Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 120 of 131
Found at i:39637103 original size:18 final size:19
Alignment explanation
Indices: 39637082--39637184 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 19
39637072 ATTTTTTAAG
39637082 TTTTACTAATTTTATT-T-T
1 TTTTA-TAATTTTATTATAT
39637100 TTTTATAA-TTTATTATAT
1 TTTTATAATTTTATTATAT
** *
39637118 TTTTATAATATTTACAAGTTT
1 TTTTATAAT-TTTATTA-TAT
*
39637139 TTTTATAACTTTA--ATAT
1 TTTTATAATTTTATTATAT
*
39637156 TCTTT-TTATTTT-TTA-AT
1 T-TTTATAATTTTATTATAT
39637173 TTTTATAATTTT
1 TTTTATAATTTT
39637185 TATACACAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
16 9 0.13
17 21 0.31
18 19 0.28
20 9 0.13
21 10 0.15
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTATTATAT
Found at i:39640036 original size:86 final size:87
Alignment explanation
Indices: 39639917--39640090 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
39639907 TATAATATAA
39639917 ATTTTTATGATTTATAACATAAGAATTTTTTTTATCATAACCATCTCAAACACTTGCACTTGCTC
1 ATTTTTATGATTTATAACATAAGAATTTTTTTTATCATAACCATCTCAAACACTTGCACTTGCTC
39639982 ATGCCTATAATATAAATTTTAT
66 ATGCCTATAATATAAATTTTAT
39640004 ATTTTTATGA-TTATAACATAAGAATTTTTTTTATCATAACCATCTCAAACACTTGCACTTGCTC
1 ATTTTTATGATTTATAACATAAGAATTTTTTTTATCATAACCATCTCAAACACTTGCACTTGCTC
39640068 ATGCCTATAATATAAATTTTAT
66 ATGCCTATAATATAAATTTTAT
39640090 A
1 A
39640091 ATTTGTGTAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 77 0.89
87 10 0.11
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (87 bp):
ATTTTTATGATTTATAACATAAGAATTTTTTTTATCATAACCATCTCAAACACTTGCACTTGCTC
ATGCCTATAATATAAATTTTAT
Found at i:39652825 original size:4 final size:4
Alignment explanation
Indices: 39652811--39652842 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
39652801 CTATTACCAT
39652811 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAA
39652843 TCGAATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:39655354 original size:2 final size:2
Alignment explanation
Indices: 39655347--39655375 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39655337 ATGATGAACA
39655347 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39655376 ATCTACCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39655522 original size:2 final size:2
Alignment explanation
Indices: 39655517--39655754 Score: 469
Period size: 2 Copynumber: 119.5 Consensus size: 2
39655507 AAAAGCTTTG
39655517 TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39655558 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39655600 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39655642 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39655684 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39655726 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39655755 TCCTCCTCTG
Statistics
Matches: 235, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
1 1 0.00
2 234 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39657288 original size:2 final size:2
Alignment explanation
Indices: 39657281--39657307 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39657271 CTAAAAGGCT
39657281 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39657308 GTTATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39667912 original size:34 final size:34
Alignment explanation
Indices: 39667874--39667993 Score: 145
Period size: 34 Copynumber: 3.6 Consensus size: 34
39667864 GCTATTGCAA
*
39667874 TGATCCATTATAAGCATGTTAATTGCTACCGTAT
1 TGATCTATTATAAGCATGTTAATTGCTACCGTAT
* **
39667908 TGATCTATTATAAGCATGATAATTGCTATTGTAT
1 TGATCTATTATAAGCATGTTAATTGCTACCGTAT
* *
39667942 CGA-CTTATTATAAACATGTT-ATTGCTACCGTAT
1 TGATC-TATTATAAGCATGTTAATTGCTACCGTAT
* *
39667975 TGATTTGTTATAAGCATGT
1 TGATCTATTATAAGCATGT
39667994 CATGTTGTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
33 26 0.37
34 45 0.63
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (34 bp):
TGATCTATTATAAGCATGTTAATTGCTACCGTAT
Found at i:39668126 original size:21 final size:23
Alignment explanation
Indices: 39668100--39668150 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
39668090 GCAGTTTATT
39668100 TACAAC-GATT-AGTGGTTCATC
1 TACAACAGATTAAGTGGTTCATC
*
39668121 TACAACATATTACAGTGGTTCATC
1 TACAACAGATTA-AGTGGTTCATC
*
39668145 CACAAC
1 TACAAC
39668151 CTACTAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 3 0.12
24 16 0.64
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (23 bp):
TACAACAGATTAAGTGGTTCATC
Found at i:39669701 original size:40 final size:40
Alignment explanation
Indices: 39669634--39669760 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
39669624 ACCAGTTTAG
* *
39669634 CACCTAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
* * * *
39669674 CACCCAGTGTCTCATCGGCTAAATCGAAGT--GAA-TTGG
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
** *
39669711 CACCCAGTGCCTCATCAAATTAATCCGAAGTAAT-AGATTGA
1 CACCCAGTGCCTCATCGGATAAAT-CGAAGTAATAAG-TTGA
39669752 CACCCAGTG
1 CACCCAGTG
39669761 TTTCATCGAC
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
37 22 0.32
38 8 0.12
39 1 0.01
40 26 0.38
41 12 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
Found at i:39670267 original size:8 final size:8
Alignment explanation
Indices: 39670254--39670283 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
39670244 TTAATATTAT
39670254 TATAATAA
1 TATAATAA
39670262 TATAATAA
1 TATAATAA
39670270 TATAAT-A
1 TATAATAA
39670277 TATAATA
1 TATAATA
39670284 TACTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAATAA
Found at i:39676951 original size:19 final size:19
Alignment explanation
Indices: 39676929--39677079 Score: 62
Period size: 19 Copynumber: 8.3 Consensus size: 19
39676919 TTCATTCACT
39676929 TAATATTATTATAATAATA
1 TAATATTATTATAATAATA
*
39676948 TAATA-TA--ATAATATATT
1 TAATATTATTATAATA-ATA
*
39676965 TAA-A-TATTA-ATTAATA
1 TAATATTATTATAATAATA
*
39676981 -CATATT-TTATTAAT-ATA
1 TAATATTATTA-TAATAATA
*
39676998 TACATATGTA-TATATTAATA
1 TA-ATAT-TATTATAATAATA
* *
39677018 AAATATGTATTAATTAAT-ATT
1 TAATAT-TATT-A-TAATAATA
39677039 TAA-ATATATTAT--T-ATA
1 TAATAT-TATTATAATAATA
*
39677055 TTATATTATTATAATAATA
1 TAATATTATTATAATAATA
39677074 TAATAT
1 TAATAT
39677080 AATAATATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 38
0.65 0.10 0.25
Matches are distributed among these distances:
15 1 0.01
16 26 0.27
17 14 0.14
18 7 0.07
19 28 0.29
20 14 0.14
21 5 0.05
22 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
TAATATTATTATAATAATA
Found at i:39676970 original size:13 final size:13
Alignment explanation
Indices: 39676938--39676962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39676928 TTAATATTAT
39676938 TATAATAATATAA
1 TATAATAATATAA
39676951 TATAATAATATA
1 TATAATAATATA
39676963 TTTAAATATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:39677059 original size:13 final size:13
Alignment explanation
Indices: 39677043--39677067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39677033 AATATTTAAA
39677043 TATATTATTATAT
1 TATATTATTATAT
39677056 TATATTATTATA
1 TATATTATTATA
39677068 ATAATATAAT
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:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATTATAT
Found at i:39677096 original size:13 final size:13
Alignment explanation
Indices: 39677064--39677088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39677054 ATTATATTAT
39677064 TATAATAATATAA
1 TATAATAATATAA
39677077 TATAATAATATA
1 TATAATAATATA
39677089 TTTAAATATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:39677152 original size:126 final size:127
Alignment explanation
Indices: 39676931--39677158 Score: 397
Period size: 126 Copynumber: 1.8 Consensus size: 127
39676921 CATTCACTTA
39676931 ATATTATTATAATAATATAATATAATAATATATTTAAATATTAATTAATACATATTTTATTAATA
1 ATATTATTATAATAATATAATATAATAATATATTTAAATATTAATTAATACATATTTTATTAATA
*
39676996 TATACATATGTATATATTAATAAAATATGT-ATTAATTAATATTTAAATATATTATTATATT
66 TATACATATGTATATATTAATAAAACATGTAATTAATTAATATTTAAATATATTATTATATT
39677057 ATATTATTATAATAATATAATATAATAATATATTTAAATATTAATTAATACATATTTTATTAATA
1 ATATTATTATAATAATATAATATAATAATATATTTAAATATTAATTAATACATATTTTATTAATA
* * *
39677122 TATACATATGTATATTATT-TTTACACATGTAATTAAT
66 TATACATATGTATA-TATTAATAAAACATGTAATTAAT
39677159 ATTACCATAC
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
126 86 0.90
127 10 0.10
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (127 bp):
ATATTATTATAATAATATAATATAATAATATATTTAAATATTAATTAATACATATTTTATTAATA
TATACATATGTATATATTAATAAAACATGTAATTAATTAATATTTAAATATATTATTATATT
Found at i:39678826 original size:2 final size:2
Alignment explanation
Indices: 39678821--39678857 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39678811 AAACACACAC
39678821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39678858 ATCCAACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39681419 original size:21 final size:21
Alignment explanation
Indices: 39681390--39681429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39681380 TAACAAATCT
*
39681390 TAATATTATTTATATTTATGA
1 TAATATTATATATATTTATGA
* *
39681411 TAATTTTATATATTTTTAT
1 TAATATTATATATATTTAT
39681430 TTTCTTAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TAATATTATATATATTTATGA
Found at i:39686728 original size:21 final size:19
Alignment explanation
Indices: 39686704--39686754 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
39686694 TGAATCAAGC
*
39686704 CGAGTGAAATGAAATCCGAGT
1 CGAGTGAAATG-AAT-CGAAT
*
39686725 CGAGTCAAATTGAATCGAAT
1 CGAGTGAAA-TGAATCGAAT
39686745 CGAGTGAAAT
1 CGAGTGAAAT
39686755 TGTTCAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 11 0.42
22 2 0.08
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (19 bp):
CGAGTGAAATGAATCGAAT
Found at i:39686961 original size:10 final size:10
Alignment explanation
Indices: 39686946--39687004 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
39686936 TTATTATTCT
39686946 AATTTTTTTA
1 AATTTTTTTA
39686956 AA-TTTTTTA
1 AATTTTTTTA
39686965 AATTTTTTTA
1 AATTTTTTTA
* *
39686975 TATACTTTTTA
1 AAT-TTTTTTA
* *
39686986 GAATATTTTTG
1 -AATTTTTTTA
39686997 AATTTTTT
1 AATTTTTT
39687005 ATAATATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 9 0.22
10 18 0.45
11 11 0.28
12 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:39686970 original size:8 final size:9
Alignment explanation
Indices: 39686949--39687005 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
