Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 85 of 100
Found at i:17169638 original size:35 final size:35
Alignment explanation
Indices: 17169592--17169722 Score: 133
Period size: 35 Copynumber: 3.8 Consensus size: 35
17169582 TTGTAAATGA
* **
17169592 TTCAAGATTCTCTGAGGTTCTAGATTCACAAAGAT
1 TTCAAGTTTCTCAAAGGTTCTAGATTCACAAAGAT
* * *
17169627 TTCAAGTTTCTCAAAGGTTTTAGATTCATAAAAAT
1 TTCAAGTTTCTCAAAGGTTCTAGATTCACAAAGAT
* ** *
17169662 TTCAA-TTT-TAAAGAGGTTCTAGATTTGCAAAGGT
1 TTCAAGTTTCTCAA-AGGTTCTAGATTCACAAAGAT
17169696 TTCAAGTTTCAT-AAAGGTTCTAGATTC
1 TTCAAGTTTC-TCAAAGGTTCTAGATTC
17169723 GCAAGAATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 3 0.04
34 23 0.29
35 49 0.63
36 2 0.03
37 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (35 bp):
TTCAAGTTTCTCAAAGGTTCTAGATTCACAAAGAT
Found at i:17169793 original size:34 final size:33
Alignment explanation
Indices: 17169750--17169851 Score: 98
Period size: 34 Copynumber: 3.0 Consensus size: 33
17169740 ACAAAAATCC
*
17169750 AAAGATTCGTAAGAATTCATATTCATAAGACTTT
1 AAAGATTCGTAAGAATTCATATTCAAAAGA-TTT
* * *
17169784 AAAGATTCGTAAAAATTTCAGATTCACAAGGATTT
1 AAAGATTCGTAAGAA-TTCATATTCA-AAAGATTT
* * *
17169819 -AAGTTTTGTAAGTACTTCATATTCAAAAGATTT
1 AAAGATTCGTAAG-AATTCATATTCAAAAGATTT
17169852 TGTTAGTGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
33 7 0.13
34 32 0.58
35 13 0.24
36 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (33 bp):
AAAGATTCGTAAGAATTCATATTCAAAAGATTT
Found at i:17169963 original size:23 final size:22
Alignment explanation
Indices: 17169937--17170047 Score: 69
Period size: 23 Copynumber: 4.9 Consensus size: 22
17169927 TCACCTCTAG
17169937 AATTCAAAGATTCTCATTTGAAA
1 AATTCAAAGATTCTCATTT-AAA
** * * *
17169960 AATTTTAAGGTTTTACATCTAAA
1 AATTCAAAGATTCT-CATTTAAA
* * *
17169983 ATTTCAAAGATTCACATTAAAAA
1 AATTCAAAGATTCTCATT-TAAA
** **
17170006 AATTTTAAGAATTCTCATCCAAA
1 AATTCAAAG-ATTCTCATTTAAA
*
17170029 ATTTCAAAGATTCTCATTT
1 AATTCAAAGATTCTCATTT
17170048 TAGAGATTTA
Statistics
Matches: 61, Mismatches: 24, Indels: 7
0.66 0.26 0.08
Matches are distributed among these distances:
22 11 0.18
23 39 0.64
24 11 0.18
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTCAAAGATTCTCATTTAAA
Found at i:17170007 original size:46 final size:46
Alignment explanation
Indices: 17169939--17170046 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
17169929 ACCTCTAGAA
** * * *
17169939 TTCAAAGATTCTCATTTGAAAAATTTTAAG-GTTTTACATCTAAAAT
1 TTCAAAGATTCTCATTAAAAAAATTTTAAGAATTCT-CATCCAAAAT
*
17169985 TTCAAAGATTCACATTAAAAAAATTTTAAGAATTCTCATCCAAAAT
1 TTCAAAGATTCTCATTAAAAAAATTTTAAGAATTCTCATCCAAAAT
17170031 TTCAAAGATTCTCATT
1 TTCAAAGATTCTCATT
17170047 TTAGAGATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 51 0.94
47 3 0.06
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (46 bp):
TTCAAAGATTCTCATTAAAAAAATTTTAAGAATTCTCATCCAAAAT
Found at i:17170042 original size:22 final size:22
Alignment explanation
Indices: 17169939--17170045 Score: 65
Period size: 22 Copynumber: 4.7 Consensus size: 22
17169929 ACCTCTAGAA
*
17169939 TTCAAAGATTCTCATTTGAAAAAT
1 TTCAAAGATTCTCA--TCAAAAAT
* * * *
17169963 TT-TAAGGTTTTACATCTAAAAT
1 TTCAAAGATTCT-CATCAAAAAT
* *
17169985 TTCAAAGATTCACATTAAAAAAAT
1 TTCAAAGATTCTCA-T-CAAAAAT
* *
17170009 TT-TAAGAATTCTCATCCAAAAT
1 TTCAAAG-ATTCTCATCAAAAAT
17170031 TTCAAAGATTCTCAT
1 TTCAAAGATTCTCAT
17170046 TTTAGAGATT
Statistics
Matches: 61, Mismatches: 16, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
22 25 0.41
23 19 0.31
24 17 0.28
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (22 bp):
TTCAAAGATTCTCATCAAAAAT
Found at i:17170173 original size:23 final size:23
Alignment explanation
Indices: 17170105--17170173 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
17170095 CGGCTTCACA
17170105 TTCAAAGATTCTCATTCGAAAAAAT
1 TTCAAAGATTCTCATTCG--AAAAT
* * * *
17170130 TT-GAGGATT-TCACATCTAAAAT
1 TTCAAAGATTCTCA-TTCGAAAAT
17170152 TTCAAAGATTCTCATTCGAAAA
1 TTCAAAGATTCTCATTCGAAAA
17170174 GCTCATTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
22 7 0.21
23 14 0.42
24 10 0.30
25 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (23 bp):
TTCAAAGATTCTCATTCGAAAAT
Found at i:17176020 original size:9 final size:9
Alignment explanation
Indices: 17175991--17176033 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
17175981 ATAGATAATC
17175991 AAATAAATA
1 AAATAAATA
* *
17176000 AAAT-ATTT
1 AAATAAATA
17176008 AAATAAATA
1 AAATAAATA
17176017 AAATAAAATA
1 AAAT-AAATA
17176027 AAATAAA
1 AAATAAA
17176034 CACTTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.21
9 13 0.46
10 9 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAATAAATA
Found at i:17181671 original size:18 final size:18
Alignment explanation
Indices: 17181637--17181671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17181627 GTATAGGTTT
*
17181637 CATACATTGCATTCATTG
1 CATACATTGCATGCATTG
*
17181655 CATACATTTCATGCATT
1 CATACATTGCATGCATT
17181672 ATATGTATCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.40
Consensus pattern (18 bp):
CATACATTGCATGCATTG
Found at i:17183332 original size:20 final size:21
Alignment explanation
Indices: 17183293--17183334 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17183283 TTTTTTTCTT
17183293 TGGTATTTTATTTATTTTTTA
1 TGGTATTTTATTTATTTTTTA
17183314 TGGT-TTTTATTTTTATTTTTT
1 TGGTATTTTA--TTTATTTTTT
17183335 TGAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (21 bp):
TGGTATTTTATTTATTTTTTA
Found at i:17185454 original size:30 final size:30
Alignment explanation
Indices: 17185381--17185454 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
17185371 ATTGAAAATC
*
17185381 AAGAGTTTATTTGAATACAAATTAAAGGTT
1 AAGAGTTTATTTGGATACAAATTAAAGGTT
* **
17185411 AAAAGTTTATTTGGATGTAAATTAAAGGTT
1 AAGAGTTTATTTGGATACAAATTAAAGGTT
*
17185441 AAGAGATTATTTGG
1 AAGAGTTTATTTGG
17185455 GTGCAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (30 bp):
AAGAGTTTATTTGGATACAAATTAAAGGTT
Found at i:17191530 original size:17 final size:18
Alignment explanation
Indices: 17191510--17191544 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
17191500 AACTTTTAAA
17191510 TTTTTA-AATTAT-TTAT
1 TTTTTATAATTATATTAT
17191526 TTTTTATAATTATATTAT
1 TTTTTATAATTATATTAT
17191544 T
1 T
17191545 AAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTATATTAT
Found at i:17191833 original size:15 final size:15
Alignment explanation
Indices: 17191813--17191842 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17191803 ATATTTTATT
17191813 ACATGAAATTAAAAC
1 ACATGAAATTAAAAC
17191828 ACATGAAATTAAAAC
1 ACATGAAATTAAAAC
17191843 TAAATATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
ACATGAAATTAAAAC
Found at i:17192331 original size:14 final size:14
Alignment explanation
Indices: 17192312--17192351 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
17192302 ATATTTATTC
*
17192312 AAATTTAAATAATT
1 AAATTTAAATAAAT
17192326 AAATTTAAA-AAAT
1 AAATTTAAATAAAT
17192339 AATATTTAAATAA
1 AA-ATTTAAATAA
17192352 GCATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 16 0.70
15 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTTAAATAAAT
Found at i:17192630 original size:3 final size:3
Alignment explanation
Indices: 17192622--17192647 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17192612 TTGAATTAAC
17192622 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
17192648 CACCAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17193509 original size:8 final size:8
Alignment explanation
Indices: 17193493--17193539 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
17193483 TTATTTTATT
17193493 TTTATTTG
1 TTTATTTG
*
17193501 TTTAATTG
1 TTTATTTG
*
17193509 TTTTATTTA
1 -TTTATTTG
17193518 TTTATTTG
1 TTTATTTG
17193526 TTTGA-TTG
1 TTT-ATTTG
17193534 TTTATT
1 TTTATT
17193540 ATTCTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
7 1 0.03
8 24 0.75
9 7 0.22
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (8 bp):
TTTATTTG
Found at i:17193514 original size:17 final size:17
Alignment explanation
Indices: 17193492--17193537 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
17193482 TTTATTTTAT
17193492 TTTTATTTGTTTAATTG
1 TTTTATTTGTTTAATTG
* *
17193509 TTTTATTTATTTATTTG
1 TTTTATTTGTTTAATTG
*
17193526 TTTGA-TTGTTTA
1 TTTTATTTGTTTA
17193538 TTATTCTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (17 bp):
TTTTATTTGTTTAATTG
Found at i:17193525 original size:25 final size:23
Alignment explanation
Indices: 17193486--17193536 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
17193476 AAGTATTTTA
17193486 TTTTATTTTTATTTGTTTAATTG
1 TTTTATTTTTATTTGTTTAATTG
*
17193509 TTTTATTTATTTATTTGTTTGATTG
1 TTTTA-TT-TTTATTTGTTTAATTG
17193534 TTT
1 TTT
17193537 ATTATTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 18 0.72
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATTTGTTTAATTG
Found at i:17194177 original size:13 final size:13
Alignment explanation
Indices: 17194159--17194183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17194149 TTTGATTTAA
17194159 ATTAAAATATAAC
1 ATTAAAATATAAC
17194172 ATTAAAATATAA
1 ATTAAAATATAA
