Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 133 of 240
Found at i:41315782 original size:28 final size:27
Alignment explanation
Indices: 41315750--41315827 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
41315740 CAATTAATTT
41315750 ATTATTTAAAATTTAAAAAATTATAAAA
1 ATTATTTAAAA-TTAAAAAATTATAAAA
* *
41315778 ATTATTTAAAAAAATT-AAAACTTATTAAA
1 ATTATTT---AAAATTAAAAAATTATAAAA
*
41315807 ATTATTTTAAAAATAAAAAAT
1 ATTA-TTTAAAATTAAAAAAT
41315828 ATGTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.12
28 12 0.29
29 15 0.37
30 5 0.12
31 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTATTTAAAATTAAAAAATTATAAAA
Found at i:41315796 original size:20 final size:21
Alignment explanation
Indices: 41315760--41315807 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
41315750 ATTATTTAAA
*
41315760 ATTTAAAAAATTATAAAAATT
1 ATTTAAAAAAATATAAAAATT
*
41315781 ATTTAAAAAAAT-TAAAACTT
1 ATTTAAAAAAATATAAAAATT
41315801 A-TTAAAA
1 ATTTAAAA
41315808 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTAAAAAAATATAAAAATT
Found at i:41315826 original size:29 final size:27
Alignment explanation
Indices: 41315750--41315827 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 27
41315740 CAATTAATTT
*
41315750 ATTATTTAAAATTTAAAAAATTATAAAA
1 ATTATTTAAAA-ATAAAAAATTATAAAA
*
41315778 ATTATTTAAAAA-AATTAAAACTTATTAAA
1 ATTATTTAAAAATAA--AAAA-TTATAAAA
41315807 ATTATTTTAAAAATAAAAAAT
1 ATTA-TTTAAAAATAAAAAAT
41315828 ATGTTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
26 2 0.05
28 16 0.37
29 15 0.35
30 8 0.19
31 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
ATTATTTAAAAATAAAAAATTATAAAA
Found at i:41318202 original size:17 final size:16
Alignment explanation
Indices: 41318177--41318222 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
41318167 TTTTTAAAGT
41318177 AAAAATAATAAATGAA
1 AAAAATAATAAATGAA
41318193 AAAAATTAATAAAATGAA
1 AAAAA-TAAT-AAATGAA
*
41318211 AAATATAATAAA
1 AAAAATAATAAA
41318223 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
18 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAATAATAAATGAA
Found at i:41318209 original size:18 final size:17
Alignment explanation
Indices: 41318177--41318229 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
41318167 TTTTTAAAGT
41318177 AAAAATAAT-AAATGAA
1 AAAAATAATAAAATGAA
41318193 AAAAATTAATAAAATGAA
1 AAAAA-TAATAAAATGAA
* *
41318211 AAATATAATAAAAAGAA
1 AAAAATAATAAAATGAA
41318228 AA
1 AA
41318230 GAAAAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 5 0.15
17 17 0.52
18 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
AAAAATAATAAAATGAA
Found at i:41320873 original size:39 final size:39
Alignment explanation
Indices: 41320830--41320974 Score: 182
Period size: 39 Copynumber: 3.7 Consensus size: 39
41320820 TTCACTTTTG
* * *
41320830 AGCATATATCACATTACACATATAATCACATAACATTTA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* ** **
41320869 AGCATATATCATAATACTCATATAATTGCATAATGTTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
* * *
41320908 AGCACATATCGCAATACTCATATGATCACATAACATTCA
1 AGCATATATCACAATACTCATATAATCACATAACATTCA
*
41320947 AGCATATATCCCAATACTCATATAATCA
1 AGCATATATCACAATACTCATATAATCA
41320975 TTTTATAGGA
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (39 bp):
AGCATATATCACAATACTCATATAATCACATAACATTCA
Found at i:41332842 original size:17 final size:18
Alignment explanation
Indices: 41332802--41332842 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41332792 AATTTTGGGT
*
41332802 CCACATGCCCGTGTTGGC
1 CCACACGCCCGTGTTGGC
*
41332820 CGACACGCCCGTG-TGGC
1 CCACACGCCCGTGTTGGC
41332837 CCACAC
1 CCACAC
41332843 ACCAAAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.15, C:0.44, G:0.27, T:0.15
Consensus pattern (18 bp):
CCACACGCCCGTGTTGGC
Found at i:41332896 original size:32 final size:32
Alignment explanation
Indices: 41332828--41332898 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
41332818 GCCGACACGC
* * *
41332828 CCGTGTGGCCCACACACCAAAATTGACCTTGC
1 CCGTGTGGCCCACACACCAAAATCGACCTAGA
* * * *
41332860 CCGTGTGGCCCAGACGCCCAAATCGGCCTAGA
1 CCGTGTGGCCCACACACCAAAATCGACCTAGA
41332892 CCGTGTG
1 CCGTGTG
41332899 ACCGACTCGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (32 bp):
CCGTGTGGCCCACACACCAAAATCGACCTAGA
Found at i:41333526 original size:6 final size:6
Alignment explanation
Indices: 41333515--41333542 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41333505 GAAGAGAGAG
41333515 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
41333543 TGTTAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:41338910 original size:38 final size:38
Alignment explanation
Indices: 41338868--41338940 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
41338858 CTTATTAAAT
*
41338868 ATACAGAGATATTAATGAATGAATGTTTTATTTTCTTA
1 ATACAAAGATATTAATGAATGAATGTTTTATTTTCTTA
41338906 ATACAAAGATATTAATGAATGAATGTTTTATTTTC
1 ATACAAAGATATTAATGAATGAATGTTTTATTTTC
41338941 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (38 bp):
ATACAAAGATATTAATGAATGAATGTTTTATTTTCTTA
Found at i:41339701 original size:21 final size:21
Alignment explanation
Indices: 41339668--41339718 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
41339658 GGCTTATCTA
* *
41339668 AGTGA-AAATGCTTTTTCTGT
1 AGTGAGAAATGCTTTCTCTGC
*
41339688 AGTGAGAAGTGCTTTCTCTGC
1 AGTGAGAAATGCTTTCTCTGC
41339709 AGTGAGAAAT
1 AGTGAGAAAT
41339719 TGCACACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (21 bp):
AGTGAGAAATGCTTTCTCTGC
Found at i:41342515 original size:7 final size:7
Alignment explanation
Indices: 41342503--41342536 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
41342493 ATATAATAAC
41342503 AAATTTT
1 AAATTTT
41342510 AAATTTT
1 AAATTTT
*
41342517 AAACTTT
1 AAATTTT
*
41342524 AAACTTT
1 AAATTTT
41342531 AAATTT
1 AAATTT
41342537 CAATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:41344181 original size:23 final size:22
Alignment explanation
Indices: 41344155--41344229 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
41344145 GTAGCCATTT
41344155 AGGCGTTATAGAATACGCCACAA
1 AGGC-TTATAGAATACGCCACAA
* *
41344178 AGGCTTAATAGATTATGCCACAA
1 AGGCTT-ATAGAATACGCCACAA
*
41344201 AGGCTCTATTAG-ATACACCACAA
1 AGGCT-TA-TAGAATACGCCACAA
41344224 AGGCTT
1 AGGCTT
41344230 CACAAATATC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (22 bp):
AGGCTTATAGAATACGCCACAA
Found at i:41347644 original size:6 final size:6
Alignment explanation
Indices: 41347633--41347659 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41347623 GTATTAACTG
41347633 TGACCA TGACCA TGACCA TGACCA TGA
1 TGACCA TGACCA TGACCA TGACCA TGA
41347660 ACACACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (6 bp):
TGACCA
Found at i:41353073 original size:12 final size:12
Alignment explanation
Indices: 41353056--41353083 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41353046 AAATGAGAGG
41353056 AATTTTAAAGGA
1 AATTTTAAAGGA
41353068 AATTTTAAAGGA
1 AATTTTAAAGGA
41353080 AATT
1 AATT
41353084 GAGGGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
AATTTTAAAGGA
Found at i:41358170 original size:25 final size:25
Alignment explanation
Indices: 41358101--41358177 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
41358091 GAGTAGACTG
* *
41358101 ATTTTCATAGATCGTGTGAACATTT
1 ATTTTCATAGCTCGTGTGAGCATTT
* *
41358126 ACTTTCATAGCTCATGTGAGCATTT
1 ATTTTCATAGCTCGTGTGAGCATTT
* *
41358151 GTTTTCATAGCTCGTGTGAGCAATT
1 ATTTTCATAGCTCGTGTGAGCATTT
41358176 AT
1 AT
41358178 AGTTATAACT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (25 bp):
ATTTTCATAGCTCGTGTGAGCATTT
Found at i:41360043 original size:29 final size:29
Alignment explanation
Indices: 41360008--41360067 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41359998 TTTTGACATG
41360008 ATTGATTATTGGAAGGTTTTATTTATGAT
1 ATTGATTATTGGAAGGTTTTATTTATGAT
41360037 ATTGATTATTGGAAGGTTTTATTTATGAT
1 ATTGATTATTGGAAGGTTTTATTTATGAT
41360066 AT
1 AT
41360068 AATTGATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (29 bp):
ATTGATTATTGGAAGGTTTTATTTATGAT
Found at i:41366998 original size:21 final size:22
Alignment explanation
Indices: 41366959--41366999 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
41366949 TTTAAGTTAT
41366959 TTATTAAATTACAAGTTTAATC
1 TTATTAAATTACAAGTTTAATC
41366981 TTATT-AATTAACAA-TTTAA
1 TTATTAAATT-ACAAGTTTAA
41367000 AACACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
TTATTAAATTACAAGTTTAATC
Found at i:41370976 original size:13 final size:13
Alignment explanation
Indices: 41370958--41370982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41370948 TAATAATTAT
41370958 TTAATATATATAA
1 TTAATATATATAA
41370971 TTAATATATATA
1 TTAATATATATA
41370983 TTTTTTATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATATATATAA
Found at i:41373350 original size:9 final size:9
Alignment explanation
Indices: 41373329--41373361 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
41373319 ATTTGTTTTT
*
41373329 TTTTTTGGA
1 TTTTTTAGA
41373338 -TTTTTAGA
1 TTTTTTAGA
41373346 TTTTTTAGA
1 TTTTTTAGA
41373355 TTTTTTA
1 TTTTTTA
41373362 TAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (9 bp):
TTTTTTAGA
Found at i:41373547 original size:28 final size:30
Alignment explanation
Indices: 41373501--41373556 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
41373491 AACTTTTAAG
* *
41373501 TTATTTTTATTATTGTAAATA-TAAAATAT
1 TTATTTTTATTATTATAAAAATTAAAATAT
41373530 TTATTTTTA-TATTATAAAAATTAAAAT
1 TTATTTTTATTATTATAAAAATTAAAAT
41373557 TAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTATTTTTATTATTATAAAAATTAAAATAT
Found at i:41373571 original size:15 final size:16
Alignment explanation
Indices: 41373547--41373580 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41373537 TATATTATAA
*
41373547 AAATTAAAATTAATAT
1 AAATTAAAATAAATAT
41373563 AAATT-AAATAAATAT
1 AAATTAAAATAAATAT
41373578 AAA
1 AAA