39686939 TTATTCTAAT
39686949 TTTTTTAAA
1 TTTTTTAAA
39686958 TTTTTTAAA
1 TTTTTTAAA
39686967 TTTTTTTATATA
1 -TTTTTTA-A-A
*
39686979 CTTTTTAGAA
1 TTTTTTA-AA
*
39686989 TATTTTTGAA
1 T-TTTTTAAA
39686999 TTTTTTA
1 TTTTTTA
39687006 TAATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 14 0.36
10 11 0.28
11 13 0.33
12 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:39687050 original size:19 final size:19
Alignment explanation
Indices: 39687028--39687094 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
39687018 AACATATAAT
*
39687028 TTTTTAATTTTTATAAATA
1 TTTTGAATTTTTATAAATA
* *
39687047 TTTTGAA-TTTTAAAAATTC
1 TTTTGAATTTTTATAAA-TA
* *
39687066 TTTTTAATTTTTGATAATTA
1 TTTTGAATTTTT-ATAAATA
39687086 TTTTGAATT
1 TTTTGAATT
39687095 ATTTTGTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
18 8 0.22
19 13 0.35
20 13 0.35
21 3 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTGAATTTTTATAAATA
Found at i:39699043 original size:4 final size:4
Alignment explanation
Indices: 39699034--39699124 Score: 182
Period size: 4 Copynumber: 22.8 Consensus size: 4
39699024 CGGATTTTTC
39699034 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
39699082 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
39699125 TAGTTTACTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 87 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:39706555 original size:84 final size:84
Alignment explanation
Indices: 39706414--39706582 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
39706404 GCGAGGAGGA
39706414 GCTAAAAAGCCCCTAGGGGTGCAGCTCTGACCACCGTTGACGGTGTAATCGTGGCGGAGAGGTGG
1 GCTAAAAAGCCCCTAGGGGTGCAGCTCTGACCACCGTTGACGGTGTAATCGTGGCGGAGAGGTGG
39706479 CAGACTGGCGGCGAAGGGT
66 CAGACTGGCGGCGAAGGGT
*
39706498 GCTAAAAAGGCCCTAGGGGTGCAGCTCTGACCACCGTTGACGGTGTAATCGTGGCGGAGAGGTGG
1 GCTAAAAAGCCCCTAGGGGTGCAGCTCTGACCACCGTTGACGGTGTAATCGTGGCGGAGAGGTGG
39706563 CAGACTGGCGGCGAAGGGT
66 CAGACTGGCGGCGAAGGGT
39706582 G
1 G
39706583 AGAGAGGTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.21, C:0.22, G:0.40, T:0.17
Consensus pattern (84 bp):
GCTAAAAAGCCCCTAGGGGTGCAGCTCTGACCACCGTTGACGGTGTAATCGTGGCGGAGAGGTGG
CAGACTGGCGGCGAAGGGT
Found at i:39707370 original size:21 final size:21
Alignment explanation
Indices: 39707344--39707385 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39707334 AGATTTATTT
*
39707344 AGATATTTTTGTTTCACATAA
1 AGATATTTCTGTTTCACATAA
39707365 AGATATTTCTGTTTCACATAA
1 AGATATTTCTGTTTCACATAA
39707386 TATATATATA
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:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
AGATATTTCTGTTTCACATAA
Found at i:39718006 original size:20 final size:21
Alignment explanation
Indices: 39717983--39718025 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
39717973 AATTTAAAAA
39717983 TAAAAAATAAAAAAATAT-TT
1 TAAAAAATAAAAAAATATATT
**
39718003 TAAAATTTAAAAAAATATATT
1 TAAAAAATAAAAAAATATATT
39718024 TA
1 TA
39718026 TTATATACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAATAAAAAAATATATT
Found at i:39719954 original size:970 final size:970
Alignment explanation
Indices: 39718074--39720013 Score: 3880
Period size: 970 Copynumber: 2.0 Consensus size: 970
39718064 CCCGAGGCCC
39718074 GGCCCGTTTTCTAAACCGACCTCGTTTTTTTGCCCAAACCCATATTTTGAGCTTATATTTTTACC
1 GGCCCGTTTTCTAAACCGACCTCGTTTTTTTGCCCAAACCCATATTTTGAGCTTATATTTTTACC
39718139 CGAACCCTCTCATATTTCAGGCGGACCGTCGGGCCGGGCTGGGTCACCCAACCCATGAGCACCTC
66 CGAACCCTCTCATATTTCAGGCGGACCGTCGGGCCGGGCTGGGTCACCCAACCCATGAGCACCTC
39718204 TAATCCCAGCCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTTCACACGGTCAAGCCACAAGC
131 TAATCCCAGCCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTTCACACGGTCAAGCCACAAGC
39718269 CCATGTGTCAGGCCGTGTATCATTCGAAATGACTTCACACGACCATGTGTTAGACCGTGTGCTGG
196 CCATGTGTCAGGCCGTGTATCATTCGAAATGACTTCACACGACCATGTGTTAGACCGTGTGCTGG
39718334 GCTGTGTAACAGCCTGACTTGCAAACATTTATAAGCTACAGGGAAAACACGACTATGTCGCCTAG
261 GCTGTGTAACAGCCTGACTTGCAAACATTTATAAGCTACAGGGAAAACACGACTATGTCGCCTAG
39718399 CCGTGTGTCACATATGGCTGAGACACACGCCCGTTCTCTGGCCGTGTGGACGAAAAATAGGTCAT
326 CCGTGTGTCACATATGGCTGAGACACACGCCCGTTCTCTGGCCGTGTGGACGAAAAATAGGTCAT
39718464 TTCCAAGCAATTTTTCTCACCCATTCAAGCACATACCTACAACCAAATTTCCACATATAAACAAG
391 TTCCAAGCAATTTTTCTCACCCATTCAAGCACATACCTACAACCAAATTTCCACATATAAACAAG
39718529 CCTTCAAAATGCACTAAAAACCTGCATAATCAAGCTATCCCAATAAGGTACATAAACATTCAACC
456 CCTTCAAAATGCACTAAAAACCTGCATAATCAAGCTATCCCAATAAGGTACATAAACATTCAACC
39718594 AATATACCCAAAGGCACCTCAATCACAACATTAAAACATGTATAACCATATGCATAATTTAACCA
521 AATATACCCAAAGGCACCTCAATCACAACATTAAAACATGTATAACCATATGCATAATTTAACCA
39718659 AAACTTACCACTTTGTTCACATATCAAATTCACATTCACAAGTACCAAATTTACCATTTTACATT
586 AAACTTACCACTTTGTTCACATATCAAATTCACATTCACAAGTACCAAATTTACCATTTTACATT
39718724 TAGCATCATAAGCTGTATATACCAACTACATTTTTCATACCAAAATGAACATTTACTATCCATCA
651 TAGCATCATAAGCTGTATATACCAACTACATTTTTCATACCAAAATGAACATTTACTATCCATCA
39718789 ACTAAGTCATTAGCACAATTAGGCACATATGTCATCTATAAACAACATATCAAATTACCACATTC
716 ACTAAGTCATTAGCACAATTAGGCACATATGTCATCTATAAACAACATATCAAATTACCACATTC
39718854 AAACTTGTCAAAGGACAACTTATAACATACATTTTTAACTACCATTTTAACCTCCATCATCTAAT
781 AAACTTGTCAAAGGACAACTTATAACATACATTTTTAACTACCATTTTAACCTCCATCATCTAAT
39718919 TACCACAAACACAAAATAATAGCCAATACAAGGCCAAATATATACATGCCAACTTAACACCATAT
846 TACCACAAACACAAAATAATAGCCAATACAAGGCCAAATATATACATGCCAACTTAACACCATAT
39718984 CATCATTCAAAATGCCATAAACACAAGCCAAAAACAAATGGCTAATTCATCAAACAAAAA
911 CATCATTCAAAATGCCATAAACACAAGCCAAAAACAAATGGCTAATTCATCAAACAAAAA
39719044 GGCCCGTTTTCTAAACCGACCTCGTTTTTTTGCCCAAACCCATATTTTGAGCTTATATTTTTACC
1 GGCCCGTTTTCTAAACCGACCTCGTTTTTTTGCCCAAACCCATATTTTGAGCTTATATTTTTACC
39719109 CGAACCCTCTCATATTTCAGGCGGACCGTCGGGCCGGGCTGGGTCACCCAACCCATGAGCACCTC
66 CGAACCCTCTCATATTTCAGGCGGACCGTCGGGCCGGGCTGGGTCACCCAACCCATGAGCACCTC
39719174 TAATCCCAGCCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTTCACACGGTCAAGCCACAAGC
131 TAATCCCAGCCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTTCACACGGTCAAGCCACAAGC
39719239 CCATGTGTCAGGCCGTGTATCATTCGAAATGACTTCACACGACCATGTGTTAGACCGTGTGCTGG
196 CCATGTGTCAGGCCGTGTATCATTCGAAATGACTTCACACGACCATGTGTTAGACCGTGTGCTGG
39719304 GCTGTGTAACAGCCTGACTTGCAAACATTTATAAGCTACAGGGAAAACACGACTATGTCGCCTAG
261 GCTGTGTAACAGCCTGACTTGCAAACATTTATAAGCTACAGGGAAAACACGACTATGTCGCCTAG
39719369 CCGTGTGTCACATATGGCTGAGACACACGCCCGTTCTCTGGCCGTGTGGACGAAAAATAGGTCAT
326 CCGTGTGTCACATATGGCTGAGACACACGCCCGTTCTCTGGCCGTGTGGACGAAAAATAGGTCAT
39719434 TTCCAAGCAATTTTTCTCACCCATTCAAGCACATACCTACAACCAAATTTCCACATATAAACAAG
391 TTCCAAGCAATTTTTCTCACCCATTCAAGCACATACCTACAACCAAATTTCCACATATAAACAAG
39719499 CCTTCAAAATGCACTAAAAACCTGCATAATCAAGCTATCCCAATAAGGTACATAAACATTCAACC
456 CCTTCAAAATGCACTAAAAACCTGCATAATCAAGCTATCCCAATAAGGTACATAAACATTCAACC
39719564 AATATACCCAAAGGCACCTCAATCACAACATTAAAACATGTATAACCATATGCATAATTTAACCA
521 AATATACCCAAAGGCACCTCAATCACAACATTAAAACATGTATAACCATATGCATAATTTAACCA
39719629 AAACTTACCACTTTGTTCACATATCAAATTCACATTCACAAGTACCAAATTTACCATTTTACATT
586 AAACTTACCACTTTGTTCACATATCAAATTCACATTCACAAGTACCAAATTTACCATTTTACATT
39719694 TAGCATCATAAGCTGTATATACCAACTACATTTTTCATACCAAAATGAACATTTACTATCCATCA
651 TAGCATCATAAGCTGTATATACCAACTACATTTTTCATACCAAAATGAACATTTACTATCCATCA
39719759 ACTAAGTCATTAGCACAATTAGGCACATATGTCATCTATAAACAACATATCAAATTACCACATTC
716 ACTAAGTCATTAGCACAATTAGGCACATATGTCATCTATAAACAACATATCAAATTACCACATTC
39719824 AAACTTGTCAAAGGACAACTTATAACATACATTTTTAACTACCATTTTAACCTCCATCATCTAAT
781 AAACTTGTCAAAGGACAACTTATAACATACATTTTTAACTACCATTTTAACCTCCATCATCTAAT
39719889 TACCACAAACACAAAATAATAGCCAATACAAGGCCAAATATATACATGCCAACTTAACACCATAT
846 TACCACAAACACAAAATAATAGCCAATACAAGGCCAAATATATACATGCCAACTTAACACCATAT
39719954 CATCATTCAAAATGCCATAAACACAAGCCAAAAACAAATGGCTAATTCATCAAACAAAAA
911 CATCATTCAAAATGCCATAAACACAAGCCAAAAACAAATGGCTAATTCATCAAACAAAAA
39720014 CACCTATACA
Statistics
Matches: 970, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
970 970 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (970 bp):
GGCCCGTTTTCTAAACCGACCTCGTTTTTTTGCCCAAACCCATATTTTGAGCTTATATTTTTACC
CGAACCCTCTCATATTTCAGGCGGACCGTCGGGCCGGGCTGGGTCACCCAACCCATGAGCACCTC
TAATCCCAGCCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTTCACACGGTCAAGCCACAAGC
CCATGTGTCAGGCCGTGTATCATTCGAAATGACTTCACACGACCATGTGTTAGACCGTGTGCTGG
GCTGTGTAACAGCCTGACTTGCAAACATTTATAAGCTACAGGGAAAACACGACTATGTCGCCTAG
CCGTGTGTCACATATGGCTGAGACACACGCCCGTTCTCTGGCCGTGTGGACGAAAAATAGGTCAT
TTCCAAGCAATTTTTCTCACCCATTCAAGCACATACCTACAACCAAATTTCCACATATAAACAAG
CCTTCAAAATGCACTAAAAACCTGCATAATCAAGCTATCCCAATAAGGTACATAAACATTCAACC
AATATACCCAAAGGCACCTCAATCACAACATTAAAACATGTATAACCATATGCATAATTTAACCA
AAACTTACCACTTTGTTCACATATCAAATTCACATTCACAAGTACCAAATTTACCATTTTACATT
TAGCATCATAAGCTGTATATACCAACTACATTTTTCATACCAAAATGAACATTTACTATCCATCA
ACTAAGTCATTAGCACAATTAGGCACATATGTCATCTATAAACAACATATCAAATTACCACATTC
AAACTTGTCAAAGGACAACTTATAACATACATTTTTAACTACCATTTTAACCTCCATCATCTAAT
TACCACAAACACAAAATAATAGCCAATACAAGGCCAAATATATACATGCCAACTTAACACCATAT
CATCATTCAAAATGCCATAAACACAAGCCAAAAACAAATGGCTAATTCATCAAACAAAAA
Found at i:39720656 original size:85 final size:85
Alignment explanation
Indices: 39720512--39720686 Score: 323
Period size: 85 Copynumber: 2.1 Consensus size: 85
39720502 GGGATAGCTA
*
39720512 ACACATAGTATGCTAACTCATATAACTATAATCTGTCAATTCTTGTACATGTATACTCACACGAG
1 ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
39720577 CTGTGAAAATAGGTCTGCTC
66 CTGTGAAAATAGGTCTGCTC
* *
39720597 ACACATCGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATGCTCACACGAG
1 ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
39720662 CTGTGAAAATAGGTCTGCTC
66 CTGTGAAAATAGGTCTGCTC
39720682 ACACA
1 ACACA
39720687 AGCTGTGGGT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (85 bp):
ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
CTGTGAAAATAGGTCTGCTC
Found at i:39721723 original size:24 final size:24
Alignment explanation
Indices: 39721689--39721758 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
39721679 GAAACCAGTC
39721689 CCACAGCTCCTCTCTTCACCCTTT
1 CCACAGCTCCTCTCTTCACCCTTT
* *
39721713 CCACTGTTCCTCTCTTCACCCTTT
1 CCACAGCTCCTCTCTTCACCCTTT
*
39721737 CCACAGCTCCTCTATTCACCCT
1 CCACAGCTCCTCTCTTCACCCT
39721759 ATCGATTGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.13, C:0.49, G:0.04, T:0.34
Consensus pattern (24 bp):
CCACAGCTCCTCTCTTCACCCTTT
Found at i:39725951 original size:33 final size:33
Alignment explanation
Indices: 39725899--39725973 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
