Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 17 of 362
Found at i:5267986 original size:30 final size:29
Alignment explanation
Indices: 5267951--5268008 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
5267941 TGGAATTAGG
5267951 TTTTGGAGGTCT-AATGAAAATTTCAAAAAT
1 TTTTGGA-GTCTAAATGAAAATTT-AAAAAT
*
5267981 TTTTGGAGTTTAAATGAAAATTTAAAAA
1 TTTTGGAGTCTAAATGAAAATTTAAAAA
5268009 GAAAAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTTGGAGTCTAAATGAAAATTTAAAAAT
Found at i:5272229 original size:174 final size:174
Alignment explanation
Indices: 5271911--5272339 Score: 629
Period size: 174 Copynumber: 2.5 Consensus size: 174
5271901 CCGCAAAGTG
* * * *
5271911 GAGGTAAATATATAGTTACTTGATGTCATTAAACATGTACCACACTATGCTAAGTTTTGG-AAGG
1 GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTATGC-AAGTTTTGGAAAAG
* * * *
5271975 AATTATGCAATAGCAAAAAGAAGCTAGCCAGGTTGAAAAGGTAAGTATGAGAGAAAATGTCTTTG
65 AATTGTGCACTAACAAAAACAAGCTAGCCAGGTTGAAAAGGTAAGTATGAGAGAAAATGTCTTTG
5272040 CTATCATAAAAAAAAAAAGATACCCCTAAAAC-TTCCAGTAAAATA
130 CTATCATAAAAAAAAAAAGATACCCCTAAAACTTTCCA-TAAAATA
* *
5272085 GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTGTGCAAAGTTTTGGAAAAA
1 GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTATGC-AAGTTTTGGAAAAG
***
5272150 AATTGTGCACTAACAAAAACAAGCTAGTTGGGTT-AACAAGGTAAGTATGAGAGAAAATGT-TTC
65 AATTGTGCACTAACAAAAACAAGCTAGCCAGGTTGAA-AAGGTAAGTATGAGAGAAAATGTCTT-
*
5272213 TGCTATCAT-CAAAAAAAAAGATACCCCTAAAACTTTCCATAAAATA
128 TGCTATCATAAAAAAAAAAAGATACCCCTAAAACTTTCCATAAAATA
5272259 GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTAT-CAAGTTTT-GAAAAGA
1 GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTATGCAAGTTTTGGAAAAGA
*
5272322 ATTGTACACTAACAAAAA
66 ATTGTGCACTAACAAAAA
5272340 AAAAAAAACT
Statistics
Matches: 233, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
171 23 0.10
172 7 0.03
173 1 0.00
174 136 0.58
175 66 0.28
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (174 bp):
GAGGTAAATATATCGTTACTTGATGTCATTAAAAATGTATCACACTATGCAAGTTTTGGAAAAGA
ATTGTGCACTAACAAAAACAAGCTAGCCAGGTTGAAAAGGTAAGTATGAGAGAAAATGTCTTTGC
TATCATAAAAAAAAAAAGATACCCCTAAAACTTTCCATAAAATA
Found at i:5279101 original size:19 final size:20
Alignment explanation
Indices: 5279057--5279093 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5279047 CACCGACTGT
*
5279057 GAGAAAGAAAAGAGAGAAAG
1 GAGAAGGAAAAGAGAGAAAG
5279077 GAGAAGGAAAAGA-AGAA
1 GAGAAGGAAAAGAGAGAA
5279094 GGAAGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GAGAAGGAAAAGAGAGAAAG
Found at i:5279397 original size:92 final size:96
Alignment explanation
Indices: 5279301--5279474 Score: 259
Period size: 97 Copynumber: 1.8 Consensus size: 96
5279291 ATTAGGTTGC
5279301 AAATTGTTAGTGTTTAGT-GTATTAGTGTATT-GTG-ATT-T-TTTTAGTAATAATATATTTAAA
1 AAATTGTTAGTGTTTAGTAGT-TTAGTGTATTAGTGTATTGTATTTTAGTAATAATATATTTAAA
5279361 AAAAAAAAATTTTATAGTTGATTTGGTTATAT
65 AAAAAAAAATTTTATAGTTGATTTGGTTATAT
** *
5279393 AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTAAA
1 AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGT-ATTTTAGTAATAATATATTTAAA
*
5279458 AAAAAACAATTTTATAG
65 AAAAAAAAATTTTATAG
5279475 CTATTTTATT
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
92 28 0.39
93 5 0.07
94 3 0.04
95 1 0.01
97 35 0.49
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.48
Consensus pattern (96 bp):
AAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTATTTTAGTAATAATATATTTAAAA
AAAAAAAATTTTATAGTTGATTTGGTTATAT
Found at i:5279518 original size:100 final size:97
Alignment explanation
Indices: 5279314--5279636 Score: 275
Period size: 112 Copynumber: 3.1 Consensus size: 97
5279304 TTGTTAGTGT
*
5279314 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATAATATATTTAAAAAAAAAAAATTTTATAGT
1 TTAGTGTATTAGTGTATTGTGATTTTTTTAG---TAATATATTT-AAAAAAAAAAATTTTATAGC
** * * *
5279379 TGATTTGGTTATATAAATT--G-TTAGTGTT-TAGTAGT-
62 T-ATTTTATTA-GTAATTTAAGATTAG-GTTATA-TATTG
5279414 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTAAAAAAAAACAATTTTATAGCTAT
1 TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTAAAAAAAAA-AATTTTATAGCTAT
5279479 TTTATTAGTAATTTAAGATTAGGTTATATAAATTG
65 TTTATTAGTAATTTAAGATTAGGTTATAT--ATTG
* * *
5279514 TTAGTGTTTAGTAGTTTAGTATATTAGCGTATTGTAATTTTTTTAGTAATATATTT--TAAAAAA
1 TTA--G--T-GTA--TTAGTGTATT-GTG-A-T-T----TTTTTAGTAATATATTTAAAAAAAAA
5279577 AATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATATTG
51 AATTTTATAGCTATTTTATTAGTAATTTAAGATTAGGTTATATATTG
5279624 TTAGTGT-TTAGTG
1 TTAGTGTATTAGTG
5279637 GTTTAGTGTG
Statistics
Matches: 190, Mismatches: 10, Indels: 44
0.78 0.04 0.18
Matches are distributed among these distances:
95 5 0.03
96 16 0.08
97 26 0.14
98 6 0.03
99 2 0.01
100 34 0.18
102 6 0.03
104 1 0.01
105 5 0.03
106 1 0.01
107 9 0.05
108 3 0.02
109 1 0.01
110 8 0.04
111 1 0.01
112 43 0.23
113 6 0.03
115 17 0.09
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (97 bp):
TTAGTGTATTAGTGTATTGTGATTTTTTTAGTAATATATTTAAAAAAAAAAATTTTATAGCTATT
TTATTAGTAATTTAAGATTAGGTTATATATTG
Found at i:5279518 original size:115 final size:112
Alignment explanation
Indices: 5279380--5279706 Score: 496
Period size: 112 Copynumber: 2.9 Consensus size: 112
5279370 TTTTATAGTT
*
5279380 GATTTGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
*
5279445 TAATATATTTAAAAAAAAACAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTT--TAAAAAA-AATTTTATAGCTATTTTATTAGTAATTTAA
* * *
5279495 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTATATTAGCGTATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
5279560 TAATATATTTTAAAAAAAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAAATTTTATAGCTATTTTATTAGTAATTTAA
* *
5279607 GATTAGGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAATGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTA--GTGTATTAGTGTATTGTGATTTTTTT
* * *
5279670 AGTAGTGTATTTTAAAAAATAATTTTATAGTTATTTT
64 AGTAATATATTTTAAAAAA-AATTTTATAGCTATTTT
5279707 GTGTTAGTAT
Statistics
Matches: 196, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
110 21 0.11
112 82 0.42
113 22 0.11
115 71 0.36
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (112 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
TAATATATTTTAAAAAAAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:5279793 original size:15 final size:16
Alignment explanation
Indices: 5279764--5279795 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5279754 TGTGATTTTT
5279764 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
5279780 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
5279795 T
1 T
5279796 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:5281890 original size:33 final size:33
Alignment explanation
Indices: 5281853--5281948 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
5281843 ATTTATCTCA
*
5281853 GTACTCTACTCCTTCC-GGCCCGTATCCACC-CAT
1 GTACTCTACTCC-TCCAGGCCCGTATCCACCGC-C
*
5281886 GTACTCAACTCCTCCAGAG-CCGTATCCACCGCC
1 GTACTCTACTCCTCCAG-GCCCGTATCCACCGCC
* *
5281919 GTACTCTACTCCTCCTGGCCCATATCCACC
1 GTACTCTACTCCTCCAGGCCCGTATCCACC
5281949 TCCATATTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.07
33 48 0.89
34 2 0.04
ACGTcount: A:0.18, C:0.46, G:0.12, T:0.24
Consensus pattern (33 bp):
GTACTCTACTCCTCCAGGCCCGTATCCACCGCC
Found at i:5287220 original size:25 final size:25
Alignment explanation
Indices: 5287191--5287240 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5287181 TCATTTTCCA
5287191 ATCGAAATAAAATTCAATTGATGGT
1 ATCGAAATAAAATTCAATTGATGGT
5287216 ATCGAAATAAAATTCAATTGATGGT
1 ATCGAAATAAAATTCAATTGATGGT
5287241 CATAATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (25 bp):
ATCGAAATAAAATTCAATTGATGGT
Found at i:5298977 original size:14 final size:15
Alignment explanation
Indices: 5298958--5298990 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5298948 ATTGAGATGA
*
5298958 TGATACTTAT-TTGT
1 TGATACTAATATTGT
5298972 TGATACTAATATTGT
1 TGATACTAATATTGT
5298987 TGAT
1 TGAT
5298991 GCTGTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (15 bp):
TGATACTAATATTGT
Found at i:5304649 original size:6 final size:6
Alignment explanation
Indices: 5304638--5304673 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
5304628 CTATAGCTTT
5304638 CAAAAA CAAAAA CAAAAAA CAAAAAA CAAAAA CAAA
1 CAAAAA CAAAAA C-AAAAA C-AAAAA CAAAAA CAAA
5304674 GATAACCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:5304655 original size:7 final size:7
Alignment explanation
Indices: 5304639--5304673 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
5304629 TATAGCTTTC
5304639 AAAAAC-
1 AAAAACA
5304645 AAAAACA
1 AAAAACA
5304652 AAAAACA
1 AAAAACA
5304659 AAAAAC-
1 AAAAACA
5304665 AAAAACA
1 AAAAACA
5304672 AA
1 AA
5304674 GATAACCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:5304657 original size:13 final size:13
Alignment explanation
Indices: 5304638--5304673 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5304628 CTATAGCTTT
5304638 CAAAAAC-AAAAA
1 CAAAAACAAAAAA
5304650 CAAAAAACAAAAAA
1 C-AAAAACAAAAAA
5304664 CAAAAACAAA
1 CAAAAACAAA
5304674 GATAACCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 15 0.68
14 6 0.27
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAACAAAAAA
Found at i:5304688 original size:25 final size:21
Alignment explanation
Indices: 5304639--5304679 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5304629 TATAGCTTTC
5304639 AAAAACAAAAACAAAA-AACA
1 AAAAACAAAAACAAAATAACA
5304659 AAAAACAAAAACAAAGATAAC
1 AAAAACAAAAACAAA-ATAAC
5304680 CCTAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 1 0.05
22 3 0.16
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.02
Consensus pattern (21 bp):
AAAAACAAAAACAAAATAACA
Found at i:5307441 original size:20 final size:22
Alignment explanation
Indices: 5307404--5307444 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5307394 TATAATACAT
*
5307404 TATATTATGTTATTTTTATAAA
1 TATATTATGTTATATTTATAAA
5307426 TATATTATG-TA-ATTTATAA
1 TATATTATGTTATATTTATAA
5307445 CACATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TATATTATGTTATATTTATAAA
Found at i:5309180 original size:15 final size:17
Alignment explanation
Indices: 5309152--5309184 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5309142 CGACCAAAGA
5309152 AAAATAAGACAAAAACC
1 AAAATAAGACAAAAACC
5309169 AAAA-AAGA-AAAAACC
1 AAAATAAGACAAAAACC
5309184 A
1 A
5309185 CGTGTTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAATAAGACAAAAACC
Found at i:5328635 original size:12 final size:12
Alignment explanation
Indices: 5328603--5328670 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