17194184 AAACAAGTGA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAATATAAC
Found at i:17204241 original size:32 final size:31
Alignment explanation
Indices: 17204200--17204275 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
17204190 CAAAAATCCA
*
17204200 CTTTGAGGGTC-AGACATTCTTGTTCTTGAATG
1 CTTTAAGGGTCTAGACA--CTTGTTCTTGAATG
* *
17204232 CTTTAAGGGTCTTTGAGACTTGTTCTTGAATG
1 CTTTAAGGGTC-TAGACACTTGTTCTTGAATG
*
17204264 CTTCAAGGGTCT
1 CTTTAAGGGTCT
17204276 TGTTGATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 1 0.03
32 34 0.89
34 3 0.08
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (31 bp):
CTTTAAGGGTCTAGACACTTGTTCTTGAATG
Found at i:17204291 original size:32 final size:32
Alignment explanation
Indices: 17204218--17204293 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
17204208 GTCAGACATT
* *
17204218 CTTGTTCTTGAATGCTTTAAGGGTCTTTGAGA
1 CTTGATCTTGAATGCTTCAAGGGTCTTTGAGA
* *
17204250 CTTGTTCTTGAATGCTTCAAGGGTC-TTGTTGA
1 CTTGATCTTGAATGCTTCAAGGGTCTTTG-AGA
*
17204282 TTTGATCTTGAA
1 CTTGATCTTGAA
17204294 CAAATGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 3 0.08
32 36 0.92
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45
Consensus pattern (32 bp):
CTTGATCTTGAATGCTTCAAGGGTCTTTGAGA
Found at i:17206834 original size:12 final size:12
Alignment explanation
Indices: 17206817--17206849 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
17206807 ATGTTATTTA
17206817 TATATATTTATG
1 TATATATTTATG
17206829 TATATATTTATG
1 TATATATTTATG
17206841 TATATATTT
1 TATATATTT
17206850 TGCCTAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (12 bp):
TATATATTTATG
Found at i:17214665 original size:24 final size:25
Alignment explanation
Indices: 17214619--17214665 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17214609 GGTGCAGCGA
***
17214619 TTGATCAAAGATGGAATGGTAATTT
1 TTGATCAAAGATGGAAAAATAATTT
17214644 TTGATCAAAGA-GGAAAAATAAT
1 TTGATCAAAGATGGAAAAATAAT
17214666 ACATAATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (25 bp):
TTGATCAAAGATGGAAAAATAATTT
Found at i:17215418 original size:10 final size:9
Alignment explanation
Indices: 17215404--17215472 Score: 63
Period size: 10 Copynumber: 7.6 Consensus size: 9
17215394 AAAAGGTCCT
17215404 AAAAAAAGA
1 AAAAAAAGA
17215413 AGAAAAAAG-
1 A-AAAAAAGA
17215422 AAAAAAAGA
1 AAAAAAAGA
17215431 AAAAACAAGA
1 AAAAA-AAGA
**
17215441 TAAAGCAAG-
1 -AAAAAAAGA
17215450 -AAAAAAGA
1 AAAAAAAGA
17215458 AAAAAAGAGA
1 AAAAAA-AGA
17215468 AAAAA
1 AAAAA
17215473 TGAATCACGT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 5 0.10
8 7 0.14
9 12 0.24
10 22 0.45
11 3 0.06
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:17216985 original size:22 final size:22
Alignment explanation
Indices: 17216951--17217009 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
17216941 GAATATTTTG
*
17216951 ATGAAAATTTTTGAGTTCTC-AA
1 ATGAGAATTTTTGAGTT-TCAAA
*
17216973 ATGAGAATCTTTGAGTTTCAAA
1 ATGAGAATTTTTGAGTTTCAAA
*
17216995 ATAAGAATTTTTGAG
1 ATGAGAATTTTTGAG
17217010 GTGTGAAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (22 bp):
ATGAGAATTTTTGAGTTTCAAA
Found at i:17217669 original size:41 final size:42
Alignment explanation
Indices: 17217612--17217858 Score: 302
Period size: 41 Copynumber: 5.9 Consensus size: 42
17217602 GTCAAGGAGT
* * *
17217612 AATTTATTTTTC-AAAGTTATGGTGCCTCTGTTTAGAGGAAC
1 AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
*
17217653 AATTTATTTTTC-AAAGTTGTGGTACCTCTGTTTAGAAGAGC
1 AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* * *
17217694 AATTTATTTTTCCAAAAGTTGTGATTACCTCTGTTTAGAGGAGC
1 AATTTATTTTT-CAAAAGTTGTG-GTGCCTCTGTTTAGAAGAGC
*
17217738 AATTTATTTTTC-AAAGTTGTGGTGCTTCTGTTTAGAAGAGC
1 AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* * * *
17217779 AATTTATTTTTTCAAAAATTGTGGTGCCTCTATTTAAAAAAGC
1 AATTTA-TTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* * * *
17217822 AATTTACTTTTCAAAAGTTATTGAGCCTCTGTTTAGA
1 AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGA
17217859 GGAGTTTTGT
Statistics
Matches: 179, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
41 70 0.39
42 40 0.22
43 40 0.22
44 29 0.16
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (42 bp):
AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
Found at i:17217752 original size:85 final size:83
Alignment explanation
Indices: 17217612--17217858 Score: 309
Period size: 85 Copynumber: 2.9 Consensus size: 83
17217602 GTCAAGGAGT
* *
17217612 AATTTATTTTTC-AAAGTTATGGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTTGTGGT
1 AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGT
17217676 ACCTCTGTTTAGAAGAGC
66 ACCTCTGTTTAGAAGAGC
* *
17217694 AATTTATTTTTCCAAAAGTTGTGATTACCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTG
1 AATTTATTTTT-CAAAAGTTGTG-GTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTG
* *
17217759 GTGCTTCTGTTTAGAAGAGC
64 GTACCTCTGTTTAGAAGAGC
* * * ** * * *
17217779 AATTTATTTTTTCAAAAATTGTGGTGCCTCTATTTAAAAAAGCAATTTACTTTTCAAAAGTTATT
1 AATTTA-TTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTC-AAAGTTGTG
17217844 G-AGCCTCTGTTTAGA
64 GTA-CCTCTGTTTAGA
17217859 GGAGTTTTGT
Statistics
Matches: 141, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
82 11 0.08
83 1 0.01
84 33 0.23
85 91 0.65
86 5 0.04
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (83 bp):
AATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGT
ACCTCTGTTTAGAAGAGC
Found at i:17217851 original size:126 final size:126
Alignment explanation
Indices: 17217606--17217862 Score: 351
Period size: 126 Copynumber: 2.0 Consensus size: 126
17217596 ATGATTGTCA
* * *
17217606 AGGAGTAATTTATTTTTCAAAGTTATGGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTT
1 AGGAGCAATTTATTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAACAATTTATTTTTCAAAATT
* * * *
17217671 GTGGTACCTCTGTTTAGAAGAGCAATTTATTTTTCCAAAAGTTGTGATTACCTCTGTTTAG
66 GTGGTACCTCTATTTAAAAAAGCAATTTACTTTTCCAAAAGTTGTGATTACCTCTGTTTAG
* * *
17217732 AGGAGCAATTTATTTTTCAAAGTTGTGGTGCTTCTGTTTAGAAGAGCAATTTATTTTTTCAAAAA
1 AGGAGCAATTTATTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAACAATTTA-TTTTTC-AAAA
*
17217797 TTGTGGTGCCTCTATTTAAAAAAGCAATTTACTTTT-CAAAAG-T-T-ATTGAGCCTCTGTTTAG
64 TTGTGGTACCTCTATTTAAAAAAGCAATTTACTTTTCCAAAAGTTGTGATT-A-CCTCTGTTTAG
17217858 AGGAG
1 AGGAG
17217863 TTTTGTTTAT
Statistics
Matches: 116, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
124 3 0.03
125 2 0.02
126 65 0.56
127 12 0.10
128 34 0.29
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (126 bp):
AGGAGCAATTTATTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAACAATTTATTTTTCAAAATT
GTGGTACCTCTATTTAAAAAAGCAATTTACTTTTCCAAAAGTTGTGATTACCTCTGTTTAG
Found at i:17217947 original size:44 final size:44
Alignment explanation
Indices: 17217824--17217998 Score: 201
Period size: 44 Copynumber: 4.0 Consensus size: 44
17217814 AAAAAAGCAA
*
17217824 TTTACTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
1 TTTATTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
** * *
17217868 TTTATTTTTTC-AAA-TTATCAAGCCTCTATTTAGAGGAATTTTG
1 TTTA-TTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
* * **
17217911 TTTATTTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCCTTG
1 TTTATTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
* * * * *
17217955 TTTATTTTTTAAAAGTCATTGAGCCTCTGATTAGAAGAGCTTTG
1 TTTATTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
17217999 ATCAAGTTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
42 6 0.06
43 32 0.29
44 66 0.61
45 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (44 bp):
TTTATTTTTCAAAAGTTATTGAGCCTCTGTTTAGAGGAGTTTTG
Found at i:17218248 original size:3 final size:3
Alignment explanation
Indices: 17218242--17218287 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
17218232 TTTTTTCCAT
*
17218242 TTA TTA TTTA TTT TTA TTA TTA TTA TTA TTA TTA TCT- TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
17218288 GTTTTTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 33 0.87
4 4 0.11
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:17218615 original size:11 final size:12
Alignment explanation
Indices: 17218600--17218631 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17218590 TTGGTTTTTT
17218600 TTTTCTAGAAAA
1 TTTTCTAGAAAA
17218612 -TTTCTA-AAAA
1 TTTTCTAGAAAA
17218622 TTTTCTAGAA
1 TTTTCTAGAA
17218632 TGCGATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (12 bp):
TTTTCTAGAAAA
Found at i:17218788 original size:22 final size:23
Alignment explanation
Indices: 17218763--17218814 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
17218753 AGAGAGAGGG
17218763 GAGAAAAAAAGGGAGAAGA-AGA
1 GAGAAAAAAAGGGAGAAGAGAGA
*
17218785 GAGAAAAAAATGGAGAAGAGAGA
1 GAGAAAAAAAGGGAGAAGAGAGA
17218808 GAGAAAA
1 GAGAAAA
17218815 GAAGAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (23 bp):
GAGAAAAAAAGGGAGAAGAGAGA
Found at i:17218820 original size:19 final size:18
Alignment explanation
Indices: 17218776--17218820 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
17218766 AAAAAAAGGG
17218776 AGAAGAAGAGAGAAAAAA
1 AGAAGAAGAGAGAAAAAA
* *
17218794 ATGGAGAAGAGAGAGAGAAA
1 A-GAAGAAGAGAGA-AAAAA
17218814 AGAAGAA