39725889 AAGATGTAGA
* *
39725899 AAAATGTTTTGTAGGAGCCCCGCTTTTCAACTC
1 AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
*
39725932 AAAAGGTTTAGTAGGAGCCCTGCTTTTCAACTC
1 AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
39725965 AAAAGGTTT
1 AAAAGGTTT
39725974 CGTCTCAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
Found at i:39729823 original size:13 final size:13
Alignment explanation
Indices: 39729807--39729832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39729797 ATTAATTTAG
39729807 TTAATTTAATTAA
1 TTAATTTAATTAA
39729820 TTAATTTAATTAA
1 TTAATTTAATTAA
39729833 GTAAATAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:39731464 original size:41 final size:41
Alignment explanation
Indices: 39731419--39731579 Score: 259
Period size: 41 Copynumber: 3.9 Consensus size: 41
39731409 ACTAGCTCTT
* * *
39731419 AGCCTGCTAGACATAATGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* *
39731460 AGCCTGCTATACTTAAAGCCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
39731501 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* *
39731542 AGCCTTCTAGACTTAAAGTCTGAAATGTTTCACTGGCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCA
39731580 ATAAACATGA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:39744897 original size:17 final size:17
Alignment explanation
Indices: 39744872--39744905 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39744862 TGTTTACACT
*
39744872 CTTTTTTTTCAGTTTTA
1 CTTTATTTTCAGTTTTA
*
39744889 CTTTATTTTTAGTTTTA
1 CTTTATTTTCAGTTTTA
39744906 AAATTTGAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.71
Consensus pattern (17 bp):
CTTTATTTTCAGTTTTA
Found at i:39745411 original size:30 final size:30
Alignment explanation
Indices: 39745363--39745468 Score: 110
Period size: 30 Copynumber: 3.5 Consensus size: 30
39745353 TTTTAGGTTA
*
39745363 CTTAAAAGTTGG-AAAAAAAATTTAAATCC
1 CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
**
39745392 CTTAAAAGTTGGTAAAAAAAATTTTCAGCC
1 CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
**
39745422 CTTAAAAGTT--TAAAAAAATATTTTTAGGGCTC
1 CTTAAAAGTTGGTAAAAAAA-A--TTTAAAGC-C
39745454 CTTAAAAGTTGGTAA
1 CTTAAAAGTTGGTAA
39745469 TTTTTTTTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.12
29 13 0.20
30 24 0.38
31 5 0.08
32 11 0.17
34 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
Found at i:39747698 original size:23 final size:22
Alignment explanation
Indices: 39747679--39747726 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
39747669 ATTAAATTTT
39747679 AAAATTTGAAATATAAAAATTAA
1 AAAATTTGAAATA-AAAAATTAA
*
39747702 AAAATTTTAAAT-AAAAA-TAA
1 AAAATTTGAAATAAAAAATTAA
39747722 AAAAT
1 AAAAT
39747727 AAATCTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
23 11 0.46
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATTTGAAATAAAAAATTAA
Found at i:39753581 original size:6 final size:6
Alignment explanation
Indices: 39753572--39753597 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39753562 GATATATATA
39753572 ATACAC ATACAC ATACAC ATACAC AT
1 ATACAC ATACAC ATACAC ATACAC AT
39753598 CCATATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATACAC
Found at i:39769186 original size:392 final size:392
Alignment explanation
Indices: 39768462--39769242 Score: 1262
Period size: 392 Copynumber: 2.0 Consensus size: 392
39768452 GCTTATTTTG
39768462 AGCTCTCCAAGCACTGTCAGCAGGAAAAGGCAGTCTAGCCTGCTTACCAAGCTGACAAACCTCAC
1 AGCTCTCCAAGCACTGTCAGCAGGAAAAGGCAGTCTAGCCTGCTTACCAAGCTGACAAACCTCAC
*
39768527 AAACATTCCCACTAACCTCAATCTTTGAAATGTCATCAACTAAATTCAGCCTATGTAGCAAATCA
66 AAACATTCCCACTAACCTCAATCTTTGAAATGTCATCAACCAAATTCAGCCTATGTAGCAAATCA
* * *
39768592 AGAGATCTAAAATTGGCATGGCCTAGTCTCTTATGCCACAAATCAGTGTTATCAGCAAGGCTGGT
131 AGAGATCTAAAATTGGCATGGCCAAGTCTCCTATGCCACAAATCAGTGTTATCAACAAGGCTGGT
*
39768657 GTATGCCTTTCTTTCTACTTGGCTAACATCCAACATGAAGCATCTATCAGTCATAGAGACTGAGA
196 GTATGCCTTTCTTTCTACTTGGCTAACATCCAACATGAAGCACCTATCAGTCATAGAGACTGAGA
* * * * *
39768722 TTAACTCCAGACCATTCATGTCTTGAACAGTACAACAACCATCCTTGAAAACTAATGTATAGCCC
261 CTAACTCCAGACCATTCATGTCTTAAACAATACAACAACCATCCTTGAAAACCAAGGTATAGCCC
*
39768787 TTTTCAACTAATTGGCCTACACTAAGCAAATTCTGGTCTAAATCAGGTACAAAAAGCACATCTGT
326 TTTTCAACCAATTGGCCTACACTAAGCAAATTCTGGTCTAAATCAGGTACAAAAAGCACATCTGT
39768852 GA
391 GA
39768854 AGCTCTCCAAGCACTGTCAGCAGGAAAAGGCAGTCTAGCCTGCTTACCAAGCTGACAAACCTCAC
1 AGCTCTCCAAGCACTGTCAGCAGGAAAAGGCAGTCTAGCCTGCTTACCAAGCTGACAAACCTCAC
* *
39768919 AAACATTCCCACTAACCTCAATCTTTGAAATGTCATTAACCAAATTCAGCCTATGTAGCAGATCA
66 AAACATTCCCACTAACCTCAATCTTTGAAATGTCATCAACCAAATTCAGCCTATGTAGCAAATCA
* * * * * *
39768984 ATAGATCTAAAGTTGGCATGGCCAAGTCTCCTATGCTATAAGTCAGTGTTGTCAACAAGGCTGGT
131 AGAGATCTAAAATTGGCATGGCCAAGTCTCCTATGCCACAAATCAGTGTTATCAACAAGGCTGGT
* * *
39769049 GTATGCC-TTCTTTTCTACTTGGCTAACATCCAGCATGAAGCACCTATCGGTCATAGAGACTGTG
196 GTATGCCTTTC-TTTCTACTTGGCTAACATCCAACATGAAGCACCTATCAGTCATAGAGACTGAG
* *
39769113 ACTAACTCCAGACCATTCATGTCTTAAACAATACAACAACCAT-TTTTAAAGACCAAGGTATA-C
260 ACTAACTCCAGACCATTCATGTCTTAAACAATACAACAACCATCCTTGAAA-ACCAAGGTATAGC
* * * *
39769176 CCTTTTTCAACCAATTGGCCTACACTAAGCAGATTCTGGTCTAAGTCAGGTGCAAAAAGTACATC
324 CC-TTTTCAACCAATTGGCCTACACTAAGCAAATTCTGGTCTAAATCAGGTACAAAAAGCACATC
39769241 TG
388 TG
39769243 AGATCAGCTT
Statistics
Matches: 358, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
391 11 0.03
392 347 0.97
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (392 bp):
AGCTCTCCAAGCACTGTCAGCAGGAAAAGGCAGTCTAGCCTGCTTACCAAGCTGACAAACCTCAC
AAACATTCCCACTAACCTCAATCTTTGAAATGTCATCAACCAAATTCAGCCTATGTAGCAAATCA
AGAGATCTAAAATTGGCATGGCCAAGTCTCCTATGCCACAAATCAGTGTTATCAACAAGGCTGGT
GTATGCCTTTCTTTCTACTTGGCTAACATCCAACATGAAGCACCTATCAGTCATAGAGACTGAGA
CTAACTCCAGACCATTCATGTCTTAAACAATACAACAACCATCCTTGAAAACCAAGGTATAGCCC
TTTTCAACCAATTGGCCTACACTAAGCAAATTCTGGTCTAAATCAGGTACAAAAAGCACATCTGT
GA
Found at i:39789681 original size:91 final size:91
Alignment explanation
Indices: 39789568--39789749 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 91
39789558 AATATTAATT
39789568 CTCAATACTTACTTAACTTATTAATTTAATTACTTTATAATATTATTATAAATATATTAAAAAAA
1 CTCAATACTTACTTAACTTATTAATTTAATTACTTTATAATATTATTATAAATATATT-AAAAAA
39789633 CAAAGAATTGCGTCAAGCAATCCCCTA
65 CAAAGAATTGCGTCAAGCAATCCCCTA
*
39789660 CTCAATACTT-CTTAACTTATTAATTTAATTACTTTATAATATTATTATAAATATATTACAAAAC
1 CTCAATACTTACTTAACTTATTAATTTAATTACTTTATAATATTATTATAAATATATTAAAAAAC
*
39789724 GAAGAATTGCGTCAAGCAATCCCCTA
66 AAAGAATTGCGTCAAGCAATCCCCTA
39789750 ATTTTGTTAG
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
90 31 0.35
91 47 0.53
92 10 0.11
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (91 bp):
CTCAATACTTACTTAACTTATTAATTTAATTACTTTATAATATTATTATAAATATATTAAAAAAC
AAAGAATTGCGTCAAGCAATCCCCTA
Found at i:39791670 original size:2 final size:2
Alignment explanation
Indices: 39791663--39791717 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
39791653 ACAATGATAC
39791663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
39791705 TT TA TA CA TA TA T
1 TA TA TA TA TA TA T
39791718 TTTGCTTCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39798144 original size:36 final size:36
Alignment explanation
Indices: 39798095--39798184 Score: 144
Period size: 36 Copynumber: 2.4 Consensus size: 36
39798085 TCTGTAAGTG
*
39798095 GTGTATAGAGATGGATGGGTGTTTTATACCCATATGGT
1 GTGT-TAG-GATGGATGAGTGTTTTATACCCATATGGT
39798133 GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
1 GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
*
39798169 GTGTTGGGATGGATGA
1 GTGTTAGGATGGATGA
39798185 AGTTGGTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
36 43 0.86
37 3 0.06
38 4 0.08
ACGTcount: A:0.22, C:0.07, G:0.34, T:0.37
Consensus pattern (36 bp):
GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
Found at i:39799130 original size:85 final size:87
Alignment explanation
Indices: 39799003--39799162 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 87
39798993 ATTTTTTTTT
* * * * *
39799003 AAAAAAAGAGTAATTAAGTCCTTATCTTTTTTTTTTGCACTCAATTAGGTACT-TGAACTTTCAA
1 AAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTA-TATGAACTTTCAA
*
39799067 AATGTATAAAAAATCTCAATTTA
65 AATATATAAAAAATCTCAATTTA
*
39799090 AAAAAAAAAGTAATTAAGCCCCT-GC-TTTTGTTTTGCACTCAATTGGGTATATGAACTTTCAAA
1 AAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTATATGAACTTTCAAA
39799153 ATATATAAAA
66 ATATATAAAA
39799163 TACCCTCGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.02
85 43 0.66
86 1 0.02
87 20 0.31
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (87 bp):
AAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTATATGAACTTTCAAA
ATATATAAAAAATCTCAATTTA
Found at i:39799416 original size:26 final size:26
Alignment explanation
Indices: 39799387--39799440 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
39799377 AATAGAAATT
*
39799387 ATAAAAAT-TATTAAATTTTAATAAAA
1 ATAAAAATGT-TTAAAATTTAATAAAA
*
39799413 ATAAAAATGTTTAAAATTTATTAAAA
1 ATAAAAATGTTTAAAATTTAATAAAA
39799439 AT
1 AT
39799441 TGAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
ATAAAAATGTTTAAAATTTAATAAAA
Found at i:39799448 original size:20 final size:19
Alignment explanation
Indices: 39799425--39799498 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
39799415 AAAAATGTTT
39799425 AAAATTTATTAAAAATTGAA
1 AAAATTTA-TAAAAATTGAA
39799445 AAAA-TTATAAAAATCAT-AA
1 AAAATTTATAAAAAT--TGAA
* *
39799464 AAAAATTATAAAAAATTGTA
1 AAAATTTAT-AAAAATTGAA
*
39799484 AAATTTTATAAAAAT
1 AAAATTTATAAAAAT
39799499 AGTAAGAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 7 0.15
19 16 0.35
20 17 0.37
21 6 0.13
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATTTATAAAAATTGAA
Found at i:39799456 original size:8 final size:9
Alignment explanation
Indices: 39799382--39799614 Score: 70
Period size: 9 Copynumber: 24.8 Consensus size: 9
39799372 AAACCAATAG
39799382 AAATTATAA
1 AAATTATAA
*
39799391 AAATTAT-T
1 AAATTATAA
*
39799399 AAATTTTAA
1 AAATTATAA
*
39799408 TAAA-AATAA
1 -AAATTATAA
*
39799417 AAATGTTTAA
1 AAAT-TATAA
*
39799427 AATTTATTAA
1 AAATTA-TAA
39799437 AAATTGA-AA
1 AAATT-ATAA
39799446 AAATTATAA
1 AAATTATAA
*
39799455 AAATCATAAAA
1 AAAT--TATAA
39799466 AAATTATAAA
1 AAATTAT-AA
*
39799476 AAATTGTAA
1 AAATTATAA
*
39799485 AATTTTATAA
1 AA-ATTATAA
39799495 AAA-TAGTAA
1 AAATTA-TAA
*
39799504 GAAA-TGT-A
1 -AAATTATAA
39799512 AAATATATAGA
1 AAAT-TATA-A
*
39799523 AAA-TAGAA
1 AAATTATAA
**
39799531 AAAAAATATA
