Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 39 of 50
Found at i:16910683 original size:2 final size:2
Alignment explanation
Indices: 16910678--16910732 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
16910668 TCTGTCACTC
* * *
16910678 AT AT AT AT AT AT AT -T TT AT AT AT A- AA AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16910718 AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT
16910733 TATTNTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16910699 original size:13 final size:13
Alignment explanation
Indices: 16910678--16910726 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
16910668 TCTGTCACTC
16910678 ATATATATATATA
1 ATATATATATATA
* * *
16910691 TTTTATATATAAA
1 ATATATATATATA
16910704 ATATATATATATA
1 ATATATATATATA
16910717 A-ATATATATA
1 ATATATATATA
16910727 ATATATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATATATATA
Found at i:16910723 original size:10 final size:9
Alignment explanation
Indices: 16910678--16910732 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
16910668 TCTGTCACTC
16910678 ATATAT-AT
1 ATATATAAT
**
16910686 ATATATTTT
1 ATATATAAT
*
16910695 ATATATAAA
1 ATATATAAT
16910704 ATATAT-AT
1 ATATATAAT
16910712 ATATA-AAT
1 ATATATAAT
16910720 ATATATAAT
1 ATATATAAT
16910729 ATAT
1 ATAT
16910733 TATTNTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 19 0.49
9 20 0.51
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATAAT
Found at i:16910853 original size:16 final size:16
Alignment explanation
Indices: 16910828--16910866 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16910818 TATAAAAATT
16910828 TATTAATTAATAGAGA
1 TATTAATTAATAGAGA
* * *
16910844 TATTATTTAATTGATA
1 TATTAATTAATAGAGA
16910860 TATTAAT
1 TATTAAT
16910867 AATTTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
TATTAATTAATAGAGA
Found at i:16912158 original size:29 final size:29
Alignment explanation
Indices: 16912080--16912211 Score: 142
Period size: 30 Copynumber: 4.6 Consensus size: 29
16912070 AATAATTTAT
*
16912080 TATAAAAATTTAATGGACTCAAAATAAAAA
1 TATAAAAATTTAAT-TACTCAAAATAAAAA
* * *
16912110 TATAAAAATTTATTTGATTTAAAATAAAAA
1 TATAAAAATTTAATT-ACTCAAAATAAAAA
* ***
16912140 TATAAAAATTTAATTATTTGTAATAAAAA
1 TATAAAAATTTAATTACTCAAAATAAAAA
* *
16912169 TATAAAAATTTGATTACTCATAAT--AAA
1 TATAAAAATTTAATTACTCAAAATAAAAA
16912196 TATAAAAATTTAATTA
1 TATAAAAATTTAATTA
16912212 AATATTTTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
27 18 0.20
29 32 0.36
30 39 0.44
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (29 bp):
TATAAAAATTTAATTACTCAAAATAAAAA
Found at i:16912179 original size:21 final size:21
Alignment explanation
Indices: 16912141--16912180 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16912131 AAATAAAAAT
* **
16912141 ATAAAAATTTAATTATTTGTA
1 ATAAAAATATAAAAATTTGTA
16912162 ATAAAAATATAAAAATTTG
1 ATAAAAATATAAAAATTTG
16912181 ATTACTCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAAAAATATAAAAATTTGTA
Found at i:16912222 original size:27 final size:27
Alignment explanation
Indices: 16912133--16912212 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 27
16912123 TTGATTTAAA
* *
16912133 ATAA-AAATATAAAAATTTAATTATTT
1 ATAATAAATATAAAAATTTAATTAATC
* * *
16912159 GTAATAAAAATATAAAAATTTGATTACTC
1 ATAAT--AAATATAAAAATTTAATTAATC
16912188 ATAATAAATATAAAAATTTAATTAA
1 ATAATAAATATAAAAATTTAATTAA
16912213 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 3 0.07
27 18 0.41
29 23 0.52
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
ATAATAAATATAAAAATTTAATTAATC
Found at i:16912324 original size:3 final size:3
Alignment explanation
Indices: 16912316--16912368 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
16912306 ATGGGCAAGG
16912316 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16912364 ATT AT
1 ATT AT
16912369 AATAGTCAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16912977 original size:29 final size:29
Alignment explanation
Indices: 16912945--16913002 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
16912935 CATAAACATA
16912945 GTTT-AAAAAATTTTAAATTTTTTTATTAT
1 GTTTGAAAAAATTTTAAA-TTTTTTATTAT
** *
16912974 GTTTGATCAAATTTTATATTTTTTATTAT
1 GTTTGAAAAAATTTTAAATTTTTTATTAT
16913003 TTATTATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (29 bp):
GTTTGAAAAAATTTTAAATTTTTTATTAT
Found at i:16913262 original size:30 final size:30
Alignment explanation
Indices: 16913227--16913295 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
16913217 AATTATTAAT
* *
16913227 TATAAAAATTT-ATTTAATTTAAAATAAAAA
1 TATAAAAATTTAATTAAATGTAAAA-AAAAA
*
16913257 TATAAAAATTTAATTAAATGTAATAAAAAA
1 TATAAAAATTTAATTAAATGTAAAAAAAAA
*
16913287 TAAAAAAAT
1 TATAAAAAT
16913296 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (30 bp):
TATAAAAATTTAATTAAATGTAAAAAAAAA
Found at i:16923414 original size:27 final size:29
Alignment explanation
Indices: 16923361--16923416 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
16923351 TATAATTAAT
*
16923361 AATTAACTAATTATCATTACTATTAAAAAA
1 AATTAACTAATCATCATTAC-ATTAAAAAA
16923391 AATTAACTAATCATCATTA-A-TAAAAA
1 AATTAACTAATCATCATTACATTAAAAA
16923417 TATTACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 1 0.04
30 18 0.72
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (29 bp):
AATTAACTAATCATCATTACATTAAAAAA
Found at i:16924541 original size:5 final size:5
Alignment explanation
Indices: 16924531--16924599 Score: 61
Period size: 5 Copynumber: 13.4 Consensus size: 5
16924521 TTATATTACA
*
16924531 TATTT TATTT TAATTT T-TTT TATTT TATTT TATTT TAATTCT AATTCT
1 TATTT TATTT T-ATTT TATTT TATTT TATTT TATTT T-ATT-T TATT-T
* *
16924579 TATAT TA-TA TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TA
16924600 ATTATAACAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 6 0.11
5 31 0.58
6 15 0.28
7 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:16924542 original size:32 final size:31
Alignment explanation
Indices: 16924467--16924606 Score: 109
Period size: 32 Copynumber: 4.5 Consensus size: 31
16924457 TGTATTTTAT
* *
16924467 TTTTATTTATTATTATAA-TCTTATA-TATATA
1 TTTTATTT-TAATTATAATTTTTATATTA-ATA
16924498 TTTTTATTTTTTAA-TATAATTTGTTATATTACATA
1 -TTTTA--TTTTAATTATAATTT-TTATATTA-ATA
16924533 TTTTATTTTAATT-T--TTTTTAT-TT--TA
1 TTTTATTTTAATTATAATTTTTATATTAATA
* *
16924558 TTTTATTTTAATTCTAATTCTTATATTATATA
1 TTTTATTTTAATTATAATTTTTATATTA-ATA
16924590 TTTTATTTTAATTATAA
1 TTTTATTTTAATTATAA
16924607 CATTACAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 26
0.74 0.04 0.21
Matches are distributed among these distances:
25 15 0.17
26 1 0.01
28 8 0.09
29 6 0.07
30 3 0.03
32 35 0.39
33 4 0.04
34 13 0.14
35 5 0.06
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.66
Consensus pattern (31 bp):
TTTTATTTTAATTATAATTTTTATATTAATA
Found at i:16927825 original size:22 final size:21
Alignment explanation
Indices: 16927795--16927848 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
16927785 TTTTAAAATG
16927795 AAAAATTATGTCTCTTCATAT
1 AAAAATTATGTCTCTTCATAT
* * *
16927816 AAAAAGTTATATTTTTTCATAT
1 AAAAA-TTATGTCTCTTCATAT
16927838 AAAAAATTATG
1 -AAAAATTATG
16927849 ATTATTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 5 0.19
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (21 bp):
AAAAATTATGTCTCTTCATAT
Found at i:16929793 original size:28 final size:28
Alignment explanation
Indices: 16929760--16929833 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
16929750 GTTATGTAAC
16929760 ATAAATAATAAAAAAATAAAAAATAAAA
1 ATAAATAATAAAAAAATAAAAAATAAAA
* ** *
16929788 ATAAATAATATATATCATAAATAATAAAA
1 ATAAATAATA-AAAAAATAAAAAATAAAA
*
16929817 A-AAATAATATAAAAATA
1 ATAAATAATAAAAAAATA
16929834 TTTTTATGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
27 4 0.11
28 18 0.49
29 15 0.41
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.24
Consensus pattern (28 bp):
ATAAATAATAAAAAAATAAAAAATAAAA
Found at i:16929814 original size:7 final size:7
Alignment explanation
Indices: 16929760--16929825 Score: 57
Period size: 7 Copynumber: 9.4 Consensus size: 7
16929750 GTTATGTAAC
16929760 ATAAATA
1 ATAAATA
*
16929767 ATAAAAAA
1 AT-AAATA
*
16929775 ATAAAAA
1 ATAAATA
16929782 ATAAA-A
1 ATAAATA
16929788 ATAAATA
1 ATAAATA
*
16929795 ATATATATC
1 ATA-A-ATA
16929804 ATAAATA
1 ATAAATA
16929811 ATAAA-A
1 ATAAATA
16929817 A-AAATA
1 ATAAATA
16929823 ATA
1 ATA
16929826 TAAAAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
5 3 0.06
6 10 0.20
7 24 0.48
8 8 0.16
9 5 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
ATAAATA
Found at i:16941286 original size:3 final size:3
Alignment explanation
Indices: 16941278--16941323 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16941268 GTAAACAAAC
16941278 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
16941324 AGGAATGAAA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16942095 original size:19 final size:17
Alignment explanation
Indices: 16942072--16942107 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16942062 AATTTTATTT
*
16942072 TTTATTAAT-TTTAAAA
1 TTTATTATTATTTAAAA
16942088 TTTATTATTATTTAAAA
1 TTTATTATTATTTAAAA
16942105 TTT
1 TTT
16942108 CTTTTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTATTATTTAAAA
Found at i:16943308 original size:2 final size:2
Alignment explanation
Indices: 16943301--16943326 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16943291 TAACAGAATG
16943301 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
16943327 CCAGATTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16962974 original size:4 final size:4
Alignment explanation
Indices: 16962960--16962991 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
16962950 AGAAAGGACT
16962960 GCTG G-TG GCTG GCTG GCTG GCTG GCTG GCTG G
1 GCTG GCTG GCTG GCTG GCTG GCTG GCTG GCTG G