1 AGAAGAA
17218821 AAATCTGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (18 bp):
AGAAGAAGAGAGAAAAAA
Found at i:17219171 original size:14 final size:15
Alignment explanation
Indices: 17219145--17219174 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17219135 TGATTTAATT
17219145 TAATAAGAAATAAAA
1 TAATAAGAAATAAAA
17219160 TAATAA-AAATAAAA
1 TAATAAGAAATAAAA
17219174 T
1 T
17219175 TTTGGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAATAAGAAATAAAA
Found at i:17220258 original size:19 final size:19
Alignment explanation
Indices: 17220234--17220274 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17220224 ATCAATGAAG
*
17220234 ATATCACACTTTTAACTAT
1 ATATCACACTTCTAACTAT
*
17220253 ATATCACACTTCTCACTAT
1 ATATCACACTTCTAACTAT
17220272 ATA
1 ATA
17220275 ATTAATGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATCACACTTCTAACTAT
Found at i:17225920 original size:26 final size:25
Alignment explanation
Indices: 17225876--17225926 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
17225866 GTTTGGTTTG
*
17225876 AGAAAATATTTTTATTTTTACTTTTT
1 AGAAAATACTTTTATTTTT-CTTTTT
17225902 AGAAAATAGCTTTTA-TTTTCTTTTT
1 AGAAAATA-CTTTTATTTTTCTTTTT
17225927 TTGTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (25 bp):
AGAAAATACTTTTATTTTTCTTTTT
Found at i:17226175 original size:12 final size:12
Alignment explanation
Indices: 17226128--17226189 Score: 61
Period size: 13 Copynumber: 5.0 Consensus size: 12
17226118 AAAATTATTA
*
17226128 ATTAATTATAAT
1 ATTAATAATAAT
*
17226140 AGTAAATAATAAT
1 A-TTAATAATAAT
*
17226153 AGTAATAAATAAT
1 ATTAAT-AATAAT
* *
17226166 ATTATTAATATT
1 ATTAATAATAAT
17226178 ATTAATAATAAT
1 ATTAATAATAAT
17226190 GATAATGTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 19 0.49
13 20 0.51
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:17229063 original size:9 final size:9
Alignment explanation
Indices: 17229051--17229092 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
17229041 AAAAAAAAGC
*
17229051 AAAACAAAA
1 AAAATAAAA
17229060 AAAATAAAA
1 AAAATAAAA
17229069 AAAATAAAAA
1 AAAAT-AAAA
17229079 AAAAGTAAAA
1 AAAA-TAAAA
17229089 AAAA
1 AAAA
17229093 ATCTCTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 13 0.43
10 16 0.53
11 1 0.03
ACGTcount: A:0.88, C:0.02, G:0.02, T:0.07
Consensus pattern (9 bp):
AAAATAAAA
Found at i:17229685 original size:116 final size:118
Alignment explanation
Indices: 17229551--17229790 Score: 448
Period size: 117 Copynumber: 2.1 Consensus size: 118
17229541 AAAAGATTTA
17229551 CCTTGAAAATGAAAATTCAGGGC-AAAAAAAAAGGGTGAATAAAGTTGTTGAAATTGATGCCAGA
1 CCTTGAAAATGAAAATTCAGGGCAAAAAAAAAAGGGTGAATAAAGTTGTTGAAATTGATGCCAGA
*
17229615 TATATTTTTT-AAAAAAAGCAAAGAAAGAAAGTCAGAGAATGCTCCTCGGGAT
66 TATATTTTTTAAAAAAAAGCAAAGAAAGAAAGTCAGAGAATGCTCCTCGAGAT
17229667 CCTTGAAAATGAAAATTCAGGGCAAAAAAAAAAGGGTGAATAAAGTTGTTGAAATTGATGCCAGA
1 CCTTGAAAATGAAAATTCAGGGCAAAAAAAAAAGGGTGAATAAAGTTGTTGAAATTGATGCCAGA
*
17229732 TATTTTTTTTAAAAAAAAGCAAAGAAAGAAAGTCAGAGAATGCTCCTCGAGAT
66 TATATTTTTTAAAAAAAAGCAAAGAAAGAAAGTCAGAGAATGCTCCTCGAGAT
17229785 CCTTGA
1 CCTTGA
17229791 CCTAATTACA
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
116 23 0.19
117 50 0.42
118 47 0.39
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (118 bp):
CCTTGAAAATGAAAATTCAGGGCAAAAAAAAAAGGGTGAATAAAGTTGTTGAAATTGATGCCAGA
TATATTTTTTAAAAAAAAGCAAAGAAAGAAAGTCAGAGAATGCTCCTCGAGAT
Found at i:17230304 original size:65 final size:65
Alignment explanation
Indices: 17230200--17230331 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
17230190 TCAAAAAGTA
17230200 ATGGTTAGTTTTGACACACATTGAAGTATCACGTTTTCAATAAAAGAAGAGTATTTTAGAAAATT
1 ATGGTTAGTTTTGACACACATTGAAGTATCACGTTTTCAATAAAAGAAGAGTATTTTAGAAAATT
17230265 ATGGTTAGTTTTGACACACATTGAAGTATCACGTTTTCAATAAAAGAAGAGTATTTTAGAAAATT
1 ATGGTTAGTTTTGACACACATTGAAGTATCACGTTTTCAATAAAAGAAGAGTATTTTAGAAAATT
17230330 AT
1 AT
17230332 CTCTTTTGTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (65 bp):
ATGGTTAGTTTTGACACACATTGAAGTATCACGTTTTCAATAAAAGAAGAGTATTTTAGAAAATT
Found at i:17231022 original size:18 final size:18
Alignment explanation
Indices: 17230974--17231022 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
17230964 ATTCATATTC
* *
17230974 TTTCATTTGCATTGACAT
1 TTTCATTAGCATCGACAT
*
17230992 TTGCATTCA-CATCGACAT
1 TTTCATT-AGCATCGACAT
17231010 TTTCATTAGCATC
1 TTTCATTAGCATC
17231023 ATTTGATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTCATTAGCATCGACAT
Found at i:17231372 original size:22 final size:22
Alignment explanation
Indices: 17231347--17231389 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17231337 ATTGATTCTT
17231347 TAAGACCTCTGAGCATAATTTC
1 TAAGACCTCTGAGCATAATTTC
* *
17231369 TAAGACCTCTGGGTATAATTT
1 TAAGACCTCTGAGCATAATTT
17231390 TGACTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (22 bp):
TAAGACCTCTGAGCATAATTTC
Found at i:17231465 original size:22 final size:22
Alignment explanation
Indices: 17231416--17231471 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
17231406 ATTAATCAAT
* *
17231416 TCTTTAAGACTTTTAGACATGA
1 TCTTTAAGACCTTTAGACATAA
* * *
17231438 TTTTTAAGACCTTTGGGCATAA
1 TCTTTAAGACCTTTAGACATAA
*
17231460 TCTTTAGGACCT
1 TCTTTAAGACCT
17231472 CCGGATATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (22 bp):
TCTTTAAGACCTTTAGACATAA
Found at i:17231578 original size:22 final size:22
Alignment explanation
Indices: 17231552--17231622 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
17231542 GTCAATTCTA
*
17231552 TAAGACTTCTGAGCATGAT-TT
1 TAAGACTTCTGAGCATAATCTT
*
17231573 CTAAGACCTCTGAGCATAATCTT
1 -TAAGACTTCTGAGCATAATCTT
17231596 TAAGATCTT-TGAGCATAATCTT
1 TAAGA-CTTCTGAGCATAATCTT
17231618 TAAGA
1 TAAGA
17231623 TTTTCAGGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 40 0.91
23 4 0.09
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (22 bp):
TAAGACTTCTGAGCATAATCTT
Found at i:17231623 original size:22 final size:22
Alignment explanation
Indices: 17231552--17231636 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
17231542 GTCAATTCTA
*
17231552 TAAGA-CTTCTGAGCATGAT-TT
1 TAAGATCTT-TGAGCATAATCTT
* *
17231573 CTAAGACCTCTGAGCATAATCTT
1 -TAAGATCTTTGAGCATAATCTT
17231596 TAAGATCTTTGAGCATAATCTT
1 TAAGATCTTTGAGCATAATCTT
*
17231618 TAAGAT-TTTCAGGCATAAT
1 TAAGATCTTTGA-GCATAAT
17231637 TTTGAATCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 4 0.07
22 47 0.85
23 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (22 bp):
TAAGATCTTTGAGCATAATCTT
Found at i:17231793 original size:22 final size:21
Alignment explanation
Indices: 17231742--17231806 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
17231732 ATCGATTTTG
*
17231742 TAAGACCTCCAGACATGATTTC
1 TAAGACCTCCAG-CATAATTTC
*
17231764 TAAAACCTCCGAGCATAATCTT-
1 TAAGACCTCC-AGCATAAT-TTC
*
17231786 TAAGACCTCTAAGCATAATTT
1 TAAGACCTC-CAGCATAATTT
17231807 TGAATTACGG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 2 0.06
22 30 0.83
23 4 0.11
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (21 bp):
TAAGACCTCCAGCATAATTTC
Found at i:17231856 original size:132 final size:132
Alignment explanation
Indices: 17231684--17232068 Score: 433
Period size: 132 Copynumber: 2.9 Consensus size: 132
17231674 TCGATTCATT
* *
17231684 GTGTTATCCCGATCGATTCTTTATTTTTTGACTTGCGATGTTGTTCCTATCGATTTTGTAAGACC
1 GTGTTATCCCGATTGATTCTTTATTTTTTGACTTACGATGTTGTTCCTATCGATTTTGTAAGACC
17231749 TCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACC-TCTAAGCATAATTTTGAATT
66 TCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTTC-AAGCATAATTTTGAATT
17231813 ACG
130 ACG
* * * * *
17231816 GTGTTATCCTGATTGATTTTTTATTTTTTGACTTATGATGTTGTCTCGGT-T-GATTCTT-TGAG
1 GTGTTATCCCGATTGATTCTTTATTTTTTGACTTACGATGTTGT-TC-CTATCGATT-TTGTAAG
* * * * * *
17231878 ACCTTCAAACATGATTTTTAAAACCTCCGGGCATAATCTTTAAGACCTTCAGGCATAATTTTGAT
63 ACCTCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTTCAAGCATAATTTTGAA
*
17231943 TTGCG
128 TTACG
* * * * * * *
17231948 ATATTATCCCAATTGATTCTTTATTTTTTGACTTACGATATT-AT-CTCAGTCAATTCTGTAAGA
1 GTGTTATCCCGATTGATTCTTTATTTTTTGACTTACGATGTTGTTCCT-A-TCGATTTTGTAAGA
* * * *
17232011 CCTCTAGGCATGATTTCTAAAATCTCC-AGGCATAATCTTTAAGATCTTCAAGCATAAT
64 CCTCCAGACATGATTTCTAAAACCTCCGA-GCATAATCTTTAAGACCTTCAAGCATAAT
17232069 CTTTAAGACC
Statistics
Matches: 208, Mismatches: 35, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
128 1 0.00
130 1 0.00
131 2 0.01
132 196 0.94
133 7 0.03
134 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (132 bp):
GTGTTATCCCGATTGATTCTTTATTTTTTGACTTACGATGTTGTTCCTATCGATTTTGTAAGACC
TCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTTCAAGCATAATTTTGAATTA
CG
Found at i:17231919 original size:22 final size:22
Alignment explanation
Indices: 17231894--17231936 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17231884 AAACATGATT
*
17231894 TTTAAAACCTCCGGGCATAATC
1 TTTAAAACCTCCAGGCATAATC
* *
17231916 TTTAAGACCTTCAGGCATAAT
1 TTTAAAACCTCCAGGCATAAT
17231937 TTTGATTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (22 bp):
TTTAAAACCTCCAGGCATAATC
Found at i:17232057 original size:22 final size:21
Alignment explanation
Indices: 17232006--17232095 Score: 81
Period size: 22 Copynumber: 4.1 Consensus size: 21