1 AAATTATA-A
*
39799541 AAATTTTATA
1 AAATTATA-A
* *
39799551 AAGTCATAAGA
1 AAATTAT-A-A
39799562 AAATTATAA
1 AAATTATAA
39799571 ACAATGTA-AA
1 A-AAT-TATAA
39799581 GAAA-TATAA
1 -AAATTATAA
* *
39799590 AATTTGTAA
1 AAATTATAA
*
39799599 AAAATATAA
1 AAATTATAA
39799608 AAATTAT
1 AAATTAT
39799615 CGTAACAAAA
Statistics
Matches: 163, Mismatches: 36, Indels: 50
0.65 0.14 0.20
Matches are distributed among these distances:
7 3 0.02
8 21 0.13
9 61 0.37
10 55 0.34
11 23 0.14
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:39799485 original size:10 final size:10
Alignment explanation
Indices: 39799425--39799497 Score: 60
Period size: 10 Copynumber: 7.4 Consensus size: 10
39799415 AAAAATGTTT
* *
39799425 AAAATTTATT
1 AAAAATTATA
*
39799435 AAAAATT-GA
1 AAAAATTATA
39799444 AAAAATTAT-
1 AAAAATTATA
*
39799453 AAAAATCATAA
1 AAAAATTAT-A
39799464 AAAAATTATA
1 AAAAATTATA
*
39799474 AAAAATTGTA
1 AAAAATTATA
**
39799484 AAATTTTATA
1 AAAAATTATA
39799494 AAAA
1 AAAA
39799498 TAGTAAGAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
9 15 0.31
10 26 0.53
11 8 0.16
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:39799588 original size:19 final size:18
Alignment explanation
Indices: 39799561--39799609 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
39799551 AAGTCATAAG
*
39799561 AAAATTATAAACA-ATGTA
1 AAAAATATAAA-ATATGTA
*
39799579 AAGAAATATAAAATTTGTA
1 AA-AAATATAAAATATGTA
39799598 AAAAATATAAAA
1 AAAAATATAAAA
39799610 ATTATCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAAATATAAAATATGTA
Found at i:39799837 original size:30 final size:30
Alignment explanation
Indices: 39799798--39799860 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
39799788 TTTTATGCAT
*
39799798 TTTATAATTTTTT-TATGATTTTTATGAAAA
1 TTTACAATTTTTTATAT-ATTTTTATGAAAA
* *
39799828 TTTACAATTTTTTATATTTTTTTATTAAAA
1 TTTACAATTTTTTATATATTTTTATGAAAA
39799858 TTT
1 TTT
39799861 GATAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTACAATTTTTTATATATTTTTATGAAAA
Found at i:39804446 original size:30 final size:30
Alignment explanation
Indices: 39804412--39804474 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39804402 ACTTAACAAG
39804412 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTTTAAAATAATAACAAAATTAA
*
39804442 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTTTAAAATAATAACAAAATTAA
39804472 CAA
1 CAA
39804475 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTTTAAAATAATAACAAAATTAA
Found at i:39804568 original size:11 final size:11
Alignment explanation
Indices: 39804554--39804584 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
39804544 TAAAATAGGG
39804554 AGAAAATAATA
1 AGAAAATAATA
39804565 AGAAAATAATA
1 AGAAAATAATA
39804576 AGAAAATAA
1 AGAAAATAA
39804585 CATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AGAAAATAATA
Found at i:39808471 original size:308 final size:307
Alignment explanation
Indices: 39807913--39808978 Score: 1459
Period size: 308 Copynumber: 3.5 Consensus size: 307
39807903 AAAAATTGTA
39807913 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * *
39807978 AAATTAGAAAAT-ATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATGCGAACAAATGGC
66 AAATTAGAAAATAAT-ATATTTTTTAAAGTAATACAATTCGG-GAAAAAAATACGAACAAAGGGC
* * **
39808042 CGAAGTAAGGGTTTTTTACTAAATTTTTAAAAAAACAGAAATAATTAATACATTTCAAACATAAT
129 CGAAATAAGGGTTTTTTACTAAAATTAAAAAAAAACAGAAATAATTAATACATTTCAAACATAAT
* *
39808107 GTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATT
194 GTACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATT
* * *
39808172 TGG-GAAAAAATACGAGCAAAAAGCCAAAATAAGGGTTTTTTTAAAAATT
259 CGGAAAAAAAATACGAGCAAAAAGCAAAAATAAGGGTTTTTTT-AAAATT
*
39808221 TATTTAAAAAACACACTAAACTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTTAAAAAACACACTAAA-TTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
*
39808286 TAAAATTAGAAAATAATAT-TTTTTTAAAGTAATACAATTCGGTAAAAAAATACGAACAAAGGGC
64 TAAAATTAGAAAATAATATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGC
* *
39808350 CGAAATAAGGGTTTTTTACTAAAATTAAAAAAAAACAGAATTAATTAATACATTTTAAACATAAT
129 CGAAATAAGGGTTTTTTACTAAAATTAAAAAAAAACAGAAATAATTAATACATTTCAAACATAAT
39808415 GTACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATT
194 GTACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATT
** * *
39808480 CGGAAAAAAAATACGAGCAAAGGGCAAAAATAATGGTTTTTTTTAAATT
259 CGGAAAAAAAATACGAGCAAAAAGCAAAAATAAGGGTTTTTTTAAAATT
*
39808529 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAGAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
39808594 AAATTAGAAAATAGTATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
66 AAATTAGAAAATAATATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
******* * ** * *
39808659 AAATAAGGGTTTTTTTACT-AAATT----TTTTTTTGAAGT--TGCAGACA--TC--GC--AATG
131 AAATAAGGG-TTTTTTACTAAAATTAAAAAAAAACAGAAATAATTAATACATTTCAAACATAAT-
* ** * * *
39808711 GCTTCATTGATTAGCAG-CAAATAAT-AAATACAAAAATAATATATTTTTATTGAAAGTAATAAA
194 G-TAC-TAAAATA-AAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAA
** * *
39808774 ATTCAGG-AAAAAAATACGAGCAAATGGCAGAAATAAGAGTTTTTTTAAAATT
256 ATTC-GGAAAAAAAATACGAGCAAAAAGCAAAAATAAGGGTTTTTTTAAAATT
39808826 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
39808891 AAATTAGAAAATAGTATATTTTTTTAAAGTAATACAATTCGGGAAAAAAAATACGAACAAAGGGT
66 AAATTAGAAAATAATATA-TTTTTTAAAGTAATACAATTCGGG-AAAAAAATACGAACAAAGGGC
39808956 CGAAATAAGGGTTTTTTACTAAA
129 CGAAATAAGGGTTTTTTACTAAA
39808979 TTTTTTTTTG
Statistics
Matches: 693, Mismatches: 51, Indels: 37
0.89 0.07 0.05
Matches are distributed among these distances:
295 3 0.00
296 1 0.00
297 167 0.24
298 46 0.07
299 36 0.05
301 5 0.01
303 4 0.01
306 56 0.08
307 63 0.09
308 197 0.28
309 58 0.08
310 55 0.08
311 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (307 bp):
TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATAATATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
AAATAAGGGTTTTTTACTAAAATTAAAAAAAAACAGAAATAATTAATACATTTCAAACATAATGT
ACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCG
GAAAAAAAATACGAGCAAAAAGCAAAAATAAGGGTTTTTTTAAAATT
Found at i:39808518 original size:155 final size:154
Alignment explanation
Indices: 39807913--39808680 Score: 961
Period size: 155 Copynumber: 5.0 Consensus size: 154
39807903 AAAAATTGTA
* *
39807913 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTAAAAAAACACAATAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * *
39807978 AAATTAGAAAAT-ATGATA-TTTTTTAAAGTAATAAAATGCGGAGAAAAAAATGCGAACAAATGG
66 AAATTAGAAAATAAT-ATATTTTTTTAAAGTAATAAAATTCGGA-AAAAAAATACGAACAAAGGG
*
39808041 CCGAAGTAAGGGTTTTTTACT-AAAT
129 CCGAAATAAGGGTTTTTTACTAAAAT
* * *
39808066 TTTTAAAAAAACAGAA-ATAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
1 TATTAAAAAAACACAATA-AATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAAT
* * * *
39808130 AAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTGG-GAAAAAATACGAGCAAAA
65 AAAATTA-GAAAATAATATATTTTT-TT-AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAG
* *
39808193 AGCCAAAATAAGGGTTTTTT--TAAAAATT
127 GGCCGAAATAAGGGTTTTTTACT-AAAA-T
* * *
39808221 TATTTAAAAAACACACTAAACTTATTTAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
1 TATTAAAAAAACACAATAAA-TTA-ATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAA
* *
39808286 TAAAATTAGAAAAT-A-ATATTTTTTTAAAGTAATACAATTCGGTAAAAAAATACGAACAAAGGG
64 TAAAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGG
39808349 CCGAAATAAGGGTTTTTTACTAAAAT
129 CCGAAATAAGGGTTTTTTACTAAAAT
* * * * * *
39808375 TA-AAAAAAAACAGAATTAATTAATACATTTTAAACATAATGTACTAAAATAAAGTAAAATAATA
1 TATTAAAAAAACACAATAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
39808439 AAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAGCAAAGG
66 AAATTA-GAAAATAATATATTTTT-TT-AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGG
** * * *
39808503 GCAAAAATAATGGTTTTTT-TTAAATT
128 GCCGAAATAAGGGTTTTTTACTAAAAT
* * *
39808529 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAGAATAATA
1 TATTAAAAAAACACAATAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * *
39808594 AAATTAGAAAATAGTATA-TTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCC
66 AAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCC
39808658 GAAATAAGGGTTTTTTTACTAAA
131 GAAATAAGGG-TTTTTTACTAAA
39808681 TTTTTTTTTG
Statistics
Matches: 527, Mismatches: 63, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
150 2 0.00
151 46 0.09
152 52 0.10
153 113 0.21
154 95 0.18
155 145 0.28
156 23 0.04
157 49 0.09
158 2 0.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (154 bp):
TATTAAAAAAACACAATAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCC
GAAATAAGGGTTTTTTACTAAAAT
Found at i:39810639 original size:12 final size:12
Alignment explanation
Indices: 39810619--39810655 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
39810609 TGATCCTAAA
39810619 CCAGAGCCCGAG
1 CCAGAGCCCGAG
*
39810631 CCGGAGCCCGAG
1 CCAGAGCCCGAG
*
39810643 CCAGATCCCGAG
1 CCAGAGCCCGAG
39810655 C
1 C
39810656 AGTCACATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.43, G:0.32, T:0.03
Consensus pattern (12 bp):
CCAGAGCCCGAG
Found at i:39811306 original size:124 final size:124
Alignment explanation
Indices: 39811086--39811585 Score: 937
Period size: 124 Copynumber: 4.0 Consensus size: 124
39811076 ATATAATGTT
39811086 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
*
39811151 CTGAATTTAAGTTAATGGGTGTTTAAACAACATTGCAACATCCGAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCGAACATTACACATAAC
*
39811210 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGTATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
* *
39811275 CTAAATTTAAGTTAATGGGTGTTAAAACAACATAGCAACATCCGAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCGAACATTACACATAAC
39811334 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
*
39811399 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCTGAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCGAACATTACACATAAC
*
39811458 AATTATTCCGAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
*
39811523 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCAAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCGAACATTACACATAAC
39811582 AATT
1 AATT
39811586 TGACAGCATT
Statistics
Matches: 365, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 365 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (124 bp):
AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCGAACATTACACATAAC
Found at i:39814532 original size:37 final size:38
Alignment explanation
Indices: 39814448--39814534 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 38
39814438 ACTAACACAA
* *
39814448 TAACAATAATAATAGTTTTATACTCAAAATAATACTAAC
1 TAACAATAATAATAGGTTTATACT-AAAATAATAATAAC
39814487 TAACAATAATAATTAGGGTTT-TACT-AAA-AATAATAAC
1 TAACAATAATAA-TA-GGTTTATACTAAAATAATAATAAC
39814524 TAACAATAATA
1 TAACAATAATA
39814535 TAATGTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
37 19 0.43
38 3 0.07
39 12 0.27
40 6 0.14
41 4 0.09
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (38 bp):
TAACAATAATAATAGGTTTATACTAAAATAATAATAAC
Found at i:39814566 original size:23 final size:23
Alignment explanation
Indices: 39814523--39814567 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39814513 AAAATAATAA
*
39814523 CTAACAATAATATAATGTAAAAC
1 CTAACAATAATATAATCTAAAAC
*
39814546 CTAACAATCATACTAA-CTAAAA
1 CTAACAATAATA-TAATCTAAAA
39814568 TAATAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (23 bp):
CTAACAATAATATAATCTAAAAC
Found at i:39820616 original size:79 final size:80
Alignment explanation
Indices: 39820506--39820664 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 80
39820496 CATTTTAATA
39820506 ACTTATATCTTTATAATTTTTAAATAATTAAATCAAATTTTTATCATTTTGAAGGGGTTAAAATG
1 ACTTATATCTTTATAATTTTTAAATAATTAAATCAAATTTTTATCATTTTGAAGGGGTTAAAATG
39820571 CAATTATACCATTAT
66 CAATTATACCATTAT
39820586 ACTTATATC-TTATAATTTTTAAATAATTAAATCAAATTTTTATCATTTTGAAGGGGTTAAAATG
1 ACTTATATCTTTATAATTTTTAAATAATTAAATCAAATTTTTATCATTTTGAAGGGGTTAAAATG
39820650 CAATTATACCATTAT
66 CAATTATACCATTAT
39820665 TAATTTAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 70 0.89
80 9 0.11
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.45
Consensus pattern (80 bp):
ACTTATATCTTTATAATTTTTAAATAATTAAATCAAATTTTTATCATTTTGAAGGGGTTAAAATG
CAATTATACCATTAT
Found at i:39822657 original size:16 final size:16
Alignment explanation
Indices: 39822636--39822666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39822626 TAGATGCATC
*
39822636 TATCAAAATCATATAA
1 TATCAAAACCATATAA
39822652 TATCAAAACCATATA
1 TATCAAAACCATATA
39822667 CATGGTGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
TATCAAAACCATATAA
Found at i:39825131 original size:41 final size:42
Alignment explanation
Indices: 39825033--39825136 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
39825023 TCTGATTCAA
* * * *
39825033 TTCACCGGCAATT-AGCCTGCTAGACTTAAAGTCCGAATTAT
1 TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
* *
39825074 TTCACCGACAC-AAAGCCTGCTAGACATAAAGTCCGAATAAC
1 TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
39825115 TTCACCGGC-CTTAAGCCTGCTA
1 TTCACCGGCACTTAAGCCTGCTA
39825137 AGTTTTAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (42 bp):
TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
Found at i:39826683 original size:13 final size:13
Alignment explanation
Indices: 39826665--39826689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39826655 TCAAACTATC
39826665 AAATTTTCACACG
1 AAATTTTCACACG
39826678 AAATTTTCACAC
1 AAATTTTCACAC
39826690 ATATAACTTA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:39829002 original size:55 final size:56
Alignment explanation
Indices: 39828927--39829035 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
39828917 AAGAACTAAG
* * *
39828927 GATGATACTGGAATCGAACCAGAATCT-GGGGCTGAAACTGTAAATAAATAAGAAT
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
*
39828982 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAATAAGA
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGA
39829036 GTCATTAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 24 0.49
56 25 0.51
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (56 bp):
GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
Found at i:39829812 original size:55 final size:56
Alignment explanation
Indices: 39829737--39829845 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
39829727 AAGAACTAAG
* * *
39829737 GATGATACTGGAATCGAACCAGAATCT-GGGGCTGAAACTGTAAATAAATAAGAAT
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
*
39829792 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAATAAGA
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGA
39829846 GTCATTAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 24 0.49
56 25 0.51
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (56 bp):
GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
Found at i:39830395 original size:810 final size:811
Alignment explanation
Indices: 39828825--39830447 Score: 3239
Period size: 810 Copynumber: 2.0 Consensus size: 811
39828815 AAAAGAAAAA
39828825 AACTAAACAGTTTAAAAAGAAAATAAAAAGCAAAATCAAAACAAACAAGAAAACTAATAATAAAC
1 AACTAAACAGTTTAAAAAGAAAATAAAAAGCAAAATCAAAACAAACAAGAAAACTAATAATAAAC
39828890 AAAAACAATTTAAAAGAAAAATAAAAAAAGAACTAAGGATGATACTGGAATCGAACCAGAATCTG
66 AAAAACAATTTAAAAGAAAAATAAAAAAAGAACTAAGGATGATACTGGAATCGAACCAGAATCTG
39828955 GGGCTGAAACTGTAAATAAATAAGAATGATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAA
131 GGGCTGAAACTGTAAATAAATAAGAATGATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAA
39829020 CTATAAATAAATAAGAGTCATTAAGGGCCGATATAGAACGTGCTTTAACAATGAGGGACTGACTG
196 CTATAAATAAATAAGAGTCATTAAGGGCCGATATAGAACGTGCTTTAACAATGAGGGACTGACTG
39829085 GGAAAATATTCCCAAGCCCTATACGCAGCGTTCCATTGTGGACCAGATTTGAGCAAACAGAAAAT
261 GGAAAATATTCCCAAGCCCTATACGCAGCGTTCCATTGTGGACCAGATTTGAGCAAACAGAAAAT
39829150 TACACCGTGAAATTAAAAAAGAGAAAAAATGACGAGCGAGGACTAAATTGCAAAGCTTCACGAAA
326 TACACCGTGAAATTAAAAAAGAGAAAAAATGACGAGCGAGGACTAAATTGCAAAGCTTCACGAAA
39829215 GCGGAAGGATCAAAGCGGTGAAAAGCCCCTTTTGTCTCAGAACGCGCAGACCCTTAGCAGGTCAA
391 GCGGAAGGATCAAAGCGGTGAAAAGCCCCTTTTGTCTCAGAACGCGCAGACCCTTAGCAGGTCAA
39829280 ACTCGGGTGAGCGGGTCAGCGACCCCCGAAACGAAGCCGTTTTGACATCTGGGGGGCCGAAATGA
456 ACTCGGGTGAGCGGGTCAGCGACCCCCGAAACGAAGCCGTTTTGACATCTGGGGGGCCGAAATGA
39829345 AACTGTGTCGTTTTAGTCCAGTCATTTAAACCCCAAAAAAGAAAATATGTCACTAGCAGCCCATT
521 AACTGTGTCGTTTTAGTCCAGTCATTTAAACCCCAAAAAAGAAAATATGTCACTAGCAGCCCATT
39829410 TTTTTACCCTAAAAAGTAAACCCCTATTCTCTCAACTCCCTCTTCCCCTTCTGGCCATAGCCAAC
586 TTTTTACCCTAAAAAGTAAACCCCTATTCTCTCAACTCCCTCTTCCCCTTCTGGCCATAGCCAAC
39829475 GTCGGTGAATGGCCACGCCGCCGCCACGGTCAACAGGCAGTGACGAAAGGTTAGGCTTTTCAGCC
651 GTCGGTGAATGGCCACGCCGCCGCCACGGTCAACAGGCAGTGACGAAAGGTTAGGCTTTTCAGCC
39829540 CCTTTTTAAGCCCGGTGGTCAGTGACTGGTGATGAGAGGCCAAATGAGGAAAAGAAAAAATCTAG
716 CCTTTTTAAGCCCGGTGGTCAGTGACTGGTGATGAGAGGCCAAATGAGGAAAAGAAAAAATCTAG
39829605 CCCCCTTTTAAGTTCAACTCCGACGACGACT
781 CCCCCTTTTAAGTTCAACTCCGACGACGACT
39829636 AACTAAACAG-TTAAAAAGAAAATAAAAAGCAAAATCAAAACAAACAAGAAAACTAATAATAAAC
1 AACTAAACAGTTTAAAAAGAAAATAAAAAGCAAAATCAAAACAAACAAGAAAACTAATAATAAAC
39829700 AAAAACAATTTAAAAGAAAAATAAAAAAAGAACTAAGGATGATACTGGAATCGAACCAGAATCTG
66 AAAAACAATTTAAAAGAAAAATAAAAAAAGAACTAAGGATGATACTGGAATCGAACCAGAATCTG
39829765 GGGCTGAAACTGTAAATAAATAAGAATGATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAA
131 GGGCTGAAACTGTAAATAAATAAGAATGATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAA
39829830 CTATAAATAAATAAGAGTCATTAAGGGCCGATATAGAACGTGCTTTAACAATGAGGGACTGACTG
196 CTATAAATAAATAAGAGTCATTAAGGGCCGATATAGAACGTGCTTTAACAATGAGGGACTGACTG
39829895 GGAAAATATTCCCAAGCCCTATACGCAGCGTTCCATTGTGGACCAGATTTGAGCAAACAGAAAAT
261 GGAAAATATTCCCAAGCCCTATACGCAGCGTTCCATTGTGGACCAGATTTGAGCAAACAGAAAAT
39829960 TACACCGTGAAATTAAAAAAGAGAAAAAATGACGAGCGAGGACTAAATTGCAAAGCTTCACGAAA
326 TACACCGTGAAATTAAAAAAGAGAAAAAATGACGAGCGAGGACTAAATTGCAAAGCTTCACGAAA
39830025 GCGGAAGGATCAAAGCGGTGAAAAGCCCCTTTTGTCTCAGAACGCGCAGACCCTTAGCAGGTCAA
391 GCGGAAGGATCAAAGCGGTGAAAAGCCCCTTTTGTCTCAGAACGCGCAGACCCTTAGCAGGTCAA
39830090 ACTCGGGTGAGCGGGTCAGCGACCCCCGAAACGAAGCCGTTTTGACATCTGGGGGGCCGAAATGA
456 ACTCGGGTGAGCGGGTCAGCGACCCCCGAAACGAAGCCGTTTTGACATCTGGGGGGCCGAAATGA
39830155 AACTGTGTCGTTTTAGTCCAGTCATTTAAACCCCAAAAAAGAAAATATGTCACTAGCAGCCCATT
521 AACTGTGTCGTTTTAGTCCAGTCATTTAAACCCCAAAAAAGAAAATATGTCACTAGCAGCCCATT
39830220 TTTTTACCCTAAAAAGTAAACCCCTATTCTCTCAACTCCCTCTTCCCCTTCTGGCCATAGCCAAC
586 TTTTTACCCTAAAAAGTAAACCCCTATTCTCTCAACTCCCTCTTCCCCTTCTGGCCATAGCCAAC
39830285 GTCGGTGAATGGCCACGCCGCCGCCACGGTCAACAGGCAGTGACGAAAGGTTAGGCTTTTCAGCC
651 GTCGGTGAATGGCCACGCCGCCGCCACGGTCAACAGGCAGTGACGAAAGGTTAGGCTTTTCAGCC
39830350 CCTTTTTAAGCCCGGTGGTCAGTGACTGGTGATGAGAGGCCAAATGAGGAAAAGAAAAAATCTAG
716 CCTTTTTAAGCCCGGTGGTCAGTGACTGGTGATGAGAGGCCAAATGAGGAAAAGAAAAAATCTAG
39830415 CCCCCTTTTAAGTTCAACTCCGACGACGACT
781 CCCCCTTTTAAGTTCAACTCCGACGACGACT
39830446 AA
1 AA
39830448 GGGACCTGCG
Statistics
Matches: 812, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
810 802 0.99
811 10 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (811 bp):
AACTAAACAGTTTAAAAAGAAAATAAAAAGCAAAATCAAAACAAACAAGAAAACTAATAATAAAC
AAAAACAATTTAAAAGAAAAATAAAAAAAGAACTAAGGATGATACTGGAATCGAACCAGAATCTG
GGGCTGAAACTGTAAATAAATAAGAATGATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAA
CTATAAATAAATAAGAGTCATTAAGGGCCGATATAGAACGTGCTTTAACAATGAGGGACTGACTG
GGAAAATATTCCCAAGCCCTATACGCAGCGTTCCATTGTGGACCAGATTTGAGCAAACAGAAAAT
TACACCGTGAAATTAAAAAAGAGAAAAAATGACGAGCGAGGACTAAATTGCAAAGCTTCACGAAA
GCGGAAGGATCAAAGCGGTGAAAAGCCCCTTTTGTCTCAGAACGCGCAGACCCTTAGCAGGTCAA
ACTCGGGTGAGCGGGTCAGCGACCCCCGAAACGAAGCCGTTTTGACATCTGGGGGGCCGAAATGA
AACTGTGTCGTTTTAGTCCAGTCATTTAAACCCCAAAAAAGAAAATATGTCACTAGCAGCCCATT
TTTTTACCCTAAAAAGTAAACCCCTATTCTCTCAACTCCCTCTTCCCCTTCTGGCCATAGCCAAC
GTCGGTGAATGGCCACGCCGCCGCCACGGTCAACAGGCAGTGACGAAAGGTTAGGCTTTTCAGCC
CCTTTTTAAGCCCGGTGGTCAGTGACTGGTGATGAGAGGCCAAATGAGGAAAAGAAAAAATCTAG
CCCCCTTTTAAGTTCAACTCCGACGACGACT
Found at i:39830709 original size:20 final size:19
Alignment explanation
Indices: 39830678--39830722 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
39830668 GTCATTATCC
39830678 TTTTTTGTCTTTTTCATTTGT
1 TTTTTTGTC-TTTT-ATTTGT
*
39830699 TTTTTTG-CTTTTGTTTGT
1 TTTTTTGTCTTTTATTTGT
39830717 TTTTTT
1 TTTTTT
39830723 CTGCCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 4 0.17
20 1 0.04
21 7 0.30
ACGTcount: A:0.02, C:0.07, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTTTGTCTTTTATTTGT
Found at i:39830927 original size:18 final size:18
Alignment explanation
Indices: 39830892--39830929 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39830882 TAAAAATGTT
*
39830892 TTTAGTTTTGGGCTAGGG
1 TTTAGTTTTAGGCTAGGG
39830910 TTTAG-TTTAGGCTGAGGG
1 TTTAGTTTTAGGCT-AGGG
39830928 TT
1 TT