5328593 GAAGTCTAAG
*
5328603 AAAATAACAAAAA
1 AAAATAA-AAATA
5328616 AAACATAAAAATA
1 AAA-ATAAAAATA
* **
5328629 GAAATAAATTTA
1 AAAATAAAAATA
*
5328641 AAAATAGAAATA
1 AAAATAAAAATA
5328653 AAAAT-AAAAT-
1 AAAATAAAAATA
5328663 AAAATAAA
1 AAAATAAA
5328671 TAGACTCAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 5 0.11
11 6 0.14
12 20 0.45
13 9 0.20
14 4 0.09
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:5328644 original size:18 final size:18
Alignment explanation
Indices: 5328620--5328672 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
5328610 CAAAAAAAAC
5328620 ATAAAAATAGAAATAAAT
1 ATAAAAATAGAAATAAAT
* *
5328638 TTAAAAATAGAAATAAAA
1 ATAAAAATAGAAATAAAT
5328656 AT-AAAATA-AAATAAAT
1 ATAAAAATAGAAATAAAT
5328672 A
1 A
5328673 GACTCAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 8 0.26
17 6 0.19
18 17 0.55
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
ATAAAAATAGAAATAAAT
Found at i:5335488 original size:32 final size:32
Alignment explanation
Indices: 5335447--5335509 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
5335437 TGACTCTCCG
5335447 TTAGCCTACCATGAAGCACACTATCCAACCAT
1 TTAGCCTACCATGAAGCACACTATCCAACCAT
5335479 TTAGCCTACCATGAAGCACACTATCCAACCA
1 TTAGCCTACCATGAAGCACACTATCCAACCA
5335510 ATCACATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.21
Consensus pattern (32 bp):
TTAGCCTACCATGAAGCACACTATCCAACCAT
Found at i:5339836 original size:47 final size:47
Alignment explanation
Indices: 5339715--5339847 Score: 180
Period size: 46 Copynumber: 2.9 Consensus size: 47
5339705 ATAATCTCAC
* * *
5339715 CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGGTG-TTCGCAT
1 CCATAATGAACTTGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* *
5339761 CCATAATGAACTTGGAACACAACTCAACGAGTTCGAATGCTT-GCAT
1 CCATAATGAACTTGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* *
5339807 CCATAGGTGAACTTGGAATGCAACTCAACGAGTTCGGATGC
1 CCATA-ATGAACTTGGAACGCAACTCAACGAGTTCGGATGC
5339848 CTCATAATTC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
46 43 0.57
47 33 0.43
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (47 bp):
CCATAATGAACTTGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
Found at i:5347472 original size:11 final size:11
Alignment explanation
Indices: 5347394--5347475 Score: 62
Period size: 11 Copynumber: 7.1 Consensus size: 11
5347384 TTCACATATG
5347394 TTATATATTTA
1 TTATATATTTA
5347405 TTA-ATTATTTA
1 TTATA-TATTTA
5347416 TATATATATTGT-
1 T-TATATATT-TA
5347428 TT-TATATGTTA
1 TTATATAT-TTA
*
5347439 TTTTATATTATA
1 TTATATATT-TA
*
5347451 TCTATTATATTTC
1 T-TA-TATATTTA
5347464 TTATATATTTA
1 TTATATATTTA
5347475 T
1 T
5347476 ATTACATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
10 7 0.12
11 23 0.40
12 17 0.29
13 5 0.09
14 6 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATATATTTA
Found at i:5359706 original size:119 final size:119
Alignment explanation
Indices: 5359495--5359973 Score: 753
Period size: 119 Copynumber: 4.0 Consensus size: 119
5359485 GAAATAAATT
* ** **
5359495 AAAGACAGCAGATCTAGA-CTTCAGACATTTATGTTGAAGCAGATCCAAGATGATTTGGTATTCT
1 AAAGATAGCAGATCTA-ACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCT
* *
5359559 TGTGTTTACAAGAAACAAGTCAAGGACATAGCAGATTTGACTCTCAGACGTTCTC
65 TGTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
*
5359614 AAAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATGATTTGGTATTCTT
1 AAAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
*
5359679 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGAATCTCAGACGTTCTC
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
* *
5359733 AAAGATAGTAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTAGTATTCTT
1 AAAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
*
5359798 GTGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
* * *
5359852 AAATATAACAGATCTAACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGATTTGGTATTCTT
1 AAAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
* * * * * *
5359917 GTGTTTACAAGGAACAAATCGAGGACATTGTAGATATGACTCTCAAATGTTCTC
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
5359971 AAA
1 AAA
5359974 CAGACTCAAG
Statistics
Matches: 335, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
118 1 0.00
119 334 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (119 bp):
AAAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTT
GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTC
Found at i:5360036 original size:83 final size:83
Alignment explanation
Indices: 5359897--5360164 Score: 394
Period size: 83 Copynumber: 3.2 Consensus size: 83
5359887 GAAGCAGATC
* * * *
5359897 CAAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAATCGAGGACATTGTAGATATGACTCTCA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
5359962 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * *
5359980 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATTGAGGATATTGCAGATATGACTCACA
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
5360045 AATGTTCTCAAACAGACT
66 AATGTTCTCAAACAGACT
* * ** *
5360063 CAAGATGATTTGGCATCCTTGTGCTTATAAGGAACAAATCGAGGACGTAACAGATATGACTCTCG
1 CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
*
5360128 AATGTTCTCAAAACAAACT
66 AATGTTCTC-AAACAGACT
5360147 CAA-ACTGATTTGGCATCC
1 CAAGA-TGATTTGGCATCC
5360165 CCACAAGTCG
Statistics
Matches: 167, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
83 143 0.86
84 24 0.14
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (83 bp):
CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCA
AATGTTCTCAAACAGACT
Found at i:5361867 original size:36 final size:35
Alignment explanation
Indices: 5361802--5361885 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
5361792 TTATTTTCAC
*
5361802 ATATGTTATATATTTATTAATTATATATATTGTTTT
1 ATATGTTATATATTTATTAATTATATATATT-TCTT
5361838 ATATGTTAT-T-TTATATTATATCTAT-TATATTTCTT
1 ATATGTTATATATT-TATTA-AT-TATATATATTTCTT
*
5361873 ATATATT-TATATT
1 ATATGTTATATATT
5361886 ACATTTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
34 3 0.07
35 16 0.39
36 19 0.46
37 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (35 bp):
ATATGTTATATATTTATTAATTATATATATTTCTT
Found at i:5361967 original size:20 final size:20
Alignment explanation
Indices: 5361941--5361992 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
5361931 ATGTATCGCC
5361941 AATTATATTTTTTATGATTA
1 AATTATATTTTTTATGATTA
* * * *
5361961 CATTATATATATTATTATTA
1 AATTATATTTTTTATGATTA
*
5361981 AATCATATTTTT
1 AATTATATTTTT
5361993 AACCTACACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTATATTTTTTATGATTA
Found at i:5363736 original size:11 final size:11
Alignment explanation
Indices: 5363720--5363762 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5363710 CCCTTTTAAA
5363720 ATTTAAAAATT
1 ATTTAAAAATT
*
5363731 ATTTAAAAATC
1 ATTTAAAAATT
**
5363742 ATAAAAAAATTT
1 ATTTAAAAA-TT
5363754 ATTTAAAAA
1 ATTTAAAAA
5363763 ATTTATAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTAAAAATT
Found at i:5363780 original size:17 final size:16
Alignment explanation
Indices: 5363754--5363787 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5363744 AAAAAAATTT
5363754 ATTTAAAAAATTTATAA
1 ATTTAAAAAA-TTATAA
*
5363771 ATTTATAAAATTATAA
1 ATTTAAAAAATTATAA
5363787 A
1 A
5363788 AATTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAAAAATTATAA
Found at i:5363931 original size:13 final size:12
Alignment explanation
Indices: 5363908--5363957 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
5363898 AAAATTTAAA
5363908 TTTTTATAATTT
1 TTTTTATAATTT
5363920 TTTTTATGAATTT
1 TTTTTAT-AATTT
* *
5363933 TGTTAAT-ATTT
1 TTTTTATAATTT
*
5363944 TGTTTATAATTT
1 TTTTTATAATTT
5363956 TT
1 TT
5363958 AATAACTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 10 0.31
12 12 0.38
13 10 0.31
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:5365804 original size:11 final size:11
Alignment explanation
Indices: 5365771--5365809 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
5365761 AACAAGACAT
5365771 ATAAATAAAATA
1 ATAAA-AAAATA
*
5365783 CATAAATAAATA
1 -ATAAAAAAATA
5365795 ATAAAAAAATA
1 ATAAAAAAATA
5365806 ATAA
1 ATAA
5365810 TAATAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 5 0.21
13 5 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:5369272 original size:27 final size:26
Alignment explanation
Indices: 5369235--5369346 Score: 152
Period size: 27 Copynumber: 4.2 Consensus size: 26
5369225 AGCATGGCTG
* *
5369235 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5369261 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5369289 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
5369316 CCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
5369343 CCAG
1 CCAG
5369347 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.09
27 54 0.69
28 17 0.22
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5369294 original size:54 final size:54
Alignment explanation
Indices: 5369235--5369346 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
5369225 AGCATGGCTG
*
5369235 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* *
5369289 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5369343 CCAG
1 CCAG
5369347 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5370981 original size:26 final size:26
Alignment explanation
Indices: 5370945--5371054 Score: 202
Period size: 26 Copynumber: 4.2 Consensus size: 26
5370935 CATGAAATTC
*
5370945 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
5370971 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5370997 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5371023 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5371049 TTATCA
1 TTATCA
5371055 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5374037 original size:20 final size:21
Alignment explanation
Indices: 5374007--5374056 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
5373997 TACTTCTCTA
*
5374007 TTTTGTTCTTTCTT-TTATTTC
1 TTTTATTCTTT-TTATTATTTC
5374028 -TTTATTCTTTTTATTATTTC
1 TTTTATTCTTTTTATTATTTC
5374048 TTTTATTCT
1 TTTTATTCT
5374057 ACTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTATTCTTTTTATTATTTC
Found at i:5374066 original size:21 final size:19
Alignment explanation
Indices: 5374017--5374066 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
5374007 TTTTGTTCTT
5374017 TCTTT-TATTTCTTTATTC
1 TCTTTATATTTCTTTATTC
*
5374035 TTTTTATTATTTCTTTTATTC
1 TCTTTA-TATTTC-TTTATTC
5374056 TACTTTATATT
1 T-CTTTATATT
