCCCTGAAGTTGCAGT-GAGCAAGATGAAGCTACAAATCATATATC
59456850 TCTGAAGTTG
Statistics
Matches: 127, Mismatches: 21, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
93 2 0.02
94 50 0.39
95 72 0.57
96 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (93 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGAGCAAGATGAAGCTACAAATCATATATCCCTAAAGAT
GCAATGGATCAGACCAAAATTACAATAG
Found at i:59456877 original size:138 final size:138
Alignment explanation
Indices: 59456713--59457001 Score: 389
Period size: 138 Copynumber: 2.1 Consensus size: 138
59456703 CTTATCTCCC
* * * *
59456713 CTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATTCTATATCCTTGAATATGTAGTGGATCAGA
1 CTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAATATGCAGTGGATCAGA
* * * * * * * *
59456778 CCAAAGTTACAATGGCGAATCTTATCTCCCTGAGGCTGCAGTGGAGCAAGATGAAGCTACAAGTC
66 CCAAAGTTACAATAGCAAATCTGATCTCCCTGAAGATACAGTGAAGCAAGATGAAGCTACAAATC
*
59456843 TTATATCT
131 CTATATCT
* *
59456851 CTGAAGTTGCAGTAGAGCAAGATGAAGCTATAAATCCTATATCCCTAAATATGCAGTGGATCGGA
1 CTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAATATGCAGTGGATCAGA
* * * *
59456916 TCAAAGTTATAATATCAAATCTGATCTCCTTGAAGATACAGTGAAGCAAGATGAAGCTACAAATC
66 CCAAAGTTACAATAGCAAATCTGATCTCCCTGAAGATACAGTGAAGCAAGATGAAGCTACAAATC
59456981 CTATATCT
131 CTATATCT
* *
59456989 CTAAAGATGCAGT
1 CTGAAGTTGCAGT
59457002 GGATCGAATT
Statistics
Matches: 130, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (138 bp):
CTGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAATATGCAGTGGATCAGA
CCAAAGTTACAATAGCAAATCTGATCTCCCTGAAGATACAGTGAAGCAAGATGAAGCTACAAATC
CTATATCT
Found at i:59456971 original size:94 final size:94
Alignment explanation
Indices: 59456860--59457084 Score: 290
Period size: 94 Copynumber: 2.4 Consensus size: 94
59456850 TCTGAAGTTG
* * * *
59456860 CAGTAGAGCAAGATGAAGCTATAAATCCTATATCCCTAAATATGCAGTGGATCGGATCAAAGTTA
1 CAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAAGATGCAGTGGATCGAATCAAAGCTA
* *
59456925 TAATATCAAATCTGATCTCCTTGAAGATA
66 CAATAGCAAATCTGATCTCCTTGAAGATA
* **
59456954 CAGT-GAAGCAAGATGAAGCTACAAATCCTATATCTCTAAAGATGCAGTGGATCGAATTGAAGCT
1 CAGTAG-AGCAAGATGAAGCTACAAATCCTATATCCCTAAAGATGCAGTGGATCGAATCAAAGCT
* * * *
59457018 ACCATAGCAAATCTTATCTCCTTGAAGTTG
65 ACAATAGCAAATCTGATCTCCTTGAAGATA
* * *
59457048 TAGTAGAGCAAGATGAAGCTACAAATCTTATACCCCT
1 CAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCT
59457085 GAAGTTGTAG
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
93 1 0.01
94 110 0.98
95 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (94 bp):
CAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAAGATGCAGTGGATCGAATCAAAGCTA
CAATAGCAAATCTGATCTCCTTGAAGATA
Found at i:59457153 original size:44 final size:43
Alignment explanation
Indices: 59457026--59457156 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 43
59457016 CTACCATAGC
* * * *
59457026 AAATCTTATCTCCTTGAAGTTGTAGTAGAGCA-AGATGAAGCTAC
1 AAATCTTATATCCCTGAAGTTGTAGTAGA--ATAGATGAAACTAA
* ** *
59457070 AAATCTTATACCCCTGAAGTTGTAGTAGTTTCGAATGAAACTAA
1 AAATCTTATATCCCTGAAGTTGTAGTAGAATAG-ATGAAACTAA
*
59457114 AAATCTCATATCCCTGAAGTTGTAGTAGAATAGATTGAAACTA
1 AAATCTTATATCCCTGAAGTTGTAGTAGAATAGA-TGAAACTA
59457157 TAACAGCAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
43 2 0.03
44 69 0.97
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (43 bp):
AAATCTTATATCCCTGAAGTTGTAGTAGAATAGATGAAACTAA
Found at i:59458899 original size:20 final size:22
Alignment explanation
Indices: 59458860--59458899 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
59458850 TTTTTTCACA
*
59458860 ATTTCAATTTAGTCCCATGTTC
1 ATTTCAATTAAGTCCCATGTTC
59458882 ATTT-AATTAAGT-CCATGT
1 ATTTCAATTAAGTCCCATGT
59458900 ACTTGCTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (22 bp):
ATTTCAATTAAGTCCCATGTTC
Found at i:59459163 original size:14 final size:13
Alignment explanation