16962992 GAGAGGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.22, G:0.53, T:0.25
Consensus pattern (4 bp):
GCTG
Found at i:16963103 original size:23 final size:24
Alignment explanation
Indices: 16963063--16963109 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
16963053 ATTTTAGAGG
16963063 ATTTAATAATAAATAAAT-AAAAT
1 ATTTAATAATAAATAAATCAAAAT
*
16963086 ATTTAATAGGTAAA-AAATCAAAAT
1 ATTTAATA-ATAAATAAATCAAAAT
16963110 CTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
ATTTAATAATAAATAAATCAAAAT
Found at i:16963771 original size:12 final size:12
Alignment explanation
Indices: 16963747--16963778 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
16963737 AAGTTTAATT
16963747 TTTTAATAATATA
1 TTTTAA-AATATA
16963760 TTTTAAAATATA
1 TTTTAAAATATA
16963772 TTTTAAA
1 TTTTAAA
16963779 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:16963893 original size:27 final size:28
Alignment explanation
Indices: 16963850--16963909 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
16963840 ATACTAATAT
16963850 TTAAATGATCAATTATTAATATTTTAAA
1 TTAAATGATCAATTATTAATATTTTAAA
16963878 TTAAAT-ATCAATTATTAATATTTTAAA
1 TTAAATGATCAATTATTAATATTTTAAA
*
16963905 ATAAA
1 TTAAA
16963910 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAAATGATCAATTATTAATATTTTAAA
Found at i:16963952 original size:88 final size:85
Alignment explanation
Indices: 16963831--16964034 Score: 202
Period size: 88 Copynumber: 2.4 Consensus size: 85
16963821 CATTTAAATT
* * * * * * *
16963831 ATAAATAA-AATACTAATATTTAAATGATCAATTATTAATATT-T-TAAATTAAA-TATCAATTA
1 ATAAATAATAATAATAATATTTAAATTATAAATTA--AATATTATAAAAAATAAATTATAAAATA
16963892 TTAATATTTT-AAAATAAAATAAA
64 -T-ATATTTTAAAAATAAAATAAA
*
16963915 ATAAAAATAACTAATAATAATATTTAAATTATAAATTAAATATTAATAANAAATAAATTTATAAA
1 AT--AAATAA-TAATAATAATATTTAAATTATAAATTAAATATT-ATAAAAAATAAA-TTATAAA
16963980 ATATATATTTTAAAAATAAAATAAA
61 ATATATATTTTAAAAATAAAATAAA
* *
16964005 ATAAATAATCATAATAACATTTAAATTATA
1 ATAAATAATAATAATAATATTTAAATTATA
16964035 TCTAAAATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
84 2 0.02
86 12 0.12
87 20 0.20
88 30 0.30
89 13 0.13
90 16 0.16
91 7 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (85 bp):
ATAAATAATAATAATAATATTTAAATTATAAATTAAATATTATAAAAAATAAATTATAAAATATA
TATTTTAAAAATAAAATAAA
Found at i:16963971 original size:29 final size:27
Alignment explanation
Indices: 16963939--16964011 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 27
16963929 TAATAATATT
*
16963939 TAAATTATAAATTAAATATTAATAANAAA
1 TAAATTATAAAATAAATATT-ATAA-AAA
* *
16963968 TAAATTTATAAAATATATATTTTAAAAA
1 TAAA-TTATAAAATAAATATTATAAAAA
16963996 TAAA--ATAAAATAAATA
1 TAAATTATAAAATAAATA
16964012 ATCATAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 11 0.28
28 7 0.18
29 7 0.18
30 14 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTATAAAATAAATATTATAAAAA
Found at i:16973659 original size:22 final size:22
Alignment explanation
Indices: 16973629--16973670 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16973619 GCTTTGAAAA
* *
16973629 CTCTCTTTATTGTTTGATATTT
1 CTCTATTTAATGTTTGATATTT
16973651 CTCTATTTAATGTTTGATAT
1 CTCTATTTAATGTTTGATAT
16973671 GATAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (22 bp):
CTCTATTTAATGTTTGATATTT
Found at i:16974124 original size:21 final size:22
Alignment explanation
Indices: 16974073--16974125 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
16974063 ATTATTAATT
*
16974073 ATATATTTTATGTTATATAAAA
1 ATATATTTTATATTATATAAAA
16974095 ATACT-TTTTATATT-T-TCAAAA
1 ATA-TATTTTATATTATAT-AAAA
16974116 ATATATTTTA
1 ATATATTTTA
16974126 AATAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 13 0.48
22 11 0.41
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATATTTTATATTATATAAAA
Found at i:16975934 original size:25 final size:25
Alignment explanation
Indices: 16975906--16975959 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
16975896 GGTTAATAAT
*
16975906 ATTAATCTTCATGCAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
* *
16975931 ATTAATCTTTATATAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
16975956 ATTA
1 ATTA
16975960 GTTTCAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATACAATAAATAAAC
Found at i:16978697 original size:85 final size:85
Alignment explanation
Indices: 16978586--16979164 Score: 536
Period size: 85 Copynumber: 6.7 Consensus size: 85
16978576 ATTACAATCA
*
16978586 TTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
16978651 CCAAACATAATTCTTAATGT
66 CCAAACATAATTCTTAATGT
* *
16978671 TTAATTCTAGCATATTACCAATCATTTT-AGTGAAAAATCTAAACAATAATTCTAAACATTAATT
1 TTAATTCTAGCATATTACCAATCATTTTAATTG-AAAATCCAAACAATAATTCTAAACATTAATT
16978735 CCCAAACATAATTCTTAATGT
65 CCCAAACATAATTCTTAATGT
** * *
16978756 TTAATTCTAGCATATTGTCAATCATTTTGATTGAAAATCCAAACAATAATTCTAAACAATAATT-
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
* *
16978820 CTAAACATTAATTCCCAAACATAAT-T
66 CCAAACA-TAATT------CTTAATGT
* * ** * *** ** *
16978846 CTTAATGTTTA--ATTTTA-GTAT-ATTATCAATCATTTTAATTAAAATCCAAACGATATTCTAA
1 -TTAAT-TCTAGCATATTACCAATCATT-TTAAT--TGAAAATCCAAA--C-AA-TA-ATTCTAA
* *
16978907 ACATTAATTTCCAAATATAATTCTTAATGT
56 ACATTAATTCCCAAACATAATTCTTAATGT
* *** *
16978937 ATAATTCTAGCATTATTGTGAATCATTTTTATTGAAAATCCAAACAATAATTCTAAACATTAATT
1 TTAATTCTAGCA-TATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATT
* * *
16979002 CCCAAACATTATTTTTAATAT
65 CCCAAACATAATTCTTAATGT
* * * *
16979023 TTAATTCTAACAAATTACCAATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAATT-
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
*
16979087 CCAAACATAATTCTTAATAT
66 CCAAACATAATTCTTAATGT
* * * *
16979107 TTAATTCTAGC--A-T-CGAATCATTTTAATT-AATTATTCAAACAATAATTCTAAGCATTAA
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAA-AATCCAAACAATAATTCTAAACATTAA
16979165 GCTCCTTGAA
Statistics
Matches: 405, Mismatches: 62, Indels: 59
0.77 0.12 0.11
Matches are distributed among these distances:
79 2 0.00
80 37 0.09
81 1 0.00
82 1 0.00
84 37 0.09
85 183 0.45
86 45 0.11
87 1 0.00
88 5 0.01
89 9 0.02
90 14 0.03
91 26 0.06
92 6 0.01
93 7 0.02
94 5 0.01
95 1 0.00
96 20 0.05
97 5 0.01
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (85 bp):
TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
CCAAACATAATTCTTAATGT
Found at i:16978726 original size:13 final size:13
Alignment explanation
Indices: 16978708--16978749 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16978698 TAGTGAAAAA
16978708 TCTAAACAATAAT
1 TCTAAACAATAAT
*
16978721 TCTAAACATTAAT
1 TCTAAACAATAAT
*
16978734 TCCCAAAC-ATAAT
1 T-CTAAACAATAAT
16978747 TCT
1 TCT
16978750 TAATGTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 1 0.04
13 18 0.75
14 5 0.21
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (13 bp):
TCTAAACAATAAT
Found at i:16978814 original size:13 final size:13
Alignment explanation
Indices: 16978796--16978847 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
16978786 TTGAAAATCC
16978796 AAACAATAATTCT
1 AAACAATAATTCT
16978809 AAACAATAATTCT
1 AAACAATAATTCT
* *
16978822 AAACATTAATTCCC
1 AAACAATAATT-CT
16978836 AAAC-ATAATTCT
1 AAACAATAATTCT
16978848 TAATGTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 1 0.03
13 28 0.82
14 5 0.15
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (13 bp):
AAACAATAATTCT
Found at i:16979001 original size:169 final size:170
Alignment explanation
Indices: 16978809--16979119 Score: 482
Period size: 169 Copynumber: 1.8 Consensus size: 170
16978799 CAATAATTCT
* * ** * *
16978809 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTTTAGTATATTATCA
1 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCA
* * * *
16978874 ATCATTTTAATT-AAAATCCAAACGAT-ATTCTAAACATTAATTTCCAAATATAATTCTTAATGT
66 ATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAA-TTCCAAACATAATTCTTAATAT
16978937 ATAATTCTAGCATTATTGTGAATCATTTTTATTGAAAATCC
130 ATAATTCTAGCATTATTGTGAATCATTTTTATTGAAAATCC
* *
16978978 AAACAATAATTCTAAACATTAATTCCCAAACATTATTTTTAATATTTAATTCTAACAAATTACCA
1 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCA
*
16979043 ATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAATTCCAAACATAATTCTTAATATT
66 ATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAATTCCAAACATAATTCTTAATATA
16979108 TAATTCTAGCAT
131 TAATTCTAGCAT
16979120 CGAATCATTT
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
169 69 0.54
170 45 0.35
171 13 0.10
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (170 bp):
AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCA
ATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAATTCCAAACATAATTCTTAATATA
TAATTCTAGCATTATTGTGAATCATTTTTATTGAAAATCC
Found at i:16979011 original size:183 final size:183
Alignment explanation
Indices: 16978626--16979119 Score: 678
Period size: 183 Copynumber: 2.8 Consensus size: 183
16978616 TTGAAAATCC
16978626 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCA
1 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCA
* *
16978691 ATCATTTTAGTGAAAAATCTAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGT
66 ATCATTTTAATGAAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGT
*
16978756 TTAATTCTAGCATATTGTCAATCATTTTGATTGAAAATCCAAACAATAATTCT
131 ATAATTCTAGCATATTGTCAATCATTTTGATTGAAAATCCAAACAATAATTCT
* * *
16978809 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTTTAGTATATTATCA
1 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCA
* * * *
16978874 ATCATTTTAAT-TAAAATCCAAACGAT-ATTCTAAACATTAATTTCCAAATATAATTCTTAATGT
66 ATCATTTTAATGAAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGT
* *
16978937 ATAATTCTAGCATTATTGTGAATCATTTTTATTGAAAAT-----C-------C-
131 ATAATTCTAGCA-TATTGTCAATCATTTTGATTGAAAATCCAAACAATAATTCT
* * * * *
16978978 AAACAATAATTCTAAACATTAATTCCCAAACATTATTTTTAATATTTAATTCTAACAAATTACCA
1 AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCA
* * *