5374067 ATTATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
20 6 0.23
21 12 0.46
22 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTATATTTCTTTATTC
Found at i:5374074 original size:29 final size:29
Alignment explanation
Indices: 5374015--5374071 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
5374005 TATTTTGTTC
* *
5374015 TTTCTTTTATTTCTTTATTCTTTTTATTA
1 TTTCTTTTATTTCTTTATTATTATTATTA
5374044 TTTCTTTTATTCTACTTTA-TATTATTAT
1 TTTCTTTTATT-T-CTTTATTATTATTAT
5374072 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 8 0.33
31 5 0.21
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTCTTTTATTTCTTTATTATTATTATTA
Found at i:5374078 original size:13 final size:13
Alignment explanation
Indices: 5374060--5374097 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5374050 TTATTCTACT
5374060 TTATATTATTATA
1 TTATATTATTATA
*
5374073 TTATATTTTTA-A
1 TTATATTATTATA
5374085 TTATAATTATTAT
1 TTAT-ATTATTAT
5374098 TTCTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:5375046 original size:14 final size:14
Alignment explanation
Indices: 5375023--5375057 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5375013 ATTGTTGGCT
5375023 TTGGGCTAGTGTAA
1 TTGGGCTAGTGTAA
* *
5375037 TTGGGTTAGTGTAG
1 TTGGGCTAGTGTAA
5375051 TTGGGCT
1 TTGGGCT
5375058 GAGGATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.40, T:0.40
Consensus pattern (14 bp):
TTGGGCTAGTGTAA
Found at i:5375136 original size:14 final size:14
Alignment explanation
Indices: 5375113--5375147 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5375103 ATTGTTGGCT
*
5375113 TTGGGCTAGTGTAA
1 TTGGGTTAGTGTAA
*
5375127 TTGGGTTAGTGTAG
1 TTGGGTTAGTGTAA
5375141 TTGGGTT
1 TTGGGTT
5375148 GAGGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.03, G:0.40, T:0.43
Consensus pattern (14 bp):
TTGGGTTAGTGTAA
Found at i:5375166 original size:90 final size:90
Alignment explanation
Indices: 5375013--5375185 Score: 337
Period size: 90 Copynumber: 1.9 Consensus size: 90
5375003 ATTTTGGGCC
5375013 ATTGTTGGCTTTGGGCTAGTGTAATTGGGTTAGTGTAGTTGGGCTGAGGATTTTTGTAAGGGACT
1 ATTGTTGGCTTTGGGCTAGTGTAATTGGGTTAGTGTAGTTGGGCTGAGGATTTTTGTAAGGGACT
5375078 TAAACTATTATTATTATTATTTGGT
66 TAAACTATTATTATTATTATTTGGT
*
5375103 ATTGTTGGCTTTGGGCTAGTGTAATTGGGTTAGTGTAGTTGGGTTGAGGATTTTTGTAAGGGACT
1 ATTGTTGGCTTTGGGCTAGTGTAATTGGGTTAGTGTAGTTGGGCTGAGGATTTTTGTAAGGGACT
5375168 TAAACTATTATTATTATT
66 TAAACTATTATTATTATT
5375186 TGGTTTTAAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (90 bp):
ATTGTTGGCTTTGGGCTAGTGTAATTGGGTTAGTGTAGTTGGGCTGAGGATTTTTGTAAGGGACT
TAAACTATTATTATTATTATTTGGT
Found at i:5376166 original size:20 final size:21
Alignment explanation
Indices: 5376136--5376180 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
5376126 AATCATAAAC
5376136 AAAATTTATTAAAAAAGTTA-T
1 AAAATTTATTAAAAAA-TTATT
5376157 AAAA-TTATTAAAAAATTATT
1 AAAATTTATTAAAAAATTATT
5376177 AAAA
1 AAAA
5376181 AATAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATTTATTAAAAAATTATT
Found at i:5376182 original size:11 final size:11
Alignment explanation
Indices: 5376110--5376183 Score: 64
Period size: 11 Copynumber: 6.5 Consensus size: 11
5376100 TTTAAAATTT
5376110 AAAAATTATTTAA
1 AAAAATTA-TT-A
* *
5376123 AAAAATCATAA
1 AAAAATTATTA
5376134 ACAAAATTTATTA
1 A-AAAA-TTATTA
5376147 AAAAAGTTA-T-
1 AAAAA-TTATTA
5376157 -AAAATTATTA
1 AAAAATTATTA
5376167 AAAAATTATTA
1 AAAAATTATTA
5376178 AAAAAT
1 AAAAAT
5376184 AATAATGTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 3 0.06
9 5 0.10
11 19 0.37
12 12 0.24
13 12 0.24
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:5377324 original size:27 final size:26
Alignment explanation
Indices: 5377287--5377398 Score: 152
Period size: 27 Copynumber: 4.2 Consensus size: 26
5377277 AGCATGGCTG
* *
5377287 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5377313 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5377341 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
5377368 CCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
5377395 CCAG
1 CCAG
5377399 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.09
27 54 0.69
28 17 0.22
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5377346 original size:54 final size:54
Alignment explanation
Indices: 5377287--5377398 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
5377277 AGCATGGCTG
*
5377287 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* *
5377341 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5377395 CCAG
1 CCAG
5377399 GACGCTTCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5379052 original size:26 final size:26
Alignment explanation
Indices: 5379016--5379151 Score: 245
Period size: 26 Copynumber: 5.2 Consensus size: 26
5379006 CATGAAATTC
*
5379016 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
5379042 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5379068 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5379094 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5379120 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5379146 TTATCA
1 TTATCA
5379152 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5380240 original size:19 final size:19
Alignment explanation
Indices: 5380216--5380306 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
5380206 AATCATATCT
*
5380216 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
5380235 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
5380253 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
* *
5380270 TCTAAGATTACATATCACA
1 TCTAAGATTGCATATCATA
5380289 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5380307 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 15 0.23
18 16 0.25
19 33 0.52
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5380274 original size:35 final size:37
Alignment explanation
Indices: 5380216--5380306 Score: 132
Period size: 35 Copynumber: 2.5 Consensus size: 37
5380206 AATCATATCT
* *
5380216 TCTAAGATTGTATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTACATATCACA
5380253 TCTAAGATTG-TATCATATCTAAGATTACATATCACA
1 TCTAAGATTGATATCATATCTAAGATTACATATCACA
5380289 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
5380307 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 18 0.37
36 15 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTACATATCACA
Found at i:5381151 original size:207 final size:207
Alignment explanation
Indices: 5380688--5381480 Score: 1345
Period size: 207 Copynumber: 3.8 Consensus size: 207
5380678 AATCTGCTTA
* * *
5380688 TTCAATTTGTTCCCTAACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACACG
1 TTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
* *
5380753 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* * ** * * *
5380818 GATC-TGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATATGTCTGTCCTCTGTCGAATATG
131 GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
5380882 GAGACGCCAAAC
196 GAGACGCCAAAC
** * *
5380894 TTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAATGTAAACACG
1 TTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
5380959 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* * *
5381024 GATCTTGCTTTAGTATAAACATCTGAAGGCCATATCTGCTATGTGTCTGCCCTCCGTCAAATATG
131 GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
*
5381089 GAGACGTCAAAC
196 GAGACGCCAAAC
*
5381101 TTCAATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
1 TTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
5381166 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* *
5381231 GATCTTGCTTCAGTATAAACATTTGAAGGCCATATCTGCTATGTGTCTGCCCTCCGTCGAATATG
131 GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
5381296 GAGACGCCAAAC
196 GAGACGCCAAAC
**
5381308 TTTGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
1 TTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
*
5381373 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCATTGTAAGCACAAGGATGCCAAACCATCTTG
66 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
5381438 GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATG
131 GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATG
5381481 CTTTAACCTG
Statistics
Matches: 553, Mismatches: 33, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
206 125 0.23
207 428 0.77
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (207 bp):
TTCAATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAACGTAAACACG
TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
GATCTTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
GAGACGCCAAAC
Found at i:5381644 original size:87 final size:83
Alignment explanation
Indices: 5381486--5381773 Score: 427
Period size: 84 Copynumber: 3.4 Consensus size: 83
5381476 CTATGCTTTA
*
5381486 ACCTGTTACCCTACTGCTTAGGGGGTTAAGGCGCA-TCTTCGATCTGTTCCACTACTGCTTAGGG
1 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTGTTCCACTACTGCTTAGGG
*
5381550 AGATAAGATCCGCAATTTT
65 AGATAAGATCTGCAATTTT
*
5381569 GACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTTGATCTGTTCCACTACTGCTTA
1 -ACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGTTCCACTACTGCTTA
*
5381634 GGGAGATAAGATCTGTAATTTT
62 GGGAGATAAGATCTGCAATTTT
* *
5381656 AGCCTGTTACCCTACTACTTAAGGGG-TTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTAGG
1 A-CCTGTTACCCTACTGCTT-AGGGGATTAAGGCGAGTCTTCGATCTGTTCCACTACTGCTTAGG
*
5381720 GAGATAAGATCTGCAAATTTA
64 GAGATAAGATCTGC-AATTTT
5381741 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
1 ACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
5381774 CTGAATTTTG
Statistics
Matches: 186, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
83 6 0.03
84 95 0.51
85 7 0.04
86 2 0.01
87 71 0.38
88 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (83 bp):
ACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGTTCCACTACTGCTTAGGGA
GATAAGATCTGCAATTTT
Found at i:5382731 original size:1 final size:1
Alignment explanation
Indices: 5382721--5382818 Score: 70
Period size: 1 Copynumber: 98.0 Consensus size: 1
5382711 GGCCTCTCCA
* * * * * * * *
5382721 TTTTTCTTTTTTTTTCTTTTTTCTTTTTTTCTTTTTTTATTTTTTTATTTTTTATTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * **
5382786 TTTCTCTTTTTCTTTTCTTTTTCCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5382819 GAAATAGAAG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:5382740 original size:8 final size:8
Alignment explanation
Indices: 5382721--5382801 Score: 85
Period size: 8 Copynumber: 10.2 Consensus size: 8
5382711 GGCCTCTCCA
5382721 TTTTTCTT
1 TTTTTCTT
*