41373581 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAAATAAATAT
Found at i:41373582 original size:16 final size:17
Alignment explanation
Indices: 41373546--41373583 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
41373536 TTATATTATA
*
41373546 AAAATTAAAATTAATAT
1 AAAATTAAAATAAATAT
41373563 -AAATT-AAATAAATAT
1 AAAATTAAAATAAATAT
41373578 AAAATT
1 AAAATT
41373584 TAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTAAAATAAATAT
Found at i:41374311 original size:22 final size:21
Alignment explanation
Indices: 41374281--41374321 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41374271 TTTTATTTAA
41374281 AAATATATTTAAAATTTTATCT
1 AAATATATTT-AAATTTTATCT
* *
41374303 AAATCTATTTATATTTTAT
1 AAATATATTTAAATTTTAT
41374322 AAATTACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATATTTAAATTTTATCT
Found at i:41379800 original size:47 final size:47
Alignment explanation
Indices: 41379716--41380075 Score: 504
Period size: 47 Copynumber: 7.6 Consensus size: 47
41379706 TATTTGAATA
41379716 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
41379765 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
41379812 AATGTGAAAGTGTATATATATGTGATATGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
41379861 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
41379908 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
** * * * * *
41379955 AATGTGAAAGTGTATATATACGACAGGGCCGAGTGACCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * *
41380002 AATGTGAAAGTGTATATATGCGACATGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
41380049 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
41380076 TCCCGAAGGG
Statistics
Matches: 284, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
47 228 0.80
49 56 0.20
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:41380295 original size:37 final size:37
Alignment explanation
Indices: 41380194--41380295 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
41380184 CCGAGCTCTA
*
41380194 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
41380231 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* * *
41380268 AAGACCCGATAACTTCATGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
41380296 CATCTGAGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:41396429 original size:25 final size:25
Alignment explanation
Indices: 41396401--41396461 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
41396391 GCGGATACTC
*
41396401 CACAGCTCATGTGAGTATTCTAATT
1 CACAGCTCATGTGAGCATTCTAATT
* **
41396426 CACAGCTCGTGTGAGCATTCTGGTT
1 CACAGCTCATGTGAGCATTCTAATT
*
41396451 TACAGCTCATG
1 CACAGCTCATG
41396462 AGGGCATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (25 bp):
CACAGCTCATGTGAGCATTCTAATT
Found at i:41425071 original size:128 final size:128
Alignment explanation
Indices: 41424905--41425428 Score: 881
Period size: 128 Copynumber: 4.1 Consensus size: 128
41424895 GCATATAACA
*
41424905 AATTTCATAGCATCACATCTTAGTTTTCA-TTCTCGCAACACATAAGCACATGTTTCAGAATTTA
1 AATTT-AT-GCATCACATCTTAGTTTTCATTTC-CGCAACACATAAGCACATATTTCAGAATTTA
* *
41424969 AACCTAAGTATGAGCAAACTTACACTCGAAATTTTGAATAGGGGTTTAGGCTACTACTAACTTCC
63 AACATAAGTATGAGCAAACTTACACTCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCC
41425034 C
128 C
*
41425035 AATTTATGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCATATATTTCAGAATTTAAAC
1 AATTTATGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCACATATTTCAGAATTTAAAC
*
41425100 ATAAGTATGAGCAAACTTACACAT-GGAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCCC
66 ATAAGTATGAGCAAACTTACAC-TCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCCC
*
41425163 AATTTAGGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCACATATTTCAGAATTTAAAC
1 AATTTATGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCACATATTTCAGAATTTAAAC
* * *
41425228 ATAAGTATGAGCAAACTTACACTTGGAATTTAGAACAGGGGTTTAGGCTACTACTAACTTCCC
66 ATAAGTATGAGCAAACTTACACTCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCCC
* * *
41425291 AATTTAGGCATCACATCTTAGTTTTCATTTCTGCAACACATAAGCACATATTTTAGAATTTAAAC
1 AATTTATGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCACATATTTCAGAATTTAAAC
*
41425356 ATAAGTATGAGCAAACTTACACTCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTTCC
66 ATAAGTATGAGCAAACTTACACTCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCCC
41425419 AATTTATGCA
1 AATTTATGCA
41425429 ATGAATCGTG
Statistics
Matches: 376, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
127 1 0.00
128 364 0.97
129 6 0.02
130 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (128 bp):
AATTTATGCATCACATCTTAGTTTTCATTTCCGCAACACATAAGCACATATTTCAGAATTTAAAC
ATAAGTATGAGCAAACTTACACTCGAAATTTAGAATAGGGGTTTAGGCTACTACTAACTTCCC
Found at i:41434265 original size:17 final size:17
Alignment explanation
Indices: 41434245--41434280 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41434235 CCGTCAGTCT
41434245 AAATAAGCCTAGTAATC
1 AAATAAGCCTAGTAATC
41434262 AAATAAGCCTAGTAATC
1 AAATAAGCCTAGTAATC
41434279 AA
1 AA
41434281 TCTTTCTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (17 bp):
AAATAAGCCTAGTAATC
Found at i:41453106 original size:17 final size:17
Alignment explanation
Indices: 41453064--41453107 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
41453054 ATTGAGTCTA
41453064 TTTTATTTT-ATTTTAT
1 TTTTATTTTCATTTTAT
41453080 TTTTAGTTTTCA-TTTATT
1 TTTTA-TTTTCATTTTA-T
41453098 TTTTATTTTC
1 TTTTATTTTC
41453108 TTAGACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 7 0.28
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTTTCATTTTAT
Found at i:41457437 original size:20 final size:20
Alignment explanation
Indices: 41457403--41457549 Score: 132
Period size: 20 Copynumber: 7.3 Consensus size: 20
41457393 GCATCATAGA
*
41457403 TGCATAACAGGGGCACCAAAG
1 TGCA-AACAGAGGCACCAAAG
* * **
41457424 TGCATACAGAGGCACGAATC
1 TGCAAACAGAGGCACCAAAG
* * **
41457444 TGCAAGCAGAGGCGCCGTAG
1 TGCAAACAGAGGCACCAAAG
* * **
41457464 TGCAAACAGAGACGCCGTAG
1 TGCAAACAGAGGCACCAAAG
*
41457484 TGCAAACAGAGACACCAAAG
1 TGCAAACAGAGGCACCAAAG
*
41457504 TGCAAACAGAGGCACCTAAG
1 TGCAAACAGAGGCACCAAAG
* *
41457524 TGCAAATAGAGGCACTAAAG
1 TGCAAACAGAGGCACCAAAG
41457544 TGCAAA
1 TGCAAA
41457550 TCTCGTACAA
Statistics
Matches: 103, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
20 99 0.96
21 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (20 bp):
TGCAAACAGAGGCACCAAAG
Found at i:41470989 original size:21 final size:19
Alignment explanation
Indices: 41470965--41471003 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
41470955 ATCCTAGTTT
41470965 ATTTATGTTATAATTGTTACA
1 ATTTATGTT-TAATT-TTACA
41470986 ATTTATGTTTAATTTTAC
1 ATTTATGTTTAATTTTAC
41471004 TAAAATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (19 bp):
ATTTATGTTTAATTTTACA
Found at i:41477634 original size:28 final size:31
Alignment explanation
Indices: 41477556--41477635 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 31
41477546 GAATCAGTCA
*
41477556 AGGCCTGAGCCCTATACAGTATCAGTTCAGTGT
1 AGGCCTTAGCCCTATACAGTA-CAG-TCAGTGT
41477589 AGGCCTTAGCCC-ATTACAGTA-A-T-AGTGT
1 AGGCCTTAGCCCTA-TACAGTACAGTCAGTGT
*
41477617 GGGCCTTAGCCCTATACAG
1 AGGCCTTAGCCCTATACAG
41477636 AAATCAGTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
28 21 0.49
29 2 0.05
31 1 0.02
32 1 0.02
33 18 0.42
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (31 bp):
AGGCCTTAGCCCTATACAGTACAGTCAGTGT
Found at i:41477997 original size:27 final size:27
Alignment explanation
Indices: 41477967--41478026 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
41477957 TCAACTCCTA
*
41477967 GGGGTATAACAGTGATTTTACCCTTTG
1 GGGGTATAACAGTGATTTTACCCTTCG
***
41477994 GGGGTATTTTAGTGATTTTACCCTTCG
1 GGGGTATAACAGTGATTTTACCCTTCG
41478021 GGGGTA
1 GGGGTA
41478027 ATTTGGTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.13, G:0.30, T:0.38
Consensus pattern (27 bp):
GGGGTATAACAGTGATTTTACCCTTCG
Found at i:41478038 original size:27 final size:27
Alignment explanation
Indices: 41477976--41478092 Score: 112
Period size: 27 Copynumber: 4.3 Consensus size: 27
41477966 AGGGGTATAA
* * *
41477976 CAGTGATTTTACCCTTTGGGGGTATTT
1 CAGTCATTTTACCCTTCGGGGGTAATT
* *
41478003 TAGTGATTTTACCCTTCGGGGGTAATT
1 CAGTCATTTTACCCTTCGGGGGTAATT
** *
41478030 TGGTCATTTTACTCTTTC-GGGGTAATT
1 CAGTCATTTTAC-CCTTCGGGGGTAATT
* *
41478057 CAGTCATTTTATCTTTCGGGGGTAATT
1 CAGTCATTTTACCCTTCGGGGGTAATT
41478084 C-GATCATTT
1 CAG-TCATTT
41478093 GTAACCCATT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.08
27 68 0.87
28 4 0.05
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGGGGGTAATT
Found at i:41478052 original size:54 final size:54
Alignment explanation
Indices: 41477981--41478092 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
41477971 TATAACAGTG
* * * * * *
41477981 ATTTTACCCTTTGGGGGTATTTTAGTGATTTTACCCTTCGGGGGTAATTTGGTC
1 ATTTTACCCTTTCGGGGTAATTCAGTCATTTTACCCTTCGGGGGTAATTCGATC
* * *
41478035 ATTTTACTCTTTCGGGGTAATTCAGTCATTTTATCTTTCGGGGGTAATTCGATC
1 ATTTTACCCTTTCGGGGTAATTCAGTCATTTTACCCTTCGGGGGTAATTCGATC
41478089 ATTT
1 ATTT
41478093 GTAACCCATT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (54 bp):
ATTTTACCCTTTCGGGGTAATTCAGTCATTTTACCCTTCGGGGGTAATTCGATC
Found at i:41479229 original size:54 final size:54
Alignment explanation
Indices: 41479152--41479268 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
41479142 AGGGGTATAA
* **
41479152 CAGTCATTTTACCCTATACGGGTAATTGGGTCATTTTACCCTTTGGGGGTAATT
1 CAGTCATTTTACCCTATAAGGGTAATTCAGTCATTTTACCCTTTGGGGGTAATT
* * *
41479206 CGGTCATTTTACCCT-TCAAGGGTAATTCATTCATTTTATCCTTTGGGGGTAATT
1 CAGTCATTTTACCCTAT-AAGGGTAATTCAGTCATTTTACCCTTTGGGGGTAATT
*
41479260 TAGTCATTT
1 CAGTCATTT
41479269 GTGGCCCATT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (54 bp):
CAGTCATTTTACCCTATAAGGGTAATTCAGTCATTTTACCCTTTGGGGGTAATT
Found at i:41479255 original size:27 final size:27
Alignment explanation