17231996 GTCAATTCTG
* *
17232006 TAAGACCTCTAGGCATGATTT
1 TAAGACCTCCAGGCATAATTT
* *
17232027 CTAAAATCTCCAGGCATAATCTT
1 -TAAGACCTCCAGGCATAAT-TT
* * *
17232050 TAAGATCTTCAAGCATAATCTT
1 TAAGACCTCCAGGCATAAT-TT
*
17232072 TAAGACCTTCAGGCATAATTT
1 TAAGACCTCCAGGCATAATTT
17232093 TAA
1 TAA
17232096 TTCACGGTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.09
22 51 0.88
23 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAGACCTCCAGGCATAATTT
Found at i:17232191 original size:37 final size:37
Alignment explanation
Indices: 17232101--17232193 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
17232091 TTTAATTCAC
**
17232101 GGTGTTATCTTGATCGATTCTTTATTTTTTGATTCGT
1 GGTGTTATCCCGATCGATTCTTTATTTTTTGATTCGT
***
17232138 GGTGTTATCTTAATCGATTCTTTATTTTTTGACTTACG-
1 GGTGTTATCCCGATCGATTCTTTATTTTTTGA-TT-CGT
*
17232176 GG-GTTGTCCCGATCGATT
1 GGTGTTATCCCGATCGATT
17232194 TTGTAAGACC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
37 43 0.88
38 4 0.08
39 2 0.04
ACGTcount: A:0.15, C:0.14, G:0.20, T:0.51
Consensus pattern (37 bp):
GGTGTTATCCCGATCGATTCTTTATTTTTTGATTCGT
Found at i:17232324 original size:455 final size:454
Alignment explanation
Indices: 17231542--17232436 Score: 1179
Period size: 455 Copynumber: 2.0 Consensus size: 454
17231532 TGTTGTCCTG
* * * **
17231542 GTCAATTCTATAAGACTTCTGAGCATGATTTCTAAGACCTCTGAGCATAATCTTTAAGATCTTTG
1 GTCAATTCTATAAGACCTCTGAGCATGATTTCTAAAACCTCAGAGCATAATCTTTAAGATCTTCA
** *
17231607 AGCATAATCTTTAAGATTTTCAGGCATAATTTTGAATCGCAGTGTTATCCCAATGATTCTTTACT
66 AGCATAATCTTTAAGACCTTCAGGCATAATTTTGAATCACAGTGTTATCCCAATGATTCTTTACT
* * * * * *
17231672 TTTCGATTCATTGTGTTATCCCGATCGATTCTTTATTTTTTGACTTGCGATGTTGTTCCTATCGA
131 TTTCGATTCATGGTGTTATCCCAATCGATTCTTTATTTTTTGACTTACGAGGTTGTCCCGATCGA
*
17231737 TTTTGTAAGACCTCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTCTAAGCAT
196 TTTTGTAAGACCTCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTCCAAGCAT
* * * **
17231802 AATTTTGAATTACGGTGTTATCCTGATTGATTTTTTATTTTTTGACTTATGATGTTGTCTCGGTT
261 AATTTTGAATTACGGTGTTATCCTAATTGATTCTTTATTTTTTGACTTACGACATTGTCTCGGTT
* * *
17231867 GATTCTTTGAGACCTTCAAACATGATTTTTAAAACCTCCGGGCATAATCTTTAAGACCTTCAGGC
326 GATTCTGTAAGACCTTCAAACATGATTTCTAAAACCTCCGGGCATAATCTTTAAGACCTTCAGGC
* * * *
17231932 ATAATTTTGATTTGCGATATTATCCCAATTGATTCTTTATTTTTTGACTTACGATATTATCTCA
391 ATAATTTCGATTTACAATATTATCCCAATTGATTCTTTATTTTTTAACTTACGATATTATCTCA
* *
17231996 GTCAATTCTGTAAGACCTCT-AGGCATGATTTCTAAAATCTCCAG-GCATAATCTTTAAGATCTT
1 GTCAATTCTATAAGACCTCTGA-GCATGATTTCTAAAACCT-CAGAGCATAATCTTTAAGATCTT
* ***
17232059 CAAGCATAATCTTTAAGACCTTCAGGCATAATTTT-AATTCACGGTGTTATCTTGATCGATTCTT
64 CAAGCATAATCTTTAAGACCTTCAGGCATAATTTTGAA-TCACAGTGTTATCCCAAT-GATTCTT
* * * ** *
17232123 TATTTTTTGATTCGTGGTGTTATCTTAATCGATTCTTTATTTTTTGACTTACGGGGTTGTCCCGA
127 TACTTTTCGATTCATGGTGTTATCCCAATCGATTCTTTATTTTTTGACTTACGAGGTTGTCCCGA
* * * *
17232188 TCGATTTTGTAAGACCTTCGAGA-ATGATTTTTAAAATCTCTGAGCATAATCTTTAAGACCTCCA
192 TCGATTTTGTAAGACC-TCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTCCA
* * ** *
17232252 GGCATAATTTTGATTTGTGGTGTTAT-CTCAATTGATTCTTTATTTTTTGACTTACGGCATTGTC
256 AGCATAATTTTGAATTACGGTGTTATCCT-AATTGATTCTTTATTTTTTGACTTACGACATTGTC
* * * * *
17232316 TTGGTTGATTCTGTAAGATCTTCGAGCATGATTTCTAAAACCTCTGGGCATAATCTTTAAGACCT
320 TCGGTTGATTCTGTAAGACCTTCAAACATGATTTCTAAAACCTCCGGGCATAATCTTTAAGACCT
** ***
17232381 TTGGGCATAATTTCGATTTACAATATTATTTTAATTGATTCTTTATTTTTTAACTT
385 TCAGGCATAATTTCGATTTACAATATTATCCCAATTGATTCTTTATTTTTTAACTT
17232437 GTGGTATTGT
Statistics
Matches: 377, Mismatches: 58, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
453 3 0.01
454 99 0.26
455 270 0.72
456 5 0.01
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (454 bp):
GTCAATTCTATAAGACCTCTGAGCATGATTTCTAAAACCTCAGAGCATAATCTTTAAGATCTTCA
AGCATAATCTTTAAGACCTTCAGGCATAATTTTGAATCACAGTGTTATCCCAATGATTCTTTACT
TTTCGATTCATGGTGTTATCCCAATCGATTCTTTATTTTTTGACTTACGAGGTTGTCCCGATCGA
TTTTGTAAGACCTCCAGACATGATTTCTAAAACCTCCGAGCATAATCTTTAAGACCTCCAAGCAT
AATTTTGAATTACGGTGTTATCCTAATTGATTCTTTATTTTTTGACTTACGACATTGTCTCGGTT
GATTCTGTAAGACCTTCAAACATGATTTCTAAAACCTCCGGGCATAATCTTTAAGACCTTCAGGC
ATAATTTCGATTTACAATATTATCCCAATTGATTCTTTATTTTTTAACTTACGATATTATCTCA
Found at i:17232499 original size:132 final size:133
Alignment explanation
Indices: 17232142--17232501 Score: 390
Period size: 132 Copynumber: 2.7 Consensus size: 133
17232132 ATTCGTGGTG
* ** * * * *
17232142 TTATCTTAATCGATTCTTTATTTTTTGACTTACGGGGTTGTCCCGATCGATTTTGTAAGACCTTC
1 TTATCTTAATTGATTCTTTATTTTTTGACTTACGGCATTGTCTCGGTTGATTTTGTAAGAACTTC
* * **
17232207 GAGA-ATGATTTT-TAAAATCTCTGAGCATAATCTTTAAGACCTCCAGGCATAATTTTGATTTGT
66 GA-ACATGATTTTATAAACTCTCTGAGCATAATCTTTAAGACCTCCAGGCATAATTTCGATTTAC
** *
17232270 GGTG
130 AATA
* * * *
17232274 TTATCTCAATTGATTCTTTATTTTTTGACTTACGGCATTGTCTTGGTTGATTCTGTAAGATCTTC
1 TTATCTTAATTGATTCTTTATTTTTTGACTTACGGCATTGTCTCGGTTGATTTTGTAAGAACTTC
* * ***
17232339 GAGCATGATTTCTA-AAAC-CTCTGGGCATAATCTTTAAGACCTTTGGGCATAATTTCGATTTAC
66 GAACATGATTT-TATAAACTCTCTGAGCATAATCTTTAAGACCTCCAGGCATAATTTCGATTTAC
17232402 AATA
130 AATA
* * ** *
17232406 TTATTTTAATTGATTCTTTATTTTTTAACTTGTGGTATTGTCTCGGTTGATTTTGTAA-AACTTC
1 TTATCTTAATTGATTCTTTATTTTTTGACTTACGGCATTGTCTCGGTTGATTTTGTAAGAACTT-
*
17232470 CGAACATGATTTTATAAACTTTCT-AGCATAAT
65 CGAACATGATTTTATAAACTCTCTGAGCATAAT
17232502 TTTGATTCGC
Statistics
Matches: 188, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
131 6 0.03
132 175 0.93
133 7 0.04
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (133 bp):
TTATCTTAATTGATTCTTTATTTTTTGACTTACGGCATTGTCTCGGTTGATTTTGTAAGAACTTC
GAACATGATTTTATAAACTCTCTGAGCATAATCTTTAAGACCTCCAGGCATAATTTCGATTTACA
ATA
Found at i:17233970 original size:17 final size:17
Alignment explanation
Indices: 17233950--17234012 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
17233940 TTTTTACCTA
*
17233950 TTTTTTATTTTTTTATT
1 TTTTTTATTTTATTATT
* *
17233967 TTTTTTAATTCTATAATT
1 TTTTTT-ATTTTATTATT
* *
17233985 TTTTATATATTATTATT
1 TTTTTTATTTTATTATT
*
17234002 TTTGTTATTTT
1 TTTTTTATTTT
17234013 GAGCTTTATT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
17 22 0.63
18 13 0.37
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTATTTTATTATT
Found at i:17234294 original size:3 final size:3
Alignment explanation
Indices: 17234288--17234350 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
17234278 AAAAAAAAGT
17234288 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17234335 TTGA A-A ATA ATA ATA A
1 AT-A ATA ATA ATA ATA A
17234351 GTTTTTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17234524 original size:21 final size:21
Alignment explanation
Indices: 17234499--17234538 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17234489 TACTAAAACC
17234499 CAAAAC-CCAAAACCTTAAAAT
1 CAAAACTCC-AAACCTTAAAAT
*
17234520 CAAAACTTCAAACCTTAAA
1 CAAAACTCCAAACCTTAAA
17234539 TCCTAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (21 bp):
CAAAACTCCAAACCTTAAAAT
Found at i:17234545 original size:28 final size:28
Alignment explanation
Indices: 17234508--17234637 Score: 122
Period size: 28 Copynumber: 4.6 Consensus size: 28
17234498 CCAAAACCCA
* * *
17234508 AAACCTTAAAATCAAAACTTCAAACCTT
1 AAACCCTAAAATCAAAACCTCAAACCTC
* * *
17234536 AAATCCTAAAA-CTAAA-CTATAAATCCTTC
1 AAACCCTAAAATCAAAACCT-CAAA-CC-TC
*
17234565 AAATCCTAAAATCAAAACCTCAAACCTC
1 AAACCCTAAAATCAAAACCTCAAACCTC
*
17234593 AAACCCTAAAA-CTAAAACCTCAAATCTC
1 AAACCCTAAAATC-AAAACCTCAAACCTC
*
17234621 AAACCCTAAAATAAAAA
1 AAACCCTAAAATCAAAA
17234638 AACCTAAACC
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.01
27 8 0.10
28 52 0.62
29 14 0.17
30 7 0.08
31 2 0.02
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (28 bp):
AAACCCTAAAATCAAAACCTCAAACCTC
Found at i:17234552 original size:20 final size:22
Alignment explanation
Indices: 17234508--17234548 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
17234498 CCAAAACCCA
17234508 AAACCTTAAAAT-C-AAAACTTC
1 AAACCTT-AAATCCTAAAACTTC
17234529 AAACCTTAAATCCTAAAACT
1 AAACCTTAAATCCTAAAACT
17234549 AAACTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCTTAAATCCTAAAACTTC
Found at i:17234591 original size:7 final size:7
Alignment explanation
Indices: 17234579--17234625 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
17234569 CCTAAAATCA
17234579 AAACCTC
1 AAACCTC
17234586 AAACCTC
1 AAACCTC
17234593 AAACC-C
1 AAACCTC
* *
17234599 TAAAACTA
1 -AAACCTC
17234607 AAACCTC
1 AAACCTC
*
17234614 AAATCTC
1 AAACCTC
17234621 AAACC
1 AAACC
17234626 CTAAAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 1 0.03
7 31 0.97
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCTC
Found at i:17234705 original size:15 final size:15
Alignment explanation
Indices: 17234685--17234740 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
17234675 CCTAAAATCC
*
17234685 AAAATCCCAAACTCT
1 AAAATCCAAAACTCT
17234700 AAAATCCAAAAC-CTT
1 AAAATCCAAAACTC-T
*
17234715 AAAATCCAAAATTCT
1 AAAATCCAAAACTCT
17234730 AAAAATCCAAA
1 -AAAATCCAAA
17234741 TTTGGTACGC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 1 0.03
15 24 0.67
16 11 0.31
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATCCAAAACTCT
Found at i:17234725 original size:22 final size:22
Alignment explanation
Indices: 17234678--17234726 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
17234668 CCCTAACCCT
* *
17234678 AAAATCCAAAATCCCAAACTCT
1 AAAATCCAAAATCCCAAAATCC
*
17234700 AAAATCCAAAA-CCTTAAAATCC
1 AAAATCCAAAATCC-CAAAATCC
17234722 AAAAT
1 AAAAT
17234727 TCTAAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAATCCAAAATCCCAAAATCC
Found at i:17234736 original size:16 final size:14
Alignment explanation
Indices: 17234678--17234740 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 14
17234668 CCCTAACCCT
*
17234678 AAAATCCAAAATCCC
1 AAAATCTAAAAT-CC
*
17234693 AAACTCTAAAATCC
1 AAAATCTAAAATCC
*
17234707 AAAACCTTAAAATCC
1 AAAATC-TAAAATCC
17234722 AAAATTCTAAAAATCC
1 AAAA-TCT-AAAATCC
17234738 AAA
1 AAA
17234741 TTTGGTACGC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.15
15 23 0.57
16 11 0.28
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATCTAAAATCC
Found at i:17241069 original size:23 final size:21
Alignment explanation
Indices: 17241015--17241069 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 21
17241005 AATATTAAAT
*
17241015 TTAATATTTGTATTTTTATATA
1 TTAAT-TTTGAATTTTTATATA
17241037 TT--TTTT-AATTTTATAATATA
1 TTAATTTTGAATTTT-T-ATATA
17241057 TTAATTTTGAATT
1 TTAATTTTGAATT
17241070 ATAACTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 8 0.30
22 6 0.22
23 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTAATTTTGAATTTTTATATA
Found at i:17241191 original size:19 final size:20
Alignment explanation
Indices: 17241154--17241191 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
17241144 CATAAACAAA
* *
17241154 TATTATTATATTAATTTTTT
1 TATTATTATAATAAATTTTT
17241174 TATT-TTATAATAAATTTT
1 TATTATTATAATAAATTTT
17241192 AAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTATAATAAATTTTT
Found at i:17244778 original size:22 final size:22
Alignment explanation
Indices: 17244734--17244778 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17244724 TTATATTTAG
* **
17244734 ATGTACATATCCTATAAGTAAA
1 ATGTACATATCCTACAAAAAAA
*
17244756 ATGTACATATCTTACAAAAAAA
1 ATGTACATATCCTACAAAAAAA
17244778 A
1 A
17244779 CAAATTAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (22 bp):
ATGTACATATCCTACAAAAAAA
Found at i:17245322 original size:19 final size:19
Alignment explanation
Indices: 17245300--17245356 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
17245290 AATTTTTTTA
17245300 ATTCTAAAAAATTTTAAAC
1 ATTCTAAAAAATTTTAAAC
** *
17245319 ATTCTAAAAGTTTTTGAAAT
1 ATTCTAAAAAATTTT-AAAC
* *
17245339 TTTCTAGAAAATTTTAAA
1 ATTCTAAAAAATTTTAAA
17245357 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTCTAAAAAATTTTAAAC
Found at i:17245361 original size:10 final size:10
Alignment explanation
Indices: 17245346--17245397 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
17245336 AATTTTCTAG
17245346 AAAATTTTAA
1 AAAATTTTAA
17245356 AAAATTTTAA
1 AAAATTTTAA
** *
17245366 AATTTTTTTA
1 AAAATTTTAA
* *
17245376 AAAATTATAG
1 AAAATTTTAA
*
17245386 AAAATTATAA
1 AAAATTTTAA
17245396 AA
1 AA
17245398 TATGAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:17245369 original size:30 final size:29
Alignment explanation
Indices: 17245330--17245398 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
17245320 TTCTAAAAGT
* *
17245330 TTTTGAAATTTTCTAGAAAATTTTAAAAAA
1 TTTTAAAATTTTCTA-AAAATTATAAAAAA
* *
17245360 TTTTAAAATTTTTTTAAAAATTATAGAAAA
1 TTTTAAAA-TTTTCTAAAAATTATAAAAAA
*
17245390 TTATAAAAT
1 TTTTAAAAT
17245399 ATGAAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 26 0.79
31 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTTAAAATTTTCTAAAAATTATAAAAAA
Found at i:17245387 original size:40 final size:40
Alignment explanation
Indices: 17245307--17245397 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
17245297 TTAATTCTAA
* ** *
17245307 AAAATTTT-AAACATTCTAAAAGTTTTTGAAATTTTCTAG
1 AAAATTTTAAAAAATTCTAAAAGTTTTTGAAAAATTATAG
* * *
17245346 AAAATTTTAAAAAATTTTAAAATTTTTTTAAAAATTATAG
1 AAAATTTTAAAAAATTCTAAAAGTTTTTGAAAAATTATAG
*
17245386 AAAATTATAAAA
1 AAAATTTTAAAA
17245398 TATGAAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 8 0.19
40 35 0.81
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (40 bp):
AAAATTTTAAAAAATTCTAAAAGTTTTTGAAAAATTATAG
Found at i:17246261 original size:34 final size:34
Alignment explanation
Indices: 17246222--17246287 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
17246212 AAACAATTCT
* *
17246222 AAAAATTTTCTAAAAATTCCAAAATA-ATTTTACA
1 AAAAATTTT-TAAAAATTCAAAAAAATATTTTACA
*
17246256 AAAAATTTTTGAAAATTCAAAAAAATATTTTA
1 AAAAATTTTTAAAAATTCAAAAAAATATTTTA
17246288 AAACTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (34 bp):
AAAAATTTTTAAAAATTCAAAAAAATATTTTACA
Found at i:17246308 original size:30 final size:30
Alignment explanation
Indices: 17246257--17246314 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17246247 AATTTTACAA
* * *
17246257 AAAATTTTTGAAAATTCAAAAAAATATTTT
1 AAAACTTTTCAAAATTAAAAAAAATATTTT
17246287 AAAACTTTTCAAAATTAAAAAAAATATT
1 AAAACTTTTCAAAATTAAAAAAAATATT
17246315 AAAAATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAACTTTTCAAAATTAAAAAAAATATTTT
Found at i:17246347 original size:19 final size:19
Alignment explanation
Indices: 17246292--17246348 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
17246282 ATTTTAAAAC
* *
17246292 TTTTCAAAATTAAAAAAAA
1 TTTTAAAAATTAAAAACAA
* * *
17246311 TATTAAAAATTATGAAACAT
1 TTTTAAAAATTA-AAAACAA
17246331 TTTTAAAAATTAAAAACA
1 TTTTAAAAATTAAAAACA
17246349 CAATTTTTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
TTTTAAAAATTAAAAACAA
Found at i:17246375 original size:22 final size:20
Alignment explanation
Indices: 17246287--17246376 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 20
17246277 AAAATATTTT
* *
17246287 AAAACTTTTCAAAATTA-AA
1 AAAATTTTTAAAAATTATAA
* * *
17246306 AAAAATATTAAAAATTATGA
1 AAAATTTTTAAAAATTATAA
* *
17246326 AACATTTTTAAAAATTAAAA
1 AAAATTTTTAAAAATTATAA
17246346 ACACAATTTTTCAAAAATTATTAA
1 A-A-AATTTTT-AAAAATTA-TAA
*
17246370 ATAATTT
1 AAAATTT
17246377 CCAAAATTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 14 0.26
20 17 0.31
21 1 0.02
22 11 0.20
23 8 0.15
24 3 0.06
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
AAAATTTTTAAAAATTATAA
Found at i:17246402 original size:10 final size:10
Alignment explanation
Indices: 17246222--17246441 Score: 56
Period size: 10 Copynumber: 21.7 Consensus size: 10
17246212 AAACAATTCT
*
17246222 AAAAATTTTCT
1 AAAAATTTT-A
**
17246233 AAAAATTCCA
1 AAAAATTTTA
17246243 AAATAATTTTACA
1 AAA-AATTTT--A
*
17246256 AAAAATTTTT
1 AAAAATTTTA
* **
17246266 GAAAATTCAA
1 AAAAATTTTA
*
17246276 AAAAATATTTT
1 AAAAAT-TTTA
*
17246287 AAAACTTTT-
1 AAAAATTTTA
* **
17246296 CAAAATTAAA
1 AAAAATTTTA
*
17246306 AAAAATATT-
1 AAAAATTTTA
* *
17246315 AAAAATTATG
1 AAAAATTTTA
* *
17246325 AAACATTTTT
1 AAAAATTTTA
**
17246335 AAAAATTAAA
1 AAAAATTTTA
*
17246345 AACACAATTTTTC
1 AA-A-AA-TTTTA
17246358 AAAAATTATTA
1 AAAAATT-TTA
* *
17246369 AATAA-TTTC
1 AAAAATTTTA
* *
17246378 CAAAATTTTT
1 AAAAATTTTA
*
17246388 TAAAATTTTA
1 AAAAATTTTA
*
17246398 AAAAATTCT-
1 AAAAATTTTA
* *
17246407 -ACAA-TTCA
1 AAAAATTTTA
17246415 AAAAATTTTA
1 AAAAATTTTA
*
17246425 CAAAATTTTA
1 AAAAATTTTA
17246435 AAAAATT
1 AAAAATT
17246442 AAAAAAGAAT
Statistics
Matches: 143, Mismatches: 52, Indels: 29
0.64 0.23 0.13
Matches are distributed among these distances:
7 1 0.01
8 3 0.02
9 20 0.14
10 76 0.53
11 26 0.18
12 9 0.06
13 8 0.06
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.37
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:17246690 original size:9 final size:9
Alignment explanation
Indices: 17246673--17246759 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 9
17246663 ATACAATTTC
*
17246673 ATATATTTT
1 ATATTTTTT
17246682 ATATTTTTT
1 ATATTTTTT
*
17246691 TTAATTTTTT
1 AT-ATTTTTT
17246701 A-ATTTTTTT
1 ATA-TTTTTT
17246710 GATATTTTTT
1 -ATATTTTTT
17246720 A-A-TTTTT
1 ATATTTTTT
17246727 ATTAATTTTTT
1 A-T-ATTTTTT
17246738 A-A-TTTTT
1 ATATTTTTT
*
17246745 AGATTTTTT
1 ATATTTTTT
17246754 A-ATTTT
1 ATATTTT
17246760 ATAGGATGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
7 12 0.18
8 9 0.14
9 22 0.34
10 15 0.23
11 7 0.11
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
ATATTTTTT
Found at i:17246698 original size:8 final size:8
Alignment explanation
Indices: 17246687--17246759 Score: 85
Period size: 9 Copynumber: 8.5 Consensus size: 8
17246677 ATTTTATATT
17246687 TTTTTTAA
1 TTTTTTAA
17246695 TTTTTTAA
1 TTTTTTAA
17246703 TTTTTTTGATA
1 -TTTTTT-A-A
17246714 TTTTTTAA
1 TTTTTTAA
17246722 TTTTTATTAA
1 -TTTT-TTAA
17246732 TTTTTTAA
1 TTTTTTAA
17246740 -TTTTTAGA
1 TTTTTTA-A
17246748 TTTTTTAA
1 TTTTTTAA
17246756 TTTT
1 TTTT
17246760 ATAGGATGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.10
8 19 0.33
9 21 0.36
10 11 0.19
11 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:17246745 original size:18 final size:18
Alignment explanation
Indices: 17246678--17246759 Score: 98
Period size: 18 Copynumber: 4.6 Consensus size: 18
17246668 ATTTCATATA
*
17246678 TTTTATATTTTTTTTAATT
1 TTTTA-ATTTTTATTAATT