Indices: 59459120--59459159 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
59459110 ATATAATATT
59459120 TTTTATTTCATCA
1 TTTTATTTCATCA
*
59459133 -TTT-TTT-ATTA
1 TTTTATTTCATCA
59459143 TTTTATTTCATCA
1 TTTTATTTCATCA
59459156 TTTT
1 TTTT
59459160 TATTGTACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.14
11 6 0.27
12 6 0.27
13 7 0.32
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTTCATCA
Found at i:59459163 original size:22 final size:22
Alignment explanation
Indices: 59459116--59459160 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
59459106 TATTATATAA
59459116 TATTTTTTATTTCATCATTTTT
1 TATTTTTTATTTCATCATTTTT
59459138 TATTATTTTATTTCATCATTTTT
1 TATT-TTTTATTTCATCATTTTT
59459161 ATTGTACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTTTATTTCATCATTTTT
Found at i:59480738 original size:24 final size:26
Alignment explanation
Indices: 59480714--59480763 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
59480704 ACAACGCATT
59480714 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
*
59480740 AATTAAAAATATTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
59480764 ATTACATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:59480870 original size:30 final size:30
Alignment explanation
Indices: 59480836--59480932 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
59480826 AAATAAAAAT
59480836 TTGATCATTAGATATAATCAAGTAAACAAC
1 TTGATCATTAGATATAATCAAGTAAACAAC
* ** * * * *
59480866 TTGATTAAAAAAAATATTCAA-TATATTA-AAA
1 TTGATCATTAGATATAATCAAGTA-A--ACAAC
59480897 TTGGATCATTAGATATAATCAAGTAAACAAC
1 TT-GATCATTAGATATAATCAAGTAAACAAC
59480928 TTGAT
1 TTGAT
59480933 TAAAAAACAA
Statistics
Matches: 47, Mismatches: 14, Indels: 12
0.64 0.19 0.16
Matches are distributed among these distances:
29 2 0.04
30 20 0.43
31 8 0.17
32 15 0.32
33 2 0.04
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (30 bp):
TTGATCATTAGATATAATCAAGTAAACAAC
Found at i:59480904 original size:62 final size:65
Alignment explanation
Indices: 59480831--59480958 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 65
59480821 AAATAAAATA
*
59480831 AAAATTTGATCATTAGATATAATCAAGTAAACAACTTGATT-AAAAA-AAATATTCAATA-TATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATTATT
*
59480893 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCATTATTATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATTATT
59480958 A
1 A
59480959 TGGTTGATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 40 0.66
63 5 0.08
64 11 0.18
65 5 0.08
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.34
Consensus pattern (65 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATTCAATATTATT
Found at i:59480981 original size:16 final size:16
Alignment explanation
Indices: 59480962--59480992 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59480952 ATTATTATGG
59480962 TTGATTAAAAAACAAC
1 TTGATTAAAAAACAAC
59480978 TTGATTAAAAAACAA
1 TTGATTAAAAAACAA
59480993 ATATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
TTGATTAAAAAACAAC
Found at i:59484210 original size:47 final size:47
Alignment explanation
Indices: 59484153--59484298 Score: 151
Period size: 47 Copynumber: 3.2 Consensus size: 47
59484143 ATATAAGAAC
* *
59484153 ATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
** *
59484200 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* * *
59484244 ATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
59484291 ATTTAATA
1 ATTTAATA
59484299 ATAATTATTT
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 32 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (47 bp):
ATTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTAT
Found at i:59484248 original size:91 final size:91
Alignment explanation
Indices: 59484136--59484351 Score: 369
Period size: 91 Copynumber: 2.4 Consensus size: 91
59484126 ATGATTTTAG
*
59484136 TAAATTCATATAAGAACATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
59484201 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* *
59484227 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
59484292 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
* * *
59484318 CAAATTCATATAAGAAAATTTATTAGTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
59484352 ATTTTAAATT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:59484282 original size:101 final size:92
Alignment explanation
Indices: 59484228--59484419 Score: 185
Period size: 101 Copynumber: 2.0 Consensus size: 92
59484218 TAAATTATAT
59484228 AAATTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGA--AATTATATATTATTATTAAATT
1 AAATTCATATAAGAAAATTTATTAGT-AAGAATTATT-TGATTAATTATATA-TATTATTAAATT
* *
59484289 ATATTTAATAATAATTATTTTAAATTATAC
63 ATATTTAATATTAATTATTTTAAATTATAT
* * *
59484319 AAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAAAATTTATTAGTAAGAATTA-TTT-GA-TTAATT--AT-ATATA--TT-AT
* *
59484384 TAAAATATATTTAATATTAATTATTTCAAATTATAT
57 TAAATTATATTTAATATTAATTATTTTAAATTATAT
59484420 TTTATAGTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
91 30 0.37
92 2 0.02
93 3 0.04
96 3 0.04
98 4 0.05
99 3 0.04
100 2 0.02
101 34 0.42
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (92 bp):
AAATTCATATAAGAAAATTTATTAGTAAGAATTATTTGATTAATTATATATATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATAT
Found at i:59484434 original size:59 final size:58
Alignment explanation
Indices: 59484369--59484677 Score: 197
Period size: 59 Copynumber: 5.2 Consensus size: 58
59484359 ATTTTATTAA
59484369 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATATTTTATAGT
* * ** * *
59484428 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTA-TT-AA-GA-ATTTTATTA-
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTAAATTATATTTTA-TAG
*
59484488 A
58 T
* * * *
59484489 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTATAGT
* * ** * *
59484548 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAGTTATTAAGAATT-T-TTTTATA-
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATATTTTATAG
59484610 T
58 T
* * *
59484611 -T-ATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATAGTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTATAGT
59484668 ATCATATATT
1 ATCATATATT
59484678 ATGGTTTGAG
Statistics
Matches: 186, Mismatches: 36, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
54 23 0.12
55 11 0.06
56 10 0.05
57 7 0.04
58 4 0.02
59 33 0.18
60 16 0.09
61 24 0.13
62 4 0.02
63 8 0.04
64 9 0.05
65 13 0.07
66 24 0.13
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATATTTTATAGT
Found at i:59484488 original size:120 final size:120
Alignment explanation
Indices: 59484358--59484775 Score: 714
Period size: 120 Copynumber: 3.5 Consensus size: 120
59484348 AATTATTTTA
* * *
59484358 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
59484422 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
59484478 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
59484543 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATT-AGTTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGA-TTATTAAG
* * *
59484598 AATTTTTTTATATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATAGTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
59484663 ATAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
59484718 TATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
59484776 ATGATTAAAT
Statistics
Matches: 282, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
119 1 0.00
120 272 0.96
121 9 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:59484496 original size:61 final size:61
Alignment explanation
Indices: 59484418--59484738 Score: 208
Period size: 61 Copynumber: 5.3 Consensus size: 61
59484408 TTCAAATTAT
*
59484418 ATTTTA-TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