16979043 ATCATTTTAATTAAAAATCCAAACAATAATTCTAAACATCAATT-CCAAACATAATTCTTAATAT
66 ATCATTTTAATGAAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGT
*
16979107 TTAATTCTAGCAT
131 ATAATTCTAGCAT
16979120 CGAATCATTT
Statistics
Matches: 282, Mismatches: 26, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
169 69 0.24
170 43 0.15
171 15 0.05
177 1 0.00
181 46 0.16
182 36 0.13
183 72 0.26
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.38
Consensus pattern (183 bp):
AAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCA
ATCATTTTAATGAAAAATCCAAACAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGT
ATAATTCTAGCATATTGTCAATCATTTTGATTGAAAATCCAAACAATAATTCT
Found at i:16979114 original size:267 final size:268
Alignment explanation
Indices: 16978586--16979099 Score: 759
Period size: 267 Copynumber: 1.9 Consensus size: 268
16978576 ATTACAATCA
*
16978586 TTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
* *
16978651 CCAAACATAATTCTTAATGTTTAATTCTAGCATATTACCAATCATTTTAGTGAAAAATCTAAACA
66 CCAAACATAATTCTTAATGTATAATTCTAGCATATTACCAATCATTTTAGTGAAAAATCCAAACA
* * * **
16978716 ATAATTCTAAACATTAATTCCCAAACATAATTCTTAATGTTTAATTCTAGCATATTGTCAATCAT
131 ATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCAATCAT
* * *
16978781 TTTGATTGAAAATCCAAACAATAATTCTAAACAATAATTCTAAACATTAATTCCCAAACATAATT
196 TTTAATTAAAAATCCAAACAATAATTCTAAACAATAATTCCAAACATTAATTCCCAAACATAATT
16978846 CTTAATGT
261 CTTAATGT
* * * * *
16978854 TTAATTTTAGTATATTATCAATCATTTTAATT-AAAATCCAAACGAT-ATTCTAAACATTAATTT
1 TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
* *** *
16978917 CCAAATATAATTCTTAATGTATAATTCTAGCATTATTGTGAATCATTTTTATTG-AAAATCCAAA
66 CCAAACATAATTCTTAATGTATAATTCTAGCA-TATTACCAATCA-TTTTAGTGAAAAATCCAAA
* *
16978981 CAATAATTCTAAACATTAATTCCCAAACATTATTTTTAATATTTAATTCTAACAAATTACCAATC
129 CAATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCAATC
16979046 ATTTTAATTAAAAATCCAAACAATAATTCTAAAC-ATCAATTCCAAACA-TAATTC
194 ATTTTAATTAAAAATCCAAACAATAATTCTAAACAAT-AATTCCAAACATTAATTC
16979100 TTAATATTTA
Statistics
Matches: 220, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
266 54 0.25
267 131 0.60
268 35 0.16
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (268 bp):
TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTAAACATTAATTC
CCAAACATAATTCTTAATGTATAATTCTAGCATATTACCAATCATTTTAGTGAAAAATCCAAACA
ATAATTCTAAACATTAATTCCCAAACATAATTCTTAATATTTAATTCTAACAAATTACCAATCAT
TTTAATTAAAAATCCAAACAATAATTCTAAACAATAATTCCAAACATTAATTCCCAAACATAATT
CTTAATGT
Found at i:16985851 original size:21 final size:21
Alignment explanation
Indices: 16985827--16985882 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
16985817 AGGCCAATAG
16985827 GCCATCAACCAGATCGCCTAA
1 GCCATCAACCAGATCGCCTAA
*
16985848 GCCATCAACCAAATCGCCTAA
1 GCCATCAACCAGATCGCCTAA
16985869 GCCATCAACACAGA
1 GCCATCAAC-CAGA
16985883 CAGCCAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (21 bp):
GCCATCAACCAGATCGCCTAA
Found at i:16989584 original size:33 final size:33
Alignment explanation
Indices: 16989537--16989613 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
16989527 AAAAGTATTA
* *
16989537 ATTAAAATTGAAGATAATTTATAAAATTTCATC
1 ATTAAAATTAAAGATAATTTACAAAATTTCATC
16989570 ATTAAAATTAAAGATAATTTACAAAATTTCATC
1 ATTAAAATTAAAGATAATTTACAAAATTTCATC
16989603 ATTAAAATTAA
1 ATTAAAATTAA
16989614 TAAATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (33 bp):
ATTAAAATTAAAGATAATTTACAAAATTTCATC
Found at i:16989927 original size:14 final size:14
Alignment explanation
Indices: 16989897--16989934 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16989887 AAATTTTTAA
16989897 AAAATAATT-TTTT
1 AAAATAATTATTTT
16989910 -AAATAATTATTTT
1 AAAATAATTATTTT
*
16989923 AAAATTATTATT
1 AAAATAATTATT
16989935 ATAACTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
14 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAAATAATTATTTT
Found at i:16990010 original size:38 final size:38
Alignment explanation
Indices: 16989952--16990030 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
16989942 TTGTTTATAA
** *
16989952 TATTTTTAAATTTAAAATTAT-TTCTTTTTAATTATTTT
1 TATTTTT-AATTTAAAATTATATAATTTTAAATTATTTT
16989990 TATTTTT-ATTTATAATATTATATAATTTTAAATTATTTT
1 TATTTTTAATTTA-AA-ATTATATAATTTTAAATTATTTT
16990029 TA
1 TA
16990031 ATAAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.14
37 2 0.06
38 12 0.34
39 16 0.46
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
TATTTTTAATTTAAAATTATATAATTTTAAATTATTTT
Found at i:17002389 original size:2 final size:2
Alignment explanation
Indices: 17002384--17002423 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
17002374 ATACACACAC
*
17002384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17002424 GAGTGGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17009214 original size:21 final size:21
Alignment explanation
Indices: 17009175--17009214 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17009165 TGATTTACAA
***
17009175 GATGAATTTGAATGCCTTTAT
1 GATGAATTTGAAAAACTTTAT
17009196 GATGAATTTGAAAAACTTT
1 GATGAATTTGAAAAACTTT
17009215 TTTTCAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
GATGAATTTGAAAAACTTTAT
Found at i:17021737 original size:22 final size:22
Alignment explanation
Indices: 17021703--17021774 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
17021693 GTAAATATTC
* *
17021703 AAAATCTCCGAATAACAATTTA
1 AAAACCTCTGAATAACAATTTA
* *
17021725 AAAACCTCTGAAT-ACATTTTC
1 AAAACCTCTGAATAACAATTTA
* ** *
17021746 AAAACCTTTGTGTAACAATTTT
1 AAAACCTCTGAATAACAATTTA
17021768 AAAACCT
1 AAAACCT
17021775 TCGAGTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (22 bp):
AAAACCTCTGAATAACAATTTA
Found at i:17021775 original size:22 final size:22
Alignment explanation
Indices: 17021712--17021775 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
17021702 CAAAATCTCC
* *
17021712 GAATAACAATTTAAAAACCTCT
1 GAATAACAATTTTAAAACCTTT
17021734 GAAT-AC-ATTTTCAAAACCTTT
1 GAATAACAATTTT-AAAACCTTT
**
17021755 GTGTAACAATTTTAAAACCTT
1 GAATAACAATTTTAAAACCTT
17021776 CGAGTAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 14 0.40
23 5 0.14
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.34
Consensus pattern (22 bp):
GAATAACAATTTTAAAACCTTT
Found at i:17021782 original size:22 final size:22
Alignment explanation
Indices: 17021648--17021782 Score: 86
Period size: 21 Copynumber: 6.3 Consensus size: 22
17021638 TCAAATTTTT
*
17021648 GAGTAACAATTTCAAAACCTTC
1 GAGTAACAATTTTAAAACCTTC
* *
17021670 GA-TAACAATTTTAAAAACTGTA
1 GAGTAACAATTTTAAAACCT-TC
* * *
17021692 G-GT-A-AATATTCAAAATCTCC
1 GAGTAACAAT-TTTAAAACCTTC
* *
17021712 GAATAACAATTTAAAAACC-TC
1 GAGTAACAATTTTAAAACCTTC
* *
17021733 TGAAT-AC-ATTTTCAAAACCTTT
1 -GAGTAACAATTTT-AAAACCTTC
*
17021755 GTGTAACAATTTTAAAACCTTC
1 GAGTAACAATTTTAAAACCTTC
17021777 GAGTAA
1 GAGTAA
17021783 TACTTTTAGA
Statistics
Matches: 85, Mismatches: 17, Indels: 22
0.69 0.14 0.18
Matches are distributed among these distances:
20 8 0.09
21 36 0.42
22 33 0.39
23 8 0.09
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (22 bp):
GAGTAACAATTTTAAAACCTTC
Found at i:17021789 original size:22 final size:22
Alignment explanation
Indices: 17021757--17021845 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 22
17021747 AAACCTTTGT
* *
17021757 GTAACAATTTTAAAACCTTCGA
1 GTAATAATTTTAAAACCTTCAA
* * *
17021779 GTAATACTTTTAGAACATTCAA
1 GTAATAATTTTAAAACCTTCAA
* *
17021801 GT-ATAATCTTCAAAACCTCCAA
1 GTAATAAT-TTTAAAACCTTCAA
17021823 GTAAT-ATTTTAAAAACCTTCAA
1 GTAATAATTTT-AAAACCTTCAA
17021845 G
1 G
17021846 CTTAATCTTC
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 6 0.12
22 44 0.85
23 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
GTAATAATTTTAAAACCTTCAA
Found at i:17021818 original size:44 final size:44
Alignment explanation
Indices: 17021768--17021863 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
17021758 TAACAATTTT
* * *
17021768 AAAACCTTCGAGTAATACTTTT-AGAACATTCAAG-TATAATCTTC
1 AAAACCTCCAAGTAATA-TTTTAAAAACATTCAAGCT-TAATCTTC
*
17021812 AAAACCTCCAAGTAATATTTTAAAAACCTTCAAGCTTAATCTTC
1 AAAACCTCCAAGTAATATTTTAAAAACATTCAAGCTTAATCTTC
17021856 AAAACCTC
1 AAAACCTC
17021864 TAGATACACT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 4 0.09
44 41 0.89
45 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (44 bp):
AAAACCTCCAAGTAATATTTTAAAAACATTCAAGCTTAATCTTC
Found at i:17021859 original size:22 final size:21
Alignment explanation
Indices: 17021796--17021862 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
17021786 TTTTAGAACA
17021796 TTCAAGTATAATCTTCAAAACC
1 TTCAAGT-TAATCTTCAAAACC
* * * *
17021818 TCCAAGTAATATTTTAAAAACC
1 TTCAAGTTA-ATCTTCAAAACC
17021840 TTCAAGCTTAATCTTCAAAACC
1 TTCAAG-TTAATCTTCAAAACC
17021862 T
1 T
17021863 CTAGATACAC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
TTCAAGTTAATCTTCAAAACC
Found at i:17024082 original size:25 final size:25
Alignment explanation
Indices: 17024054--17024133 Score: 112
Period size: 25 Copynumber: 3.2 Consensus size: 25
17024044 CCATTTATTT
17024054 TTATTTCTTATTGGGTCATGCCCAC
1 TTATTTCTTATTGGGTCATGCCCAC
17024079 TTATTT-TCTA-TGGGTCATGCCCAC
1 TTATTTCT-TATTGGGTCATGCCCAC
*
17024103 TTATTGTC-TATTGGGTCATGCCCAT
1 TTATT-TCTTATTGGGTCATGCCCAC
17024128 TTATTT
1 TTATTT
17024134 ATTTTTTTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
24 23 0.46
25 27 0.54
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (25 bp):
TTATTTCTTATTGGGTCATGCCCAC
Found at i:17024094 original size:24 final size:25
Alignment explanation
Indices: 17024057--17024133 Score: 120
Period size: 24 Copynumber: 3.1 Consensus size: 25
17024047 TTTATTTTTA
17024057 TTTCTTATTGGGTCATGCCCACTTAT
1 TTTC-TATTGGGTCATGCCCACTTAT
17024083 TTTCTA-TGGGTCATGCCCACTTAT
1 TTTCTATTGGGTCATGCCCACTTAT
* *
17024107 TGTCTATTGGGTCATGCCCATTTAT
1 TTTCTATTGGGTCATGCCCACTTAT
17024132 TT
1 TT