17246697 TTTTAATTTTT-TTGATATT
1 TTTTAATTTTTATT-A-ATT
17246716 TTTTAATTTTTATTAATT
1 TTTTAATTTTTATTAATT
*
17246734 TTTTAATTTTTA--GATT
1 TTTTAATTTTTATTAATT
17246750 TTTTAATTTT
1 TTTTAATTTT
17246760 ATAGGATGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
16 13 0.22
17 2 0.03
18 22 0.37
19 20 0.34
20 2 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTAATTTTTATTAATT
Found at i:17247002 original size:19 final size:19
Alignment explanation
Indices: 17246978--17247057 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
17246968 ATATTCTTAA
17246978 TTTTTATAAGTTTTAAAAT
1 TTTTTATAAGTTTTAAAAT
* *
17246997 TTTTTATAATTTTTGAAAT
1 TTTTTATAAGTTTTAAAAT
* *
17247016 TTTTTCTAA-TTTTAGAAT
1 TTTTTATAAGTTTTAAAAT
** * *
17247034 AATTCAAAAGTTTTAAGAAT
1 TTTTTATAAGTTTTAA-AAT
17247054 TTTT
1 TTTT
17247058 AAAATTTTTG
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
18 11 0.24
19 30 0.65
20 5 0.11
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTTATAAGTTTTAAAAT
Found at i:17247061 original size:19 final size:19
Alignment explanation
Indices: 17247039--17247080 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17247029 AGAATAATTC
*
17247039 AAAAGTTTTAAGAATTTTT
1 AAAAGTTTTAAGAAATTTT
* *
17247058 AAAATTTTTGAGAAATTTT
1 AAAAGTTTTAAGAAATTTT
17247077 AAAA
1 AAAA
17247081 AAATTTGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (19 bp):
AAAAGTTTTAAGAAATTTT
Found at i:17247075 original size:11 final size:9
Alignment explanation
Indices: 17246976--17247080 Score: 52
Period size: 10 Copynumber: 11.2 Consensus size: 9
17246966 TCATATTCTT
*
17246976 AATTTTTAT
1 AATTTTTAA
*
17246985 AAGTTTTAA
1 AATTTTTAA
*
17246994 AATTTTTTAT
1 AA-TTTTTAA
17247004 AATTTTTGAA
1 AATTTTT-AA
* **
17247014 ATTTTTTCT
1 AATTTTTAA
*
17247023 AA-TTTTAG
1 AATTTTTAA
* *
17247031 AATAATTCAA
1 AAT-TTTTAA
*
17247041 AAGTTTTAA
1 AATTTTTAA
17247050 GAATTTTTAA
1 -AATTTTTAA
17247060 AATTTTTGAGA
1 AATTTTT-A-A
17247071 AA-TTTTAA
1 AATTTTTAA
17247079 AA
1 AA
17247081 AAATTTGCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
8 9 0.13
9 27 0.38
10 32 0.45
11 3 0.04
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (9 bp):
AATTTTTAA
Found at i:17247213 original size:20 final size:20
Alignment explanation
Indices: 17247181--17247327 Score: 81
Period size: 19 Copynumber: 7.5 Consensus size: 20
17247171 ATTATTTTTC
*
17247181 AATTTTTAT-AAGTTTTTAA
1 AATTTTTTTGAAGTTTTTAA
*
17247200 AATTTTTTTGAAG-TTTTGA
1 AATTTTTTTGAAGTTTTTAA
* *
17247219 AATTTTTTAGAAATTTTTAGA
1 AATTTTTTTGAAGTTTTTA-A
* * * **
17247240 AA-TGTTTAGAATTATTTTTG
1 AATTTTTTTGAAGT-TTTTAA
* *
17247260 AATTTTTAT-AACTTTTTAA
1 AATTTTTTTGAAGTTTTTAA
*
17247279 ATTTTGTTTTGAAG-TTTTAA
1 AATTT-TTTTGAAGTTTTTAA
* * *
17247299 AACTTTTTAGAA-TTCTTAA
1 AATTTTTTTGAAGTTTTTAA
17247318 AATGTTTTTT
1 AAT-TTTTTT
17247328 AAAAAATAAT
Statistics
Matches: 95, Mismatches: 24, Indels: 17
0.70 0.18 0.12
Matches are distributed among these distances:
19 45 0.47
20 38 0.40
21 12 0.13
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (20 bp):
AATTTTTTTGAAGTTTTTAA
Found at i:17247264 original size:30 final size:30
Alignment explanation
Indices: 17247230--17247312 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
17247220 ATTTTTTAGA
*
17247230 AATTTTTAGAAATGTTTAGAATTAT-TTTTG
1 AATTTTTA-AAATTTTTAGAATTATGTTTTG
* *
17247260 AATTTTTATAACTTTTTA-AATTTTGTTTTG
1 AATTTTTA-AAATTTTTAGAATTATGTTTTG
*
17247290 AAGTTTTAAAACTTTTTAGAATT
1 AATTTTTAAAA-TTTTTAGAATT
17247313 CTTAAAATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 7 0.16
30 33 0.75
31 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (30 bp):
AATTTTTAAAATTTTTAGAATTATGTTTTG
Found at i:17247264 original size:79 final size:78
Alignment explanation
Indices: 17247169--17247324 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 78
17247159 TAAAAAAATT
* * *
17247169 GAATTATTTTTCAATTTTTATAAGTTTTTAAAATTT-TTTTGAAGTTTTGAAATTTTTTAGAAAT
1 GAATTATTTTTCAATTTTTATAACTTTTTAAAATTTGTTTTGAAGTTTTAAAACTTTTTAG-AAT
*
17247233 TTTTAGAAATGTTTA
65 TCTTA-AAATGTTTA
* *
17247248 GAATTATTTTTGAATTTTTATAACTTTTTAAATTTTGTTTTGAAGTTTTAAAACTTTTTAGAATT
1 GAATTATTTTTCAATTTTTATAACTTTTTAAAATTTGTTTTGAAGTTTTAAAACTTTTTAGAATT
17247313 CTTAAAATGTTT
66 CTTAAAATGTTT
17247325 TTTAAAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
78 8 0.11
79 40 0.57
80 22 0.31
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (78 bp):
GAATTATTTTTCAATTTTTATAACTTTTTAAAATTTGTTTTGAAGTTTTAAAACTTTTTAGAATT
CTTAAAATGTTTA
Found at i:17247371 original size:9 final size:9
Alignment explanation
Indices: 17247359--17247521 Score: 83
Period size: 9 Copynumber: 16.9 Consensus size: 9
17247349 TTGTTTACTA
17247359 TTTTTAAATT
1 TTTTTAAA-T
* *
17247369 TTTTTTAGT
1 TTTTTAAAT
* *
17247378 TTTTAAAAA
1 TTTTTAAAT
*
17247387 TTTTAAAAGT
1 TTTTTAAA-T
* *
17247397 TCTTAAAAAT
1 TTTTTAA-AT
*
17247407 TTTTATAATT
1 TTTT-TAAAT
*
17247417 TTTTTAGAT
1 TTTTTAAAT
17247426 TTGTTTAAAAT
1 TT-TTT-AAAT
*
17247437 TTTTAAAAT
1 TTTTTAAAT
17247446 TTTTTAGAAT
1 TTTTTA-AAT
17247456 TTGTTTAGAAT
1 TT-TTTA-AAT
* *
17247467 GTTTTAAAA
1 TTTTTAAAT
* *
17247476 CTTTTAGAT
1 TTTTTAAAT
*
17247485 TTTTTAAAA
1 TTTTTAAAT
*
17247494 TTTTAAAATT
1 TTTTTAAA-T
17247504 TTTTATAAAT
1 TTTT-TAAAT
17247514 TTTTTAAA
1 TTTTTAAA
17247522 ATATGACATA
Statistics
Matches: 117, Mismatches: 27, Indels: 19
0.72 0.17 0.12
Matches are distributed among these distances:
9 53 0.45
10 44 0.38
11 20 0.17
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.58
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:17247390 original size:10 final size:10
Alignment explanation
Indices: 17247377--17247523 Score: 117
Period size: 10 Copynumber: 15.0 Consensus size: 10
17247367 TTTTTTTTAG
17247377 TTTTTAAAA-
1 TTTTTAAAAT
* *
17247386 ATTTTAAAAG
1 TTTTTAAAAT
* *
17247396 TTCTTAAAAA
1 TTTTTAAAAT
*
17247406 TTTTTATAAT
1 TTTTTAAAAT
* *
17247416 TTTTTTAGAT
1 TTTTTAAAAT
17247426 TTGTTTAAAA-
1 TT-TTTAAAAT
17247436 TTTTTAAAAT
1 TTTTTAAAAT
*
17247446 TTTTTAGAAT
1 TTTTTAAAAT
*
17247456 TTGTTTAGAAT
1 TT-TTTAAAAT
*
17247467 GTTTTAAAA-
1 TTTTTAAAAT
* *
17247476 CTTTT-AGAT
1 TTTTTAAAAT
17247485 TTTTTAAAA-
1 TTTTTAAAAT
17247494 -TTTTAAAAT
1 TTTTTAAAAT
17247503 TTTTTATAAAT
1 TTTTTA-AAAT
17247514 TTTTTAAAAT
1 TTTTTAAAAT
17247524 ATGACATAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
8 10 0.09
9 23 0.21
10 53 0.48
11 24 0.22
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:17247918 original size:18 final size:18
Alignment explanation
Indices: 17247886--17247923 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17247876 AATCATTGTG
*
17247886 ATTTGAATTAATAATTTA
1 ATTTGAATTAATAATATA
17247904 ATTT-AATTAATTAATATA
1 ATTTGAATTAA-TAATATA
17247922 AT
1 AT
17247924 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTGAATTAATAATATA
Found at i:17247962 original size:7 final size:7
Alignment explanation
Indices: 17247952--17247990 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
17247942 ATTTAACATG
17247952 TTTAAAA
1 TTTAAAA
17247959 TTTAAAA
1 TTTAAAA
17247966 TTTAAAA
1 TTTAAAA
17247973 TTTAAAA
1 TTTAAAA
17247980 TTTATAAA
1 TTTA-AAA
17247988 TTT
1 TTT
17247991 TTTATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TTTAAAA
Found at i:17248006 original size:22 final size:22
Alignment explanation
Indices: 17247973--17248015 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
17247963 AAATTTAAAA
17247973 TTTAAAATTTATAAATTTTTTAT
1 TTTAAAATTTAT-AATTTTTTAT
*
17247996 TTTAAAA-TTATGATTTTTTA
1 TTTAAAATTTATAATTTTTTA
17248016 ATGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTAAAATTTATAATTTTTTAT
Found at i:17248352 original size:62 final size:63
Alignment explanation
Indices: 17248246--17248370 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 63
17248236 TCGACGATGA
* * * * *
17248246 CAAACAAAGCCATGCGTTACACACGACTTGTTGACGATGTCTCTTTGCCTAAGGAAACGCAAT
1 CAAACAAAGCCATGCGTTACACACCACTTGATGACGACGGCTCTTTGCCTAAGGAAACCCAAT
* * * *
17248309 CAAACAAA-CCATGCGTTTCATACCACTTGATGACGGCGGCTCTTTGTCTAAGGAAACCCAAT
1 CAAACAAAGCCATGCGTTACACACCACTTGATGACGACGGCTCTTTGCCTAAGGAAACCCAAT
17248371 AAGTTGGAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 45 0.85
63 8 0.15
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (63 bp):
CAAACAAAGCCATGCGTTACACACCACTTGATGACGACGGCTCTTTGCCTAAGGAAACCCAAT
Found at i:17248850 original size:19 final size:19
Alignment explanation
Indices: 17248807--17248850 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17248797 AATAAAATGC
*
17248807 TAATTATTTATTAACATAA
1 TAATTATTTATTAACAAAA
*
17248826 TTATTATTTAATTAA-AAAA
1 TAATTATTT-ATTAACAAAA
17248845 TAATTA
1 TAATTA
17248851 ATAATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTATTTATTAACAAAA
Found at i:17249230 original size:16 final size:16
Alignment explanation
Indices: 17249209--17249255 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
17249199 TAGAGGTTAT
**
17249209 AAAATAAATTTGAGTA
1 AAAATAAATTTGAAAA
*
17249225 AAAATAATTTTGGAAAA
1 AAAATAAATTT-GAAAA
17249242 AAAATAAATTTGAA
1 AAAATAAATTTGAA
17249256 TTTACTTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.30
Consensus pattern (16 bp):
AAAATAAATTTGAAAA