Indices: 41479152--41479268 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
41479142 AGGGGTATAA
* **
41479152 CAGTCATTTTACCCTATACGGGTAATT
1 CAGTCATTTTACCCTTTGGGGGTAATT
**
41479179 GGGTCATTTTACCCTTTGGGGGTAATT
1 CAGTCATTTTACCCTTTGGGGGTAATT
* ***
41479206 CGGTCATTTTACCCTTCAAGGGTAATT
1 CAGTCATTTTACCCTTTGGGGGTAATT
* *
41479233 CATTCATTTTATCCTTTGGGGGTAATT
1 CAGTCATTTTACCCTTTGGGGGTAATT
*
41479260 TAGTCATTT
1 CAGTCATTT
41479269 GTGGCCCATT
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTTTGGGGGTAATT
Found at i:41482873 original size:19 final size:19
Alignment explanation
Indices: 41482851--41482891 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
41482841 TTTTCAATCA
41482851 TCACTCATCCCATCA-TCTC
1 TCACTCAT-CCATCATTCTC
41482870 TCACTCATCCATCATTCTC
1 TCACTCATCCATCATTCTC
41482889 TCA
1 TCA
41482892 AATATTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.34
Consensus pattern (19 bp):
TCACTCATCCATCATTCTC
Found at i:41485771 original size:12 final size:14
Alignment explanation
Indices: 41485744--41485776 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
41485734 TCTTGTAATG
41485744 AAAGAAAGTCAGAA
1 AAAGAAAGTCAGAA
41485758 AAAGAAA-TCA-AA
1 AAAGAAAGTCAGAA
41485770 AAAGAAA
1 AAAGAAA
41485777 AAGAGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (14 bp):
AAAGAAAGTCAGAA
Found at i:41485797 original size:21 final size:19
Alignment explanation
Indices: 41485754--41485803 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
41485744 AAAGAAAGTC
*
41485754 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATAAAAAA
41485772 AGAAAAAGAGAATGAAAAAA
1 AGAAAAAGAGAAT-AAAAAA
41485792 AGGAAAAAGAGA
1 A-GAAAAAGAGA
41485804 TTGACAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 6 0.21
21 10 0.36
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (19 bp):
AGAAAAAGAGAATAAAAAA
Found at i:41491984 original size:19 final size:18
Alignment explanation
Indices: 41491943--41491995 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
41491933 AATCTATTCA
41491943 TTTTATT-TTATTATTTTAT
1 TTTTATTGTTA-T-TTTTAT
41491962 TTTTATTGTTATTTTTAT
1 TTTTATTGTTATTTTTAT
* *
41491980 GTTTTTTTGATATTTT
1 -TTTTATTGTTATTTT
41491996 CTTCTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.20
19 21 0.70
20 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTATTGTTATTTTTAT
Found at i:41495508 original size:422 final size:422
Alignment explanation
Indices: 41494715--41495562 Score: 1543
Period size: 422 Copynumber: 2.0 Consensus size: 422
41494705 TTGACATTGC
*
41494715 ATATCTTAGATAATTTTCAGAAAGATCTAATATCTAACTCAGAAATCTGTTTATTTGCTAACCAA
1 ATATCTTAGATAATCTTCAGAAAGATCTAATATCTAACTCAGAAATCTGTTTATTTGCTAACCAA
*
41494780 CTCTCGACTATGACCACATTATTACTCATTCATCTGCTCAACTCTTTAGCTTAACACTTGTGGAC
66 CTCTCGACTATGACCACATTATTACTCATTCATCCGCTCAACTCTTTAGCTTAACACTTGTGGAC
*
41494845 TTTTCACAATAGAATTCTGTTATATAAAATTTTGAGAACGAGGGGGTGGAGATCGCAATGCCACA
131 TTTTCACAATAGAATTCTATTATATAAAATTTTGAGAACGAGGGGGTGGAGATCGCAATGCCACA
*
41494910 AAATTTAATTCTCATGTGAACACATCAAATATAACATTCATTATTAACATAACATTATGAACCTC
196 AAATTTAATTCTCATGTGAACACATCAAACATAACATTCATTATTAACATAACATTATGAACCTC
*
41494975 TACTCTAACCTTTATGAAATTTAGCTCATCATTAGCAACATTTTAATCAGATATTCGAGTATTGC
261 TACTCTAACCTTTATGAAATTTAGCTCATCATTAGCAACATTTTAATCAGATATTCAAGTATTGC
* *
41495040 TTTCAACATTATCGGAATTAACTCAGTTGGAAACCATCTTTGTCTATAAGTGAAACAAATCCCAT
326 TTTCAACATTATCGGAATTAACTCAGTTGGAAAACATCTCTGTCTATAAGTGAAACAAATCCCAT
41495105 CAGAGTCAAGAGGCATCACGCTATCACAGGTT
391 CAGAGTCAAGAGGCATCACGCTATCACAGGTT
* *
41495137 ATATCTTAGATAATCTTCAGAAAGATCTAATATCTAACTCAGAAATCTGTTTATTTTCTAACTAA
1 ATATCTTAGATAATCTTCAGAAAGATCTAATATCTAACTCAGAAATCTGTTTATTTGCTAACCAA
* *
41495202 CTCTCGACTATGACCACATTATTACTCATTCATCCGTTGAACTCTTTAGCTTAACACTTGTGGAC
66 CTCTCGACTATGACCACATTATTACTCATTCATCCGCTCAACTCTTTAGCTTAACACTTGTGGAC
* *
41495267 TTTTCACAATAGAATTCTATTATATAAAATTTTGAGAACGAGGGGGTGGAGATTGTAATGCCACA
131 TTTTCACAATAGAATTCTATTATATAAAATTTTGAGAACGAGGGGGTGGAGATCGCAATGCCACA
*
41495332 AAATTTAATTCTCATGTGAACACATCAAACATAACATTCATTATTAATATAACATTATGAACCTC
196 AAATTTAATTCTCATGTGAACACATCAAACATAACATTCATTATTAACATAACATTATGAACCTC
* *
41495397 TACTCTAACCTTTATGAAATTTAGCTCATCATTAGCAGCATTTTAATCAGATATTTAAGTATTGC
261 TACTCTAACCTTTATGAAATTTAGCTCATCATTAGCAACATTTTAATCAGATATTCAAGTATTGC
41495462 TTTCAACATTATCGGAATTAACTCAGTTGGAAAACATCTCTGTCTATAAGTGAAACAAATCCCAT
326 TTTCAACATTATCGGAATTAACTCAGTTGGAAAACATCTCTGTCTATAAGTGAAACAAATCCCAT
*
41495527 CAGAGTCAAGAGGCATCACGCTATCATAGGTT
391 CAGAGTCAAGAGGCATCACGCTATCACAGGTT
41495559 ATAT
1 ATAT
41495563 AATGACATGT
Statistics
Matches: 409, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
422 409 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (422 bp):
ATATCTTAGATAATCTTCAGAAAGATCTAATATCTAACTCAGAAATCTGTTTATTTGCTAACCAA
CTCTCGACTATGACCACATTATTACTCATTCATCCGCTCAACTCTTTAGCTTAACACTTGTGGAC
TTTTCACAATAGAATTCTATTATATAAAATTTTGAGAACGAGGGGGTGGAGATCGCAATGCCACA
AAATTTAATTCTCATGTGAACACATCAAACATAACATTCATTATTAACATAACATTATGAACCTC
TACTCTAACCTTTATGAAATTTAGCTCATCATTAGCAACATTTTAATCAGATATTCAAGTATTGC
TTTCAACATTATCGGAATTAACTCAGTTGGAAAACATCTCTGTCTATAAGTGAAACAAATCCCAT
CAGAGTCAAGAGGCATCACGCTATCACAGGTT
Found at i:41505523 original size:27 final size:27
Alignment explanation
Indices: 41505484--41505649 Score: 224
Period size: 27 Copynumber: 6.1 Consensus size: 27
41505474 AGAGGTCAAT
* *
41505484 AAATGACCAAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
*
41505511 AAATGACCGAATTACCCCCACAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
* * * *
41505538 AAATAACTGAATTACCCTCATAAGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
*
41505565 AAATGATCGAATTACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
* *
41505592 AAATGACTGAATGACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
* *
41505619 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAATTACCCCCATAGGGTA
41505646 AAAT
1 AAAT
41505650 AACAGTTATA
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (27 bp):
AAATGACCGAATTACCCCCATAGGGTA
Found at i:41506058 original size:28 final size:28
Alignment explanation
Indices: 41506013--41506203 Score: 292
Period size: 28 Copynumber: 6.8 Consensus size: 28
41506003 ACTGTATCGA
** *
41506013 TACTGTATTGGGAGAAGGCCCATATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
41506041 TACTGTATTGGGCTAAGGCCCACATTAT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
41506069 TATTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
41506097 TACTATATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
41506125 TATTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
41506153 TACTGTATTGGGCTAAGGCCTATATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
41506181 TGCTGTATTGGGCTAAGGCCCAC
1 TACTGTATTGGGCTAAGGCCCAC
41506204 TGTGACAGCC
Statistics
Matches: 147, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 147 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:41508043 original size:40 final size:40
Alignment explanation
Indices: 41507806--41508035 Score: 267
Period size: 40 Copynumber: 5.8 Consensus size: 40
41507796 TTGAATGCTG
*
41507806 TCCGGGCTAAGTCCCGAAGGC-TTGTGCTA--AGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATT-TG-TACGAGTTACTAA-A
* * *
41507845 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
41507885 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
* *
41507924 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
* * *
41507964 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* *
41508005 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAG
41508036 GAGCTATATC
Statistics
Matches: 168, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 55 0.33
40 107 0.64
41 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:41511200 original size:28 final size:28
Alignment explanation
Indices: 41511169--41511235 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
41511159 CGGCTATGAC
*
41511169 TTAGACATCATTAA-AGCATGTAATAAAA
1 TTAGACA-CATTAATAACATGTAATAAAA
41511197 TTAGACACATTAATAACATGTAATAAAA
1 TTAGACACATTAATAACATGTAATAAAA
41511225 TATA-ACACATT
1 T-TAGACACATT
41511236 TATCACAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 6 0.17
28 28 0.78
29 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (28 bp):
TTAGACACATTAATAACATGTAATAAAA
Found at i:41514308 original size:6 final size:6
Alignment explanation
Indices: 41514299--41514395 Score: 61
Period size: 6 Copynumber: 15.7 Consensus size: 6
41514289 TAATGAAATC
* ** * **
41514299 GAAAAA GAAAAC GAAAAA GAAAAA GAAATT GCAAAA GAAAAA GAAATC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * *
41514347 GAAAAA GTGAGA GAAAAA GAAAGTGAA -AAAAA GAAAATT GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAA---AA GAAAAA GAAAA-A GAAAAA GAAA
41514396 TTGAGATTGA
Statistics
Matches: 66, Mismatches: 20, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
5 2 0.03
6 54 0.82
7 5 0.08
8 3 0.05
9 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:41514320 original size:18 final size:18
Alignment explanation
Indices: 41514299--41514353 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
41514289 TAATGAAATC
*
41514299 GAAAAAGAAAACGAAAAA
1 GAAAAAGAAATCGAAAAA
* *
41514317 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
41514335 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
41514353 G
1 G
41514354 TGAGAGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.71, C:0.05, G:0.18, T:0.05
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:41514379 original size:14 final size:16
Alignment explanation
Indices: 41514350--41514382 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
41514340 AGAAATCGAA
41514350 AAAGTGAGAGAAAAAG
1 AAAGTGAGAGAAAAAG
41514366 AAAGTGA-A-AAAAAG
1 AAAGTGAGAGAAAAAG
41514380 AAA
1 AAA
41514383 ATTGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAGTGAGAGAAAAAG
Found at i:41514414 original size:18 final size:18