17024134 ATTTTTTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 23 0.49
25 20 0.43
26 4 0.09
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (25 bp):
TTTCTATTGGGTCATGCCCACTTAT
Found at i:17027497 original size:34 final size:34
Alignment explanation
Indices: 17027442--17027574 Score: 198
Period size: 34 Copynumber: 4.0 Consensus size: 34
17027432 TCAGGTCGTG
*
17027442 ACAG-TCCAAGTTTT-TGCACAAATTGGCAGCAA
1 ACAGCTCCAATTTTTCTGCACAAATTGGCAGCAA
*
17027474 ACAGCTCCAATTTTTCTGTACAAATTGGCAGCAA
1 ACAGCTCCAATTTTTCTGCACAAATTGGCAGCAA
*
17027508 ACAGCTCTAATTTTTCTGCACAAATTGGCAGCAA
1 ACAGCTCCAATTTTTCTGCACAAATTGGCAGCAA
* * *
17027542 ATAGCTCCAATTTTTCTACACAAATTAGCAGCA
1 ACAGCTCCAATTTTTCTGCACAAATTGGCAGCA
17027575 CTTTGCTACC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 4 0.04
33 9 0.10
34 78 0.86
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (34 bp):
ACAGCTCCAATTTTTCTGCACAAATTGGCAGCAA
Found at i:17029580 original size:220 final size:220
Alignment explanation
Indices: 17029198--17029640 Score: 802
Period size: 220 Copynumber: 2.0 Consensus size: 220
17029188 TATTCTCGAA
17029198 AATAAAACTCCAATACTTTCATGATCGAGTGCTCATTAGAAAATTTCAACTTATACCACAAGACA
1 AATAAAACTCCAATACTTTCATGATCGAGTGCTCATTAGAAAATTTCAACTTATACCACAAGACA
17029263 TTTCGATAATTAATAATATTCTTGTATATATCTTTATAATCTTAATCAATCTCTTTAATCAATAA
66 TTTCGATAATTAATAATATTCTTGTATATATCTTTATAATCTTAATCAATCTCTTTAATCAATAA
*
17029328 CTAATTTGTTCATCATCAACCGCATACAACATATCTAACTTGAAATTCC-TC-AATTTACTCTAA
131 CTAATTTGTTCATCATCAACCGCATACAACATATCTAACTTGAAA--CCGTCAAATTTACTCCAA
17029391 ATGCCAAA-TCTCACGGTCTCATTACT
194 ATGCCAAACTCTCACGGTCTCATTACT
17029417 NAATAAAACTCCAATACTTTCATGATCGAGTGCTCATTAGAAAATTTCAACTTATACCACAAGAC
1 -AATAAAACTCCAATACTTTCATGATCGAGTGCTCATTAGAAAATTTCAACTTATACCACAAGAC
**
17029482 ATTTCGATAATTAATAATATTCTTGTATATATCTTTATCTTCTTAATCAATCTCTTTAATCAATA
65 ATTTCGATAATTAATAATATTCTTGTATATATCTTTATAATCTTAATCAATCTCTTTAATCAATA
17029547 ACTAATTTGTTCATCATCAACCGCATACAACATATCTAACTTGAAACCGTCAAATTTACTCCAAA
130 ACTAATTTGTTCATCATCAACCGCATACAACATATCTAACTTGAAACCGTCAAATTTACTCCAAA
17029612 TGCCAAATCTCTCACGGTCTCATTACT
195 TGCCAAA-CTCTCACGGTCTCATTACT
17029639 AA
1 AA
17029641 AACCTTTGCT
Statistics
Matches: 216, Mismatches: 3, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
218 2 0.01
219 2 0.01
220 192 0.89
221 2 0.01
222 18 0.08
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (220 bp):
AATAAAACTCCAATACTTTCATGATCGAGTGCTCATTAGAAAATTTCAACTTATACCACAAGACA
TTTCGATAATTAATAATATTCTTGTATATATCTTTATAATCTTAATCAATCTCTTTAATCAATAA
CTAATTTGTTCATCATCAACCGCATACAACATATCTAACTTGAAACCGTCAAATTTACTCCAAAT
GCCAAACTCTCACGGTCTCATTACT
Found at i:17037618 original size:25 final size:25
Alignment explanation
Indices: 17037593--17037663 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
17037583 TTTATTTTTA
* *
17037593 TTTCTTATTGGGCCATGCCCGCTTAT
1 TTTC-TATTGGGTCATGCCCACTTAT
17037619 TTTCTATTGGGTCATGCCCACTTAT
1 TTTCTATTGGGTCATGCCCACTTAT
17037644 TTTCTATTGGGTCATGCCCA
1 TTTCTATTGGGTCATGCCCA
17037664 TTTGTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
25 39 0.91
26 4 0.09
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.42
Consensus pattern (25 bp):
TTTCTATTGGGTCATGCCCACTTAT
Found at i:17037781 original size:22 final size:22
Alignment explanation
Indices: 17037753--17037822 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
17037743 CATGGCTTCC
17037753 CTTCACCACCGTGGCTTCCTCT
1 CTTCACCACCGTGGCTTCCTCT
*
17037775 CTTCACCACCATGGCTTCCTCT
1 CTTCACCACCGTGGCTTCCTCT
*
17037797 CTTCATCACCGTGGCTTCCTCT
1 CTTCACCACCGTGGCTTCCTCT
17037819 CTTC
1 CTTC
17037823 CTTTCCTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.10, C:0.44, G:0.11, T:0.34
Consensus pattern (22 bp):
CTTCACCACCGTGGCTTCCTCT
Found at i:17037808 original size:44 final size:41
Alignment explanation
Indices: 17037742--17037822 Score: 126
Period size: 44 Copynumber: 1.9 Consensus size: 41
17037732 TTTTTCCAGC
17037742 CCATGGCTTCCCTTCACCACCGTGGCTTCCTCTCTTCACCA
1 CCATGGCTTCCCTTCACCACCGTGGCTTCCTCTCTTCACCA
*
17037783 CCATGGCTTCCTCTCTTCATCACCGTGGCTTCCTCTCTTC
1 CCATGGCTT-C-C-CTTCACCACCGTGGCTTCCTCTCTTC
17037823 CTTTCCTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
41 9 0.25
42 1 0.03
43 1 0.03
44 25 0.69
ACGTcount: A:0.10, C:0.44, G:0.12, T:0.33
Consensus pattern (41 bp):
CCATGGCTTCCCTTCACCACCGTGGCTTCCTCTCTTCACCA
Found at i:17038001 original size:34 final size:34
Alignment explanation
Indices: 17037956--17038050 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
17037946 CACAAAGCTG
17037956 TCCAA-TTTTCTGCACAAATTGGCAGCAAACAGC
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
* * *
17037989 TCTAATTTTTCTGCACAAATTGGTAGCAAATAGC
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
*
17038023 TCCAATTTATCTGCACAAATTGGCAGCA
1 TCCAATTTTTCTGCACAAATTGGCAGCA
17038051 CTTTGCTGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 4 0.07
34 51 0.93
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (34 bp):
TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
Found at i:17038358 original size:14 final size:14
Alignment explanation
Indices: 17038316--17038375 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
17038306 TCCCACGGTT
17038316 TTCTCTTCTTTTTTC
1 TTCTCTT-TTTTTTC
* * *
17038331 TTTTCATTTCTTTC
1 TTCTCTTTTTTTTC
17038345 TTC-CTTTATTTTTC
1 TTCTCTTT-TTTTTC
*
17038359 TTCTCTTTTTCTTC
1 TTCTCTTTTTTTTC
17038373 TTC
1 TTC
17038376 ACTAACCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
13 3 0.08
14 24 0.67
15 9 0.25
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTCTTTTTTTTC
Found at i:17039381 original size:22 final size:21
Alignment explanation
Indices: 17039331--17039382 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17039321 TTACACTATC
*
17039331 TAAAACCTCTGGATATATCTT
1 TAAAACCTCTGAATATATCTT
** *
17039352 CCAAACCTTTGAATATATGCTT
1 TAAAACCTCTGAATATAT-CTT
17039374 TAAAACCTC
1 TAAAACCTC
17039383 CTGATAACCA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (21 bp):
TAAAACCTCTGAATATATCTT
Found at i:17041555 original size:53 final size:53
Alignment explanation
Indices: 17041441--17041570 Score: 129
Period size: 53 Copynumber: 2.4 Consensus size: 53
17041431 ATTTCCAACA
* * * * *
17041441 GAATTTTCTGTTGAAAAAACATTTCCCACGAAATTCCGTTAGAAAGTTTCAAT
1 GAATTTTCTGTTGGAAAAACATTTCCCACGAAATTCCGTCACAAAGTTGCAAG
* * *
17041494 AAAGTTTTCTGTTGGAAAAGCATTT-CCACGAAATTCTGTCACAAA-TTGCTAACG
1 GAA-TTTTCTGTTGGAAAAACATTTCCCACGAAATTCCGTCACAAAGTTGC-AA-G
* *
17041548 GAATTTTCCGTTGGAAATACATT
1 GAATTTTCTGTTGGAAAAACATT
17041571 GTCAAACCCT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
52 3 0.05
53 38 0.61
54 21 0.34
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (53 bp):
GAATTTTCTGTTGGAAAAACATTTCCCACGAAATTCCGTCACAAAGTTGCAAG
Found at i:17048893 original size:35 final size:35
Alignment explanation
Indices: 17048827--17049096 Score: 267
Period size: 35 Copynumber: 7.7 Consensus size: 35
17048817 TACTTGACTA
* *
17048827 AAATTGTTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
** * *
17048859 AAATTGCTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
*
17048894 AAATTATTTAATTAAGTAATTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* *** *
17048929 AGATTAAAAAATTAAGTTATTGGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
17048964 AAATTTGTTTAATTAAGTCATAGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
17049000 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* *
17049036 AAATTATTTAATTAAGTTATTGGGCCTATTTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
***
17049071 AAATTAAACAATTAAGTTAATTGGGC
1 AAATTATTTAATTAAGTT-ATTGGGC
17049097 TTCTTAAGGA
Statistics
Matches: 197, Mismatches: 35, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
32 14 0.07
35 121 0.61
36 59 0.30
37 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:17049024 original size:142 final size:139
Alignment explanation
Indices: 17048820--17049096 Score: 394
Period size: 142 Copynumber: 2.0 Consensus size: 139
17048810 TCTCAAGTAC
*
17048820 TTGACTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTGCTTAATTAAATCATTGGGCC
1 TTGACTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGCTTAATTAAATCATTGGGCC
*
17048885 TAATTAATTAAATTATTTAATTAAGTAATTGGGCCTAATTAATTAGATTAAAAAATTAAGTT-AT
66 TAATTAATTAAATTATTTAATTAAGTAATTGGGCCTAATTAATTAAATTAAAAAATTAAGTTAAT
17048949 TGGGCCTAA
131 TGGGCCTAA
* * * * **
17048958 TTGATTAAATTTGTTTAATTAAGTCATAGGGCCTAATTGATTAAAATTGTTTAATTAAATTGTTG
1 TTGACTAAAATTGTTTAATTAAGT--T-GGGCCTAATTAATT-AAATTGCTTAATTAAATCATTG
* * * * *
17049023 GGCTTAATTAATTAAATTATTTAATTAAGTTATTGGGCCTATTTGATTAAATTAAACAATTAAGT
62 GGCCTAATTAATTAAATTATTTAATTAAGTAATTGGGCCTAATTAATTAAATTAAAAAATTAAGT
17049088 TAATTGGGC
127 TAATTGGGC
17049097 TTCTTAAGGA
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
138 22 0.18
140 1 0.01
141 12 0.10
142 79 0.65
143 7 0.06
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (139 bp):
TTGACTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGCTTAATTAAATCATTGGGCC
TAATTAATTAAATTATTTAATTAAGTAATTGGGCCTAATTAATTAAATTAAAAAATTAAGTTAAT
TGGGCCTAA
Found at i:17049031 original size:107 final size:106
Alignment explanation
Indices: 17048847--17049075 Score: 307
Period size: 107 Copynumber: 2.2 Consensus size: 106
17048837 ATTAAGTTGT
* * *
17048847 GCCTAATTAATTAAA-TTGCTTAATTAAATCATTGGGCCTAATTAATTAAATTATTTAATTAAGT
1 GCCTAATTGATTAAATTTGCTTAATTAAATCATAGGGCCTAATTAATTAAATTATTTAATTAAAT
*
17048911 AATTGGGCCTAATTAATTAGATTAAAAAATTAAGTTATTGG
66 AATTGGGCCTAATTAATTAAATTAAAAAATTAAGTTATTGG
* * * *
17048952 GCCTAATTGATTAAATTTGTTTAATTAAGTCATAGGGCCTAATTGATTAAAATTGTTTAATTAAA
1 GCCTAATTGATTAAATTTGCTTAATTAAATCATAGGGCCTAATTAATT-AAATTATTTAATTAAA
** * ***
17049017 TTGTTGGGCTTAATTAATTAAATTATTTAATTAAGTTATTGG
65 TAATTGGGCCTAATTAATTAAATTAAAAAATTAAGTTATTGG
*
17049059 GCCTATTTGATTAAATT
1 GCCTAATTGATTAAATT