Found at i:17249242 original size:15 final size:16
Alignment explanation
Indices: 17249209--17249254 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
17249199 TAGAGGTTAT
*
17249209 AAAATAAATTTGAGTA
1 AAAATAAATTTGAGAA
* *
17249225 AAAATAATTTTGGAAAA
1 AAAATAAATTT-GAGAA
17249242 AAAATAAATTTGA
1 AAAATAAATTTGA
17249255 ATTTACTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (16 bp):
AAAATAAATTTGAGAA
Found at i:17249859 original size:15 final size:15
Alignment explanation
Indices: 17249839--17249868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17249829 AATTGTAATT
17249839 ATTTTATATTATAAA
1 ATTTTATATTATAAA
*
17249854 ATTTTATATTTTAAA
1 ATTTTATATTATAAA
17249869 GCTAATATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATATTATAAA
Found at i:17250257 original size:17 final size:17
Alignment explanation
Indices: 17250237--17250276 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17250227 ATTACGAGTG
17250237 ATAAAATCACCTTAGTA
1 ATAAAATCACCTTAGTA
* * *
17250254 ATAAGATCACTTTGGTA
1 ATAAAATCACCTTAGTA
17250271 ATAAAA
1 ATAAAA
17250277 AATGTCTATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (17 bp):
ATAAAATCACCTTAGTA
Found at i:17250480 original size:23 final size:23
Alignment explanation
Indices: 17250454--17250498 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
17250444 TTTTCCATTA
*
17250454 TTTGAAAGTGTTTAGGAAAAAAC
1 TTTGAAAGTGTTCAGGAAAAAAC
***
17250477 TTTGTGGGTGTTCAGGAAAAAA
1 TTTGAAAGTGTTCAGGAAAAAA
17250499 TTTTTCTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (23 bp):
TTTGAAAGTGTTCAGGAAAAAAC
Found at i:17250832 original size:19 final size:19
Alignment explanation
Indices: 17250791--17250834 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17250781 GATCTATTAC
* *
17250791 TATTAAAATATTATTAATG
1 TATTAAAAAATTATTAATA
**
17250810 TATTAAAAAATTATTTTTA
1 TATTAAAAAATTATTAATA
17250829 TATTAA
1 TATTAA
17250835 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTAAAAAATTATTAATA
Found at i:17251594 original size:31 final size:30
Alignment explanation
Indices: 17251558--17251620 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
17251548 ACACCTATCC
* *
17251558 AACATTATAAAATGATCATTTTACATTTTTT
1 AACATTATAAAATGACCATTTTAC-TCTTTT
17251589 AACATTATAAAATGACCATTTTACTCTTTT
1 AACATTATAAAATGACCATTTTACTCTTTT
17251619 AA
1 AA
17251621 TCAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (30 bp):
AACATTATAAAATGACCATTTTACTCTTTT
Found at i:17251630 original size:31 final size:31
Alignment explanation
Indices: 17251564--17251632 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
17251554 ATCCAACATT
* * **
17251564 ATAAAATGATCATTTTACATTTTTTAACATT
1 ATAAAATGACCATTTTACATCTTTTAACAAA
17251595 ATAAAATGACCATTTTAC-TCTTTTAATCAAA
1 ATAAAATGACCATTTTACATCTTTTAA-CAAA
17251626 ATAAAAT
1 ATAAAAT
17251633 AATCTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (31 bp):
ATAAAATGACCATTTTACATCTTTTAACAAA
Found at i:17251752 original size:151 final size:152
Alignment explanation
Indices: 17251464--17251752 Score: 344
Period size: 151 Copynumber: 1.9 Consensus size: 152
17251454 TATAGAATGA
*
17251464 TTAATCAAAATAAATTAAATTAAAATGTTAATACTAAAAATATTTAAAATAAATTAAACAAATTT
1 TTAATCAAAATAAAATAAATTAAAATGTTAATAC-AAAAATATTTAAAATAAATTAAACAAATTT
* * * *
17251529 CCAAAGAAATTACATTTTGACACCTATCCAACATTATAAAATGATCATTTTACATTTTTTAACAT
65 CCAAAGAAATTACATTTTGACACCTATACAACATTATAAAATGATCATTTTACATTTATGAACAA
17251594 TATAAAATGACCATTTTACTCTT
130 TATAAAATGACCATTTTACTCTT
*
17251617 TTAATCAAAATAAAAT-AATCTAAAATGTTAATA-AAGAAA-ATTTAATAATATATTAAA-AGAA
1 TTAATCAAAATAAAATAAAT-TAAAATGTTAATACAA-AAATATTTAA-AATAAATTAAACA-AA
* * * *
17251678 -TT-CAAA-AAAGCTTATATTTTGACACTTGTACAACATTATAAAATGATCATTTTATCCTTTAA
62 TTTCCAAAGAAA--TTACATTTTGACACCTATACAACATTATAAAATGATCATTTTA-CATTT-A
17251740 TGAA-AATA-AAAAT
123 TGAACAATATAAAAT
17251753 AATCTAAAAT
Statistics
Matches: 118, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
149 3 0.03
150 4 0.03
151 55 0.47
152 25 0.21
153 31 0.26
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (152 bp):
TTAATCAAAATAAAATAAATTAAAATGTTAATACAAAAATATTTAAAATAAATTAAACAAATTTC
CAAAGAAATTACATTTTGACACCTATACAACATTATAAAATGATCATTTTACATTTATGAACAAT
ATAAAATGACCATTTTACTCTT
Found at i:17251768 original size:22 final size:22
Alignment explanation
Indices: 17251738--17251783 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17251728 TTTATCCTTT
*
17251738 AATGAAAATAA-AAATAATCTAA
1 AATGAAAATAATAAAAAAT-TAA
*
17251760 AATGTAAATAATAAAAAATTAA
1 AATGAAAATAATAAAAAATTAA
17251782 AA
1 AA
17251784 ATATGAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (22 bp):
AATGAAAATAATAAAAAATTAA
Found at i:17252015 original size:18 final size:18
Alignment explanation
Indices: 17251992--17252026 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17251982 AAAAATTTAG
17251992 TATGAATTATCTTTAATA
1 TATGAATTATCTTTAATA
17252010 TATGAATTATCTTTAAT
1 TATGAATTATCTTTAAT
17252027 TTCAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TATGAATTATCTTTAATA
Found at i:17252578 original size:19 final size:19
Alignment explanation
Indices: 17252535--17252578 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
17252525 TTATTTCTAA
17252535 AATTTT-TAGAATTTTTTG
1 AATTTTCTAGAATTTTTTG
*
17252553 AAATTTCTAG-ATTTTGTTG
1 AATTTTCTAGAATTTT-TTG
17252572 AATTTTC
1 AATTTTC
17252579 CAGCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (19 bp):
AATTTTCTAGAATTTTTTG
Found at i:17253401 original size:96 final size:95
Alignment explanation
Indices: 17253230--17253530 Score: 252
Period size: 96 Copynumber: 3.1 Consensus size: 95
17253220 GTTTAGAAAT
* * * * * * *
17253230 TTTTAAATTATGAATTCTACCGAATGATT-AGAGAATTTCATAATGATTTTGAAAAACTATTTTT
1 TTTTGAATTATGAATTCTACCAAACGATTGA-ATAATTTCATAATAATTTTGAAAAACTAATTCT
*
17253294 TCAATCCTACCAAATGAAT-GGAGGATCTT-AA
65 TCAATCCTACCAAAT-AATAGAAGGAT-TTAAA
* * *
17253325 TTTTGAATTATGAATCCTACCAAAGGATTGAATAATTTTATAATAAATTTTGGAAAAA-TAATTC
1 TTTTGAATTATGAATTCTACCAAACGATTGAATAATTTCATAAT-AATTTT-GAAAAACTAATTC
*
17253389 TTCAATCCTACCAAATTATAGAAGGATTTAAA
64 TTCAATCCTACCAAATAATAGAAGGATTTAAA
* * * * * **
17253421 TATCGAATTATAAATTCTACCAAACGATTGGATAATTTCATATTGAATTTTTAGAAAAAAAATAT
1 TTTTGAATTATGAATTCTACCAAACGATTGAATAATTTCATAAT-AA-TTTT-GAAAAACTA-AT
* * * *
17253486 TCTTTTAATCTTACCAAACAATTAGAA-AATTTAAA
62 TC-TTCAATCCTACCAAATAA-TAGAAGGATTTAAA
*
17253521 TCTTGAATTA
1 TTTTGAATTA
17253531 AAACTTACCA
Statistics
Matches: 167, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
95 40 0.24
96 72 0.43
97 16 0.10
98 1 0.01
99 4 0.02
100 29 0.17
101 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (95 bp):
TTTTGAATTATGAATTCTACCAAACGATTGAATAATTTCATAATAATTTTGAAAAACTAATTCTT
CAATCCTACCAAATAATAGAAGGATTTAAA
Found at i:17258702 original size:8 final size:8
Alignment explanation
Indices: 17258689--17258776 Score: 88
Period size: 8 Copynumber: 10.6 Consensus size: 8
17258679 ACTTCACTTG
17258689 AAAGAAAA
1 AAAGAAAA
17258697 AAAGAAAA
1 AAAGAAAA
17258705 AAATGAAGAA
1 AAA-GAA-AA
17258715 AAATGAAAA
1 AAA-GAAAA
*
17258724 AATGAAAA
1 AAAGAAAA
*
17258732 AATGAAAA
1 AAAGAAAA
*
17258740 AATGAAAA
1 AAAGAAAA
*
17258748 AATGAAAA
1 AAAGAAAA
*
17258756 AATGAAAA
1 AAAGAAAA
17258764 AGAA-AAAA
1 A-AAGAAAA
17258772 AAAGA
1 AAAGA
17258777 CTCAAATCAA
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
7 2 0.03
8 55 0.74
9 8 0.11
10 9 0.12
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAGAAAA
Found at i:17258732 original size:16 final size:16
Alignment explanation
Indices: 17258692--17258764 Score: 110
Period size: 16 Copynumber: 4.4 Consensus size: 16
17258682 TCACTTGAAA
*
17258692 GAAAAAAAGAAAAAAAT
1 GAAAAAATG-AAAAAAT
17258709 GAAGAAAAATGAAAAAAT
1 G-A-AAAAATGAAAAAAT
17258727 GAAAAAATGAAAAAAT
1 GAAAAAATGAAAAAAT
17258743 GAAAAAATGAAAAAAT
1 GAAAAAATGAAAAAAT
17258759 GAAAAA
1 GAAAAA
17258765 GAAAAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
16 36 0.68
17 2 0.04
18 9 0.17
19 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
GAAAAAATGAAAAAAT
Found at i:17258773 original size:24 final size:24
Alignment explanation
Indices: 17258692--17258771 Score: 110
Period size: 24 Copynumber: 3.3 Consensus size: 24
17258682 TCACTTGAAA
*
17258692 GAAAAAAAGAAAAAAATGAAGAAAAAT
1 GAAAAAATG-AAAAAATG-A-AAAAAT
17258719 GAAAAAATGAAAAAATGAAAAAAT
1 GAAAAAATGAAAAAATGAAAAAAT
17258743 GAAAAAATGAAAAAATG-AAAAA-
1 GAAAAAATGAAAAAATGAAAAAAT
17258765 GAAAAAA
1 GAAAAAA
17258772 AAAGACTCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
22 7 0.13
23 5 0.10
24 23 0.44
25 1 0.02
26 8 0.15
27 8 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (24 bp):
GAAAAAATGAAAAAATGAAAAAAT
Found at i:17259984 original size:40 final size:40
Alignment explanation
Indices: 17259936--17260022 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
17259926 TGAATAAGCC
** *
17259936 TTATTTTTAAAGTAGTGTGCTTTCATGGTAAATGAGGCTT
1 TTATTTTTAAAGTAGTGTGCCGTCACGGTAAATGAGGCTT
* *
17259976 TTATTTTTAAAGTTGTGTGCCGTCACGGTGAATGAGGCTT
1 TTATTTTTAAAGTAGTGTGCCGTCACGGTAAATGAGGCTT
17260016 TATATTT
1 T-TATTT
17260023 AAAATTATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (40 bp):
TTATTTTTAAAGTAGTGTGCCGTCACGGTAAATGAGGCTT