Alignment explanation
Indices: 41514383--41514417 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41514373 AAAAAAGAAA
41514383 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
41514401 ATTGAGAAAA-AAATTGA
1 ATTGA-AAAAGAAATTGA
41514418 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:41516396 original size:20 final size:19
Alignment explanation
Indices: 41516355--41516411 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
41516345 TTTTTGTTTC
*
41516355 AGCTCATTCGAGCTCAATTT
1 AGCTCATT-GAGCTCGATTT
*
41516375 AGCTCATTGAGCTCGTTATT
1 AGCTCATTGAGCTCGAT-TT
*
41516395 AGCTC-TTTAGCTCGATT
1 AGCTCATTGAGCTCGATT
41516412 AATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 15 0.47
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (19 bp):
AGCTCATTGAGCTCGATTT
Found at i:41520171 original size:16 final size:16
Alignment explanation
Indices: 41520152--41520186 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41520142 TAGTAATTTT
41520152 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
41520168 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
41520184 AAT
1 AAT
41520187 TACAAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:41522468 original size:18 final size:18
Alignment explanation
Indices: 41522445--41522480 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41522435 GTATCGATAC
*
41522445 TAAAACAATACCTAATTG
1 TAAAACAATACCAAATTG
41522463 TAAAACAATACCAAATTG
1 TAAAACAATACCAAATTG
41522481 CTATACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAAACAATACCAAATTG
Found at i:41524478 original size:31 final size:29
Alignment explanation
Indices: 41524422--41524479 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
41524412 GTTTATCTAC
41524422 AAGATAAACATTAAATTAAATTTAATATT
1 AAGATAAACATTAAATTAAATTTAATATT
41524451 AAGATAATCACATTAATATTAAA-TTAATA
1 AAGATAA--ACATTAA-ATTAAATTTAATA
41524480 AAATACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
31 13 0.50
32 6 0.23
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
AAGATAAACATTAAATTAAATTTAATATT
Found at i:41524503 original size:37 final size:36
Alignment explanation
Indices: 41524469--41524538 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
41524459 CACATTAATA
*
41524469 TTAAATTAATA-AAATACTATTACAATAACTATTAAAT
1 TTAAATTAATATAAA-ACTATTAAAATAA-TATTAAAT
* *
41524506 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
41524539 TTTCCAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 22 0.76
38 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:41525835 original size:17 final size:17
Alignment explanation
Indices: 41525813--41525847 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41525803 CTATGCATGC
*
41525813 AAAATATAAAAGACATA
1 AAAATACAAAAGACATA
41525830 AAAATACAAAAGACATA
1 AAAATACAAAAGACATA
41525847 A
1 A
41525848 TAGTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATACAAAAGACATA
Found at i:41527842 original size:15 final size:17
Alignment explanation
Indices: 41527822--41527858 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41527812 AAAAAGTGAT
41527822 AAAAATTT-G-AGTTAA
1 AAAAATTTCGAAGTTAA
*
41527837 AAAAATTTCGAATTTAA
1 AAAAATTTCGAAGTTAA
41527854 AAAAA
1 AAAAA
41527859 CAGTGTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (17 bp):
AAAAATTTCGAAGTTAA
Found at i:41548510 original size:17 final size:16
Alignment explanation
Indices: 41548479--41548519 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
41548469 GAATTTAGAA
41548479 GAATTTTTGAATTAGT
1 GAATTTTTGAATTAGT
*
41548495 GAATTTTGTGATTTAGT
1 GAATTTT-TGAATTAGT
41548512 GAATTTTT
1 GAATTTTT
41548520 TGCGATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (16 bp):
GAATTTTTGAATTAGT
Found at i:41548526 original size:19 final size:17
Alignment explanation
Indices: 41548490--41548528 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
41548480 AATTTTTGAA
*
41548490 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGCGAT
41548507 TTAGTGAATTTTTTGCGAT
1 TTAGTGAA--TTTTGCGAT
41548526 TTA
1 TTA
41548529 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.54
Consensus pattern (17 bp):
TTAGTGAATTTTGCGAT
Found at i:41549332 original size:46 final size:46
Alignment explanation
Indices: 41549265--41549403 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
41549255 TGGCAAAGTG
* * * *
41549265 TGAAAGGTAGGTATGGTGTTTCGGTGAAGAAAGCCATATTGAGTTA
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
41549311 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
* *
41549357 TGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
41549403 T
1 T
41549404 AGCAATGTGA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:41551827 original size:40 final size:40
Alignment explanation
Indices: 41551384--41551813 Score: 682
Period size: 40 Copynumber: 10.8 Consensus size: 40
41551374 GAGAATTGAG
* *
41551384 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551424 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
41551464 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551504 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551544 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551584 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551624 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
41551664 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
41551704 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTTGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
41551744 AGTAATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCT
* * * *
41551784 GGTGTTATATCCGGGCTAGGTCCCGAAGAG
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAG
41551814 TAATCATGCT
Statistics
Matches: 370, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.00
40 367 0.99
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:41555438 original size:47 final size:47
Alignment explanation
Indices: 41555385--41555793 Score: 636
Period size: 47 Copynumber: 8.7 Consensus size: 47
41555375 TTAGGATTCT
41555385 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41555432 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41555479 ATGTGATGAATGTG-AAGTGTATATATATGTGATAA-GCCT-ATGG-CG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
41555524 ATGTGATGAATGTG---GT-TATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
41555567 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
41555616 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
41555665 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
41555712 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
41555759 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41555794 TCCCGAAGGG
Statistics
Matches: 341, Mismatches: 10, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
40 14 0.04
41 4 0.01
42 4 0.01
43 18 0.05
45 16 0.05
46 11 0.03
47 164 0.48
48 14 0.04
49 96 0.28
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:41555968 original size:37 final size:37
Alignment explanation
Indices: 41555912--41555990 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41555902 CCGAGCTCTA
* * *
41555912 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41555949 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41555986 AAGAC
1 AAGAC
41555991 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41560483 original size:15 final size:15
Alignment explanation
Indices: 41560456--41560485 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41560446 GAGAAGTATG
41560456 GTAATGAGAAGTGCA
1 GTAATGAGAAGTGCA
41560471 GTAATGAGAAGTGCA
1 GTAATGAGAAGTGCA
41560486 TGTCTAGGAT
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:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
GTAATGAGAAGTGCA
Found at i:41567204 original size:8 final size:8
Alignment explanation
Indices: 41567191--41567218 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41567181 AATTAAATTT
41567191 AATATTAA
1 AATATTAA
41567199 AATATTAA
1 AATATTAA
41567207 AATATTAA
1 AATATTAA
41567215 AATA
1 AATA
41567219 ATATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATATTAA
Found at i:41567599 original size:13 final size:13
Alignment explanation
Indices: 41567581--41567605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41567571 TAGGTCCAAT
41567581 TTTCAAATTCAAG
1 TTTCAAATTCAAG
41567594 TTTCAAATTCAA
1 TTTCAAATTCAA
41567606 TTTTTTGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTCAAATTCAAG
Found at i:41569259 original size:41 final size:40
Alignment explanation
Indices: 41569214--41569346 Score: 126
Period size: 40 Copynumber: 3.3 Consensus size: 40
41569204 AGCGGCATTT
41569214 TTAGCGGCG-TTTGGATAAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGCTTT--ATAAAAAACGCCGCTAAAGATCGAGCA
* ** * *
41569255 TTAGCGGCGCTTTTTGGAAAACGCCGCTAAAGATTGAGTA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
* ** * * *
41569295 TTAGCGGCGCTTTTTGGAAAACGCCTCTAAA-AACAAGCA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
*
41569334 TTAGCGGTGCTTT
1 TTAGCGGCGCTTT
41569347 CCAAAAAGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 16 0.20
40 52 0.65
41 9 0.11
42 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (40 bp):
TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGATCGAGCA
Found at i:41569282 original size:40 final size:40
Alignment explanation
Indices: 41569232--41569346 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 40
41569222 GTTTGGATAA
41569232 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
* *
41569272 AAAACGCCGCTAAAGATTGAGTATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
* * * *
41569312 AAAACGCCTCTAAA-AACAAGCATTAGCGGTGCTTT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTT
41569347 CCAAAAAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 16 0.24
40 51 0.76
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