39830930 AATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.13, C:0.05, G:0.37, T:0.45
Consensus pattern (18 bp):
TTTAGTTTTAGGCTAGGG
Found at i:39831582 original size:44 final size:46
Alignment explanation
Indices: 39831532--39831647 Score: 150
Period size: 45 Copynumber: 2.6 Consensus size: 46
39831522 TACTCCGCTG
* *
39831532 CAACTTTAGGGAGATAAGA-TTGG-TATCTTTAACTTGCTCCATTA
1 CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
* *
39831576 CAACTTTAGGGAGATAA-AGTTGGTTATCTTTAGCCTGCTCCACTG
1 CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
* *
39831621 CAACTTCAGGGAGATAAGACTT-GTTAT
1 CAACTTTAGGGAGATAAGAGTTGGTTAT
39831648 GGTAGATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 1 0.02
44 21 0.33
45 38 0.60
46 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (46 bp):
CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
Found at i:39831720 original size:44 final size:44
Alignment explanation
Indices: 39831474--39831779 Score: 135
Period size: 44 Copynumber: 6.9 Consensus size: 44
39831464 GATCCATCAT
** * *
39831474 TTTAATCCATTCCACTGTAACTTCAGGAAGATAGGA-T--TAGC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* ** * * * * *
39831515 TTCAATCTACTCCGCTGCAACTTTAGGGAGATAAGATTGGTATC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* * ** * * *
39831559 TTTAA-CTTGCTCCATTACAACTTTAGGGAGATA-AAGTTGGTTATC
1 TTTAATC-CGCTCCACTGTAACTTTAGGGAGATAGGA-TTAG-TAGC
* * * * *
39831604 TTT-AGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGA
1 TTTAATCC-GCTCCACTGTAACTTTAGGGAGATAGGA----TTA--GTAGC
* * * *
39831654 TTTAATCCGAC-CTACTGCAACTTTAGAGG-TATAGGATTCA-TTGC
1 TTTAATCCG-CTCCACTGTAACTTTAG-GGAGATAGGATT-AGTAGC
*
39831698 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTAGC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* * * *
39831742 TTCAATCTGCTCCGCTGTAACTTTAGGGAGATAAGATT
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATT
39831780 GGTATCTTCA
Statistics
Matches: 204, Mismatches: 40, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
41 28 0.14
42 1 0.00
43 6 0.03
44 101 0.50
45 30 0.15
46 3 0.01
47 1 0.00
49 3 0.01
50 24 0.12
51 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
Found at i:39831789 original size:44 final size:44
Alignment explanation
Indices: 39831518--39831787 Score: 181
Period size: 44 Copynumber: 6.0 Consensus size: 44
39831508 GATTAGCTTC
* *
39831518 AATCTACTCCGCTGCAACTTTAGGGAGATAAGATTGGTATCTTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
* *
39831562 AA-CTTGCTCCATTACAACTTTAGGGAGATAA-AGTTGGTTATCTTT
1 AATC-TGCTCCACTGCAACTTTAGGGAGATAAGA-TTGG-TATCTTT
** * **
39831607 AGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA-----T-TGGTATCTTT
* * * * **
39831657 AATCCGAC-CTACTGCAACTTTAGAGG-TATAGGATTCAT-TGCTTT
1 AATCTG-CTCCACTGCAACTTTAG-GGAGATAAGATTGGTAT-CTTT
* * * * * * *
39831701 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
* *
39831745 AATCTGCTCCGCTGTAACTTTAGGGAGATAAGATTGGTATCTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTT
39831788 CAGTCTAATT
Statistics
Matches: 174, Mismatches: 36, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
43 5 0.03
44 101 0.58
45 33 0.19
46 2 0.01
50 27 0.16
51 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
Found at i:39831932 original size:100 final size:100
Alignment explanation
Indices: 39831803--39832654 Score: 1034
Period size: 100 Copynumber: 8.5 Consensus size: 100
39831793 TAATTAACTA
** ** * * **
39831803 CAATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTCCCACTACACCGTTAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
*
39831868 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * *
39831903 CAATGTCGGGGAAGCAAGA-TCTGCCGTTGTAGCTTTAATCTGTTCCATTGCGCTGCCAGGGAAG
1 CAATGTCGGGGAAACAAGATTC-GCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAG
39831967 TAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
65 TAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * *
39832003 CAATGTCGGGGAAACAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGTACCGCTAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** *
39832068 AAGATTTGCCGTTGTGGCTTCAATCTTTTTAATTA
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * *
39832103 CAATGTTGGGGAAACAAGATTC-AC-TGGGTTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
1 CAATGTCGGGGAAACAAGATTCGCCAT-TG-TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
* *
39832166 GTAAGATTCACCGTTCTGGCTTCAATCTTTATAATTG
64 GTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* **
39832203 TAATGTCGGGGAAACAAGATT---CATTGGGTTAGCTTCAATCTGTTCCACTATACCGCCAGGGA
1 CAATGTCGGGGAAACAAGATTCGCCATT--G-TAGCTTCAATCTGTTCCACTGCACCGCCAGGGA
* * *
39832265 AGTAAGATTCGCCGTTCTGGCTTCAATCTTTATAATTG
63 AGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * * *
39832303 TAATGTCGGGGAAACAAGATTAGCCATTGTAGCTTTAATCTATTCCACTGCACCACCTGAGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
39832368 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * *
39832403 CAATGTCGGGGAAACAATATTCGCTATTGTAGCTTTAATCTGTTCTACTGCACCGCCAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* *
39832468 AAGATTCGCCGTTTTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * *
39832503 CAATGTCGAGGAAATAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGGAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** *
39832568 AAGATTTGCCATTGTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * * ** *
39832603 AAATGTCAGAGAGACAAGATACGTC-GGGTTAGCTTCAATATGTTCCACTGCA
1 CAATGTCGGGGAAACAAGATTCGCCATTG-TAGCTTCAATCTGTTCCACTGCA
39832655 ATGCCAAATA
Statistics
Matches: 657, Mismatches: 84, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
98 2 0.00
99 6 0.01
100 642 0.98
101 3 0.00
103 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (100 bp):
CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
Found at i:39832777 original size:89 final size:89
Alignment explanation
Indices: 39832678--39833029 Score: 517
Period size: 89 Copynumber: 4.0 Consensus size: 89
39832668 AGGACTAATC
* *
39832678 TCTTCAATCTGCTTCACTGCCAGTATAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
*
39832743 AAACTTAGGGAGGTCAGGCTGGTG
66 AAACTCAGGGAGGTCAGGCTGGTG
* * * * *
39832767 TCTTCGATCTGCTTCGCTACCAGTACAGGAAGACAAGATCTATAATCTTCAGTCTGCTCCGCTGC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
* *
39832832 AAACTCAAGGA-GACGAGGCTGGTG
66 AAACTCAGGGAGGTC-AGGCTGGTG
* * * *
39832856 TCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
*
39832921 AAACTCAGGGAGGTTAGGCTGGTG
66 AAACTCAGGGAGGTCAGGCTGGTG
* * * *
39832945 TCTTCGATCTGCTTCACTGCCAGTGCAGGAAGATAAGATCTGCTATCTTCAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
39833010 AAACTCAGGGAGGTCAGGCT
66 AAACTCAGGGAGGTCAGGCT
39833030 AGATATGACG
Statistics
Matches: 236, Mismatches: 25, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
88 2 0.01
89 233 0.99
90 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (89 bp):
TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
AAACTCAGGGAGGTCAGGCTGGTG
Found at i:39832867 original size:44 final size:44
Alignment explanation
Indices: 39832819--39832957 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 44
39832809 TAATCTTCAG
*
39832819 TCTGCTCCGCTGCAAACTCAAGGAGACGAGGCTGGTGTCTTCGA
1 TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
* * * * *
39832863 TCTGCTTCGCTGCCAA-T-ACAGGAAGACAAGATCTGCTATCTTC-A
1 TCTGCTCCGCTGCAAACTCA-AGG-AGACAAG-GCTGGTGTCTTCGA
* * * ***
39832907 GTCTGCTCCACTACAAACTCAGGGAGGTTAGGCTGGTGTCTTCGA
1 -TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
39832952 TCTGCT
1 TCTGCT
39832958 TCACTGCCAG
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
42 1 0.01
43 4 0.06
44 36 0.51
45 26 0.37
46 3 0.04
47 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (44 bp):
TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
Found at i:39832912 original size:45 final size:44
Alignment explanation
Indices: 39832774--39833002 Score: 128
Period size: 45 Copynumber: 5.1 Consensus size: 44
39832764 GTGTCTTCGA
* * *
39832774 TCTGCTTCGCTACCAGTACAGGAAGACAAGATCT-ATAATCTTCAG
1 TCTGCTTCGCTGCCAAT-CAGGAAGACAAGATCTGCT-ATCTTCAG
* * * * * *
39832819 TCTGCTCCGCTGCAAACTCAAGG-AGACGAG-GCTGGTGTCTTC-G
1 TCTGCTTCGCTGCCAA-TC-AGGAAGACAAGATCTGCTATCTTCAG
39832862 ATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG
1 -TCTGCTTCGCTGCCAAT-CAGGAAGACAAGATCTGCTATCTTCAG
* * * * * *** * * *
39832908 TCTGCTCCACTACAAACTCAGGGAGGTTAG-GCTGGTGTCTTC-G
1 TCTGCTTCGCTGCCAA-TCAGGAAGACAAGATCTGCTATCTTCAG
* * *
39832951 ATCTGCTTCACTGCCAGTGCAGGAAGATAAGATCTGCTATCTTCAG
1 -TCTGCTTCGCTGCCAAT-CAGGAAGACAAGATCTGCTATCTTCAG
39832997 TCTGCT
1 TCTGCT
39833003 CCACTACAAA
Statistics
Matches: 136, Mismatches: 35, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
43 7 0.05
44 58 0.43
45 64 0.47
46 7 0.05
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTGCTTCGCTGCCAATCAGGAAGACAAGATCTGCTATCTTCAG
Found at i:39833992 original size:10 final size:10
Alignment explanation
Indices: 39833977--39834010 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
39833967 TTTTTCGTTA
39833977 TTCTTTTTTT
1 TTCTTTTTTT
39833987 TTCTTTTTTT
1 TTCTTTTTTT
39833997 TTCGTTTCTTTT
1 TTC-TTT-TTTT
39834009 TT
1 TT
39834011 TAAGTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 3 0.14
12 6 0.27
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:39834516 original size:9 final size:8
Alignment explanation
Indices: 39834479--39834515 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
39834469 TTTTATTTTA
39834479 TTTTTACT
1 TTTTTACT
**
39834487 TTTTGGCT
1 TTTTTACT
39834495 TTTTTACT
1 TTTTTACT
39834503 TTTTTACT
1 TTTTTACT
39834511 TTTTT
1 TTTTT
39834516 TGCCTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (8 bp):
TTTTTACT
Found at i:39836378 original size:24 final size:25
Alignment explanation
Indices: 39836350--39836402 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
39836340 GGGTTTTTCG
*
39836350 TGAAATTTAATGCAAATG-ATGCAA
1 TGAAATGTAATGCAAATGAATGCAA
* *
39836374 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATGCAAATGAATGCAA
39836399 TGAA
1 TGAA
39836403 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGCAA
Found at i:39838872 original size:56 final size:56
Alignment explanation
Indices: 39838810--39838919 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 56
39838800 AAGAACTAAG
* * * *
39838810 GATGATACTGGAATCGAACCAGAATTTGGGGGCTGAAACTGTAAATAAATAAGAAT