17049076 AAACAATTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 14 0.13
106 28 0.26
107 65 0.61
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.43
Consensus pattern (106 bp):
GCCTAATTGATTAAATTTGCTTAATTAAATCATAGGGCCTAATTAATTAAATTATTTAATTAAAT
AATTGGGCCTAATTAATTAAATTAAAAAATTAAGTTATTGG
Found at i:17053578 original size:21 final size:21
Alignment explanation
Indices: 17053549--17053593 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17053539 AGTTATAGAA
*
17053549 ATACTTATATGTA-AATTAAAT
1 ATACGTATAT-TAGAATTAAAT
*
17053570 ATACGTATATTAGAATTATAT
1 ATACGTATATTAGAATTAAAT
17053591 ATA
1 ATA
17053594 TAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (21 bp):
ATACGTATATTAGAATTAAAT
Found at i:17079659 original size:31 final size:30
Alignment explanation
Indices: 17079624--17079707 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 30
17079614 TGTATTATAA
* *
17079624 AATTTTATTTAATTTAGTCCTTGTAC-TTCAC
1 AATTTTGTTTAATTTAGTCCTT-TACACT-AC
* *
17079655 AATTTTGTTCAATTTAATCCATTTACACTAC
1 AATTTTGTTTAATTTAGTCC-TTTACACTAC
*
17079686 AATTTTGTTTAATTTGGTCCTT
1 AATTTTGTTTAATTTAGTCCTT
17079708 ATGACATGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 2 0.05
31 39 0.89
32 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.51
Consensus pattern (30 bp):
AATTTTGTTTAATTTAGTCCTTTACACTAC
Found at i:17091211 original size:90 final size:91
Alignment explanation
Indices: 17091105--17091283 Score: 245
Period size: 90 Copynumber: 2.0 Consensus size: 91
17091095 AGTTTTAGTG
* **
17091105 TTATTTTGTTTTCATCATCTTCAAG-TTTCAAAAGGATTTCAATGATTGGTCTTTAATTTTTAAT
1 TTATTTTGTTTTCATCATCTCCAAGCTTT-AAAAAAATTTCAATGATTGGTCTTTAATTTTTAAT
* *
17091169 TTTAGCAAATCAAATAAGTG-CTTGTA
65 TGTAACAAATCAAATAAGTGACTTGTA
* * **
17091195 TTATTTTGTTTTCATCATCTCCAAGCTTTAAAAAAATTTCAATGCTTGGTCTTTAGTTTTTGGTT
1 TTATTTTGTTTTCATCATCTCCAAGCTTTAAAAAAATTTCAATGATTGGTCTTTAATTTTTAATT
*
17091260 GTAACAAATCAAGTAAGTGACTTG
66 GTAACAAATCAAATAAGTGACTTG
17091284 ATATCTCTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 70 0.91
91 7 0.09
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (91 bp):
TTATTTTGTTTTCATCATCTCCAAGCTTTAAAAAAATTTCAATGATTGGTCTTTAATTTTTAATT
GTAACAAATCAAATAAGTGACTTGTA
Found at i:17091576 original size:27 final size:27
Alignment explanation
Indices: 17091501--17091576 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
17091491 TATTCTAAGA
* * * *
17091501 ATAATTTTATCCACCAGAAGTAGATGC
1 ATAACTTTACCCACTAGAAGTGGATGC
* * *
17091528 ATAACTTTACCCATTAAAAGTGGATGG
1 ATAACTTTACCCACTAGAAGTGGATGC
17091555 ATAACTTTACCCACTAGAAGTG
1 ATAACTTTACCCACTAGAAGTG
17091577 AATGAATACT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (27 bp):
ATAACTTTACCCACTAGAAGTGGATGC
Found at i:17091590 original size:27 final size:27
Alignment explanation
Indices: 17091499--17091588 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 27
17091489 TTTATTCTAA
* * *
17091499 GAATAATTTTATCCACCAGAAGT-AGAT
1 GAATAACTTTACCCACTAGAAGTGA-AT
* * * *
17091526 GCATAACTTTACCCATTAAAAGTGGAT
1 GAATAACTTTACCCACTAGAAGTGAAT
*
17091553 GGATAACTTTACCCACTAGAAGTGAAT
1 GAATAACTTTACCCACTAGAAGTGAAT
17091580 GAAT-ACTTT
1 GAATAACTTT
17091589 TAACCCACCA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
26 5 0.10
27 45 0.90
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (27 bp):
GAATAACTTTACCCACTAGAAGTGAAT
Found at i:17092040 original size:13 final size:13
Alignment explanation
Indices: 17092022--17092069 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
17092012 ATGTTTTTAT
17092022 TATATTTAAATTA
1 TATATTTAAATTA
**
17092035 TATATTTTTATTA
1 TATATTTAAATTA
* *
17092048 CATGTTTAAATTA
1 TATATTTAAATTA
17092061 TATATTTAA
1 TATATTTAA
17092070 TTTTCTCTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
TATATTTAAATTA
Found at i:17092043 original size:24 final size:25
Alignment explanation
Indices: 17092015--17092067 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
17092005 TATTTTTATG
17092015 TTTTTATT-ATATTTAAATTATATA
1 TTTTTATTAATATTTAAATTATATA
*
17092039 TTTTTATTACATGTTTAAATTATATA
1 TTTTTATTA-ATATTTAAATTATATA
17092065 TTT
1 TTT
17092068 AATTTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 8 0.31
26 18 0.69
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTATTAATATTTAAATTATATA
Found at i:17101227 original size:42 final size:44
Alignment explanation
Indices: 17101179--17101298 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 44
17101169 ATTAAATTTA
*
17101179 CAAGTTCAACTAATATAAATTAATTTTATATTTATTACTTT-G-
1 CAAGTTCAACTAATATAAATTAATTTTATATTTATAACTTTCGT
*
17101221 CAAGTTCAACTAATATAAA--AATTTTATATATT-TAAGTTTGCGT
1 CAAGTTCAACTAATATAAATTAATTTTATAT-TTATAACTTT-CGT
*
17101264 CATAGTTCAACTAATATAAATTAATTTTACATTTA
1 CA-AGTTCAACTAATATAAATTAATTTTATATTTA
17101299 GTAGTTTATA
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
40 15 0.22
41 2 0.03
42 20 0.30
43 2 0.03
44 17 0.25
45 2 0.03
46 9 0.13
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (44 bp):
CAAGTTCAACTAATATAAATTAATTTTATATTTATAACTTTCGT
Found at i:17104258 original size:20 final size:20
Alignment explanation
Indices: 17104233--17104275 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17104223 TACAAATATG
17104233 CATCAATCATCTCATACTGA
1 CATCAATCATCTCATACTGA
17104253 CATCAATCATCTCATACTGA
1 CATCAATCATCTCATACTGA
17104273 CAT
1 CAT
17104276 ACCATCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (20 bp):
CATCAATCATCTCATACTGA
Found at i:17104283 original size:18 final size:19
Alignment explanation
Indices: 17104240--17104284 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
17104230 ATGCATCAAT
*
17104240 CATCTCATACTGACATCAAT
1 CATCTCATACTGACAT-AAC
17104260 CATCTCATACTGACAT-AC
1 CATCTCATACTGACATAAC
17104278 CATCTCA
1 CATCTCA
17104285 AACGCACAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.29
Consensus pattern (19 bp):
CATCTCATACTGACATAAC
Found at i:17105250 original size:17 final size:17
Alignment explanation
Indices: 17105228--17105262 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17105218 AACATGACAT
17105228 ATCAGTAT-TTTTCTGTA
1 ATCAGTATCTTTT-TGTA
17105245 ATCAGTATCTTTTTGTA
1 ATCAGTATCTTTTTGTA
17105262 A
1 A
17105263 AAATAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (17 bp):
ATCAGTATCTTTTTGTA
Found at i:17105984 original size:2 final size:2
Alignment explanation
Indices: 17105977--17106009 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
17105967 ATAACAGATG
*
17105977 GA GA GA GA GA GA GA GA GA AA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17106010 AGGAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17113885 original size:15 final size:15
Alignment explanation
Indices: 17113855--17113887 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
17113845 TGAGATTTAG
17113855 TTTATTTTATTGTGA
1 TTTATTTTATTGTGA
17113870 TTTAGTTTTATT-TGA
1 TTTA-TTTTATTGTGA
17113885 TTT
1 TTT
17113888 TTAGTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (15 bp):
TTTATTTTATTGTGA
Found at i:17119604 original size:55 final size:54
Alignment explanation
Indices: 17119510--17119693 Score: 170
Period size: 55 Copynumber: 3.4 Consensus size: 54
17119500 TAGAGTTATT
* * *
17119510 TTAGCGTGTCACGGCTGTTCCTGGCGTGTTGTGGTTTAACTAGTTTTTTGGGTTG
1 TTAGCGTGTCACGGCTGTTCCTAGCGTGTCGTGGGTTAACT-GTTTTTTGGGTTG
* * * * * * *
17119565 TTAGCGTGTCATGGTTGTTCCTAGTGTGTCATGGGTTAACTGAATTTATGGGTTT
1 TTAGCGTGTCACGGCTGTTCCTAGCGTGTCGTGGGTTAACTG-TTTTTTGGGTTG
* * * * * *
17119620 TTGGCGTGTCACGGCTATTCCTAGCATGTCGTGGGTTAATTGGTTTTTTGGATTT
1 TTAGCGTGTCACGGCTGTTCCTAGCGTGTCGTGGGTTAACT-GTTTTTTGGGTTG
** *
17119675 TTAATGTATCACGGCTGTT
1 TTAGCGTGTCACGGCTGTT
17119694 GATGTAACGA
Statistics
Matches: 101, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
54 1 0.01
55 99 0.98
56 1 0.01
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (54 bp):
TTAGCGTGTCACGGCTGTTCCTAGCGTGTCGTGGGTTAACTGTTTTTTGGGTTG
Found at i:17119748 original size:23 final size:23
Alignment explanation
Indices: 17119722--17119777 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
17119712 TTACAGTGAT
17119722 TGGCGTGTCACAACAATGATGCA
1 TGGCGTGTCACAACAATGATGCA
* * * *
17119745 TGGCATGTCACGATAGTGATGCA
1 TGGCGTGTCACAACAATGATGCA
17119768 TGGCGTGTCA
1 TGGCGTGTCA
17119778 TGACATTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (23 bp):
TGGCGTGTCACAACAATGATGCA
Found at i:17119798 original size:31 final size:31
Alignment explanation
Indices: 17119763--17119837 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
17119753 CACGATAGTG
* *
17119763 ATGCATGGCGTGTCATGACATTTGACTTGAT
1 ATGCATGGCGTGTCACGACAATTGACTTGAT
*
17119794 ATGCATGGCGTGTCACGATAATTGACTTGAT
1 ATGCATGGCGTGTCACGACAATTGACTTGAT
17119825 ATGCATGGCGTGT
1 ATGCATGGCGTGT
17119838 TACAACATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (31 bp):
ATGCATGGCGTGTCACGACAATTGACTTGAT
Found at i:17123263 original size:19 final size:19
Alignment explanation
Indices: 17123208--17123263 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
17123198 ACCCGGCTCA
17123208 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
17123227 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
17123246 TGTACATCCCCCCACATC
1 TGTACATCCCCCCACATC
17123264 TTGCACATGG
Statistics
Matches: 25, Mismatches: 10, Indels: 4
0.64 0.26 0.10
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.23, C:0.43, G:0.12, T:0.21
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:17128975 original size:13 final size:13
Alignment explanation
Indices: 17128957--17128981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17128947 ATTTTCAAAA
17128957 ATTTTATAAAATT
1 ATTTTATAAAATT
17128970 ATTTTATAAAAT
1 ATTTTATAAAAT
17128982 CCCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:17129301 original size:29 final size:29
Alignment explanation
Indices: 17129240--17129303 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