Found at i:41569466 original size:41 final size:41
Alignment explanation
Indices: 41569405--41569777 Score: 446
Period size: 41 Copynumber: 9.1 Consensus size: 41
41569395 CTTTCGGGGC
* *
41569405 TTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTAAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
** *
41569446 TTTAGCGGCGTTTTTGAGAAAGCGTAGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
*
41569487 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* * *
41569528 TTTAGCGGTGTTTTTGATAAAGCGCAGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* *
41569569 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCAGGAA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* * *
41569610 TTTAGCGGCTTTTTTGAGAAAGCACCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* * *
41569651 TTTAGCGGCATTTTTGAGAAAGCGTCGCTAATGCTCAGGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGG-A
* * * * * * **
41569693 TTTAGTGGCGATTTTCATAAAGCTCCGCGAATGCTCTA--TT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC-AGGGA
* * *
41569733 TTTAGTGGCGTTTTCT-AAAAAGCGCCGCTACTGCTCAGGGA
1 TTTAGCGGCGTTTT-TGAGAAAGCGCCGCTAATGCTCAGGGA
41569774 TTTA
1 TTTA
41569778 AAATAATTTA
Statistics
Matches: 285, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.00
40 30 0.11
41 225 0.79
42 28 0.10
43 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
Found at i:41569916 original size:13 final size:13
Alignment explanation
Indices: 41569898--41569924 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41569888 TTCTTATATA
41569898 ATCGTTAGAGTAT
1 ATCGTTAGAGTAT
41569911 ATCGTTAGAGTAT
1 ATCGTTAGAGTAT
41569924 A
1 A
41569925 GGGTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
ATCGTTAGAGTAT
Found at i:41569996 original size:7 final size:7
Alignment explanation
Indices: 41569978--41570031 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
41569968 GTGTTACCGT
*
41569978 TTTAAGG
1 TTTATGG
41569985 TTTATGG
1 TTTATGG
*
41569992 ATTATGGG
1 TTTAT-GG
*
41570000 TTTAGGG
1 TTTATGG
*
41570007 GTTATGG
1 TTTATGG
41570014 TTTATGG
1 TTTATGG
41570021 TTTATGG
1 TTTATGG
41570028 TTTA
1 TTTA
41570032 AAGGCTAGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:41570079 original size:7 final size:7
Alignment explanation
Indices: 41570069--41570126 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 7
41570059 ATGTGTTAAA
41570069 GGTTTATG
1 GGTTTA-G
*
41570077 GTTTTAG
1 GGTTTAG
41570084 GGTTTTAG
1 GG-TTTAG
41570092 GGTTTTAG
1 GG-TTTAG
41570100 GGTTTA-
1 GGTTTAG
* *
41570106 AGTTTAT
1 GGTTTAG
41570113 GGTTTAG
1 GGTTTAG
41570120 GGTTTAG
1 GGTTTAG
41570127 ATTAACTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
6 5 0.12
7 18 0.42
8 20 0.47
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (7 bp):
GGTTTAG
Found at i:41570087 original size:8 final size:8
Alignment explanation
Indices: 41570071--41570104 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
41570061 GTGTTAAAGG
*
41570071 TTTATGGT
1 TTTAGGGT
41570079 TTTAGGGT
1 TTTAGGGT
41570087 TTTAGGGT
1 TTTAGGGT
41570095 TTTAGGGT
1 TTTAGGGT
41570103 TT
1 TT
41570105 AAGTTTATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (8 bp):
TTTAGGGT
Found at i:41570124 original size:14 final size:14
Alignment explanation
Indices: 41569923--41570126 Score: 94
Period size: 14 Copynumber: 14.2 Consensus size: 14
41569913 CGTTAGAGTA
*
41569923 TAGGGTTTTTGGTT
1 TAGGGTTTATGGTT
*
41569937 TAGGGTATATGGTT
1 TAGGGTTTATGGTT
* * *
41569951 TAGAGCTTAAGGTT
1 TAGGGTTTATGGTT
* *
41569965 TA-GGTGTTACCGTTT
1 TAGGGT-TTA-TGGTT
* *
41569980 TAAGGTTTATGGAT
1 TAGGGTTTATGGTT
* *
41569994 TATGGGTTTAGGGGT
1 TA-GGGTTTATGGTT
*
41570009 TATGGTTTATGGTT
1 TAGGGTTTATGGTT
* * *
41570023 TATGGTTTAAAGG-C
1 TAGGGTTT-ATGGTT
41570037 TAGGGTTTGA-GGTT
1 TAGGGTTT-ATGGTT
41570051 TAGAGG-TTATGTGTT
1 TAG-GGTTTATG-GTT
* *
41570066 AAAGGTTTATGGTTT
1 TAGGGTTTATGG-TT
*
41570081 TAGGGTTTTAGGGTTT
1 TAGGG-TTTATGG-TT
*
41570097 TAGGGTTTA-AGTT
1 TAGGGTTTATGGTT
* *
41570110 TATGGTTTAGGGTT
1 TAGGGTTTATGGTT
41570124 TAG
1 TAG
41570127 ATTAACTAGT
Statistics
Matches: 144, Mismatches: 33, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
13 14 0.10
14 71 0.49
15 42 0.29
16 17 0.12
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (14 bp):
TAGGGTTTATGGTT
Found at i:41570444 original size:7 final size:7
Alignment explanation
Indices: 41570434--41570481 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
41570424 AGGTTTAAGG
41570434 GTTAGGA
1 GTTAGGA
*
41570441 GTTAGGG
1 GTTAGGA
41570448 GTTAGGA
1 GTTAGGA
41570455 GTTAGTG-
1 GTTAG-GA
41570462 GTTAGG-
1 GTTAGGA
41570468 GATTAGGA
1 G-TTAGGA
41570476 GTTAGG
1 GTTAGG
41570482 GATTTAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 2 0.06
7 32 0.89
8 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (7 bp):
GTTAGGA
Found at i:41570451 original size:14 final size:14
Alignment explanation
Indices: 41570432--41570481 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
41570422 TAAGGTTTAA
41570432 GGGTTAGGAGTTAG
1 GGGTTAGGAGTTAG
41570446 GGGTTAGGAGTTAG
1 GGGTTAGGAGTTAG
*
41570460 TGGTTAGG-GATTAG
1 GGGTTAGGAG-TTAG
*
41570474 GAGTTAGG
1 GGGTTAGG
41570482 GATTTAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 1 0.03
14 31 0.97
ACGTcount: A:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGGTTAGGAGTTAG
Found at i:41570458 original size:21 final size:20
Alignment explanation
Indices: 41570434--41570482 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
41570424 AGGTTTAAGG
*
41570434 GTTAGGAGTTAGGGGTTAGGA
1 GTTAGG-GTTAGGGATTAGGA
41570455 GTTAGTGGTTAGGGATTAGGA
1 GTTAG-GGTTAGGGATTAGGA
41570476 GTTAGGG
1 GTTAGGG
41570483 ATTTAAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (20 bp):
GTTAGGGTTAGGGATTAGGA
Found at i:41570506 original size:22 final size:22
Alignment explanation
Indices: 41570470--41570512 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41570460 TGGTTAGGGA
* *
41570470 TTAGGAGTTAGGGATTTAAGGT
1 TTAGGAGTTAAGGATTCAAGGT
*
41570492 TTAGGATTTAAGGATTCAAGG
1 TTAGGAGTTAAGGATTCAAGG
41570513 GTCGGGTTAG
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:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (22 bp):
TTAGGAGTTAAGGATTCAAGGT
Found at i:41571819 original size:23 final size:23
Alignment explanation
Indices: 41571789--41571834 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41571779 GTGTTTCATG
41571789 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
41571812 TCTGCTGCCTGATTAAGTTACAT
1 TCTGCTGCCTGATTAAGTTACAT
41571835 ACTAGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (23 bp):
TCTGCTGCCTGATTAAGTTACAT
Found at i:41572113 original size:25 final size:26
Alignment explanation
Indices: 41572078--41572126 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
41572068 TCTCCAATTC
*
41572078 TTAAACTTGATTTTGA-AATAAAAAA
1 TTAAACATGATTTTGATAATAAAAAA
*
41572103 TTAAACATGATTTTTATAATAAAA
1 TTAAACATGATTTTGATAATAAAA
41572127 CTTATTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (26 bp):
TTAAACATGATTTTGATAATAAAAAA
Found at i:41572190 original size:45 final size:46
Alignment explanation
Indices: 41572141--41572231 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
41572131 TTCTTCACAG
*
41572141 AATTAAA-TTCATACTATAAAATTTTTAAAAAATACAACCACTATA
1 AATTAAATTTCATACTATAAAATTTTCAAAAAATACAACCACTATA
* * * *
41572186 AATTAAATTTCCTACTTTGAAATTTTCAAAAAATACAATCACTATA
1 AATTAAATTTCATACTATAAAATTTTCAAAAAATACAACCACTATA
41572232 GACATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 7 0.17
46 33 0.82
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.35
Consensus pattern (46 bp):
AATTAAATTTCATACTATAAAATTTTCAAAAAATACAACCACTATA
Found at i:41577386 original size:120 final size:120
Alignment explanation
Indices: 41577189--41578051 Score: 1636
Period size: 120 Copynumber: 7.2 Consensus size: 120
41577179 TTTTCAAGTT
41577189 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577254 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41577309 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577374 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41577429 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577494 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41577549 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
41577614 TAATATAAGAATATTAATTATTAAGATTTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41577669 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577734 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
* *
41577789 ATATATTTAATAATAATTATGTTAATTTATATTTTACAATATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577854 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41577909 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
41577974 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
41578029 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
41578052 TAAATATGAT
Statistics
Matches: 727, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 727 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:41577788 original size:18 final size:17
Alignment explanation
Indices: 41577760--41577794 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41577750 ATTATTAAGA
*
41577760 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41577777 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41577795 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41578028 original size:18 final size:17
Alignment explanation
Indices: 41578000--41578034 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41577990 ATTATTAAGA
*
41578000 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41578017 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41578035 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41578291 original size:16 final size:16
Alignment explanation
Indices: 41578270--41578338 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