1 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGAAT
39838866 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGA
1 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGA
39838920 GTCATTAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (56 bp):
GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGAAT
Found at i:39839797 original size:23 final size:22
Alignment explanation
Indices: 39839745--39839801 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
39839735 TCGTTTGTCA
39839745 TTATTCTTTTTTGTCTTTTTCAT
1 TTATT-TTTTTTGTCTTTTTCAT
* *
39839768 TTGTTTTTTTTG-CTTTTGTTAGT
1 TTATTTTTTTTGTCTTTT-TCA-T
39839791 TTATTTTTTTT
1 TTATTTTTTTT
39839802 CTCTACCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 9 0.31
23 15 0.52
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (22 bp):
TTATTTTTTTTGTCTTTTTCAT
Found at i:39840007 original size:17 final size:19
Alignment explanation
Indices: 39839979--39840016 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
39839969 TAAAAATTTT
39839979 TTTAGTTTTGGGCT-AGGG
1 TTTAGTTTTGGGCTGAGGG
39839997 TTTAG-TTTGGGCTGAGGG
1 TTTAGTTTTGGGCTGAGGG
39840015 TT
1 TT
39840017 AATTTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.11, C:0.05, G:0.39, T:0.45
Consensus pattern (19 bp):
TTTAGTTTTGGGCTGAGGG
Found at i:39840022 original size:17 final size:17
Alignment explanation
Indices: 39839985--39840022 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
39839975 TTTTTTTAGT
*
39839985 TTTGGGCTAGGGTTTAG
1 TTTGGGCTAGGGTTTAA
39840002 TTTGGGCTGAGGG-TTAA
1 TTTGGGCT-AGGGTTTAA
39840019 TTTG
1 TTTG
39840023 TATTTGGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.13, C:0.05, G:0.39, T:0.42
Consensus pattern (17 bp):
TTTGGGCTAGGGTTTAA
Found at i:39840978 original size:27 final size:28
Alignment explanation
Indices: 39840930--39840986 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
39840920 ATTGAATTTT
* *
39840930 ATTTTTTATTTTTATTCAATATATAATTA
1 ATTTTTAATTTTTATT-AATATAAAATTA
39840959 ATTTTTAATTTTTATT-ATATAAAATTA
1 ATTTTTAATTTTTATTAATATAAAATTA
39840986 A
1 A
39840987 ATATTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
29 15 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTAATTTTTATTAATATAAAATTA
Found at i:39849809 original size:18 final size:17
Alignment explanation
Indices: 39849774--39849839 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
39849764 CTCGTCATGA
39849774 TCATCATTATCATC-ATCT
1 TCATC-TTATC-TCTATCT
39849792 TCATCTCTATCTCTATCT
1 TCATCT-TATCTCTATCT
* * *
39849810 CCAATGTTATCTTTATCT
1 TC-ATCTTATCTCTATCT
39849828 TCATCTTCATCT
1 TCATCTT-ATCT
39849840 TGTTTTTCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.18
18 29 0.74
19 3 0.08
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
TCATCTTATCTCTATCT
Found at i:39853436 original size:28 final size:28
Alignment explanation
Indices: 39853404--39853484 Score: 72
Period size: 33 Copynumber: 2.7 Consensus size: 28
39853394 CCATTTCCAG
*
39853404 TATCAGTGTGGGCTTTAGCCCAATACAA
1 TATCAGTGTGGGCTTTAGCCCAACACAA
* *
39853432 TATCAGAACAGTGTGGGCCTTAGCCCAACATAA
1 TAT-----CAGTGTGGGCTTTAGCCCAACACAA
* *
39853465 TAACAGTGTGGGCTTAAGCC
1 TATCAGTGTGGGCTTTAGCC
39853485 TGTTATAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
28 18 0.43
33 24 0.57
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (28 bp):
TATCAGTGTGGGCTTTAGCCCAACACAA
Found at i:39853691 original size:27 final size:27
Alignment explanation
Indices: 39853648--39853712 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
39853638 AGCCGAGCTG
*
39853648 CCAGT-ACAGTATATGTGGCATAGCCA
1 CCAGTAACAGTATATGTGGCAGAGCCA
39853674 CCAGTAACAGTGAT-TGTGGCAGAGCCA
1 CCAGTAACAGT-ATATGTGGCAGAGCCA
*
39853701 CCAGAAACAGTA
1 CCAGTAACAGTA
39853713 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 6 0.17
27 27 0.77
28 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCAGAGCCA
Found at i:39853913 original size:27 final size:27
Alignment explanation
Indices: 39853869--39853949 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
39853859 CCGGTCAATC
*
39853869 TACCCTTCTGGAGGTATTTCAATAATTT
1 TACCCTAC-GGAGGTATTTCAATAATTT
*
39853897 TACCCTACGGAGGTATTTCGATAA-TT
1 TACCCTACGGAGGTATTTCAATAATTT
* *
39853923 TACCC-ATCGGGGGTATTTCAGTAATTT
1 TACCCTA-CGGAGGTATTTCAATAATTT
39853950 ACCTATTGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.02
26 21 0.46
27 17 0.37
28 7 0.15
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
TACCCTACGGAGGTATTTCAATAATTT
Found at i:39853937 original size:26 final size:26
Alignment explanation
Indices: 39853881--39854260 Score: 371
Period size: 26 Copynumber: 14.6 Consensus size: 26
39853871 CCCTTCTGGA
*
39853881 GGTATTTCAATAATTTTACCC-TACG-G
1 GGTATTTCGATAA-TTTACCCAT-CGAG
*
39853907 AGGTATTTCGATAATTTACCCATCGGG
1 -GGTATTTCGATAATTTACCCATCGAG
* *
39853934 GGTATTTC-AGTAATTTACCTATTGAG
1 GGTATTTCGA-TAATTTACCCATCGAG
* * *
39853960 AGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
39853986 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* **
39854012 GGTATTTTGGCAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
*
39854038 GGT-TTTCGATAATTTACCCATTGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
39854063 GGTATTTCTG-TGATTTACCCATTGAG
1 GGTATTTC-GATAATTTACCCATCGAG
*
39854089 GGTATTTCTG-TGATTTACCCATCGAG
1 GGTATTTC-GATAATTTACCCATCGAG
*
39854115 GGTATTTCGATAATTTACCCATCGAT
1 GGTATTTCGATAATTTACCCATCGAG
* *
39854141 GGTATTTC-AGTAATTTACCTATTGAG
1 GGTATTTCGA-TAATTTACCCATCGAG
**
39854167 GGTATTTCTG-TAATTTACCCATTAAG
1 GGTATTTC-GATAATTTACCCATCGAG
* * * *
39854193 GGTATTTTGGTAATTTACACATTGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
39854219 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGATAATTTACCCATCGAG
* *
39854245 GGTATTTTGGTAATTT
1 GGTATTTCGATAATTT
39854261 TTATCCGTGT
Statistics
Matches: 313, Mismatches: 29, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
25 25 0.08
26 273 0.87
27 15 0.05
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
GGTATTTCGATAATTTACCCATCGAG
Found at i:39853974 original size:52 final size:52
Alignment explanation
Indices: 39853881--39854260 Score: 428
Period size: 52 Copynumber: 7.3 Consensus size: 52
39853871 CCCTTCTGGA
* ** * * *
39853881 GGTATTTCAATAATTTTACCCTACGGA-GGTATTTCGATAATTTACCCATCGGG
1 GGTATTTCAGTAA-TTTACCC-ATTGAGGGTATTTTGGTAATTTACCCATCGAG
* *
39853934 GGTATTTCAGTAATTTACCTATTGAGAGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
** * *
39853986 GGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGCAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
* *
39854038 GGT-TTTC-GATAATTTACCCATTGAGGGTATTTCT-GTGATTTACCCATTGAG
1 GGTATTTCAG-TAATTTACCCATTGAGGGTATTT-TGGTAATTTACCCATCGAG
* * * * * *
39854089 GGTATTTCTGTGATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAT
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
* **
39854141 GGTATTTCAGTAATTTACCTATTGAGGGTATTTCT-GTAATTTACCCATTAAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTT-TGGTAATTTACCCATCGAG
** *
39854193 GGTATTTTGGTAATTTACACATTGAGGGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
**
39854245 GGTATTTTGGTAATTT
1 GGTATTTCAGTAATTT
39854261 TTATCCGTGT
Statistics
Matches: 278, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.00
51 46 0.17
52 218 0.78
53 13 0.05
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (52 bp):
GGTATTTCAGTAATTTACCCATTGAGGGTATTTTGGTAATTTACCCATCGAG
Found at i:39853991 original size:78 final size:78
Alignment explanation
Indices: 39853881--39854260 Score: 410
Period size: 78 Copynumber: 4.9 Consensus size: 78
39853871 CCCTTCTGGA
* * *
39853881 GGTATTTCAATAATTTTACCC-TACG-GAGGTATTTCGATAATTTACCCATCGGGGGTATTTCAG
1 GGTATTTCGATAA-TTTACCCAT-CGAG-GGTATTTCGATAATTTACCCATCGAGGGTATTTCGG
* *
39853944 TAATTTACCTATTGAG
63 TAATTTACCCATCGAG
* * * * * * *
39853960 AGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGCAA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
39854025 TTTACCCATCGAG
66 TTTACCCATCGAG
* * * * *
39854038 GGT-TTTCGATAATTTACCCATTGAGGGTATTTCTG-TGATTTACCCATTGAGGGTATTTCTGTG
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTC-GATAATTTACCCATCGAGGGTATTTCGGTA
39854101 ATTTACCCATCGAG
65 ATTTACCCATCGAG
* * * *
39854115 GGTATTTCGATAATTTACCCATCGATGGTATTTC-AGTAATTTACCTATTGAGGGTATTTCTGTA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGA-TAATTTACCCATCGAGGGTATTTCGGTA
**
39854179 ATTTACCCATTAAG
65 ATTTACCCATCGAG
* * * * * * *
39854193 GGTATTTTGGTAATTTACACATTGAGGGTATTTTGGTAATTTACCCATCGAGGGTATTTTGGTAA
1 GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
39854258 TTT
66 TTT
39854261 TTATCCGTGT
Statistics
Matches: 253, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
77 65 0.26
78 177 0.70
79 11 0.04
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (78 bp):
GGTATTTCGATAATTTACCCATCGAGGGTATTTCGATAATTTACCCATCGAGGGTATTTCGGTAA
TTTACCCATCGAG
Found at i:39856001 original size:25 final size:25
Alignment explanation
Indices: 39855973--39856028 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
39855963 ATTCAGGAAT
39855973 GCTCATAAGAGCACATA-AACGAGAA
1 GCTCATAAGAGC-CATATAACGAGAA
* ** *
39855998 GCTCTTCCGAGCCATATAACGGGAA
1 GCTCATAAGAGCCATATAACGAGAA
39856023 GCTCAT
1 GCTCAT
39856029 GTGAGCCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGAGAA
Found at i:39856179 original size:25 final size:25
Alignment explanation
Indices: 39856143--39856218 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
39856133 CCGGAAAGCC
39856143 ATTAATCAGGAAGCTCATAAGAGCTA
1 ATTAA-CAGGAAGCTCATAAGAGCTA
* * ** *
39856169 ATTATCGGGAAGCTCCGAAGAGCCA
1 ATTAACAGGAAGCTCATAAGAGCTA
39856194 ATTAACAGGACA-CTCATAAGAGCTA
1 ATTAACAGGA-AGCTCATAAGAGCTA
39856219 CGGTGTGTCC
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
25 34 0.87
26 5 0.13
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (25 bp):
ATTAACAGGAAGCTCATAAGAGCTA
Found at i:39856180 original size:50 final size:50
Alignment explanation
Indices: 39856122--39856218 Score: 146
Period size: 50 Copynumber: 1.9 Consensus size: 50
39856112 AGAGCCTTTA
39856122 ATCGGGAAGCTCCGGAA-AGCC-ATTAATCAGGA-AGCTCATAAGAGCTAATT
1 ATCGGGAAGCTCC-GAAGAGCCAATTAA-CAGGACA-CTCATAAGAGCTAATT
39856172 ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTA
1 ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTA
39856219 CGGTGTGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
49 3 0.07
50 35 0.80
51 6 0.14
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (50 bp):