17129230 GTAAATTTTT
**
17129240 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
* *
17129269 AAAAATTACATTTTTA-CCCCAAAAATTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
17129297 AAAAATT
1 AAAAATT
17129304 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAAGTG
Found at i:17133813 original size:29 final size:29
Alignment explanation
Indices: 17133752--17133815 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
17133742 GCAAATTTTT
** *
17133752 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
*
17133781 AAAAATTACATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
17133809 AAAAATT
1 AAAAATT
17133816 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:17137156 original size:21 final size:21
Alignment explanation
Indices: 17137132--17137179 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
17137122 TTCTCGGTTT
17137132 GCATATGGTTCGGTTTTTCAA
1 GCATATGGTTCGGTTTTTCAA
17137153 GCATATGGTTCGGTTTTTCAA
1 GCATATGGTTCGGTTTTTCAA
17137174 GCATAT
1 GCATAT
17137180 CTTCCACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (21 bp):
GCATATGGTTCGGTTTTTCAA
Found at i:17137635 original size:38 final size:40
Alignment explanation
Indices: 17137546--17137651 Score: 162
Period size: 38 Copynumber: 2.7 Consensus size: 40
17137536 CACACCCGGC
*
17137546 TCATGTACATCCCCCCACATCGTGCACATAGCTGGTGTCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCTAGTGTCA
* *
17137586 TCATGTGCATCCCCCCACATCGTGCACA-ATC-AGTGTCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCTAGTGTCA
*
17137624 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
17137652 CGGGCACTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 32 0.52
39 2 0.03
40 27 0.44
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.24
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCTAGTGTCA
Found at i:17139341 original size:31 final size:31
Alignment explanation
Indices: 17139303--17139394 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
17139293 ACACTGAGTG
* *
17139303 GAAGCAGATTTATGGGTTTACAAGCTGAATA
1 GAAGCAGATTTATGGGCTGACAAGCTGAATA
* * *
17139334 GAAGCAGATTTATGGGCTGACACGCTGAGTG
1 GAAGCAGATTTATGGGCTGACAAGCTGAATA
* * *
17139365 GAAGTAGATTTATTGGCTGACATGCTGAAT
1 GAAGCAGATTTATGGGCTGACAAGCTGAAT
17139395 GCTAGTGGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (31 bp):
GAAGCAGATTTATGGGCTGACAAGCTGAATA
Found at i:17139406 original size:31 final size:31
Alignment explanation
Indices: 17139308--17139406 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
17139298 GAGTGGAAGC
* * * *
17139308 AGATTTATGGGTTTACAAGCTGAATAG-AAGC
1 AGATTTATGGGCTGACACGCTGAAT-GCAAGT
* *
17139339 AGATTTATGGGCTGACACGCTGAGTGGAAGT
1 AGATTTATGGGCTGACACGCTGAATGCAAGT
* * *
17139370 AGATTTATTGGCTGACATGCTGAATGCTAGT
1 AGATTTATGGGCTGACACGCTGAATGCAAGT
*
17139401 GGATTT
1 AGATTT
17139407 GCAACGTCAC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.31
Consensus pattern (31 bp):
AGATTTATGGGCTGACACGCTGAATGCAAGT
Found at i:17139468 original size:93 final size:92
Alignment explanation
Indices: 17139338--17139559 Score: 259
Period size: 93 Copynumber: 2.4 Consensus size: 92
17139328 TGAATAGAAG
* * * ** *
17139338 CAGATTTATGGGCTGACACGCTGAGTGGAAGTAGATTTATTGGCTGACATGCTGAATGCTAGTGG
1 CAGATTTATGGG-TGACACACTGAGTGCAAGCAGATTTATCAGCTGACACGCTGAATGCTAGTGG
17139403 -ATT-TGCAACGTCACACACTGACTTCTTA
65 AATTATG--ACGTCACACACTGACTTCTTA
** * *
17139431 CAGATTTATGTGGTGACACTTTGAGTGCAAGCAGATTTATCAGCTGACACGCTGAGTGTTAGTGG
1 CAGATTTATG-GGTGACACACTGAGTGCAAGCAGATTTATCAGCTGACACGCTGAATGCTAGTGG
** *
17139496 AATTATGACGTCACATGCTGACTTTTTA
65 AATTATGACGTCACACACTGACTTCTTA
*
17139524 CAAATTTATGGGGTGACACACTGAGTGCAAGCAGAT
1 CAGATTTAT-GGGTGACACACTGAGTGCAAGCAGAT
17139560 GGTTGTGGGG
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
93 102 0.93
94 6 0.05
95 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (92 bp):
CAGATTTATGGGTGACACACTGAGTGCAAGCAGATTTATCAGCTGACACGCTGAATGCTAGTGGA
ATTATGACGTCACACACTGACTTCTTA
Found at i:17139718 original size:19 final size:20
Alignment explanation
Indices: 17139677--17139723 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
17139667 ATTTGGTATC
17139677 AAATTAATTGTGTATAGGCAAAA
1 AAATTAATTGTGTAT--G-AAAA
17139700 AAATTAATTGTGTAT-AAAA
1 AAATTAATTGTGTATGAAAA
*
17139719 CAATT
1 AAATT
17139724 GTATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
23 15 0.65
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATTAATTGTGTATGAAAA
Found at i:17139795 original size:30 final size:30
Alignment explanation
Indices: 17139756--17139880 Score: 106
Period size: 30 Copynumber: 4.5 Consensus size: 30
17139746 AGAAAGAATT
* *
17139756 AATTTTGTATACAATGAATTGCATAAAATA
1 AATTGTGTATACAATGAATTGTATAAAATA
* * *
17139786 AATTATGTATACAAT-AATTATATAAAGTA
1 AATTGTGTATACAATGAATTGTATAAAATA
* * *
17139815 TATTGTGTATAC-A-G-A----A-AGAATT
1 AATTGTGTATACAATGAATTGTATAAAATA
*
17139837 AATTCTGTATACAATGAATTGTATAAAATA
1 AATTGTGTATACAATGAATTGTATAAAATA
17139867 AATTGTGTATACAA
1 AATTGTGTATACAA
17139881 AAAATTTATG
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
22 13 0.18
23 2 0.03
24 1 0.01
25 1 0.01
27 1 0.01
28 1 0.01
29 22 0.31
30 31 0.43
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (30 bp):
AATTGTGTATACAATGAATTGTATAAAATA
Found at i:17139823 original size:29 final size:30
Alignment explanation
Indices: 17139756--17139827 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
17139746 AGAAAGAATT
* *
17139756 AATTTTGTATACAATGAATTGCATAAAATA
1 AATTATGTATACAATGAATTACATAAAATA
* *
17139786 AATTATGTATACAAT-AATTATATAAAGTA
1 AATTATGTATACAATGAATTACATAAAATA
* *
17139815 TATTGTGTATACA
1 AATTATGTATACA
17139828 GAAAGAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (30 bp):
AATTATGTATACAATGAATTACATAAAATA
Found at i:17139834 original size:81 final size:81
Alignment explanation
Indices: 17139699--17139880 Score: 292
Period size: 81 Copynumber: 2.2 Consensus size: 81
17139689 TATAGGCAAA
* * * *
17139699 AAAATTAATTGTGTATAAAACAATTGTATAAAGTATATTGTGTATAAAGAAAGAATTAATTTTGT
1 AAAATAAATTGTGTATACAACAATTATATAAAGTATATTGTGTATAAAGAAAGAATTAATTCTGT
17139764 ATACAATGAATTGCAT
66 ATACAATGAATTGCAT
* * *
17139780 AAAATAAATTATGTATACAATAATTATATAAAGTATATTGTGTATACAGAAAGAATTAATTCTGT
1 AAAATAAATTGTGTATACAACAATTATATAAAGTATATTGTGTATAAAGAAAGAATTAATTCTGT
*
17139845 ATACAATGAATTGTAT
66 ATACAATGAATTGCAT
17139861 AAAATAAATTGTGTATACAA
1 AAAATAAATTGTGTATACAA
17139881 AAAATTTATG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 92 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.36
Consensus pattern (81 bp):
AAAATAAATTGTGTATACAACAATTATATAAAGTATATTGTGTATAAAGAAAGAATTAATTCTGT
ATACAATGAATTGCAT
Found at i:17139837 original size:47 final size:45
Alignment explanation
Indices: 17139785--17139931 Score: 159
Period size: 47 Copynumber: 3.1 Consensus size: 45
17139775 TGCATAAAAT
* * *
17139785 AAATTATGTATACAATAATTATATAAAGTATATTGTGTATACAGAA
1 AAATTATGTATACAATAATTGTATAAAATAAATTGTGTATACA-AA
17139831 AGAATTAATTCTGTATACAATGAATTGTATAAAATAAATTGTGTATACAAA
1 A-AATT-A---TGTATACAAT-AATTGTATAAAATAAATTGTGTATACAAA
* * *
17139882 AAATTTATGTATAAAATTAATTGTATAAAAAAAATTCTGTATACAAA
1 AAA-TTATGTATACAA-TAATTGTATAAAATAAATTGTGTATACAAA
17139929 AAA
1 AAA
17139932 ATTGTACAGA
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
46 1 0.01
47 42 0.48
48 2 0.02
50 3 0.03
51 15 0.17
52 24 0.28
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (45 bp):
AAATTATGTATACAATAATTGTATAAAATAAATTGTGTATACAAA
Found at i:17139861 original size:14 final size:14
Alignment explanation
Indices: 17139842--17139937 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 14
17139832 GAATTAATTC
* *
17139842 TGTATACAATGAAT
1 TGTATAAAATAAAT
17139856 TGTATAAAATAAATT
1 TGTATAAAATAAA-T
17139871 GTGTATACAAA-AAATTT
1 -TGTATA-AAATAAA--T
*
17139888 ATGTATAAAATTAAT
1 -TGTATAAAATAAAT
*
17139903 TGTATAAAAAAAATT
1 TGTATAAAATAAA-T
*
17139918 CTGTATACAAAAAAAT
1 -TGTATA-AAATAAAT
17139934 TGTA
1 TGTA
17139938 CAGACAATGG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
14 22 0.32
15 7 0.10
16 19 0.28
17 20 0.29
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (14 bp):
TGTATAAAATAAAT
Found at i:17139875 original size:16 final size:16
Alignment explanation
Indices: 17139856--17139936 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 16
17139846 TACAATGAAT
*
17139856 TGTATAAAATAAATTG
1 TGTATAAAAAAAATTG
* *
17139872 TGTATACAAAAAATTTA
1 TGTATA-AAAAAAATTG
**
17139889 TGTATAAAATTAA-T-
1 TGTATAAAAAAAATTG
*
17139903 TGTATAAAAAAAATTC
1 TGTATAAAAAAAATTG
17139919 TGTATACAAAAAAATTG
1 TGTATA-AAAAAAATTG
17139936 T
1 T
17139937 ACAGACAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 16 0.31
17 23 0.44
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (16 bp):
TGTATAAAAAAAATTG
Found at i:17139935 original size:31 final size:31
Alignment explanation
Indices: 17139856--17139937 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
17139846 TACAATGAAT
* *
17139856 TGTATAAAATAAATTGTGTATACAAAAAATTTA
1 TGTATAAAA-AAAAT-TGTATACAAAAAAATTA
** *
17139889 TGTATAAAATTAATTGTATA-AAAAAAATTC
1 TGTATAAAAAAAATTGTATACAAAAAAATTA
17139919 TGTATACAAAAAAATTGTA
1 TGTATA-AAAAAAATTGTA
17139938 CAGACAATGG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 14 0.34
31 16 0.39
32 2 0.05
33 9 0.22
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (31 bp):
TGTATAAAAAAAATTGTATACAAAAAAATTA
Found at i:17142226 original size:155 final size:156
Alignment explanation
Indices: 17141875--17142330 Score: 612
Period size: 155 Copynumber: 2.9 Consensus size: 156
17141865 CGACTAGGTC
* * *
17141875 AACTGCAATAACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAATATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
* * * * * *
17141940 TTACAACTTTAATATCATAACCGACGGCTCGTTAGCAGTTTGAGGTGGAGCTGGACCGATCGATG