5382729 TTTTTTTCT
1 TTTTTCT-T
5382738 TTTTTCTT
1 TTTTTCTT
5382746 TTTTTCTT
1 TTTTTCTT
*
5382754 TTTTTATT
1 TTTTTCTT
*
5382762 TTTTT-AT
1 TTTTTCTT
*
5382769 TTTTT-AT
1 TTTTTCTT
*
5382776 TTTTTATT
1 TTTTTCTT
*
5382784 TTTTTCTC
1 TTTTTCTT
5382792 TTTTTCTT
1 TTTTTCTT
5382800 TT
1 TT
5382802 CTTTTTCCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
7 13 0.21
8 43 0.68
9 7 0.11
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5382816 original size:15 final size:15
Alignment explanation
Indices: 5382729--5382801 Score: 85
Period size: 15 Copynumber: 4.8 Consensus size: 15
5382719 CATTTTTCTT
5382729 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
*
5382744 TTTTTTTCTTTTTTTA
1 TTTTTTTC-TTTTTTC
* *
5382760 TTTTTTTATTTTTTA
1 TTTTTTTCTTTTTTC
5382775 TTTTTTAT-TTTTTTC
1 TTTTTT-TCTTTTTTC
*
5382790 TCTTTTTCTTTT
1 TTTTTTTCTTTT
5382802 CTTTTTCCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
14 1 0.02
15 36 0.71
16 14 0.27
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:5387519 original size:12 final size:11
Alignment explanation
Indices: 5387486--5387515 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5387476 TTTTTATGAA
5387486 TTTTT-ATATT
1 TTTTTAATATT
5387496 TTTTTAATATT
1 TTTTTAATATT
5387507 TTTTTAATA
1 TTTTTAATA
5387516 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:5393426 original size:44 final size:42
Alignment explanation
Indices: 5393360--5393445 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 42
5393350 CCATTAAGAA
* *
5393360 AAACTTCAGAAACAAGAGAGCTTTAAAGCAACCAGACTAAGTTT
1 AAACTTCAGAAACAAGAAAGCTTT-AAGAAACCAGA-TAAGTTT
* *
5393404 AAACTTGAGAAGA-AAGAAAGCTTTAAGAAATCAGATAAGTTT
1 AAACTTCAGAA-ACAAGAAAGCTTTAAGAAACCAGATAAGTTT
5393446 CTAGTGCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 7 0.19
43 9 0.24
44 20 0.54
45 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACTTCAGAAACAAGAAAGCTTTAAGAAACCAGATAAGTTT
Found at i:5394843 original size:44 final size:43
Alignment explanation
Indices: 5394776--5395169 Score: 146
Period size: 44 Copynumber: 8.7 Consensus size: 43
5394766 TATGGCGGAT
* *
5394776 CTTATCTTTCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGC
1 CTTATC-TCCTGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGC
* *** * *
5394820 CTTATCTCCTCGAAGTTGTAGTGGAGCAGACTGAATATAGCGAATC
1 CTTATCTCCT-GAAGTTGCAGTGGAGCAGACTGAAGCCA-C-CAGC
* * * * *
5394866 C-CATTTCCATAAAGTTGCAGTGGAGAAGATTGAAGCCACCAGC
1 CTTATCTCC-TGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGC
** ** * **
5394909 CTTATCTCCTTGAAGTTGCAGTAAAGCAGACTGAAGATAGCGAAT
1 CTTATCTCC-TGAAGTTGCAGTGGAGCAGACTGAAGCCA-CCAGC
* * * * * * * *
5394954 CTCATTTCTCTGAAATTGCAGTGGAGCAGATTAAAACTACAAGTTGCGAGT
1 CTTATCTC-CTGAAGTTGCAGTGGAGCAGACTGAAGC--C-A----CCAGC
* * ** * *
5395005 CTTATCTCCCTCAAGTTGCCGTAGGAGCAGACTGAAGATAGCAGAT
1 CTTATCT-CCTGAAGTTGCAGT-GGAGCAGACTGAAGCCACCAG-C
* * * *
5395051 CTTATATCCCTGAAGTTGCATTGGAGCAGA-TCGAAGCCACAATC
1 CTTATCT-CCTGAAGTTGCAGTGGAGCAGACT-GAAGCCACCAGC
* * ** * *
5395095 CTTATCTCCCTGAAGTTGCAATGGAGCAAGA-TAAAAATACACAAAC
1 CTTATCT-CCTGAAGTTGCAGTGGAGC-AGACT--GAAGCCACCAGC
5395141 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 CTTATCT-CCTGAAGTTGCAGTGGAGCAG
5395170 GTTAAAATTA
Statistics
Matches: 258, Mismatches: 73, Indels: 37
0.70 0.20 0.10
Matches are distributed among these distances:
43 6 0.02
44 83 0.32
45 77 0.30
46 58 0.22
48 1 0.00
49 1 0.00
51 20 0.08
52 12 0.05
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (43 bp):
CTTATCTCCTGAAGTTGCAGTGGAGCAGACTGAAGCCACCAGC
Found at i:5394939 original size:89 final size:90
Alignment explanation
Indices: 5394784--5395114 Score: 309
Period size: 89 Copynumber: 3.6 Consensus size: 90
5394774 ATCTTATCTT
* **
5394784 TCTG-AAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGTAGTGGAGCA
1 TCTGAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGCA
*
5394848 GACTGAATATAGCGAATCCCATTTC
66 GACTGAAGATAGCGAATCCCATTTC
* *
5394873 -CAT-AAAGTTGCAGTGGAGAAGATTGAAGCCACCAGCCTTATCTCCTTGAAGTTGCAGTAAAGC
1 TC-TGAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGC
*
5394936 AGACTGAAGATAGCGAATCTCATTTC
65 AGACTGAAGATAGCGAATCCCATTTC
* * * * *
5394962 TCTGAAA-TTGCAGTGGAGCAGATTAAAACTACAAGTTGCGAGTCTTATCTCCCTC-AAGTTGCC
1 TCTGAAAGTTGCAGTGGAGCAGATTGAAGC--C-A----CCAGCCTTATCT-CCTCGAAGTTGCA
* ** *
5395025 GTAGGAGCAGACTGAAGATAGC-AGATCTTATATC
58 GTA-AAGCAGACTGAAGATAGCGA-ATCCCATTTC
* * * * *
5395059 CCTG-AAGTTGCATTGGAGCAGATCGAAGCCACAATCCTTATCTCC-CTGAAGTTGCA
1 TCTGAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTC-GAAGTTGCA
5395115 ATGGAGCAAG
Statistics
Matches: 199, Mismatches: 26, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
88 2 0.01
89 101 0.51
90 20 0.10
91 1 0.01
92 1 0.01
94 1 0.01
95 1 0.01
96 23 0.12
97 49 0.25
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (90 bp):
TCTGAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTCGAAGTTGCAGTAAAGCA
GACTGAAGATAGCGAATCCCATTTC
Found at i:5394982 original size:45 final size:45
Alignment explanation
Indices: 5394839--5394983 Score: 116
Period size: 45 Copynumber: 3.2 Consensus size: 45
5394829 TCGAAGTTGT
* *
5394839 AGTGGAGCAGACTGAATATAGCGAATCCCATTTCCAT-AAAGTTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAA-TTGC
* * ** * ** * * * *
5394884 AGTGGAGAAGATTGAAGCCA-CCAGCCTTATCTCCTTGAAGTTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAATTGC
**
5394928 AGTAAAGCAGACTGAAGATAGCGAATCTCATTTCTC-TGAAATTGC
1 AGTGGAGCAGACTGAAGATAGCGAATCTCATTTC-CATGAAATTGC
5394973 AGTGGAGCAGA
1 AGTGGAGCAGA
5394984 TTAAAACTAC
Statistics
Matches: 70, Mismatches: 27, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
44 27 0.39
45 42 0.60
46 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (45 bp):
AGTGGAGCAGACTGAAGATAGCGAATCTCATTTCCATGAAATTGC
Found at i:5395176 original size:46 final size:46
Alignment explanation
Indices: 5395051--5395211 Score: 166
Period size: 46 Copynumber: 3.6 Consensus size: 46
5395041 GATAGCAGAT
* * ** **
5395051 CTTATATCCCTGAAGTTGCATTGGAGC-AGAT-CGAAGCCACAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATACACAATC
* *
5395095 CTTATCTCCCTGAAGTTGCAATGGAGCAAGATAAAAATACACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATACACAATC
* * * *
5395141 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAATTAC-CAATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATACACAATC
* * *
5395186 CTTATATCCTTGAAGTTACAGTGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
5395212 TAGATCGAAG
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
44 25 0.25
45 30 0.30
46 44 0.44
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAAATACACAATC
Found at i:5396699 original size:23 final size:24
Alignment explanation
Indices: 5396644--5396700 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
5396634 TTCAACCCTT
* *
5396644 TTTATGTTTAAAATTTATTTATTTA
1 TTTATCTTT-AAATTTATATATTTA
*
5396669 TCT-TCTTTAAATTTATATA-TTA
1 TTTATCTTTAAATTTATATATTTA
5396691 TTTATCTTTA
1 TTTATCTTTA
5396701 CTATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 5 0.19
23 16 0.59
24 4 0.15
25 2 0.07
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATCTTTAAATTTATATATTTA
Found at i:5396725 original size:21 final size:22
Alignment explanation
Indices: 5396681--5396739 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 22
5396671 TTCTTTAAAT
5396681 TTATATATTATTTATCTTTACTA
1 TTAT-TATTATTTATCTTTACTA
5396704 TTATTATTA-TTAT-TTTATCTA
1 TTATTATTATTTATCTTTA-CTA
5396725 TTATTATTTATTTAT
1 TTATTA-TTATTTAT
5396740 ATATGCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 8 0.24
23 8 0.24
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTATTATTTATCTTTACTA
Found at i:5396726 original size:15 final size:14
Alignment explanation
Indices: 5396704--5396733 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5396694 ATCTTTACTA
5396704 TTATTATTATTATT
1 TTATTATTATTATT
5396718 TTATCTATTATTATT
1 TTAT-TATTATTATT
5396733 T
1 T
5396734 ATTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:5414672 original size:21 final size:22
Alignment explanation
Indices: 5414638--5414678 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5414628 TGAAAGGTCA
5414638 AAAATTTGTCTAACTTTTTCCT
1 AAAATTTGTCTAACTTTTTCCT
5414660 AAAATTT-TCTAACTTTTTC
1 AAAATTTGTCTAACTTTTTC
5414679 TAACTGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAATTTGTCTAACTTTTTCCT
Found at i:5418882 original size:19 final size:18
Alignment explanation
Indices: 5418847--5418882 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5418837 GAAGCAAGCA
*
5418847 ATGATTGAAGAAATCAGG
1 ATGATTGAAAAAATCAGG
5418865 ATGATTGAAAAGAATCAG
1 ATGATTGAAAA-AATCAG
5418883 ACCTGGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (18 bp):
ATGATTGAAAAAATCAGG
Found at i:5437961 original size:20 final size:19
Alignment explanation
Indices: 5437920--5437964 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5437910 TTATTCATAA
5437920 TATTATATTTTATTATTGT
1 TATTATATTTTATTATTGT
* * *
5437939 TATTATGTTTGTATTTTTTT
1 TATTATATTT-TATTATTGT
5437959 TATTAT
1 TATTAT
5437965 TTATTAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (19 bp):
TATTATATTTTATTATTGT
Found at i:5438207 original size:11 final size:11
Alignment explanation
Indices: 5438170--5438264 Score: 63
Period size: 11 Copynumber: 8.5 Consensus size: 11
5438160 TTTCAAATAT
*
5438170 TATATATGTATA
1 TATATAT-TATG
5438182 TATATATTATG
1 TATATATTATG
5438193 --TATATTATG
1 TATATATTATG
5438202 TATATATT-T-
1 TATATATTATG
5438211 TAATATATTATG
1 T-ATATATTATG
* *
5438223 TGTATATTTTG
1 TATATATTATG
* *
5438234 TTTTGTATTTCATG
1 -TATATA-TT-ATG
*
5438248 TACATATTATG
1 TATATATTATG
5438259 TATATA
1 TATATA
5438265 CATTTAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
9 10 0.15
10 8 0.12
11 26 0.40
12 14 0.22
13 5 0.08
14 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (11 bp):
TATATATTATG
Found at i:5451015 original size:45 final size:45
Alignment explanation
Indices: 5450876--5451123 Score: 188
Period size: 45 Copynumber: 5.6 Consensus size: 45
5450866 GACAAAGGAC
* ** *
5450876 CTTAACCCCCTAAACAGTAGGGTAACAGG-TTGA-ATTCACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGATTGACAGAT
* * * * ** * *
5450919 ATTAACGCCCTAAACAGTAGGGAAACA-AATCAAAG-GTGACA-AGC
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAAGATTGACAGA-T
* *
5450963 CTTAACCCCCTAAGTAGTAGGGTAATAGGCTAAAGATTGACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGATTGACAGAT
* * * ** ** *
5451008 CTTAACCCCCTAAGCAATAGGGAAACA-GATCAAA-AGCGATGGCT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCT-AAAGATTGACAGAT