41578260 GATTAGCTAT
41578270 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41578286 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
41578303 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
41578319 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
41578335 TACA
1 TACA
41578339 GCGAACTCTC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41578312 original size:33 final size:32
Alignment explanation
Indices: 41578270--41578338 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
41578260 GATTAGCTAT
41578270 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
41578303 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
41578335 TACA
1 TACA
41578339 GCGAACTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:41581097 original size:43 final size:43
Alignment explanation
Indices: 41581036--41581122 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
41581026 TAATGATGTA
* *
41581036 CAAGATTTCTTTGATTAAGTAAATGTATT-ATATCTTTTATTAC
1 CAAGATTTCTTTGATTAAGAAAATGCATTGA-ATCTTTTATTAC
*
41581079 CAAGATTTAC-TTGATTAAGAAAATGCATTGAATGTTTTATTAC
1 CAAGATTT-CTTTGATTAAGAAAATGCATTGAATCTTTTATTAC
41581122 C
1 C
41581123 TTGCATATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 37 0.95
44 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (43 bp):
CAAGATTTCTTTGATTAAGAAAATGCATTGAATCTTTTATTAC
Found at i:41581666 original size:146 final size:145
Alignment explanation
Indices: 41581399--41581675 Score: 335
Period size: 146 Copynumber: 1.9 Consensus size: 145
41581389 TTTAGCGGCA
* * *
41581399 TTTGTGTGAAAAGCGACGCTAAAGGTCTGATCTTTTGCGGCGTTTGTGAGAAAAGCGCCACTAAA
1 TTTGTGGGAAAAGCGACGCTAAAAGTCTGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCACTAAA
* * * *
41581464 AGTGATGATTTATAGCCGCATTTGTGGTAAAAGCGTCGATAAAAGTCATGACCTATAGCGGTGTT
66 AGTCATGATTTATAGCCGCATTTATGGAAAAAGCGTCGATAAAAGTCATGACCTATAGCGGAGTT
41581529 TTCTCTATAGTAGCG
131 TTCTCTATAGTAGCG
* * **
41581544 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGA-CTTATAGCGGCGTTTGTGGGAAAAGCGCTGCTA
1 TTTGTGGGAAAAGCGACGCTAAAAGTC-TGATCTT-TAGCGGCGTTTGTGAGAAAAGCGCCACTA
** * * * **
41581608 AAAGTCATGATCTT-TAGTGGCGTTTATGGAAAAAGCG-CTGCTAAAAGTCTTGTTCTATAGCGG
64 AAAGTCATGAT-TTATAGCCGCATTTATGGAAAAAGCGTC-GATAAAAGTCATGACCTATAGCGG
41581671 AGTTT
127 AGTTT
41581676 GTGTGAAAAG
Statistics
Matches: 110, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
145 28 0.25
146 80 0.73
147 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (145 bp):
TTTGTGGGAAAAGCGACGCTAAAAGTCTGATCTTTAGCGGCGTTTGTGAGAAAAGCGCCACTAAA
AGTCATGATTTATAGCCGCATTTATGGAAAAAGCGTCGATAAAAGTCATGACCTATAGCGGAGTT
TTCTCTATAGTAGCG
Found at i:41581701 original size:43 final size:43
Alignment explanation
Indices: 41581532--41581715 Score: 226
Period size: 43 Copynumber: 4.3 Consensus size: 43
41581522 CGGTGTTTTC
** *
41581532 TCTATAGTAGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATG-
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGT
* *
41581574 ACTTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGA
1 TC-TATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGT
* * * * *
41581618 TCTTTAGTGGCGTTTATGGAAAAAGCGCTGCTAAAAGTCTTGT
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGT
* * * *
41581661 TCTATAGCGGAGTTTGTGTGAAAAGCGCTGCTAAAGGTCTTGT
1 TCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGT
41581704 TCTATAGCGGCG
1 TCTATAGCGGCG
41581716 GTGTCAATAG
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 119 0.98
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (43 bp):
TCTATAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAAGTCATGT
Found at i:41584355 original size:25 final size:22
Alignment explanation
Indices: 41584326--41584386 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
41584316 AAAATAAAAT
41584326 AATTAATTTTTTGAATTTTAATGAA
1 AATTAATTTTTT-AATTTTAAT--A
** *
41584351 AATTAATAATTTAATTTTTATA
1 AATTAATTTTTTAATTTTAATA
41584373 AATTAATTTATTTA
1 AATTAATTT-TTTA
41584387 TAAAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 8 0.27
23 4 0.13
24 8 0.27
25 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
AATTAATTTTTTAATTTTAATA
Found at i:41584388 original size:16 final size:15
Alignment explanation
Indices: 41584362--41584400 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
41584352 ATTAATAATT
*
41584362 TAATT-TTTATAAAT
1 TAATTATTTATAAAA
41584376 TAATTTATTTATAAAA
1 TAA-TTATTTATAAAA
41584392 TAATTATTT
1 TAATTATTT
41584401 TTCAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 8 0.36
16 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTATTTATAAAA
Found at i:41587909 original size:66 final size:66
Alignment explanation
Indices: 41587827--41587963 Score: 256
Period size: 66 Copynumber: 2.1 Consensus size: 66
41587817 TTTTAACGTA
41587827 GTTTTTCTATGTTTTCCATTTGTTAAAATTAGTCCACAAGCTCGCCTCACTCGAAAAAATTAAAT
1 GTTTTTCTATGTTTTCCATTTGTTAAAATTAGTCCACAAGCTCGCCTCACTCGAAAAAATTAAAT
41587892 T
66 T
* *
41587893 GTTTTTCTATGTTTTCCATTTGTTAAAATTAGTCCACGAGCTCGCCTCACTGGAAAAAATTAAAT
1 GTTTTTCTATGTTTTCCATTTGTTAAAATTAGTCCACAAGCTCGCCTCACTCGAAAAAATTAAAT
41587958 T
66 T
41587959 GTTTT
1 GTTTT
41587964 AAAAAATAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (66 bp):
GTTTTTCTATGTTTTCCATTTGTTAAAATTAGTCCACAAGCTCGCCTCACTCGAAAAAATTAAAT
T
Found at i:41587991 original size:28 final size:28
Alignment explanation
Indices: 41587955--41588009 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41587945 GAAAAAATTA
41587955 AATTGTTTTAAAAAAT-AAAAATATAGG
1 AATTGTTTTAAAAAATAAAAAATATAGG
*
41587982 AATTAGTTTTAACAAATAAAAAATATAG
1 AATT-GTTTTAAAAAATAAAAAATATAG
41588010 AAAAAATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 10 0.40
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (28 bp):
AATTGTTTTAAAAAATAAAAAATATAGG
Found at i:41588072 original size:21 final size:21
Alignment explanation
Indices: 41588019--41588081 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
41588009 GAAAAAATAC
* *
41588019 GTTAAAAGAAATAGAAAAGAGA
1 GTTAAAAG-AATAAAAAAGAAA
* *
41588041 G-GAAAATAATAAAAAAGAAA
1 GTTAAAAGAATAAAAAAGAAA
*
41588061 GTTAAAAGAATATAAAAGAAA
1 GTTAAAAGAATAAAAAAGAAA
41588082 AAAATTAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 12 0.36
21 20 0.61
22 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
GTTAAAAGAATAAAAAAGAAA
Found at i:41589306 original size:21 final size:20
Alignment explanation
Indices: 41589269--41589313 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41589259 ACAAGTTCTA
41589269 TTTTCCTTTTTTATTTTTAC
1 TTTTCCTTTTTTATTTTTAC
*
41589289 TTTTCTCTTTATTT-TTTTTTC
1 TTTTC-CTTT-TTTATTTTTAC
41589310 TTTT
1 TTTT
41589314 TTCGTAACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 14 0.64
22 3 0.14
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCCTTTTTTATTTTTAC
Found at i:41594852 original size:9 final size:9
Alignment explanation
Indices: 41594838--41594875 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
41594828 TCAGACTCAA
41594838 AAAAAAATC
1 AAAAAAATC
41594847 AAAAAAATC
1 AAAAAAATC
41594856 AAAAAAAT-
1 AAAAAAATC
*
41594864 AAAAAAACC
1 AAAAAAATC
41594873 AAA
1 AAA
41594876 GTCAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATC
Found at i:41594861 original size:17 final size:18
Alignment explanation
Indices: 41594838--41594875 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
41594828 TCAGACTCAA
* *
41594838 AAAAAAATCAAAAAAATC
1 AAAAAAATAAAAAAAACC
41594856 AAAAAAAT-AAAAAAACC
1 AAAAAAATAAAAAAAACC
41594873 AAA
1 AAA
41594876 GTCAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAAAAATAAAAAAAACC
Found at i:41597115 original size:43 final size:43
Alignment explanation
Indices: 41597066--41597203 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
41597056 GAAGCAGGTC
41597066 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTT
* ** * * *
41597109 GAAGACAAAAGACCTTGCCT-TC-CTGCAT-TGAAAGCGAAGCAGGTC
1 GAAGACACAA-ACCTTGCCTCTCTC-GGTTGTGATA--G-AGCTGGTT
* * *
41597154 GAAGACTCAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTT
41597197 GAAGACA
1 GAAGACA
41597204 AAAGATCTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
42 5 0.07
43 25 0.35
44 20 0.28
45 17 0.24
46 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTT
Found at i:41597258 original size:44 final size:44
Alignment explanation
Indices: 41597021--41597260 Score: 161
Period size: 44 Copynumber: 5.4 Consensus size: 44
41597011 ACAGATCAGT
* * *
41597021 GAAGACAAAAGATCTTGTCTTCCTGCATTGACAACGAAGCAGGTC
1 GAAGACAAAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
* ** * * *
41597066 GAAGACACAAACCTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTT
1 GAAGACAAAAACCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTC
*
41597109 GAAGACAAAAGACCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTC
1 GAAGACAAAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
** * * * ** * *
41597154 GAAGACTCAAACCTTGCC-TCTTTCGGTTGTGATG-G-AGCTGGTT
1 GAAGACAAAAACCTTGCCTTCCTGC-ATTGACA-GCGAAGCAGGTC
*
41597197 GAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
1 GAAGACAAAA-ACCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
* *
41597242 GAAAACATAAACCTTGCCT
1 GAAGACAAAAACCTTGCCT
41597261 CCATCGGTGG
Statistics
Matches: 145, Mismatches: 36, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
42 4 0.03
43 38 0.26
44 53 0.37
45 46 0.32
46 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (44 bp):
GAAGACAAAAACCTTGCCTTCCTGCATTGACAGCGAAGCAGGTC
Found at i:41597268 original size:88 final size:87
Alignment explanation
Indices: 41597020--41597349 Score: 400
Period size: 88 Copynumber: 3.8 Consensus size: 87
41597010 AACAGATCAG
* * *
41597020 TGAAGACAAAAGATCTTGTCTTCCTGCATTGACAACGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAAACATAAACCTTGCCT
*
41597085 CTCTCGGTTGTGATAGAGCTGGT
66 C-CTCGGTTGTGATGGAGCTGGT