1 ATTTTATTA-TATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
* * * * * * * **
59484479 ATTTTATTAAATTATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTA--AATT
1 ATTTTATTATATTATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATTATTAAGA
*
59484536 ATCTTT-TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATT-AGTTATTAAGA
1 AT-TTTAT-TA-TATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGA-TTATTAAGA
* * * * * * *
59484599 ATTTTTTTATATTATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAAATTATAG
1 ATTTTATTATATTATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT--ATTA-AG
59484660 -
61 A
* * *
59484660 --TTTA-TAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTGATTATTAAGT
1 ATTTTATTA-TATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
*
59484719 ATTTTATTAAATTATATATT
1 ATTTTATTATATTATATATT
59484739 TTAATTATAA
Statistics
Matches: 193, Mismatches: 38, Indels: 58
0.67 0.13 0.20
Matches are distributed among these distances:
57 5 0.03
58 11 0.06
59 54 0.28
60 34 0.18
61 71 0.37
62 13 0.07
63 5 0.03
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (61 bp):
ATTTTATTATATTATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
Found at i:59484513 original size:16 final size:16
Alignment explanation
Indices: 59484492--59484537 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
59484482 TTATTAAATT
59484492 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
59484508 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
59484523 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
59484538 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:59484631 original size:16 final size:16
Alignment explanation
Indices: 59484612--59484658 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
59484602 TTTTTATATT
59484612 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
59484628 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
59484643 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
59484659 GTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:59484636 original size:15 final size:15
Alignment explanation
Indices: 59484604--59484658 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
59484594 TAAGAATTTT
59484604 TTTATATTAT-ATAT-
1 TTTA-ATTATAATATA
59484618 TTTAATTATAATATA
1 TTTAATTATAATATA
*
59484633 TTTAATAATAAT-TA
1 TTTAATTATAATATA
59484647 TGTTAAATTATA
1 T-TT-AATTATA
59484659 GTTTATAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 5 0.14
14 11 0.31
15 13 0.37
16 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTAATTATAATATA
Found at i:59484753 original size:16 final size:16
Alignment explanation
Indices: 59484718--59484773 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
59484708 GATTATTAAG
* *
59484718 TATTTTATTAAATTATA
1 TATTTTAAT-AATAATA
*
59484735 TATTTTAATTATAATA
1 TATTTTAATAATAATA
59484751 TA-TTTAATAATAAT-
1 TATTTTAATAATAATA
59484765 TATGTTTAA
1 TAT-TTTAA
59484774 ATATGATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 12 0.36
17 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTTTAATAATAATA
Found at i:59484758 original size:15 final size:15
Alignment explanation
Indices: 59484723--59484764 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
59484713 TTAAGTATTT
*
59484723 TATTAAATTAT-ATA
1 TATTTAATTATAATA
59484737 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
59484751 TATTTAATAATAAT
1 TATTTAATTATAAT
59484765 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:59485679 original size:131 final size:131
Alignment explanation
Indices: 59485445--59485706 Score: 524
Period size: 131 Copynumber: 2.0 Consensus size: 131
59485435 AAAATATACG
59485445 TTTCTCCAACATTGGCAGTGAACTTTCAGGAAAAAAGCAAAACCATTGTGGAAAATGCAATTTGT
1 TTTCTCCAACATTGGCAGTGAACTTTCAGGAAAAAAGCAAAACCATTGTGGAAAATGCAATTTGT
59485510 CAGTAAGAATAAGATGTTGATGGAGATATTTCAATGAATACTCATCCTTGCTTTAAACTGACACC