* *
5451052 -TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
1 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGATTGACAGAT
*
5451096 CTTAACCCCCTAAGCAGTAGGGAAACAG
1 CTTAACCCCCTAAGCAGTAGGGTAACAG
5451124 ATCAAAAGCG
Statistics
Matches: 153, Mismatches: 41, Indels: 20
0.71 0.19 0.09
Matches are distributed among these distances:
43 51 0.33
44 44 0.29
45 57 0.37
46 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (45 bp):
CTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAGATTGACAGAT
Found at i:5451066 original size:43 final size:43
Alignment explanation
Indices: 5451009--5451160 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
5450999 TTGACAGATC
* *
5451009 TTAACCCCCTAAGCAATAGGGAAACAGATCAAAAGCGATGGCT
1 TTAAACCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGCT
* * * * ** ** *
5451052 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGAT
1 TTAAACCCCTAAGCAGTAGGGAAACA-GATCAAAAGCGATGGCT
* *
5451096 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGCC
1 -TTAAACCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGCT
*
5451140 TTAAACCCTTAAGCAGTAGGG
1 TTAAACCCCTAAGCAGTAGGG
5451161 TAATAGACTG
Statistics
Matches: 83, Mismatches: 24, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
43 42 0.51
44 17 0.20
45 24 0.29
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (43 bp):
TTAAACCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGCT
Found at i:5451096 original size:88 final size:86
Alignment explanation
Indices: 5450703--5451326 Score: 566
Period size: 87 Copynumber: 7.2 Consensus size: 86
5450693 GAATCCACAA
* * *
5450703 GCCTTAAACCCCGAAGTAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCATAAGCAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
** * *
5450768 TGG-AGTAGATCGAATA-CGGTGG
66 -GGAAACAGATC-AAAAGCGAT-G
* * * * * *
5450790 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAA-TTACAGATCTTGTCTCCCTAAGCAG-AG
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
* * *
5450853 TGG-AGCAGAT--AAAGACAAAG
66 -GGAAACAGATCAAAAG-CGATG
* * * * * * * * *
5450873 GACCTTAACCCCCTAAACAGTAGGGTAACAGGTTGAATTCACAGATATTAACGCCCTAAACAGTA
1 G-CCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTA
* * * **
5450938 GGGAAACAAATCAAAGGTGACAA
65 GGGAAACAGATCAAAAGCGA-TG
* * * * * * *
5450961 GCCTTAACCCCCTAAGTAGTAGGGTAATAGGCTAAAGATTGACAGATCTTAACCCCCTAAGCAAT
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCT-GA-ATTTACAGATCTTATCTCCCTAAGCAGT
5451026 AGGGAAACAGATCAAAAGCGATG
64 AGGGAAACAGATCAAAAGCGATG
* * * * *
5451049 GCTTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTGACAGATCTTAACCCCCTAAGCAGT
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTG-A-ATTTACAGATCTTATCTCCCTAAGCAGT
5451114 AGGGAAACAGATCAAAAGCGATG
64 AGGGAAACAGATCAAAAGCGATG
* * * * *
5451137 GCCTTAAACCCTTAAGCAGTAGGGTAATAGACTGAATTTACAGATCTCATCACCCTAAGTAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
* * * *
5451202 GGAAACAGATCGAAGGTGAAGG
66 GGAAACAGATCAAAAGCG-ATG
5451224 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
*
5451289 TGG-AGCAGATC-AAAGACGATG
66 -GGAAACAGATCAAAAG-CGATG
*
5451310 AGCCTT-GACCCCTAAGC
1 -GCCTTAAACCCCTAAGC
5451327 TGTAACGCCC
Statistics
Matches: 446, Mismatches: 75, Indels: 33
0.81 0.14 0.06
Matches are distributed among these distances:
82 2 0.00
83 2 0.00
84 31 0.07
85 32 0.07
86 85 0.19
87 134 0.30
88 119 0.27
89 41 0.09
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (86 bp):
GCCTTAAACCCCTAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCCTAAGCAGTAG
GGAAACAGATCAAAAGCGATG
Found at i:5451283 original size:43 final size:42
Alignment explanation
Indices: 5451149--5451288 Score: 113
Period size: 43 Copynumber: 3.2 Consensus size: 42
5451139 CTTAAACCCT
* *
5451149 TAAGCAGTAGGGTAATAGACTGAATTTACAGATCTCATCACCC
1 TAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATC-CCC
* * * * * * ** *
5451192 TAAGTAGTAGGGAAACA-GATCGAAGGTGA-AGGGCCTTAAACCCC
1 TAAGCAGTAGGGTAATAGGCT-GAA-TTTACA-GATCTT-ATCCCC
5451236 TAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCTCCC
1 TAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATC-CCC
5451279 TAAGCAGTAG
1 TAAGCAGTAG
5451289 TGGAGCAGAT
Statistics
Matches: 70, Mismatches: 20, Indels: 14
0.67 0.19 0.13
Matches are distributed among these distances:
42 3 0.04
43 37 0.53
44 26 0.37
45 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (42 bp):
TAAGCAGTAGGGTAATAGGCTGAATTTACAGATCTTATCCCC
Found at i:5455798 original size:22 final size:23
Alignment explanation
Indices: 5455768--5455812 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5455758 ACCTGATCAG
5455768 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
*
5455790 AATATGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
5455813 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:5456027 original size:23 final size:24
Alignment explanation
Indices: 5456001--5456098 Score: 92
Period size: 28 Copynumber: 3.8 Consensus size: 24
5455991 AAATGTCCAA
5456001 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
5456024 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
5456052 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
5456081 CCAAAACACACCAG-TATA
1 CCAAAACACACCAGATATA
5456099 GCACAAAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
23 14 0.22
24 4 0.06
28 33 0.51
29 14 0.22
ACGTcount: A:0.46, C:0.33, G:0.04, T:0.17
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:5456047 original size:28 final size:28
Alignment explanation
Indices: 5456015--5456098 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
5456005 AACACACCAG
*
5456015 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGTATAA
* *
5456043 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGTATAA
5456071 TATAATCCATCCAAAACACACCAGTATA
1 TATAATCC-TCCAAAACACACCAGTATA
5456099 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 33 0.66
29 17 0.34
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGTATAA
Found at i:5456162 original size:13 final size:13
Alignment explanation
Indices: 5456144--5456168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5456134 TAAACATCAG
5456144 CATATCCAAATCT
1 CATATCCAAATCT
5456157 CATATCCAAATC
1 CATATCCAAATC
5456169 CCTTCTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (13 bp):
CATATCCAAATCT
Found at i:5461167 original size:27 final size:27
Alignment explanation
Indices: 5461136--5461194 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 27
5461126 GTACATAGTA
*
5461136 CCTGATCAGAATACGACACATAAGGTG
1 CCTGATCAGAATACGACACATAAAGTG
*
5461163 CCTG---A-AATATGACACATAAAGTG
1 CCTGATCAGAATACGACACATAAAGTG
5461186 CCTGATCAG
1 CCTGATCAG
5461195 TAAAGCCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
23 20 0.77
24 1 0.04
26 1 0.04
27 4 0.15
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (27 bp):
CCTGATCAGAATACGACACATAAAGTG
Found at i:5461176 original size:23 final size:23
Alignment explanation
Indices: 5461145--5461190 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5461135 ACCTGATCAG
*
5461145 AATACGACACATAAGGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
*
5461168 AATATGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
5461191 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:5461406 original size:23 final size:24
Alignment explanation
Indices: 5461380--5461474 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
5461370 AAATGTCCAA
5461380 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
5461403 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
5461431 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
5461460 CCAAAACACACCAGA
1 CCAAAACACACCAGA
5461475 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:5461476 original size:29 final size:28
Alignment explanation
Indices: 5461394--5461477 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
5461384 AACACACCAG
* *
5461394 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
5461422 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
5461450 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
5461478 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:5465626 original size:26 final size:26
Alignment explanation
Indices: 5465597--5465704 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5465587 TGGTACAAAT
5465597 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5465623 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5465649 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5465675 TGATAATGGTTTAGGGAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5465701 TGAT
1 TGAT
5465705 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5467342 original size:27 final size:27
Alignment explanation
Indices: 5467302--5467438 Score: 183
Period size: 27 Copynumber: 5.1 Consensus size: 27
5467292 AGGAAGCGTC
*
5467302 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
5467329 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
5467355 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
5467383 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
5467410 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
5467437 CT
1 CT
5467439 AGTGACTTCG
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
26 11 0.11
27 83 0.85
28 4 0.04
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:5467381 original size:54 final size:54
Alignment explanation
Indices: 5467299--5467438 Score: 246
Period size: 54 Copynumber: 2.6 Consensus size: 54
5467289 TGGAGGAAGC
5467299 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
5467353 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* *
5467407 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCT
5467439 AGTGACTTCG
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
53 6 0.07
54 77 0.93
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:5467454 original size:81 final size:80
Alignment explanation
Indices: 5467302--5467460 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 80
5467292 AGGAAGCGTC
* *
5467302 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTAT
5467367 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * *
5467383 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTAGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGTGGCTCTGCCACATATATCTGT-CCTAGTGACT
*
5467446 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
5467461 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 17 0.25
81 52 0.75