66 TTACAACTTTAATATCCTTACCGACGGCTCGTTAGCTGTTTGAGGTAGAGCCGGACCGATCGGTG
* *
17142005 CTTGAGGACCTATCGTCGCTTTCGCA
131 CTTGAGGACCTGTCGTAGCTTTCGCA
* * * *
17142031 AACTGCAATTACATATATAATTGTGTTAATCAATAATCATGCATGGAATTGTTGAACATTAATCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
*
17142096 TTACAACTTTAATATCCTTACCGTCGGCTCGTTAGCTGTTTG-GGTAGAGCCGGACCGATCGGTG
66 TTACAACTTTAATATCCTTACCGACGGCTCGTTAGCTGTTTGAGGTAGAGCCGGACCGATCGGTG
*
17142160 CTTGAGGACTTGTCGTAGCTTTCGCA
131 CTTGAGGACCTGTCGTAGCTTTCGCA
* * *
17142186 AACTACAATTACATATATAACTATATTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
* ** * * * * * * *
17142251 TTACAAC-TTAATATCCTTACCGCCTACTCATTA-ATCGTCTGCGGTTGAGCCGGACAGATTGGT
66 TTACAACTTTAATATCCTTACCGACGGCTCGTTAGCT-GTTTGAGGTAGAGCCGGACCGATCGGT
17142314 GCTTGAGGACCTGTCGT
130 GCTTGAGGACCTGTCGT
17142331 CACTTCCATA
Statistics
Matches: 264, Mismatches: 34, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
153 1 0.00
154 26 0.10
155 141 0.53
156 96 0.36
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (156 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
TTACAACTTTAATATCCTTACCGACGGCTCGTTAGCTGTTTGAGGTAGAGCCGGACCGATCGGTG
CTTGAGGACCTGTCGTAGCTTTCGCA
Found at i:17142398 original size:155 final size:155
Alignment explanation
Indices: 17141904--17142408 Score: 433
Period size: 155 Copynumber: 3.3 Consensus size: 155
17141894 ACTGTGTTAT
* * * * * * *
17141904 TCAATAATCATATATGGAATTGTTGAATATTAACCGTTACAACTTTAATATCATAACCGACGGCT
1 TCAATAAACATATATGGAATTGTAGAACATTAACCGTTACAACTTTAATATCCTTACCGCCGACT
* * * * * * * * * * *
17141969 CGTTAGCAGTTTGAGGTGGAGCTGGACCGATCGATGCTTGAGGACCTATCGTCGCTTTCGCAAAC
66 CATTAGCTGTCTG-GGTAGAGCCGGACAGATCGGTGCTTGAGGACCTGTCGTAGCTTCCACAAAC
* * * * * * *
17142034 TGCAATTACATATATAATTGTGTTAA
130 TACAATTACAGAAATAACTATATTAC
* ** * * * *
17142060 TCAATAATCATGCATGGAATTGTTGAACATTAATCGTTACAACTTTAATATCCTTACCGTCGGCT
1 TCAATAAACATATATGGAATTGTAGAACATTAACCGTTACAACTTTAATATCCTTACCGCCGACT
* * * * * *
17142125 CGTTAGCTGTTTGGGTAGAGCCGGACCGATCGGTGCTTGAGGACTTGTCGTAGCTTTCGCAAACT
66 CATTAGCTGTCTGGGTAGAGCCGGACAGATCGGTGCTTGAGGACCTGTCGTAGCTTCCACAAACT
* * *
17142190 ACAATTACATATATAACTATATTAT
131 ACAATTACAGAAATAACTATATTAC
* * * *
17142215 TCAATAATCATGTATGGAATTGTTGAACATTAACCGTTACAAC-TTAATATCCTTACCGCCTACT
1 TCAATAAACATATATGGAATTGTAGAACATTAACCGTTACAACTTTAATATCCTTACCGCCGACT
* * * *
17142279 CATTA-ATCGTCTGCGGTTGAGCCGGACAGATTGGTGCTTGAGGACCTGTCGTCA-CTTCCATAA
66 CATTAGCT-GTCTG-GGTAGAGCCGGACAGATCGGTGCTTGAGGACCTGTCGT-AGCTTCCACAA
* * * *
17142342 ACTACAATTATAGAAATTACTGTGTTAC
128 ACTACAATTACAGAAATAACTATATTAC
* * *
17142370 TCGATAAACATATGTGAGAA-TGTAGAACATAAACCGTTA
1 TCAATAAACATATATG-GAATTGTAGAACATTAACCGTTA
17142409 AAATCGATCT
Statistics
Matches: 298, Mismatches: 47, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
153 1 0.00
154 26 0.09
155 197 0.66
156 74 0.25
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (155 bp):
TCAATAAACATATATGGAATTGTAGAACATTAACCGTTACAACTTTAATATCCTTACCGCCGACT
CATTAGCTGTCTGGGTAGAGCCGGACAGATCGGTGCTTGAGGACCTGTCGTAGCTTCCACAAACT
ACAATTACAGAAATAACTATATTAC
Found at i:17144046 original size:31 final size:31
Alignment explanation
Indices: 17144011--17144201 Score: 301
Period size: 31 Copynumber: 6.2 Consensus size: 31
17144001 AAATAAGAAA
* *
17144011 AAAATGTTGTGACACGTCATGCATAACAAGC
1 AAAATGTTGTGACACGCCATGCATAACAAGT
*
17144042 AAAATGTTGTGACACGCCATGCATTACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
*
17144073 AAAATGTTGTGACACACCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
*
17144104 TAAATGTTGTGACACGCCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* *
17144135 TAAATGTTGTGACACACCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
**
17144166 AAAATGTTGTGACACGCCATGCATATTAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
17144197 AAAAT
1 AAAAT
17144202 TGTCACGACT
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 148 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (31 bp):
AAAATGTTGTGACACGCCATGCATAACAAGT
Found at i:17145542 original size:13 final size:13
Alignment explanation
Indices: 17145524--17145548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17145514 TTCCAAAAAA
17145524 TTTATAAAATCAT
1 TTTATAAAATCAT
17145537 TTTATAAAATCA
1 TTTATAAAATCA
17145549 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17147278 original size:36 final size:31
Alignment explanation
Indices: 17147184--17147273 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
17147174 GGGCTTGACA
* *
17147184 AAAATGATGTCACACGCCATG-ATATCAAGT
1 AAAATGCTCTCACACGCCATGCATATCAAGT
* *
17147214 AAAATGTTCTCACATGCCATGCATATCAAGT
1 AAAATGCTCTCACACGCCATGCATATCAAGT
17147245 AAAATGCTCTCACACGCCATGCATATCAA
1 AAAATGCTCTCACACGCCATGCATATCAA
17147274 ATCAAATCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 18 0.33
31 36 0.67
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (31 bp):
AAAATGCTCTCACACGCCATGCATATCAAGT
Found at i:17147941 original size:47 final size:47
Alignment explanation
Indices: 17147872--17148220 Score: 391
Period size: 47 Copynumber: 7.4 Consensus size: 47
17147862 TAAACCATGA
* *
17147872 CCATGGCATGTCACCAACTCTGAACTCTGACGTGTCACAGCTTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCT
* *
17147919 CCATGGCGTGTCACCAACTCTGAACTCTAGA-GTATCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCT-GACGTGTCACAGATTCCCT
* * * * * *
17147966 CCATGGCATCTCACGAACTCTAAACGCT-AGCGTGTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTGA-CGTGTCACAGATTCCCT
* * *
17148013 CCATGGCGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCT
* * *
17148060 CCATGGCGTCTCACAAACTCTGAACACT-AGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTGA-CGTGTCACAGATTCCCT
* * * * *
17148107 CCATGCCATGTCACCAACTCTTAACTCT-AGCGTGTCATAGATTCCCA
1 CCATGGCGTGTCACCAACTCTGAACTCTGA-CGTGTCACAGATTCCCT
* * * *
17148154 CCATGGCCCTGTCACCAACTCTTAACTCTGGCGTCTCACAGATTCCCT
1 CCATGG-CGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCT
*
17148202 CCATGGCGTCTCACCAACT
1 CCATGGCGTGTCACCAACT
17148221 TTGAGCGGTG
Statistics
Matches: 255, Mismatches: 40, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
45 1 0.00
47 211 0.83
48 43 0.17
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCT
Found at i:17148000 original size:94 final size:94
Alignment explanation
Indices: 17147872--17148220 Score: 450
Period size: 94 Copynumber: 3.7 Consensus size: 94
17147862 TAAACCATGA
* *
17147872 CCATGGCATGTCACCAACTCTGAACTCT-GACGTGTCACAGCTTCCCTCCATGGCGTGTCACCAA
1 CCATGGCATCTCACCAACTCTGAACTCTAG-CGTGTCACAGATTCCCTCCATGGCGTGTCACCAA
* *
17147936 CTCTGAACTCTAGAGTATCATAGATTCCCT
65 CTCTTAACTCTAGAGTGTCATAGATTCCCT
* * * *
17147966 CCATGGCATCTCACGAACTCTAAACGCTAGCGTGTCATAGATTCCCTCCATGGCGTGTCACCAAC
1 CCATGGCATCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
* *
17148031 TCTTAACTCTGGCA-TGTCACAGATTCCCT
66 TCTTAACTCTAG-AGTGTCATAGATTCCCT
* * * * *
17148060 CCATGGCGTCTCACAAACTCTGAACACTAGCGTGTCACAGATTCCCTCCATGCCATGTCACCAAC
1 CCATGGCATCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
* *
17148125 TCTTAACTCTAGCGTGTCATAGATTCCCA
66 TCTTAACTCTAGAGTGTCATAGATTCCCT
* * * * * *
17148154 CCATGGCCCTGTCACCAACTCTTAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCAA
1 CCATGG-CATCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAA
17148219 CT
65 CT
17148221 TTGAGCGGTG
Statistics
Matches: 220, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
94 168 0.76
95 52 0.24
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (94 bp):
CCATGGCATCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
TCTTAACTCTAGAGTGTCATAGATTCCCT
Found at i:17148049 original size:141 final size:141
Alignment explanation
Indices: 17147871--17148220 Score: 520
Period size: 141 Copynumber: 2.5 Consensus size: 141
17147861 CTAAACCATG
* * * *
17147871 ACCATGGCATGTCACCAACTCTGAACTCTGACGTGTCACAGCTTCCCTCCATGGCGTGTCACCAA
1 ACCATGGCATGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCAA
* * * *
17147936 CTCTGAACTCTAGAGTATCATAGATTCCCTCCATGGCATCTCACGAACTCTAAACGCTAGCGTGT
66 CTCTGAACACTAGAGTATCACAGATTCCCTCCATGCCATCTCACCAACTCTAAACGCTAGCGTGT
17148001 CATAGATTCCC
131 CATAGATTCCC
* * * *
17148012 TCCATGGCGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCTCCATGGCGTCTCACAAA
1 ACCATGGCATGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCAA
* * * * *
17148077 CTCTGAACACTAGCGTGTCACAGATTCCCTCCATGCCATGTCACCAACTCTTAACTCTAGCGTGT
66 CTCTGAACACTAGAGTATCACAGATTCCCTCCATGCCATCTCACCAACTCTAAACGCTAGCGTGT
17148142 CATAGATTCCC
131 CATAGATTCCC
* *
17148153 ACCATGGCCCTGTCACCAACTCTTAACTCTGGCGTCTCACAGATTCCCTCCATGGCGTCTCACCA
1 ACCATGG-CATGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCA
17148218 ACT
65 ACT
17148221 TTGAGCGGTG
Statistics
Matches: 186, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
141 130 0.70
142 56 0.30
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (141 bp):
ACCATGGCATGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCAA
CTCTGAACACTAGAGTATCACAGATTCCCTCCATGCCATCTCACCAACTCTAAACGCTAGCGTGT
CATAGATTCCC
Found at i:17158946 original size:62 final size:62
Alignment explanation
Indices: 17158880--17159012 Score: 151
Period size: 62 Copynumber: 2.1 Consensus size: 62
17158870 ATTCTTGCAG
* **
17158880 GTTAGAATAGCTTCTAAAATAAAAGAATCGATTCTTTAGAA-TTGAGAAGTCAATTCCTACAA
1 GTTAGAATAGCTTCTAAAATAAAAGAATCAATTC-TTAGAAGTCAAGAAGTCAATTCCTACAA
* * ** * * *
17158942 GTTAGAATAGTTTTTGGACTAAAAGAATCAATTCTTGGAAGTCAAGAAGTCAATTCTTACAA
1 GTTAGAATAGCTTCTAAAATAAAAGAATCAATTCTTAGAAGTCAAGAAGTCAATTCCTACAA
17159004 GTCTAGAAT
1 GT-TAGAAT
17159013 TTTAAGAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
61 5 0.08
62 48 0.81
63 6 0.10
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (62 bp):
GTTAGAATAGCTTCTAAAATAAAAGAATCAATTCTTAGAAGTCAAGAAGTCAATTCCTACAA
Found at i:17159005 original size:22 final size:21
Alignment explanation