66 CAGTAAGAATAAGATGTTGATGGAGATATTTCAATGAATACTCATCCTTGCTTTAAACTGACACC
59485575 A
131 A
59485576 TTTCTCCAACATTGGCAGTGAACTTTCAGGAAAAAAGCAAAACCATTGTGGAAAATGCAATTTGT
1 TTTCTCCAACATTGGCAGTGAACTTTCAGGAAAAAAGCAAAACCATTGTGGAAAATGCAATTTGT
59485641 CAGTAAGAATAAGATGTTGATGGAGATATTTCAATGAATACTCATCCTTGCTTTAAACTGACACC
66 CAGTAAGAATAAGATGTTGATGGAGATATTTCAATGAATACTCATCCTTGCTTTAAACTGACACC
59485706 A
131 A
59485707 CACGGGTGGT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (131 bp):
TTTCTCCAACATTGGCAGTGAACTTTCAGGAAAAAAGCAAAACCATTGTGGAAAATGCAATTTGT
CAGTAAGAATAAGATGTTGATGGAGATATTTCAATGAATACTCATCCTTGCTTTAAACTGACACC
A
Found at i:59488532 original size:22 final size:22
Alignment explanation
Indices: 59488504--59488546 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
59488494 GCAAACCTCT
59488504 ATTCACCAAACACTACAATTAG
1 ATTCACCAAACACTACAATTAG
59488526 ATTCACCAAACACTACAATTA
1 ATTCACCAAACACTACAATTA
59488547 AAGAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (22 bp):
ATTCACCAAACACTACAATTAG
Found at i:59491163 original size:53 final size:54
Alignment explanation
Indices: 59491079--59491263 Score: 213
Period size: 53 Copynumber: 3.5 Consensus size: 54
59491069 ATTTATTTAG
* *
59491079 GTGCTGGGACACTGATGG-TCGGCACCATTGTACCAAA-TTAAAAAAAAATTTGA
1 GTGCTGGGACACTGATGGCT-GGCACCCTTGTACCAAATTTAAAAAAAAATTGGA
* * * *
59491132 GTGCTGGGACATTGATGGCTAGCACCCTTGTACCAAACTT-AAAAAAAATTGGG
1 GTGCTGGGACACTGATGGCTGGCACCCTTGTACCAAATTTAAAAAAAAATTGGA
* *
59491185 GTGTTGGGACACTGATGGCTGGCACCCTAGTACCAAATTTTAAAAAAAAA-T-G-
1 GTGCTGGGACACTGATGGCTGGCACCCTTGTACCAAA-TTTAAAAAAAAATTGGA
*
59491237 GTGCTAGGACACTGATGG-TCGGCACCC
1 GTGCTGGGACACTGATGGCT-GGCACCC
59491264 CTTCAATATA
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
51 1 0.01
52 23 0.20
53 77 0.67
54 6 0.05
55 8 0.07
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (54 bp):
GTGCTGGGACACTGATGGCTGGCACCCTTGTACCAAATTTAAAAAAAAATTGGA
Found at i:59495980 original size:21 final size:22
Alignment explanation
Indices: 59495933--59495974 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59495923 AATATAATTG
*
59495933 CAAAATGGTAGCAAAACAATAT
1 CAAAATGGCAGCAAAACAATAT
59495955 CAAAATGGCAGC-AAACAATA
1 CAAAATGGCAGCAAAACAATA
59495975 ATAAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (22 bp):
CAAAATGGCAGCAAAACAATAT
Found at i:59503248 original size:15 final size:15
Alignment explanation
Indices: 59503230--59503263 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
59503220 ACGATTTGGT
59503230 TAGAAATTAATAGAA
1 TAGAAATTAATAGAA
59503245 TAGAAATTAATAGAA
1 TAGAAATTAATAGAA
59503260 TAGA
1 TAGA
59503264 TGAACCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (15 bp):
TAGAAATTAATAGAA
Found at i:59504076 original size:21 final size:21
Alignment explanation
Indices: 59504050--59504105 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
59504040 AACAACGGTG
*
59504050 GCGGTGAGATTAGCTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
59504071 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
**
59504092 GTAGTGAGATTAGA
1 GCGGTGAGATTAGA
59504106 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:59505018 original size:331 final size:325
Alignment explanation
Indices: 59504422--59505082 Score: 1207
Period size: 331 Copynumber: 2.0 Consensus size: 325
59504412 TTATTTTCAT
59504422 AAATAGTAACATTATACTTGGATCAAATTTTGAAGTATCTAAACAGATGATTTTTAATAAAAAAA
1 AAATAGTAACATTATACTTGGATCAAATTTTGAAGTATCTAAACAGATGATTTTTAATAAAAAAA
**
59504487 AAGACATAACAAGTTTCATTATTACTGGAAATTAGGTTATGATACAAAATGTTTTTACAAATATG
66 AAGACATAACAAGTAACATTATTACTGGAAATTAGGTTATGATACAAAATGTTTTTACAAATATG
59504552 GATTCATTAAACTAGTTGCAATGGTTTCCCTTAGCATCGCGATTTCAAGGTCAGTTTCACTGTTA
131 GATTCATTAAACTAGTTGCAATGGTTTCCCTTAGCATCGCGATTTCAAGGTCAGTTTCACTGTTA
59504617 GAAGAACTTGATTCACCTCTATCAAAATAGCCTGAAGAGACTAGCATGTCGGGTATATTCTCAAA