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTAT
GCCACAATATCTGAT
Found at i:5469036 original size:19 final size:19
Alignment explanation
Indices: 5469014--5469057 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5469004 TTATTCATAA
5469014 TATTATATTT-TATTATTGT
1 TATTATATTTGTATT-TTGT
* *
5469033 TATTATGTTTGTATTTTTT
1 TATTATATTTGTATTTTGT
5469052 TATTAT
1 TATTAT
5469058 TTATTAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (19 bp):
TATTATATTTGTATTTTGT
Found at i:5469290 original size:11 final size:11
Alignment explanation
Indices: 5469265--5469347 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
5469255 TAGATGTATA
5469265 TATATATTATG
1 TATATATTATG
5469276 --TATATTATG
1 TATATATTATG
5469285 TATATATT-T-
1 TATATATTATG
5469294 TAATATATTATG
1 T-ATATATTATG
* *
5469306 TGTATATTTTG
1 TATATATTATG
* *
5469317 TTTTGTATTTCATG
1 -TATATA-TT-ATG
*
5469331 TACATATTATG
1 TATATATTATG
5469342 TATATA
1 TATATA
5469348 CATTTAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
9 10 0.18
10 8 0.15
11 23 0.42
12 7 0.13
13 5 0.09
14 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (11 bp):
TATATATTATG
Found at i:5469403 original size:3 final size:3
Alignment explanation
Indices: 5469395--5469457 Score: 65
Period size: 3 Copynumber: 20.3 Consensus size: 3
5469385 TATGTAATGT
* * *
5469395 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCT- TTGCA TTT TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT--A TTA TTA TTA
5469442 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
5469458 ACCTTTCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 46 0.92
4 1 0.02
5 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5473120 original size:16 final size:17
Alignment explanation
Indices: 5473090--5473122 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5473080 AATAGAAAAA
*
5473090 AAGATAAAAATACAAAG
1 AAGAGAAAAATACAAAG
5473107 AAGAGAAAAA-ACAAAG
1 AAGAGAAAAATACAAAG
5473123 TTCAAAGCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGAGAAAAATACAAAG
Found at i:5473852 original size:13 final size:13
Alignment explanation
Indices: 5473834--5473872 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5473824 TATTTGTTTC
5473834 TTTATATTTTTAT
1 TTTATATTTTTAT
* *
5473847 TTTATATTTTAAA
1 TTTATATTTTTAT
*
5473860 TTTATATTATTAT
1 TTTATATTTTTAT
5473873 GTATTCTGCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTTTTAT
Found at i:5473912 original size:3 final size:3
Alignment explanation
Indices: 5473904--5473950 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
5473894 TCATTATTGC
* *
5473904 TAT TAT TAT TAT TAT TATT TAC TAT TAT TATT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT
5473951 CATTTCTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5473931 original size:13 final size:13
Alignment explanation
Indices: 5473904--5473948 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5473894 TCATTATTGC
5473904 TATTA-TTATTAT
1 TATTATTTATTAT
*
5473916 TATTATTTACTAT
1 TATTATTTATTAT
5473929 TATTATTTATTAT
1 TATTATTTATTAT
*
5473942 CATTATT
1 TATTATT
5473949 ATCATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 5 0.17
13 24 0.83
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:5473946 original size:16 final size:16
Alignment explanation
Indices: 5473904--5473950 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5473894 TCATTATTGC
*
5473904 TATTATTATTATTA-T
1 TATTATCATTATTATT
5473919 TATT-TACTATTATTATT
1 TATTAT-C-ATTATTATT
5473936 TATTATCATTATTAT
1 TATTATCATTATTAT
5473951 CATTTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 15 0.56
17 6 0.22
18 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATCATTATTATT
Found at i:5474195 original size:3 final size:3
Alignment explanation
Indices: 5474180--5474239 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
5474170 CACTTGACTG
* * * *
5474180 TTA TTA CTA TTA TTA TTA TTA TT- TT- TTA TTG TTA TTA TTA TCA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5474226 TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TT
5474240 TGTTGATGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5476149 original size:26 final size:26
Alignment explanation
Indices: 5476120--5476227 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5476110 TGATACAAAT
5476120 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5476146 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5476172 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5476198 TGATAATGGTTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
5476224 TGAT
1 TGAT
5476228 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5482059 original size:3 final size:3
Alignment explanation
Indices: 5482053--5482101 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5482043 TTTTTCTTTT
5482053 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5482101 A
1 A
5482102 AGAGGCTTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5482727 original size:3 final size:3
Alignment explanation
Indices: 5482719--5483015 Score: 273
Period size: 3 Copynumber: 98.7 Consensus size: 3
5482709 ATTAATTAAA
* *
5482719 ATT ATT ATT ATT -TCT ACT ATT ATTT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * *
5482765 ACT ATT ATT ATT ATT -TT ACT ATT ATT ATTT ATT ATC ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
* * * * *
5482810 ATT ACT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT TTT ACT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
5482858 ATT ATT TTCT ATT ATT ATA ATT ATT ATT ACT ATC ATT ATT ATT ACT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
5482904 ATT ATT ATT ATT ATT ATT -TT ACT ATT ATT ATT -TCGT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT--T ATT ATT ATT
* * *
5482949 GTT ATT ATT ACT ATT ATT ATT -TT -TT ACT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * *
5482993 GTT GTT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
5483016 CTTTTTAATT
Statistics
Matches: 236, Mismatches: 46, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
2 10 0.04
3 213 0.90
4 12 0.05
5 1 0.00
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5483120 original size:18 final size:18
Alignment explanation
Indices: 5483082--5483120 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5483072 TATTTGCTTA
* *
5483082 TTTATTTATTCTTTTAGT
1 TTTATTTATTATTTTACT
*
5483100 TTTATTTATTATTTTTCT
1 TTTATTTATTATTTTACT
5483118 TTT
1 TTT
5483121 TACTAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTTATTATTTTACT
Found at i:5485301 original size:15 final size:15
Alignment explanation
Indices: 5485275--5485319 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
5485265 TATGCATTCA
5485275 TGCATCTACATTACAT
1 TGCAT-TACATTACAT
5485291 TGCATTACATTACAT
1 TGCATTACATTACAT
*
5485306 TGCATCACA-TACAT
1 TGCATTACATTACAT
5485320 CACATTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 5 0.18
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (15 bp):
TGCATTACATTACAT
Found at i:5487822 original size:46 final size:46
Alignment explanation
Indices: 5487755--5487924 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
5487745 TGTAACCCGC
*
5487755 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTTGCAT
* *
5487801 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATG--T--TTGCAT
* * * ** *
5487851 -C-TCA-CGAACTTGGACTCAACTCAACGAGCTCGAACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTTGCAT
* *
5487894 CCATAAGTGAACTCAGACTCAACTCAACGAG
1 CCATAAGCGAACTCGGACTCAACTCAACGAG
5487925 ATCAGATGCC
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 3 0.03
46 58 0.57
47 27 0.26
48 3 0.03
49 1 0.01
50 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGTTTGCAT
Found at i:5487869 original size:93 final size:93
Alignment explanation
Indices: 5487762--5487934 Score: 265
Period size: 93 Copynumber: 1.9 Consensus size: 93
5487752 CGCCCATAAG
**** * *
5487762 CGAACTCGGACTCAACTCAACGAGCTCGGGTGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
* *
5487827 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGATCAGATGCCTAGTTACATCTCA
*
5487855 CGAACTTGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
5487920 ACGAGATCAGATGCC
66 ACGAGATCAGATGCC
5487935 AAAATATCCT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGATCAGATGCCTAGTTACATCTCA
Found at i:5501853 original size:19 final size:20
Alignment explanation
Indices: 5501829--5501866 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5501819 GTTCACTTTA
5501829 TTTTCTTTGTTT-TTCTCTT
1 TTTTCTTTGTTTCTTCTCTT
5501848 TTTTCTTTGTTTCTTCTCT
1 TTTTCTTTGTTTCTTCTCT
5501867 CGATTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTCTTTGTTTCTTCTCTT
Found at i:5506959 original size:143 final size:142
Alignment explanation
Indices: 5506604--5507069 Score: 639
Period size: 143 Copynumber: 3.3 Consensus size: 142
5506594 TATAGCAAAC
* * ** *
5506604 CTTATCTTCCTGAAGTTGCGGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCT-AATGTTGC
1 CTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAA-GTTGC
* * *
5506668 AGTGGAACGGATTGAAGCTACAAATTATGGCAAATATTATCTTCCTAAAGTTGCAGTGGAGCAGA
65 AGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
*
5506733 TTGAAGCCACCAC
130 TTGAAGCCACCAT
* * *
5506746 CTTATCTCCCTAAAGTTGCAGCAGAGCAGACTGAAGA-AATTGAATCTTATTTCCCTGAAGTTGC
1 CTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAA-CGAATCTTATTTCCCTGAAGTTGC
* ** * * * *
5506810 AATGGAATAGATTAAAGCTACAAATTATGGCGAATCTTATCTTTCTGAGGTTGTAGTGGAGCAGA
65 AGTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
5506875 TTGAAGCCACCAGT
130 TTGAAGCCACCA-T
* * * *
5506889 GTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAACGAATCTTATTTCCTTGACGTTGTA
1 CTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAAGTTGCA
*
5506954 GTGGAACGGATTGAAGATACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
66 GTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
5507019 TGAAGCCACCAAT
131 TGAAGCCACC-AT
* *
5507032 CTTATCTCCCTGAAGTTGCAATAGGAGCAGACTGAAGA
1 CTTATCTCCCTAAAGTTGCAA-CGGAGCAGACTGAAGA
5507070 TAGCGGACCC
Statistics
Matches: 283, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
141 1 0.00
142 120 0.42
143 144 0.51
144 18 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (142 bp):
CTTATCTCCCTAAAGTTGCAACGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGAAGTTGCA
GTGGAACGGATTGAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGAT
TGAAGCCACCAT
Found at i:5508546 original size:3 final size:3
Alignment explanation
Indices: 5508540--5508585 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5508530 TTATTTATTG