* *
41597108 TGAAGACAAAAGACCTTGCCTTCCTGCATTGA-AAGCGAAGCAGGTCGAAGAC-TCAAACCTTGC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAA-CGAAGCAGGTCGAAAACAT-AAACCTTGC
*
41597171 CTCTTTCGGTTGTGATGGAGCTGGT
64 CTC-CTCGGTTGTGATGGAGCTGGT
*
41597196 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAAACATAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAAACATAAACCTTGCCT
*
41597261 CCATCGG-TG-GCAGTGGAGCTAGT
66 CC-TCGGTTGTG-A-TGGAGCTGGT
* ** * * * * * *
41597284 TGAAGATAGCAGATCTTGCCTTCATGCGTTAACAACGAAGCAGATCAAAAACA-AAGCCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAAACATAAACCTTGCCT
41597348 CC
66 CC
41597350 CTGAGATTAC
Statistics
Matches: 215, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
86 1 0.00
87 17 0.08
88 195 0.91
89 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (87 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAACGAAGCAGGTCGAAAACATAAACCTTGCCT
CCTCGGTTGTGATGGAGCTGGT
Found at i:41597396 original size:44 final size:43
Alignment explanation
Indices: 41597346--41598333 Score: 348
Period size: 44 Copynumber: 22.6 Consensus size: 43
41597336 AAAGCCTTGC
* *
41597346 CTCCCTGAGATTACAGCGGAGCAGATTAAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
** * * *
41597390 CTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* ** * *** * *
41597434 CTCTCTGA-AGTTACAGCAGAGTAGA-TCGCGTCAG-GTCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
* ** **
41597475 TTCCCTGAGATTACAGTGGAATAGACCAAAGAATGTCAG-ATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAG--T-T-AGAATCTTAT
* * *
41597521 CTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
* ** * * *
41597565 CTCCCTGAGATTACCGTGGAGTGGATTAAAATGAAGGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* * *** ** * *
41597609 CTCTCTGA-AGTTACAGTAGAGCAGATCGCA-CCAG-GTCGTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
* * * * *
41597650 TTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAG-GTCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-T-TA-AAGTT-AGAATCTTAT
* * * ** *
41597696 TTCCCTGAGATTACGGTGGAACAGACCGAAGAATT-GCAGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-TTAA-AGTTAG-A-ATCTTAT
* * * *
41597742 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
* * * * *
41597786 CTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* ** * *** *
41597830 CTCTCTGA-AGTTACAGTACAGTAGA-TCGTGTCAG-ATCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
* * *
41597871 CTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
** * * *
41597915 CTCCCTGAGATTACCA-TGGAGTGGATTAAAATGAAGGATCTTAT
1 CTCCCTGAGATTA-CAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* * *** ** *
41597959 CTCTCTGA-AGTTACAGTAGAGCAGATCGTA-CCAG-GTCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
* * * * *
41598000 TTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAG-GTCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-T-TA-AAGTT-AGAATCTTAT
* * * ** *
41598046 TTCCCTGAGATTACGGTGGAAC-GACCGAAGAATT-GCAGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGA-TTAA-AGTTAG-A-ATCTTAT
** * * *
41598091 CTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
* * * * *
41598135 CTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* ** * *** *
41598179 CTCTCTGA-AGTTACAGTACAGTAGA-TCGTGTCAG-ATCTTAT
1 CTCCCTGAGA-TTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
* * *
41598220 CTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAG-AATCTTAT
* ** * * *
41598264 CTCCCTGAGATTACCGTGGAGTGGATTAAAATGAAGGATCTTAT
1 CTCCCTGAGATTACAGTGGAGCAGATTAAAGT-TAGAATCTTAT
* * *
41598308 CTCTCTGA-AGTTACAGTAGAGTAGAT
1 CTCCCTGAGA-TTACAGTGGAGCAGAT
41598334 CTCACCAGGT
Statistics
Matches: 692, Mismatches: 199, Indels: 106
0.69 0.20 0.11
Matches are distributed among these distances:
41 123 0.18
42 31 0.04
43 17 0.02
44 347 0.50
45 50 0.07
46 124 0.18
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
CTCCCTGAGATTACAGTGGAGCAGATTAAAGTTAGAATCTTAT
Found at i:41597738 original size:221 final size:221
Alignment explanation
Indices: 41597464--41597901 Score: 689
Period size: 221 Copynumber: 2.0 Consensus size: 221
41597454 GTAGATCGCG
*
41597464 TCAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACCAAAGAATGTCAGATCTTATCTCCCTGA
1 TCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATGTCAGATCTTATCTCCCTGA
* * *
41597529 GATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACCGTGGAGTGGATTAA
66 GATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAA
* * * *
41597594 AATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACCAGGTCGTATTTCCCTGAG
131 AATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGCAGATCGCACCAGATCGTATCTCCCTGAG
*
41597659 ATTACAGTGGAACAGACTGAAGAATT
196 ATTACAGCGGAACAGACTGAAGAATT
* *
41597685 TCAGGTCTTATTTCCCTGAGATTACGGTGGAACAGACCGAAGAAT-TGCAGATCTTATCTCCCTG
1 TCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATGT-CAGATCTTATCTCCCTG
*
41597749 AGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTA
65 AGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTA
* *** *
41597814 AAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCGTGTCAGATCTTATCTCCCTGA
130 AAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGCAGATCGCACCAGATCGTATCTCCCTGA
* *
41597879 GATTACAGCGGAGCAGATTGAAG
195 GATTACAGCGGAACAGACTGAAG
41597902 TTAGTAATCC
Statistics
Matches: 197, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
220 1 0.01
221 196 0.99
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (221 bp):
TCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATGTCAGATCTTATCTCCCTGA
GATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAA
AATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGCAGATCGCACCAGATCGTATCTCCCTGAG
ATTACAGCGGAACAGACTGAAGAATT
Found at i:41597878 original size:129 final size:129
Alignment explanation
Indices: 41597346--41598030 Score: 537
Period size: 129 Copynumber: 5.2 Consensus size: 129
41597336 AAAGCCTTGC
* *
41597346 CTCCCTGAGATTACAGCGGAGCAGATTAAAGTTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
* * * *
41597411 TGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGGTCTTAT
66 CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTAT
* * ** *** * * *
41597475 TTCCCTGAGATTACAGTGGAATAGACCAAAG-AATGTCAGATCTTATCTCCCTGAGATTACAGCG
1 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTA-GT-A-ATCCTATCTCCCTGAGATTACAGTG
* * * * * * * * * * ** *
41597539 GAGCAGATTGAAGT-TAGTAATCCTATCTCCCTG-AGATTACCGTGGAGTGGATTAAAATG-AAG
63 GAGCGGATTAAAATAAAG-GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGA-T--CGTGTCA-
41597601 GATCTTAT
122 GATCTTAT
* ** * * * * * *
41597609 CTCTCTGA-AGTTACAGTAGAGCAGATCGCA-CCAG--GTCGTATTTCCCTGAGATTACAGTGGA
1 CTCCCTGAGA-TTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGA
* * * ** * * * * ** * *
41597670 ACAGACTGAAGAATTTCAGG-TCTTATTTCCCTG-AGATTACGGTGGAACAGACCGAAGAATTGC
65 GCGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATCG-TG---T-C
41597733 AGATCTTAT
121 AGATCTTAT
*
41597742 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAG
1 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
*
41597807 CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCGTGTCAGATCTTAT
66 CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTAT
*
41597871 CTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGATTACCA-TGGA
1 CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTA-CAGTGGA
* * * ** *
41597935 GTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGTACCAGGTCTTAT
65 GCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTAT
* * * *
41598000 TTCCCTGAGATTACAGTGGAACAGACTGAAG
1 CTCCCTGAGATTACAGCGGAGCAGATTGAAG
41598031 AATTTCAGGT
Statistics
Matches: 435, Mismatches: 93, Indels: 56
0.74 0.16 0.10
Matches are distributed among these distances:
128 1 0.00
129 209 0.48
130 10 0.02
131 82 0.19
132 2 0.00
133 41 0.09
134 59 0.14
135 5 0.01
136 26 0.06
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (129 bp):
CTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTGTCAGATCTTAT
Found at i:41598096 original size:45 final size:46
Alignment explanation
Indices: 41597994--41598106 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 46
41597984 TCGTACCAGG
* * *
41597994 TCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGG
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGA
*
41598040 TCTTATTTCCCTGAGATTACGGTGGAAC-GACCGAAGAATTGCAGA
1 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGA
*
41598085 TCTTATCTCCCTGAGATTACAG
1 TCTTATTTCCCTGAGATTACAG
41598107 AAGAGCAGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 34 0.56
46 27 0.44
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGA
Found at i:41598227 original size:129 final size:129
Alignment explanation
Indices: 41598081--41598364 Score: 444
Period size: 129 Copynumber: 2.2 Consensus size: 129
41598071 CGAAGAATTG
*
41598081 CAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGATAT
1 CAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
**
41598146 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCGT-GT
66 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATC-TCAC
** *
41598210 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
* * * *
41598275 TACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCTCAC
66 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCTCAC
* *
41598339 CAGGTCTTATTTCCCTGAGATTACAG
1 CAGATCTTATCTCCCTGAGATTACAG
41598365 TGGAACAGAC
Statistics
Matches: 142, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 1 0.01
129 141 0.99
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (129 bp):
CAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTACAGTAGATCTCAC
Found at i:41598276 original size:349 final size:350
Alignment explanation
Indices: 41597508--41598387 Score: 1665
Period size: 349 Copynumber: 2.5 Consensus size: 350
41597498 GACCAAAGAA