196 GAAGAACTTGATTCACCTCTATCAAAATAGCCTGAAGAGACTAGCATGTCGGGTATATTCTCAAA
59504682 TTGTCGAAAATCCTCATCATTTGACCAAGCATGTCTTCGAATGTTATTATGCAAAACCATTATTG
261 TTGTCGAAAATCCTCATCATTTGACCAAGCATGTCTTCGAATGTTATTATGCAAAACCATTATTG
59504747 AAATAGTAACATTATACTTGGATCAAATTTTGAAGTATCTAAACAGATGATTTTTAATAAAAAAA
1 AAATAGTAACATTATACTTGGATCAAATTTTGAAGTATCTAAACAGATGATTTTTAATAAAAAAA
* *
59504812 TAGTAACATAAGACA-TAACAAGTTCCATTACTGGAAATTAGGTTATGATACAAAATGTTTTTAC
66 AAG--ACATAACA-AGTAAC-A-TT--ATTACTGGAAATTAGGTTATGATACAAAATGTTTTTAC
59504876 AAATATGGATTCATTAAACTAGTTGCAATGGTTTCCCTTAGCATCGCGATTTCAAGGTCAGTTTC
124 AAATATGGATTCATTAAACTAGTTGCAATGGTTTCCCTTAGCATCGCGATTTCAAGGTCAGTTTC
59504941 ACTGTTAGAAGAACTTGATTCACCTCTATCAAAATAGCCTGAAGAGACTAGCATGTCGGGTATAT
189 ACTGTTAGAAGAACTTGATTCACCTCTATCAAAATAGCCTGAAGAGACTAGCATGTCGGGTATAT
59505006 TCTCAAATTGTCGAAAATCCTCATCATTTGACCAAGCATGTCTTCGAATGTTATTATGCAAAACC
254 TCTCAAATTGTCGAAAATCCTCATCATTTGACCAAGCATGTCTTCGAATGTTATTATGCAAAACC
59505071 ATTATTG
319 ATTATTG
*
59505078 CAATA
1 AAATA
59505083 ACTATTAAAA
Statistics
Matches: 324, Mismatches: 5, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
325 67 0.21
327 9 0.03
328 2 0.01
329 2 0.01
331 244 0.75
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (325 bp):
AAATAGTAACATTATACTTGGATCAAATTTTGAAGTATCTAAACAGATGATTTTTAATAAAAAAA
AAGACATAACAAGTAACATTATTACTGGAAATTAGGTTATGATACAAAATGTTTTTACAAATATG
GATTCATTAAACTAGTTGCAATGGTTTCCCTTAGCATCGCGATTTCAAGGTCAGTTTCACTGTTA
GAAGAACTTGATTCACCTCTATCAAAATAGCCTGAAGAGACTAGCATGTCGGGTATATTCTCAAA
TTGTCGAAAATCCTCATCATTTGACCAAGCATGTCTTCGAATGTTATTATGCAAAACCATTATTG
Found at i:59511219 original size:32 final size:31
Alignment explanation
Indices: 59511174--59511269 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
59511164 CTTAGATAAT
59511174 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
59511205 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
59511237 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
59511268 TT
1 TT
59511270 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:59511513 original size:31 final size:31
Alignment explanation
Indices: 59511476--59511537 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
59511466 AGATAATTTT
59511476 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
59511507 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
59511538 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:59512555 original size:21 final size:21
Alignment explanation
Indices: 59512529--59512600 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
59512519 CAAAAAAGAT
*
59512529 GGGAGAAACCAGCAAGAATGA
1 GGGAGAAACCAGCAAGAACGA
59512550 GGGAGAAACCAGCAAGAACGA
1 GGGAGAAACCAGCAAGAACGA
59512571 GGGAGAAACCAGCAAGAACGA
1 GGGAGAAACCAGCAAGAACGA
59512592 GGGGAGAAA
1 -GGGAGAAA
59512601 TGGTTGTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 41 0.84
22 8 0.16
ACGTcount: A:0.47, C:0.15, G:0.36, T:0.01
Consensus pattern (21 bp):
GGGAGAAACCAGCAAGAACGA
Found at i:59518877 original size:15 final size:17
Alignment explanation
Indices: 59518846--59518879 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
59518836 AAAAATAATT
59518846 ATTTATTATGAGTTATA
1 ATTTATTATGAGTTATA
59518863 ATTTA-TATG-GTTATA
1 ATTTATTATGAGTTATA
59518878 AT
1 AT
59518880 CCTTAATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
ATTTATTATGAGTTATA
Found at i:59519982 original size:46 final size:45
Alignment explanation
Indices: 59519915--59520112 Score: 265
Period size: 46 Copynumber: 4.6 Consensus size: 45
59519905 TTTGAGTACT
* *
59519915 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
59519961 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
59519997 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
59520043 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
59520088 TCTGATCAAG-G-ACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