5508540 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5508586 TATTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5508590 original size:3 final size:3
Alignment explanation
Indices: 5508584--5508753 Score: 173
Period size: 3 Copynumber: 56.7 Consensus size: 3
5508574 CATCATCATC
* * **
5508584 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ACT ATT ACC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
5508632 ATT ATT ATT ACT ATT ACT ATT ATT TTCT ATT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * *
5508678 AGT ATC ATT ATT ATT ATT ACT ATT ATT ATT -TT -TT ACT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * *
5508722 ATT ATT ATT GTT GTT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5508754 CTTTTTAATT
Statistics
Matches: 136, Mismatches: 28, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
2 4 0.03
3 127 0.93
4 5 0.04
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5508773 original size:65 final size:65
Alignment explanation
Indices: 5508589--5508753 Score: 170
Period size: 65 Copynumber: 2.5 Consensus size: 65
5508579 TCATCATTAT
* * ** * *
5508589 TATTATTATTATTATTATTATTATTTTTATTACTATTACCATTATTATTATTACTATTACTATTA
1 TATTATTATAATTATTATTAGTATCATTATTATTATTA--A-TATTATTATT--TTTTACTATTA
5508654 TTTTC
61 TTTTC
*
5508659 TATTATTATAATTATTATTAGTATCATTATTATTATTACTATTATTATTTTTTACTATTATTTAT
1 TATTATTATAATTATTATTAGTATCATTATTATTATTAATATTATTATTTTTTACTATTATTT-T
5508724 -
65 C
* ** *
5508724 TATTATTGTTGTTATTATTATTATCATTAT
1 TATTATTATAATTATTATTAGTATCATTAT
5508754 CTTTTTAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
65 39 0.47
66 1 0.01
67 10 0.12
70 33 0.40
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (65 bp):
TATTATTATAATTATTATTAGTATCATTATTATTATTAATATTATTATTTTTTACTATTATTTTC
Found at i:5513088 original size:28 final size:31
Alignment explanation
Indices: 5513046--5513108 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 31
5513036 ATTATATTTG
5513046 TAAAATTTTATAAATA-AT-TT-TAATAAAA
1 TAAAATTTTATAAATATATATTATAATAAAA
*
5513074 TAAAATTTT-TAAAATATATATTATAATTAAA
1 TAAAATTTTAT-AAATATATATTATAATAAAA
5513105 TAAA
1 TAAA
5513109 TTTATTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 14 0.47
29 2 0.07
30 2 0.07
31 11 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAAATTTTATAAATATATATTATAATAAAA
Found at i:5515445 original size:144 final size:147
Alignment explanation
Indices: 5515162--5515458 Score: 438
Period size: 144 Copynumber: 2.0 Consensus size: 147
5515152 TCATATAAGT
* *
5515162 AAAGAGATCTATTCATTGATAAGAAAAACAAAAAACATGAGTAGTGATTGGATTGATGATAAAAT
1 AAAGAGATCTATTCATTGATAAG-AAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAAT
* * * * * *
5515227 AAAACCTTGGATCACGAATAGTGATTCGATTAATGATAAAGAAATAAATTTTTTTATTCTGTTTT
65 AAAACCTTGGATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGATTT
*
5515292 TCACCTTAACAA-AAAAA
130 CCACCTTAACAACAAAAA
*
5515309 AAAGAGATCTATTCATTGATAAG-AAA-AAAAAACGTGAGTAGTAATTGGATTGATAATAAAATA
1 AAAGAGATCTATTCATTGATAAGAAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAATA
* *
5515372 AAATCTTGGATCATGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGATTTC
66 AAACCTTGGATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGATTTC
* *
5515437 CACTTTAACAACAGAAA
131 CACCTTAACAACAAAAA
5515454 AAAGA
1 AAAGA
5515459 ATTGATAAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 100 0.74
145 12 0.09
147 23 0.17
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (147 bp):
AAAGAGATCTATTCATTGATAAGAAAACAAAAAACATGAGTAGTAATTGGATTGATAATAAAATA
AAACCTTGGATCACGAACAGTGATTCGATTAATGATAAAGAAATAAAATTCTTGATTCAGATTTC
CACCTTAACAACAAAAA
Found at i:5519147 original size:18 final size:18
Alignment explanation
Indices: 5519089--5519153 Score: 53
Period size: 20 Copynumber: 3.5 Consensus size: 18
5519079 AAATATAAAT
5519089 TATTCTATTTATATTT-TA
1 TATT-TATTTATATTTATA
* **
5519107 T-TTTATATATATAAATAA
1 TATTTATTTATATTTAT-A
5519125 TTATTTATTTATATTTATA
1 -TATTTATTTATATTTATA
5519144 TATTTTATTT
1 TA-TTTATTT
5519154 GCTAACGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
16 8 0.22
17 3 0.08
18 4 0.11
19 9 0.25
20 12 0.33
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATTTATATTTATA
Found at i:5528039 original size:30 final size:28
Alignment explanation
Indices: 5528004--5528071 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
5527994 ACCTTATTTT
5528004 TATATTAT-ATATTATAAAATTATTTTATTA
1 TATATTATCATATTAT--AATTA-TTTATTA
*
5528034 TATATTATTTCATATTATTATTATTTATTA
1 TATATTA--TCATATTATAATTATTTATTA
5528064 TATATTAT
1 TATATTAT
5528072 TTTTCACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 1 0.03
30 21 0.62
31 4 0.12
32 1 0.03
33 7 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATATTATCATATTATAATTATTTATTA
Found at i:5528048 original size:10 final size:10
Alignment explanation
Indices: 5528028--5528072 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
5528018 TAAAATTATT
5528028 TTATTATATA
1 TTATTATATA
5528038 TTATT-TCATA
1 TTATTAT-ATA
5528048 TTATTAT-TA
1 TTATTATATA
5528057 TTTATTATATA
1 -TTATTATATA
5528068 TTATT
1 TTATT
5528073 TTTCACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.10
10 25 0.81
11 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTATATA
Found at i:5528072 original size:23 final size:23
Alignment explanation
Indices: 5527998--5528072 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
5527988 TTTTTAACCT
*
5527998 TATTTTTA-TATTATATATTATAA
1 TATTATTATTATTATATATTAT-A
* *
5528021 AATTATT-TTATTATATATTATT
1 TATTATTATTATTATATATTATA
*
5528043 TCA-TATTATTATTATTTATTATA
1 T-ATTATTATTATTATATATTATA
5528066 TATTATT
1 TATTATT
5528073 TTTCACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.12
23 37 0.88
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATTATTATTATATATTATA
Found at i:5528441 original size:21 final size:23
Alignment explanation
Indices: 5528396--5528441 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5528386 ATTAATTACT
* *
5528396 TATTTTATACTTATATTTATATA
1 TATTATATAATTATATTTATATA
5528419 TATTATATAATTAT-TTTAT-TA
1 TATTATATAATTATATTTATATA
5528440 TA
1 TA
5528442 AATATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATATAATTATATTTATATA
Found at i:5528513 original size:17 final size:17
Alignment explanation
Indices: 5528493--5528549 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
5528483 TTCTAAACCA
*
5528493 ATATATTTTTTATTTTT
1 ATATAATTTTTATTTTT
*
5528510 ATATAATTATTATGCTTTT
1 ATATAATTTTTAT--TTTT
* *
5528529 ATA-AATTTTTGTTATT
1 ATATAATTTTTATTTTT
5528545 ATATA
1 ATATA
5528550 TTATATATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 7 0.22
19 7 0.22
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (17 bp):
ATATAATTTTTATTTTT
Found at i:5532127 original size:75 final size:73
Alignment explanation
Indices: 5532018--5532162 Score: 263
Period size: 75 Copynumber: 2.0 Consensus size: 73
5532008 ATAATTAGAA
5532018 TGTCGTAACCATTTTTAAAAAAAAAAGGGAATCGACTTGGATTTTGAAAATAAAAGAACGGGAGT
1 TGTCGTAACCATTTTTAAAAAAAAAAGGGAATCGACTTGGATTTTGAAAATAAAAGAACGGGAGT
5532083 CGCCATGC
66 CGCCATGC
*
5532091 TGTCGTAACCATTTTTTTGAAAAAAAAAGGGAATCGACTTGGATTTTGAAAATAAAAGAACGGGA
1 TGTCGTAACCA--TTTTTAAAAAAAAAAGGGAATCGACTTGGATTTTGAAAATAAAAGAACGGGA
5532156 GTCGCCA
64 GTCGCCA
5532163 CCGATCCTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 11 0.16
75 58 0.84
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (73 bp):
TGTCGTAACCATTTTTAAAAAAAAAAGGGAATCGACTTGGATTTTGAAAATAAAAGAACGGGAGT
CGCCATGC
Found at i:5533190 original size:13 final size:13
Alignment explanation
Indices: 5533172--5533198 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5533162 AATAGAAGTA
5533172 ATAAGAAATATAT
1 ATAAGAAATATAT
5533185 ATAAGAAATATAT
1 ATAAGAAATATAT
5533198 A
1 A
5533199 CATACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
ATAAGAAATATAT
Found at i:5533727 original size:3 final size:3
Alignment explanation
Indices: 5533719--5533815 Score: 58
Period size: 3 Copynumber: 32.7 Consensus size: 3
5533709 ATGTATATAT
* * * * * *
5533719 ATA ATA ATA ATA ATA ATG GT- GTA GTA AAA ATA ATA ATA AT- ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
5533765 ATGA AT- ATG ATA ATA ATA ATA ATA ATA ACA GTTA AT- ATA ATA ATAA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A
5533811 ATA AT
1 ATA AT
5533816 GCTACAAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
2 8 0.11
3 60 0.80
4 7 0.09
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5534796 original size:31 final size:31
Alignment explanation
Indices: 5534758--5534829 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
5534748 AGGAAAAATG
5534758 GGTGGTGGAGCAGAGGCCACTTGCAGGCATC
1 GGTGGTGGAGCAGAGGCCACTTGCAGGCATC
* *
5534789 GGTGGTGGAGCAGAGGCCTCTTGCAGGCGTC
1 GGTGGTGGAGCAGAGGCCACTTGCAGGCATC
5534820 GGTGGTGGAG
1 GGTGGTGGAG
5534830 GGGTGGGGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.15, C:0.19, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTGGTGGAGCAGAGGCCACTTGCAGGCATC
Found at i:5535269 original size:43 final size:43
Alignment explanation
Indices: 5535220--5536134 Score: 287
Period size: 43 Copynumber: 20.9 Consensus size: 43
5535210 TTTCAGCCTA
* * *
5535220 TTACCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGTTTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
* * ** * * *
5535263 TTACCCTACTGCTTAGGGGGTTTAGCTCAT-TATCTTCGATTTG
1 TTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAATTTGGTCTG
* * * * *
5535306 TTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
* * * * * * *
5535349 TTACCCTACTACTTAGGGGTTTAAG-GCTCATCACTTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCT-GTAAATTT-GGTCTG
* * *
5535393 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
* ** * *
5535436 TTACCCTACTGCTTAGGGGTTTAAGACTCAT-TACCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTTAAGA-TC-TGTAAATTTGGTCTG
* * **
5535480 TTTCCCTACTGCTTAAGGGGTTAAGATCTGTAAATTTTCAATCTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA-TTT-GGTCTG
* * ** ** ** ** * *
5535525 CTT-CACTGCAACTTCAGGAAGACAAGAT-TCGCTGGATTCGATCTG
1 -TTACCCTACTGCTT-AGGGGGTTAAGATCT-G-TAAATTTGGTCTG
* ** * * ** * * * * *
5535570 TT-CCACTGCAACTTCAAGGAGACAAAATCTGTAATTTTTAGCCTA
1 TTACC-CTACTGCTT-AGGGGGTTAAGATCTGTAA-ATTTGGTCTG
* * *
5535615 TTACCCTACTACTTATGGGGTTAAGGTCTGTAAATTTGG-CTTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTC-TG
* ** * *
5535658 TTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAATTTGGTCTG
* * * * * *
5535702 TTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTA
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
* * * ** * *
5535745 TTACCCTACTGCTTAGGGGTTTAAGGCTCAT-CACCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTTAA-GATC-TGTAAATTTGGTCTG
* *
5535789 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTTCAGTCTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAA-TTT-GGTCTG
* * ** * * * * * *
5535834 CTT-CACTGCAACTTCAGGAAGG-CAAGAT-TCGCTAGATTCGATTTG
1 -TTACCCTACTGCTT-AGG-GGGTTAAGATCT-G-TAAATTTGGTCTG
* ** ** *** * * * *
5535879 TT-CCACTGCAACTTCAGGAAGACCAGATCTGTAATTTTCAGCCTA
1 TTACC-CTACTGCTT-AGGGGGTTAAGATCTGTAAATTT-GGTCTG
** *
5535924 TTACCCTACTATTTAGGGGGTTAAGGTCTGTAAATTTGG-CTTG
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTC-TG
* ** * *
5535967 TTACCCTACTGCTTAGGGGGTTAAAGCTCAT-TATCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTT-AAGATC-TGTAAATTTGGTCTG
* * * * * *
5536011 TTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTA
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
* * * ** * *
5536054 TTACCCTACTGCTTAGGGGTTTAAGGCTCAT-CACCTTCGATCTG
1 TTACCCTACTGCTTAGGGGGTTAA-GATC-TGTAAATTTGGTCTG
*
5536098 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
1 TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
5536135 TCAGTCTGCT
Statistics
Matches: 622, Mismatches: 204, Indels: 92
0.68 0.22 0.10
Matches are distributed among these distances:
42 10 0.02
43 238 0.38
44 231 0.37
45 104 0.17
46 32 0.05
47 7 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (43 bp):
TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTGGTCTG
Found at i:5535409 original size:87 final size:87
Alignment explanation
Indices: 5535223--5535516 Score: 432
Period size: 87 Copynumber: 3.4 Consensus size: 87
5535213 CAGCCTATTA
* * * **
5535223 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGTTTGTTACCCTACTGCTTAGGGGGTTT-A
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTA-GGGGTTTAA
*
5535287 -GCTCATTA-TCTTCGATTTGTTT
65 GGCTCATTACT-TTCGATCTGTTT
* * *
5535309 CCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTGTTACCCTACTACTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
*
5535374 GCTCATCACTTTCGATCTGTTT
66 GCTCATTACTTTCGATCTGTTT
5535396 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
* *
5535461 ACTCATTACCTTCGATCTGTTT
66 GCTCATTACTTTCGATCTGTTT
*
5535483 CCCTACTGCTTAAGGGGTTAAGATCTGTAAATTT
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
5535517 TCAATCTGCT
Statistics
Matches: 188, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
85 7 0.04
86 48 0.26
87 132 0.70
88 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
GCTCATTACTTTCGATCTGTTT
Found at i:5535774 original size:87 final size:86
Alignment explanation
Indices: 5535618--5535825 Score: 299
Period size: 87 Copynumber: 2.4 Consensus size: 86
5535608 TAGCCTATTA
* * * * *
5535618 CCCTACTACTTATGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 CCCTACTGCTTA-GGGGTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAA
* *
5535683 GCTCATTATCTTCGATCTGTTT
65 GCTCATCACCTTCGATCTGTTT
* * *
5535705 CCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGG-GTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAA
5535770 GCTCATCACCTTCGATCTGTTT
65 GCTCATCACCTTCGATCTGTTT
5535792 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
1 CCCTACTGCTTA-GGGGTTAAGATCTGTAAATTT
5535826 TCAGTCTGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
86 3 0.03
87 102 0.94
88 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (86 bp):
CCCTACTGCTTAGGGGTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAAG
CTCATCACCTTCGATCTGTTT
Found at i:5535874 original size:309 final size:309
Alignment explanation
Indices: 5535309--5536269 Score: 1647
Period size: 309 Copynumber: 3.1 Consensus size: 309
5535299 CGATTTGTTT
* * * * * * * * *
5535309 CCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTGTTACCCTACTACTTAGGGGTTTAAG
1 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
* * * *
5535374 GCTCATCA-CTTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTGTT
66 GCTCATTATC-TTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATT
* * *
5535438 ACCCTACTGCTTAGGGGTTTAAGACTCATTACCTTCGATCTGTTTCCCTACTGCTTAAGGGGTTA
130 ACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTA
*
5535503 AGATCTGTAAATTTTCAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATC
195 AGATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATC
* *
5535568 TGTTCCACTGCAACTTCAAGGAGACAAAATCTGTAATTTTTAGCCTATTA
260 TGTTCCACTGCAACTTCAAGGAGACCAGATCTGTAATTTTTAGCCTATTA
*
5535618 CCCTACTACTTATGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
5535683 GCTCATTATCTTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTA
66 GCTCATTATCTTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTA
5535748 CCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAA
131 CCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAA
* * *
5535813 GATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGGCAAGATTCGCTAGATTCGATTT
196 GATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATCT
*
5535878 GTTCCACTGCAACTTC-AGGAAGACCAGATCTGTAATTTTCAGCCTATTA
261 GTTCCACTGCAACTTCAAGG-AGACCAGATCTGTAATTTTTAGCCTATTA
*
5535927 CCCTACTATTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
5535992 GCTCATTATCTTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTA
66 GCTCATTATCTTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTA
5536057 CCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAA
131 CCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAA
5536122 GATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATCT
196 GATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATCT
*
5536187 GTTCCACTGCAACTTCAGGGAGACCAGATCTGTAATTTTTAGCCTATTA
261 GTTCCACTGCAACTTCAAGGAGACCAGATCTGTAATTTTTAGCCTATTA
*
5536236 CCCTACTACTTAGGGGGTTAAGGTCCGTAAATTT
1 CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTT
5536270 ACTGATTCTA
Statistics
Matches: 616, Mismatches: 33, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
308 3 0.00
309 610 0.99
310 3 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (309 bp):
CCCTACTACTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
GCTCATTATCTTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTA
CCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAA
GATCTGTAAATTTTCAGTCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGCTGGATTCGATCT
GTTCCACTGCAACTTCAAGGAGACCAGATCTGTAATTTTTAGCCTATTA
Found at i:5536047 original size:396 final size:394
Alignment explanation
Indices: 5535169--5535918 Score: 1017
Period size: 396 Copynumber: 1.9 Consensus size: 394
5535159 GGTTTGTTTT
* * *
5535169 GATCTGCTCCACTGCAACTTCAAGGAGAGAAAATCTGTAATTTTC-AGCCTATTACCCTACTACT
1 GATCTGTTCCACTACAACTTCAAGGAGACAAAATCTGTAA-TTTCGAGCCTATTACCCTACTACT
* *
5535233 TAGGGGGTTAAGGTCTGTAAATTTGGTTTGTTACCCTACTGCTTAGGGGGTT-TAGCTCATTATC
65 TA-GGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATC
* *
5535297 TTCGATTTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTGTTACCCTACTACT
129 TTCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTACT
*
5535362 TAGGGGTTTAAGGCTCATCACTTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
194 TAGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA
* ** * * * **
5535427 TTTAGCCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATTACCTTCGATCTGTTTCCCTACTGC
259 TTTAGCCTGTTACACTACAACTTAGGGG-TCAAGACTCACTACATTCGATCTGTTTCCCTACAAC
* ** * * *
5535492 TTAAGGGGTTAAGATCTGTAAATTTTCAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGC
323 TTAAGGAGACAAGATCTGTAAATTTTCAACCTGATTCACTACAACTTCAGGAAGACAAGATTCGC
**
5535557 TGGATTC
388 TAAATTC
* **
5535564 GATCTGTTCCACTGCAACTTCAAGGAGACAAAATCTGTAATTTTTAGCCTATTACCCTACTACTT
1 GATCTGTTCCACTACAACTTCAAGGAGACAAAATCTGTAATTTCGAGCCTATTACCCTACTACTT
5535629 ATGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCT
66 A-GGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCT
*
5535694 TCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTGCTT
130 TCGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTACTT
5535759 AGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
195 AGGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA-
* * * * * *
5535824 TTTCAGTCTGCTT-CACTGCAACTTCAGGAAGG-CAAGATTCGCTAGATTCGATTTG-TTCCACT
259 TTT-AGCCTG-TTACACTACAACTT-AGG--GGTCAAGACTCACTACATTCGATCTGTTTCC-CT
* * *
5535886 GCAACTTCAGGAAGACCAGATCTGT-AATTTTCA
318 ACAACTTAAGG-AGACAAGATCTGTAAATTTTCA
5535919 GCCTATTACC
Statistics
Matches: 315, Mismatches: 30, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
394 3 0.01
395 107 0.34
396 137 0.43
397 3 0.01
398 16 0.05
399 38 0.12
400 9 0.03
401 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (394 bp):
GATCTGTTCCACTACAACTTCAAGGAGACAAAATCTGTAATTTCGAGCCTATTACCCTACTACTT
AGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTATCTT
CGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTACTTA
GGGGTTTAAGGCTCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATT
TAGCCTGTTACACTACAACTTAGGGGTCAAGACTCACTACATTCGATCTGTTTCCCTACAACTTA
AGGAGACAAGATCTGTAAATTTTCAACCTGATTCACTACAACTTCAGGAAGACAAGATTCGCTAA
ATTC
Found at i:5536083 original size:87 final size:87
Alignment explanation
Indices: 5535927--5536134 Score: 308
Period size: 87 Copynumber: 2.4 Consensus size: 87
5535917 CAGCCTATTA
** * * * *
5535927 CCCTACTATTTAGGGGGTTAAGGTCTGTAAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAA
* *
5535992 GCTCATTATCTTCGATCTGTTT
66 GCTCATCACCTTCGATCTGTTT
* * * *
5536014 CCCTACTGCTTAGGGTGATAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGTTTAAG
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAA
5536079 GCTCATCACCTTCGATCTGTTT
66 GCTCATCACCTTCGATCTGTTT
5536101 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
1 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTT
5536135 TCAGTCTGCT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 107 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCCTATTACCCTACTGCTTAGGGGGTTAAA
GCTCATCACCTTCGATCTGTTT
Found at i:5540968 original size:18 final size:18
Alignment explanation
Indices: 5540945--5541007 Score: 108
Period size: 18 Copynumber: 3.5 Consensus size: 18
5540935 TTCTTCCAAG
5540945 TCCTTTCCCTGGCAAGGC
1 TCCTTTCCCTGGCAAGGC
5540963 TCCTTTCCCTGGCAAGGC
1 TCCTTTCCCTGGCAAGGC
*
5540981 TCCTTTCCCTAGCAAGGC
1 TCCTTTCCCTGGCAAGGC
*
5540999 TCCCTTCCC
1 TCCTTTCCC
5541008 AACCATCAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.11, C:0.43, G:0.17, T:0.29
Consensus pattern (18 bp):
TCCTTTCCCTGGCAAGGC
Done.