41597508 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
*
41597573 GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGC
66 GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGT
*
41597638 ACCAGGTCGTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGGTCTTATTTCCCTG
131 ACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGGTCTTATTTCCCTG
**
41597703 AGATTACGGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGAT
196 AGATTACGGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGAT
41597768 TGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
261 TGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
41597833 TCTGAAGTTACAGTACAGTAGATCG
326 TCTGAAGTTACAGTACAGTAGATCG
41597858 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
*
41597923 GATTACCATGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGT
66 GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGT
41597988 ACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGGTCTTATTTCCCTG
131 ACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGGTCTTATTTCCCTG
41598053 AGATTACGGTGGAAC-GACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGAT
196 AGATTACGGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGAT
41598117 TGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
261 TGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
41598182 TCTGAAGTTACAGTACAGTAGATCG
326 TCTGAAGTTACAGTACAGTAGATCG
41598207 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
1 TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
*
41598272 GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC-T
66 GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGT
* *
41598336 CACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAGGAATTTCAG
131 -ACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAG
41598388 ATTTTATCTC
Statistics
Matches: 520, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
348 1 0.00
349 312 0.60
350 207 0.40
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (350 bp):
TGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTGA
GATTACCGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGT
ACCAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATTTCAGGTCTTATTTCCCTG
AGATTACGGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGAT
TGAAGCTAGTAATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTC
TCTGAAGTTACAGTACAGTAGATCG
Found at i:41599188 original size:21 final size:20
Alignment explanation
Indices: 41599146--41599196 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
41599136 TTGGTACAAG
*
41599146 TTCTATTTTCCTTTTTTATT
1 TTCTCTTTTCCTTTTTTATT
41599166 TT-TACTTTTCTCTTTATTT-TT
1 TTCT-CTTTTC-CTTT-TTTATT
41599187 TTCTCTTTTC
1 TTCTCTTTTC
41599197 GTAACTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 7 0.27
21 14 0.54
22 4 0.15
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (20 bp):
TTCTCTTTTCCTTTTTTATT
Found at i:41599855 original size:3 final size:3
Alignment explanation
Indices: 41599847--41599876 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41599837 ACAAATTTCA
41599847 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41599877 ACTCTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41604128 original size:13 final size:13
Alignment explanation
Indices: 41604110--41604135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41604100 TGTAACATTG
41604110 GTACATATAATTT
1 GTACATATAATTT
41604123 GTACATATAATTT
1 GTACATATAATTT
41604136 ATTTTAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
GTACATATAATTT
Found at i:41605765 original size:51 final size:51
Alignment explanation
Indices: 41605686--41605922 Score: 284
Period size: 51 Copynumber: 4.6 Consensus size: 51
41605676 AGTTACTAGA
41605686 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
* *
41605737 TCATGTGTGTAGTACTATGTGCAGGCTACTACTATGTGTA-CTGGAATG-ATA-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAC---GTGTATC-GG-ATGAAAATGG
* * * * * *** *
41605790 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT-GG
41605841 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
*
41605892 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
41605923 TGTGAACCGG
Statistics
Matches: 155, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
49 2 0.01
50 6 0.04
51 102 0.66
52 2 0.01
53 31 0.20
54 9 0.06
55 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
Found at i:41605871 original size:104 final size:102
Alignment explanation
Indices: 41605686--41605924 Score: 297
Period size: 104 Copynumber: 2.3 Consensus size: 102
41605676 AGTTACTAGA
* * * * * *
41605686 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCATGTGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGATCACGTGTGTAGTA
*
41605751 CTATGTGCAGGCTACTACTATGTGTA-CTGGAATG-ATA-GG
66 CTATGTGCAGGCTACTAC---GTGTATC-GG-ATGAAAATGG
* ***
41605790 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGATCACGTGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAAT-GATCACGTGTGTAGT
41605854 ACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
65 ACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
41605892 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
41605925 TGAACCGGGT
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
100 3 0.03
101 9 0.08
102 35 0.29
103 2 0.02
104 70 0.59
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGATCACGTGTGTAGTA
CTATGTGCAGGCTACTACGTGTATCGGATGAAAATGG
Found at i:41605926 original size:26 final size:26
Alignment explanation
Indices: 41605846--41605926 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
41605836 TTCGATCACG
41605846 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * ***
41605872 CGTGTA-T-CGGATGAAAATGG-TCAC-A
1 TGTGTAGTAC-TATGTGCA-GGCT-ACTA
41605897 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
41605923 TGTG
1 TGTG
41605927 AACCGGGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 20 0.53
27 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:41609081 original size:22 final size:20
Alignment explanation
Indices: 41609056--41609109 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 20
41609046 TAATGTTGTC
41609056 TTTTCTCTCTTTCTTTTTCATT
1 TTTTCTCTCTTT-TTTTTC-TT
41609078 TTTTCTCTCTTTTTTTTCTT
1 TTTTCTCTCTTTTTTTTCTT
41609098 TTTTCTCGTCTT
1 TTTTCTC-TCTT
41609110 AGCCCTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.29
21 10 0.32
22 12 0.39
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTCTCTCTTTTTTTTCTT
Found at i:41609084 original size:20 final size:20
Alignment explanation
Indices: 41609056--41609109 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
41609046 TAATGTTGTC
41609056 TTTTCTCTCTTTCTTTTTCATT
1 TTTTCTCTC-TTCTTTTTC-TT
*
41609078 TTTTCTCTCTTTTTTTTCTT
1 TTTTCTCTCTTCTTTTTCTT
41609098 TTTTCTCGTCTT
1 TTTTCTC-TCTT
41609110 AGCCCTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.30
21 12 0.40
22 9 0.30
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTCTCTCTTCTTTTTCTT
Found at i:41614972 original size:21 final size:21
Alignment explanation
Indices: 41614946--41614987 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41614936 CCATTTAAAC
41614946 CTTTCCCAAGACTCATATAAT
1 CTTTCCCAAGACTCATATAAT
*
41614967 CTTTCCTAAGACTCATATAAT
1 CTTTCCCAAGACTCATATAAT
41614988 GACTCACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (21 bp):
CTTTCCCAAGACTCATATAAT
Found at i:41618833 original size:21 final size:19
Alignment explanation
Indices: 41618806--41618860 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
41618796 TAATGAGAGA
*
41618806 AAATGAGAGAAAAGTAAAAG
1 AAATGAGAGAAAA-AAAAAG
* *
41618826 AATTTGAGATAAGAAAAAAAG
1 AA-ATGAGAGAA-AAAAAAAG
41618847 AAATGAGAGAAAAA
1 AAATGAGAGAAAAA
41618861 GAAACTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.11
20 9 0.32
21 14 0.50
22 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (19 bp):
AAATGAGAGAAAAAAAAAG
Found at i:41620769 original size:51 final size:50
Alignment explanation
Indices: 41620667--41620808 Score: 214
Period size: 51 Copynumber: 2.8 Consensus size: 50
41620657 TAAATAAAGT
* *
41620667 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTGCATCATAAATTATGA
1 CATGCTTTATGTAACTCTCATGTTAGTTAAATTTGCATCATAAATTATGA
* * *
41620716 CATGCTTTATGTTACTCTCGTTTTAGTTAAATTTTGCATCATAAATTATGA
1 CATGCTTTATGTAACTCTCATGTTAGTTAAA-TTTGCATCATAAATTATGA
41620767 CATGCTTTATGTAACTCTCATGTTAGTTAAAGTTTGCATCAT
1 CATGCTTTATGTAACTCTCATGTTAGTTAAA-TTTGCATCAT
41620809 TACATAAAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 24 0.29
50 2 0.02
51 56 0.68
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (50 bp):
CATGCTTTATGTAACTCTCATGTTAGTTAAATTTGCATCATAAATTATGA
Found at i:41633760 original size:45 final size:45
Alignment explanation
Indices: 41633696--41633788 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
41633686 TCATAATTAA
*
41633696 GTAGAAAAGATAAATGAATCGAATGATATTTTGAGAAATAACAAT
1 GTAGAAAAGATAAATGAATCGAATGATATTTTGAGAAATAAAAAT
41633741 GTAGAAAAGATAAATGAATCGAATGATATTTTGAGAAATAAAAAT
1 GTAGAAAAGATAAATGAATCGAATGATATTTTGAGAAATAAAAAT
41633786 GTA
1 GTA
41633789 ATTAATACAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.27
Consensus pattern (45 bp):
GTAGAAAAGATAAATGAATCGAATGATATTTTGAGAAATAAAAAT
Found at i:41633779 original size:24 final size:24
Alignment explanation
Indices: 41633707--41633779 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
41633697 TAGAAAAGAT
41633707 AAATGAATCGAATGATATTTTGAG
1 AAATGAATCGAATGATATTTTGAG
**** *
41633731 AAAT-AA-C-AATG-TAGAAAAGAT
1 AAATGAATCGAATGATA-TTTTGAG
41633752 AAATGAATCGAATGATATTTTGAG
1 AAATGAATCGAATGATATTTTGAG
41633776 AAAT
1 AAAT
41633780 AAAAATGTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 2 0.06
21 10 0.29
22 3 0.09
23 3 0.09
24 14 0.41
25 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (24 bp):
AAATGAATCGAATGATATTTTGAG
Done.