59520113 ATCATACGTA
Statistics
Matches: 138, Mismatches: 4, Indels: 23
0.84 0.02 0.14
Matches are distributed among these distances:
36 29 0.21
38 1 0.01
39 2 0.01
40 4 0.03
42 4 0.03
43 15 0.11
44 2 0.01
45 22 0.16
46 59 0.43
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:59519997 original size:36 final size:36
Alignment explanation
Indices: 59519951--59520069 Score: 139
Period size: 36 Copynumber: 3.0 Consensus size: 36
59519941 GGTAGCTTTA
*
59519951 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
59519987 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA---GT
59520026 AGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GC--TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
59520069 G
1 G
59520070 GTAGCCTAGC
Statistics
Matches: 72, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
36 33 0.46
39 2 0.03
40 2 0.03
42 3 0.04
43 2 0.03
44 1 0.01
46 29 0.40
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:59520018 original size:82 final size:82
Alignment explanation
Indices: 59519915--59520069 Score: 292
Period size: 82 Copynumber: 1.9 Consensus size: 82
59519905 TTTGAGTACT
*
59519915 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
59519980 GATAAGTGCTATACTTA
66 GATAAGTGCTATACTTA
*
59519997 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
59520062 GATAAGTG
66 GATAAGTG
59520070 GTAGCCTAGC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTATACTTA
Found at i:59525923 original size:41 final size:40
Alignment explanation
Indices: 59525878--59525968 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
59525868 AGCGGCATTT
*
59525878 TTAGCGGTG-TTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-GAC-AAAAACGCCACTAAAAATCAAGCA
* * * **
59525919 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAGATTGAGCA
1 TTAGCGGCGCTTTGACAAAAACGCCACTAAAAATCAAGCA
59525959 TTAGCGGCGC
1 TTAGCGGCGC
59525969 ATTTTGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
40 30 0.70
41 10 0.23
42 3 0.07
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGACAAAAACGCCACTAAAAATCAAGCA
Found at i:59525949 original size:40 final size:38
Alignment explanation
Indices: 59525895--59526030 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 38
59525885 TGTTTGGACA
*
59525895 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAC
1 AAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTT-C
* * *
59525935 AAAAACGCCGCTAAAGATTGAGCATTAGCGGCGCATTTTG
1 AAAAACGCCGCTAAA-AATAAGCATTAGCGGCGC-TTTTC
* * * *
59525975 GAAAACGCTGCTAAAAATAAGCATTCGCAGCG-TTTTCC
1 AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTT-C
*
59526013 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
59526031 CCTAAGCCCA
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.05
38 4 0.05
39 23 0.29
40 41 0.53
41 6 0.08
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTC
Found at i:59526128 original size:41 final size:41
Alignment explanation
Indices: 59526071--59526306 Score: 314
Period size: 41 Copynumber: 5.8 Consensus size: 41
59526061 TTTGGGGTAC
** *
59526071 TTAGCGGCGTTTTTGAAAAATTGCCGCTAATGCT-TAGGGCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCT-GGCCT
59526112 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
* * * * *
59526153 TTAGCGGCGTTTTTCAAAAAGTGCTGCTAATGCTCGGGGCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
* * *
59526194 TTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAGCCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
* *
59526235 TTAGAGGCGTTTTTGAAAAAGCGCCACTAATGCTCTGGCCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
*
59526276 TTAGCGGCGATTTT-AGAAAAGCGCCGCTAAT
1 TTAGCGGCGTTTTTGA-AAAAGCGCCGCTAAT
59526307 TATAAAATCT
Statistics
Matches: 171, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 169 0.99
42 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCT
Done.