Indices: 17158964--17159012 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
17158954 TTTGGACTAA
**
17158964 AAGAATCAATTCTTGGAAGTC
1 AAGAATCAATTCTTACAAGTC
17158985 AAGAAGTCAATTCTTACAAGTC
1 AAGAA-TCAATTCTTACAAGTC
*
17159007 TAGAAT
1 AAGAAT
17159013 TTTAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (21 bp):
AAGAATCAATTCTTACAAGTC
Found at i:17162553 original size:21 final size:19
Alignment explanation
Indices: 17162527--17162565 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
17162517 AAATTTTTCA
17162527 CCTTTTCATTTATTACATATT
1 CCTTTTCA-TT-TTACATATT
*
17162548 CCTTTTTATTTTACATAT
1 CCTTTTCATTTTACATAT
17162566 GTTTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (19 bp):
CCTTTTCATTTTACATATT
Found at i:17166910 original size:2 final size:2
Alignment explanation
Indices: 17166905--17166943 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
17166895 TCTCTCTCTC
17166905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
17166944 GCACACACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17168285 original size:2 final size:2
Alignment explanation
Indices: 17168278--17168317 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
17168268 CTTGGAGTTC
* * *
17168278 AT AT AT AT GT GT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17168318 TTCAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17178804 original size:19 final size:20
Alignment explanation
Indices: 17178768--17178806 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17178758 AAATTTGATT
* *
17178768 AAAATAATTTTTAGTTTTTG
1 AAAATAATTTATAATTTTTG
17178788 AAAAT-ATTTATAATTTTTG
1 AAAATAATTTATAATTTTTG
17178807 CGCATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
AAAATAATTTATAATTTTTG
Found at i:17196438 original size:2 final size:2
Alignment explanation
Indices: 17196423--17196471 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
17196413 ACATTATGTN
* *
17196423 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17196465 TA TA TA T
1 TA TA TA T
17196472 GTTGTGCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17198198 original size:20 final size:21
Alignment explanation
Indices: 17198169--17198223 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
17198159 ACATTGGAGT
17198169 AATGTATTGATAGACGGGA-C
1 AATGTATTGATAGACGGGACC
* * *
17198189 AATTTATTGATACATGGGACC
1 AATGTATTGATAGACGGGACC
*
17198210 AATGTATCGATAGA
1 AATGTATTGATAGA
17198224 TCAGGCTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (21 bp):
AATGTATTGATAGACGGGACC
Found at i:17198635 original size:32 final size:32
Alignment explanation
Indices: 17198606--17198710 Score: 147
Period size: 32 Copynumber: 3.3 Consensus size: 32
17198596 TTTGCTTATG
* *
17198606 CTTGGAAAAATGGGATTTGTTTTATGCTTATA
1 CTTGGAAAAATGGGATTTGATTTATGCTTACA
* * *
17198638 CTTGGAAAAGTGGGATTTGAATTATGCTTACG
1 CTTGGAAAAATGGGATTTGATTTATGCTTACA
* *
17198670 TTTGGAAAAATGGGATTTGATTTAAGCTTACA
1 CTTGGAAAAATGGGATTTGATTTATGCTTACA
17198702 CTTGGAAAA
1 CTTGGAAAA
17198711 GCAAGTTCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (32 bp):
CTTGGAAAAATGGGATTTGATTTATGCTTACA
Found at i:17200187 original size:2 final size:2
Alignment explanation
Indices: 17200182--17200230 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
17200172 CAAACCTCTC
* *
17200182 TA TA TA GTA AA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17200225 TA TA TA
1 TA TA TA
17200231 AACACGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:17200335 original size:36 final size:38
Alignment explanation
Indices: 17200295--17200392 Score: 123
Period size: 36 Copynumber: 2.7 Consensus size: 38
17200285 TAGCCGGAGT
17200295 CATCGTGTGCACCCCCACATTGTGCACA-A-CTAATAC
1 CATCGTGTGCACCCCCACATTGTGCACATAGCTAATAC
* *
17200331 CATCGTGTGCACCCCCACA-T-TGCATATAGCTAATGC
1 CATCGTGTGCACCCCCACATTGTGCACATAGCTAATAC
* * *
17200367 CATCATGTGCACCCCTACATCGTGCA
1 CATCGTGTGCACCCCCACATTGTGCA
17200393 TAGGCAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.09
35 2 0.04
36 42 0.79
38 4 0.08
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (38 bp):
CATCGTGTGCACCCCCACATTGTGCACATAGCTAATAC
Found at i:17200452 original size:34 final size:34
Alignment explanation
Indices: 17200414--17200528 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
17200404 ATCATCAGTG
17200414 TGTGCACTCACACAGCACACCACTATCACCGTCA
1 TGTGCACTCACACAGCACACCACTATCACCGTCA
* * * * *
17200448 TGTGCACTTCCACACCGCACAAGGCATATATCATCAGT-G
1 TGTGCAC-T-CACACAGCAC-A-CCA-CTATCA-CCGTCA
* *
17200487 TGTGCACTCACATAGCACACCACTATCATCGTCA
1 TGTGCACTCACACAGCACACCACTATCACCGTCA
17200521 TGTGCACT
1 TGTGCACT
17200529 TCCACACCAC
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
33 2 0.03
34 20 0.32
35 3 0.05
36 10 0.16
37 9 0.15
38 3 0.05
39 12 0.19
40 3 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (34 bp):
TGTGCACTCACACAGCACACCACTATCACCGTCA
Found at i:17200495 original size:73 final size:75
Alignment explanation
Indices: 17200394--17200541 Score: 255
Period size: 73 Copynumber: 2.0 Consensus size: 75
17200384 CATCGTGCAT
17200394 AGGCAATATCATCATCAGTGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCC
1 AGGCAATATCATCATCAGTGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCC
*
17200459 ACACCGCACA
66 ACACCACACA
* *
17200469 AGGC-ATAT-ATCATCAGTGTGTGCACTCACATAGCACACCACTATCATCGTCATGTGCACTTCC
1 AGGCAATATCATCATCAGTGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCC
17200532 ACACCACACA
66 ACACCACACA
17200542 CGCACGGTCA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 62 0.89
74 4 0.06
75 4 0.06
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (75 bp):
AGGCAATATCATCATCAGTGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCC
ACACCACACA
Found at i:17202851 original size:36 final size:36
Alignment explanation
Indices: 17202782--17202918 Score: 147
Period size: 36 Copynumber: 3.9 Consensus size: 36
17202772 GCTTGAACAT
* * * *
17202782 GTGTGGTATTCTTACCCTCACATTTAGGTTTTATTC
1 GTGTGGTATTCTTACCCCCACATCTGGGCTTTATTC
** *
17202818 GTACGGTATTCTTACCCCCATATCTGGGCTTTATTC
1 GTGTGGTATTCTTACCCCCACATCTGGGCTTTATTC
*
17202854 GTGTGGTA---TT-CCCTCACATCTGGGCTTTATTC
1 GTGTGGTATTCTTACCCCCACATCTGGGCTTTATTC
* * *
17202886 GTGTGGTATTTTTTCCCCCACATCTGGGATTTA
1 GTGTGGTATTCTTACCCCCACATCTGGGCTTTA
17202919 ATAATTATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
32 28 0.33
33 2 0.02
35 2 0.02
36 52 0.62
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (36 bp):
GTGTGGTATTCTTACCCCCACATCTGGGCTTTATTC
Found at i:17213640 original size:2 final size:2
Alignment explanation
Indices: 17213635--17213659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17213625 TATATATATG
17213635 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
17213660 TACATTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17214402 original size:2 final size:2
Alignment explanation
Indices: 17214395--17214419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17214385 TACAAGAATA
17214395 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17214420 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17218213 original size:60 final size:60
Alignment explanation
Indices: 17218136--17218318 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 60
17218126 TATTTGATAA
* * * * ** * *
17218136 TAAAGGGTGACCTGAAGCCTTA-ACTTATATTTAGTGATGTAGGGAGTTCTCACAAGTAGG
1 TAAAGGGGGACTTGAAGCC-CAGACTCATATTTAGTGACATAGGGAATTCCCACAAGTAGG
* *
17218196 TAAAGGGGGACTTGAAGCCCAGACTCATATTTAGTGACATGGGGAATTCCCACGAGTAGG
1 TAAAGGGGGACTTGAAGCCCAGACTCATATTTAGTGACATAGGGAATTCCCACAAGTAGG
* * * * * * * **
17218256 TAAAAGGGGACTTGAAACCCCGACTCA-ATTTAATGGCATGGGGAGTTCCCATGAGTAGG
1 TAAAGGGGGACTTGAAGCCCAGACTCATATTTAGTGACATAGGGAATTCCCACAAGTAGG
17218315 TAAA
1 TAAA
17218319 AGGGTTCCTA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
59 33 0.31
60 72 0.69
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (60 bp):
TAAAGGGGGACTTGAAGCCCAGACTCATATTTAGTGACATAGGGAATTCCCACAAGTAGG
Found at i:17218315 original size:59 final size:60
Alignment explanation
Indices: 17218190--17218322 Score: 196
Period size: 59 Copynumber: 2.2 Consensus size: 60
17218180 AGTTCTCACA
* * *
17218190 AGTAGGTAAAGGGGGACTTGAAGCCCAGACTCATATTTAGTGACATGGGGAATTCCCACG
1 AGTAGGTAAAAGGGGACTTGAAACCCAGACTCATATTTAATGACATGGGGAATTCCCACG
* * * *
17218250 AGTAGGTAAAAGGGGACTTGAAACCCCGACTCA-ATTTAATGGCATGGGGAGTTCCCATG
1 AGTAGGTAAAAGGGGACTTGAAACCCAGACTCATATTTAATGACATGGGGAATTCCCACG
17218309 AGTAGGTAAAAGGG
1 AGTAGGTAAAAGGG
17218323 TTCCTAAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
59 36 0.55
60 30 0.45
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.21
Consensus pattern (60 bp):
AGTAGGTAAAAGGGGACTTGAAACCCAGACTCATATTTAATGACATGGGGAATTCCCACG
Found at i:17218397 original size:60 final size:60
Alignment explanation
Indices: 17218162--17218434 Score: 245
Period size: 60 Copynumber: 4.6 Consensus size: 60
17218152 GCCTTAACTT
* * *
17218162 ATATTTAGT-G-ATGTAGGGAGTTCTCACAAGTAGGTAAAGGGGGACTTGAAG-CCCAGACTC
1 ATATTTAGTGGCATG-A-GGAGTTCCCACGAGTAGGTAAAAGGGGACTTGAAGACCC-GACTC
* * *
17218222 ATATTTAGTGACATGGGGAATTCCCACGAGTAGGTAAAAGGGGACTTGAA-ACCCCGACTC
1 ATATTTAGTGGCATGAGGAGTTCCCACGAGTAGGTAAAAGGGGACTTGAAGA-CCCGACTC
* * * ** * * *
17218282 A-ATTTAATGGCATGGGGAGTTCCCATGAGTAGGTAAAAGGGTTCCTAAAGTCCCGACTC
1 ATATTTAGTGGCATGAGGAGTTCCCACGAGTAGGTAAAAGGGGACTTGAAGACCCGACTC
* ** * * * *
17218341 ATATTTGGTGGTGTGAGGAGTTTCCATGAGTAGGT-AAAGGGAAACTTGAAGACCCGACTG
1 ATATTTAGTGGCATGAGGAGTTCCCACGAGTAGGTAAAAGGG-GACTTGAAGACCCGACTC
* *
17218401 ATATTTGGTGGCATGAGGAG-TCTCACGAGTAGGT
1 ATATTTAGTGGCATGAGGAGTTCCCACGAGTAGGT
17218435 GTTGCTATTA
Statistics
Matches: 174, Mismatches: 32, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
59 66 0.38
60 102 0.59
61 3 0.02
62 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (60 bp):
ATATTTAGTGGCATGAGGAGTTCCCACGAGTAGGTAAAAGGGGACTTGAAGACCCGACTC
Done.