Found at i:17260151 original size:40 final size:39
Alignment explanation
Indices: 17259863--17260159 Score: 213
Period size: 39 Copynumber: 7.5 Consensus size: 39
17259853 AGTCTTAACC
* * *
17259863 TTTTAAAGTTGTGTGCCTTTATGTTGAATGAACCTTTAT
1 TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
* * * * *
17259902 TTTTAAAATTGTGTGCCTTCCTATTGAATAAGCC-TTAT
1 TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
* * * *
17259940 TTTTAAAGTAGTGTGCTTTCATGGTAAATGAGGCTTTTAT
1 TTTTAAAGTTGTGTGCCTTCATGTTAAATGA-GCCTTTAT
* * * * *
17259980 TTTTAAAGTTGTGTGCCGTCACGGTGAATGAGGCTTTAT
1 TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
* * * * * *
17260019 ATTTAAAATTATGTGCCTTCTTGTTAAAGGAGCCCTTAT
1 TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
* * * *
17260058 TCTTTCAAAGTT-TGCATGCCTTTAAGTTGAAA-AAGCCCTTAGT
1 T-TTT-AAAGTTGTG--TGCCTTCATGTT-AAATGAGCCTTTA-T
* * *
17260101 ATTTTAAAGTTGTGTGCCTTAATGTTAAAGGAGTCTTTAT
1 -TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
*
17260141 TTTTAAAAGTTATGTGCCT
1 TTTT-AAAGTTGTGTGCCT
17260160 CTATTTTCGA
Statistics
Matches: 201, Mismatches: 45, Indels: 23
0.75 0.17 0.09
Matches are distributed among these distances:
38 27 0.13
39 68 0.34
40 52 0.26
41 21 0.10
42 23 0.11
43 9 0.04
44 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (39 bp):
TTTTAAAGTTGTGTGCCTTCATGTTAAATGAGCCTTTAT
Found at i:17261531 original size:24 final size:22
Alignment explanation
Indices: 17261479--17261532 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17261469 CTTTGTTTTG
* *
17261479 TTTTATTCATTTAAATTTTATT
1 TTTTATTAATTTAAATTTTAAT
*
17261501 TTATTATTAATTTTAATTGTTAAAT
1 TT-TTATTAATTTAAATT-TT-AAT
17261526 TTTTATT
1 TTTTATT
17261533 TTATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 13 0.50
24 7 0.27
25 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATTAATTTAAATTTTAAT
Found at i:17261547 original size:33 final size:31
Alignment explanation
Indices: 17261489--17261567 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 31
17261479 TTTTATTCAT
*
17261489 TTAAATTTTATTTTATTATTAATTTTAATTG
1 TTAAATTTTATTTTATTATTAATTTTAATTA
* *
17261520 TTAAATTTTTATTTTATTTATTTATTTTAGTTA
1 TTAAA-TTTTATTTTA-TTATTAATTTTAATTA
17261553 TGTAAATTTTATTTT
1 T-TAAATTTTATTTT
17261568 TAATTGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 5 0.12
32 10 0.24
33 23 0.55
34 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (31 bp):
TTAAATTTTATTTTATTATTAATTTTAATTA
Found at i:17262269 original size:78 final size:78
Alignment explanation
Indices: 17262140--17262294 Score: 301
Period size: 78 Copynumber: 2.0 Consensus size: 78
17262130 ATTTGAAGAT
*
17262140 AAATTTTCAATAATTAAATTGTTTGGTAAATTACAAAAAAGTTCTAAGGCTTTGATAACATGAAA
1 AAATTTTCAATAATTAAATTGTTTGGTAAATTACAAAAAAGTTCTAAGGCTTGGATAACATGAAA
17262205 TGAAATTGGTACC
66 TGAAATTGGTACC
17262218 AAATTTTCAATAATTAAATTGTTTGGTAAATTACAAAAAAGTTCTAAGGCTTGGATAACATGAAA
1 AAATTTTCAATAATTAAATTGTTTGGTAAATTACAAAAAAGTTCTAAGGCTTGGATAACATGAAA
17262283 TGAAATTGGTAC
66 TGAAATTGGTAC
17262295 AATCCTTTGA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (78 bp):
AAATTTTCAATAATTAAATTGTTTGGTAAATTACAAAAAAGTTCTAAGGCTTGGATAACATGAAA
TGAAATTGGTACC
Found at i:17264744 original size:17 final size:17
Alignment explanation
Indices: 17264716--17264758 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
17264706 ATTATGATAT
17264716 TATTTATTAAT-AAAATA
1 TATTT-TTAATAAAAATA
17264733 CTATTTTTAATAGAAAATA
1 -TATTTTTAATA-AAAATA
17264752 TATTTTT
1 TATTTTT
17264759 GAAATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 12 0.52
19 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TATTTTTAATAAAAATA
Found at i:17264868 original size:32 final size:32
Alignment explanation
Indices: 17264832--17264909 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
17264822 AAAATTTTCT
*
17264832 ATATCAATTTAAAAAATTAAATAAAAAACTCC
1 ATATCATTTTAAAAAATTAAATAAAAAACTCC
* * * * *
17264864 ATATCGTTTTAAAATATTAAGTAAAAAATTTC
1 ATATCATTTTAAAAAATTAAATAAAAAACTCC
*
17264896 ATATTATTTTAAAA
1 ATATCATTTTAAAA
17264910 GTAGATTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (32 bp):
ATATCATTTTAAAAAATTAAATAAAAAACTCC
Found at i:17264950 original size:19 final size:18
Alignment explanation
Indices: 17264923--17264960 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17264913 GATTTATTAA
17264923 TCTATTAAAAACCTATTT
1 TCTATTAAAAACCTATTT
*
17264941 TCTATCTAAAAATCTATTT
1 TCTAT-TAAAAACCTATTT
17264960 T
1 T
17264961 GAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTATTAAAAACCTATTT
Found at i:17265256 original size:32 final size:31
Alignment explanation
Indices: 17265197--17265282 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
17265187 ATTTGCAAAT
* * *
17265197 TTTTTTACTTAATATTTTAAGAAGATATGAAG
1 TTTTTTACTTAATTTTTTAA-AAGATATAAAA
* *
17265229 TTTTTTATTTAATTTTTTAAATTGATATAAAA
1 TTTTTTACTTAATTTTTTAAA-AGATATAAAA
* *
17265261 ATTTTCACTTAATTTTTTAAAA
1 TTTTTTACTTAATTTTTTAAAA
17265283 AATTATTTGG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.53
Consensus pattern (31 bp):
TTTTTTACTTAATTTTTTAAAAGATATAAAA
Found at i:17266922 original size:2 final size:2
Alignment explanation
Indices: 17266915--17266940 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17266905 TACCTTATTC
17266915 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17266941 GACTAGTTTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17271307 original size:195 final size:195
Alignment explanation
Indices: 17270973--17271350 Score: 679
Period size: 195 Copynumber: 1.9 Consensus size: 195
17270963 TTTTTATTTA
17270973 TTAAAAAAAAATTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATG
1 TTAAAAAAAAATTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATG
17271038 TTCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTAC
66 TTCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTAC
* *
17271103 TCGGAATACTTTTAGAATCTCATCTTT-GAAGG-CTCGAATTTATTTTTCGTAAGAAAATGTTAT
131 TCGGAATACTTTTAGAATCTCATCTTTGGAAGGTCT-AAATTTACTTTTCGTAAGAAAATGTTAT
17271166 G
195 G
17271167 TTAAAAAAAAATTTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAAT
1 TTAAAAAAAAA-TTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAAT
*
17271232 GTTTCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTA
65 GTTCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTA
**
17271297 CTTTGAATACTTTTAGAATCTCATCTTTGGAAGGTCTAAATTTACTTTTCGTAA
130 CTCGGAATACTTTTAGAATCTCATCTTTGGAAGGTCTAAATTTACTTTTCGTAA
17271351 AAATTATGTC
Statistics
Matches: 176, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
194 11 0.06
195 143 0.81
196 20 0.11
197 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (195 bp):
TTAAAAAAAAATTATTCTCGAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATG
TTCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTAC
TCGGAATACTTTTAGAATCTCATCTTTGGAAGGTCTAAATTTACTTTTCGTAAGAAAATGTTATG
Found at i:17271864 original size:26 final size:28
Alignment explanation
Indices: 17271835--17271894 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
17271825 TTCCTATATT
17271835 TTTATTAGTT-TATTATTATTATTAAA-
1 TTTATTAGTTATATTATTATTATTAAAG
* * *
17271861 TTTATT-TTTATATTATTGTTTTTAAAG
1 TTTATTAGTTATATTATTATTATTAAAG
17271888 TTTATTA
1 TTTATTA
17271895 AAAATTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.71
27 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (28 bp):
TTTATTAGTTATATTATTATTATTAAAG
Found at i:17285938 original size:15 final size:16
Alignment explanation
Indices: 17285913--17285942 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17285903 TAATATATAA
17285913 AAAATAAGAAAAATTC
1 AAAATAAGAAAAATTC
17285929 AAAA-AAGAAAAATT
1 AAAATAAGAAAAATT
17285943 TTTTACCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAATAAGAAAAATTC
Found at i:17286827 original size:21 final size:21
Alignment explanation
Indices: 17286792--17286833 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17286782 CTAAGAGAGC
17286792 TGGTCAGAGGATTGGTTGGGT
1 TGGTCAGAGGATTGGTTGGGT
17286813 TGGTC-GAGGAGTTGGTTGGGT
1 TGGTCAGAGGA-TTGGTTGGGT
17286834 GGCTGATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.05, G:0.50, T:0.33
Consensus pattern (21 bp):
TGGTCAGAGGATTGGTTGGGT
Found at i:17287267 original size:12 final size:12
Alignment explanation
Indices: 17287250--17287275 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17287240 GTGTAGGGTC
17287250 TGGTGGCAGTGG
1 TGGTGGCAGTGG
17287262 TGGTGGCAGTGG
1 TGGTGGCAGTGG
17287274 TG
1 TG
17287276 CCGGGGATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.58, T:0.27
Consensus pattern (12 bp):
TGGTGGCAGTGG
Found at i:17287361 original size:18 final size:17
Alignment explanation
Indices: 17287338--17287398 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
17287328 TTTTTTTTAT
17287338 ATTTTTATTATGTATTTC
1 ATTTTT-TTATGTATTTC
*
17287356 ATTTTTTT-TGTAGTTC
1 ATTTTTTTATGTATTTC
*
17287372 GTATTTTTTTATTATATTTC
1 --ATTTTTTTA-TGTATTTC
*
17287392 ATATTTT
1 ATTTTTT
17287399 ATACTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.20
17 2 0.06
18 20 0.57
20 6 0.17
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.69
Consensus pattern (17 bp):
ATTTTTTTATGTATTTC
Done.