ATCGGGAAGCTCCGAAGAGCCAATTAACAGGACACTCATAAGAGCTAATT
Found at i:39858287 original size:13 final size:13
Alignment explanation
Indices: 39858271--39858308 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
39858261 AAAATTCTTT
39858271 AAAAAA-TGTAAA
1 AAAAAATTGTAAA
39858283 AAAAAATTGTTAAA
1 AAAAAATTG-TAAA
*
39858297 TAAAAATTGTAA
1 AAAAAATTGTAA
39858309 TATTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (13 bp):
AAAAAATTGTAAA
Found at i:39863835 original size:20 final size:20
Alignment explanation
Indices: 39863793--39863835 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
39863783 AATTCGACCA
*
39863793 TCACATATTCATTTCACATT
1 TCACATATTCATTTCAAATT
*
39863813 TCACAT-TTCGTTTCAAATAT
1 TCACATATTCATTTCAAAT-T
39863833 TCA
1 TCA
39863836 TATCAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
TCACATATTCATTTCAAATT
Found at i:39868477 original size:20 final size:20
Alignment explanation
Indices: 39868435--39868477 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
39868425 AATTCAACCA
*
39868435 TCACATATTCATTTCACATT
1 TCACATATTCATTTCAAATT
*
39868455 TCACAT-TTCGTTTCAAATAT
1 TCACATATTCATTTCAAAT-T
39868475 TCA
1 TCA
39868478 TATCAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
TCACATATTCATTTCAAATT
Found at i:39870675 original size:19 final size:19
Alignment explanation
Indices: 39870651--39870688 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39870641 CCACTATCAC
39870651 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
39870670 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
39870689 TATTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:39874289 original size:17 final size:18
Alignment explanation
Indices: 39874267--39874304 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39874257 TATTCTGCTA
39874267 TTTCAA-ATTTCTTTTAG
1 TTTCAACATTTCTTTTAG
* *
39874284 TTTCAACATTTTTTTTTG
1 TTTCAACATTTCTTTTAG
39874302 TTT
1 TTT
39874305 AATTACTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTCAACATTTCTTTTAG
Found at i:39876720 original size:36 final size:36
Alignment explanation
Indices: 39876680--39876758 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
39876670 GGAGCCATTA
*
39876680 GTGTGTTATCAGGTAGATT-GCTCTTATGAGCATCTG
1 GTGTGTT-TCAGATAGATTAGCTCTTATGAGCATCTG
* *
39876716 GTGTGTTTCAGATGGATTAGCTCTTATGATCATCTG
1 GTGTGTTTCAGATAGATTAGCTCTTATGAGCATCTG
39876752 GTGTGTT
1 GTGTGTT
39876759 CCAGTTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.42
Consensus pattern (36 bp):
GTGTGTTTCAGATAGATTAGCTCTTATGAGCATCTG
Found at i:39879552 original size:43 final size:43
Alignment explanation
Indices: 39879473--39879623 Score: 205
Period size: 43 Copynumber: 3.5 Consensus size: 43
39879463 TGTCTTGTTC
* * *
39879473 TTTAGCGGCACTTTCCCCACAAACGCTGCTAAAGGTCATGACT
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
* * * *
39879516 TTTAGCGGCTCTTTTCCCGCAAATGCCGCTATAGGTCATGACC
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
*
39879559 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCATGACT
1 TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
**
39879602 TTTAGCGGTGC-TTTCCCACAAA
1 TTTAGCGGCACTTTTCCCACAAA
39879624 TGCTACTATT
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 11 0.12
43 83 0.88
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCACTTTTCCCACAAACGCCGCTATAGGTCATGACT
Found at i:39879653 original size:86 final size:86
Alignment explanation
Indices: 39879472--39879632 Score: 236
Period size: 86 Copynumber: 1.9 Consensus size: 86
39879462 TTGTCTTGTT
* * *
39879472 CTTTAGCGGCACTTTCCCCACAAACGCTGCTAAAGGTCATGACTTTTAGCGGCTCTTTTCCCGCA
1 CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCTCTTTTCCCACA
*
39879537 AATGCCGCTATAGGTCATGAC
66 AATGCCACTATAGGTCATGAC
* *
39879558 CTTTAGCGGCACTTTTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGG-TGC-TTTCCCAC
1 CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCT-CTTTTCCCAC
*
39879621 AAATGCTACTAT
65 AAATGCCACTAT
39879633 TGTTTGGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 18 0.27
86 49 0.73
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (86 bp):
CTTTAGCGGCACTTTCCCCACAAACGCCGCTAAAGATCATGACTTTTAGCGGCTCTTTTCCCACA
AATGCCACTATAGGTCATGAC
Found at i:39880371 original size:21 final size:21
Alignment explanation
Indices: 39880347--39880390 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39880337 TGTTTATATA
39880347 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
39880368 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
39880389 TA
1 TA
39880391 TTATGTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:39880378 original size:12 final size:12
Alignment explanation
Indices: 39880363--39880387 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39880353 TCTATATAAG
39880363 TTATGTAAGTTA
1 TTATGTAAGTTA
39880375 TTATGTAAGTTA
1 TTATGTAAGTTA
39880387 T
1 T
39880388 GTATTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:39880545 original size:17 final size:18
Alignment explanation
Indices: 39880515--39880570 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
39880505 TTTGAAAAAA
*
39880515 TATATAAATTTTAAATAAG
1 TATAT-AATATTAAATAAG
39880534 TATAT-ATATTAAA-AATG
1 TATATAATATTAAATAA-G
39880551 TATATAAATATT-AATAAG
1 TATAT-AATATTAAATAAG
39880569 TA
1 TA
39880571 ATGTAAGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.41
18 5 0.16
19 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TATATAATATTAAATAAG
Found at i:39881084 original size:14 final size:14
Alignment explanation
Indices: 39881065--39881094 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39881055 ATCGAAGAGC
*
39881065 AAGATGATTAACTA
1 AAGATGATCAACTA
39881079 AAGATGATCAACTA
1 AAGATGATCAACTA
39881093 AA
1 AA
39881095 AAACCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (14 bp):
AAGATGATCAACTA
Found at i:39882100 original size:16 final size:16
Alignment explanation
Indices: 39882081--39882131 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
39882071 CTCTGACGAC
39882081 AGAGGAGTGCGACGGT
1 AGAGGAGTGCGACGGT
***
39882097 AGAGGACAACGACGGT
1 AGAGGAGTGCGACGGT
* *
39882113 TGACGAGTGCGACGGT
1 AGAGGAGTGCGACGGT
39882129 AGA
1 AGA
39882132 TGAGCAACGA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.43, T:0.12
Consensus pattern (16 bp):
AGAGGAGTGCGACGGT
Found at i:39882674 original size:41 final size:41
Alignment explanation
Indices: 39882601--39882833 Score: 351
Period size: 41 Copynumber: 5.6 Consensus size: 41
39882591 CTTTCGGGGA
39882601 TTTAGCGGCGTTTTTAAGG-AAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTT--GGAAAAGCGCCGCTAATGCTCAGATC
* *
39882643 TTTAGCGGTGTTTTTGGAAAAGCGCCGCTAATGCCCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* *
39882684 TTTAGCGGCGTTTTTGGAAAAGCGCCGCCAATGCCCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* *
39882725 TTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGGTCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
*
39882766 TTTAGCGGCGTTTTTGAAAGAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAATGCTCAGATC
* *
39882808 TTTAGCGGCATTTTTGAAAAAGCGCC
1 TTTAGCGGCGTTTTTGGAAAAGCGCC
39882834 ACAAAAACAT
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
40 2 0.01
41 123 0.69
42 52 0.29
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
Found at i:39882980 original size:26 final size:26
Alignment explanation
Indices: 39882932--39882982 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
39882922 AAAATGGATA
** * *
39882932 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
39882958 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
39882983 ATTATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:39883272 original size:14 final size:15
Alignment explanation
Indices: 39883241--39883273 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39883231 AAGGTTTATA
*
39883241 GATTATGGAATTATG
1 GATTATGGAATTAGG
39883256 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
39883270 GATT
1 GATT
39883274 CTGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:39884464 original size:19 final size:19
Alignment explanation
Indices: 39884440--39884486 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
39884430 ATGGAATCTG
39884440 TTATAAATTAGAATGCCTA
1 TTATAAATTAGAATGCCTA
*
39884459 TTATAAACTAGAATGCCTA
1 TTATAAATTAGAATGCCTA
39884478 TTATAAATT
1 TTATAAATT
39884487 TTGGTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATAAATTAGAATGCCTA
Found at i:39884917 original size:8 final size:8
Alignment explanation
Indices: 39884904--39884928 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39884894 TATATCCCCT
39884904 TGGTTAAA
1 TGGTTAAA
39884912 TGGTTAAA
1 TGGTTAAA
39884920 TGGTTAAA
1 TGGTTAAA
39884928 T
1 T
39884929 TTTTTTTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (8 bp):
TGGTTAAA
Found at i:39888339 original size:43 final size:43
Alignment explanation
Indices: 39888243--39888504 Score: 263
Period size: 43 Copynumber: 6.3 Consensus size: 43
39888233 AGATTATGTT
* * * * * * *
39888243 TTTAGCGGCGTTTTTGCGAGAAGCGCCACAAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
39888285 TTTAGCGGCGTTTGTGAAAAAAGCGCGGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
39888328 TATAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGCCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
39888370 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGATC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
39888413 TTTTGCAGCGTTTGTGATAAAAGCGCCGC-------CATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
39888449 TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
39888492 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
39888505 ATTTCTAAAA
Statistics
Matches: 178, Mismatches: 33, Indels: 17
0.78 0.14 0.07
Matches are distributed among these distances:
36 29 0.16
42 64 0.36
43 85 0.48
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:39888503 original size:79 final size:81
Alignment explanation
Indices: 39888283--39888504 Score: 254
Period size: 79 Copynumber: 2.7 Consensus size: 81
39888273 AAAGGTTTGT
** * * * * *
39888283 TCTTTAGCGGCGTTTGTGAAAAAAGCGCGGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAA
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGAAA
39888348 AGCGCCGCTAAAGGCCATGG
66 AGCGCCGC---A-GCCATGG
* * * *
39888368 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTTATGATCTTTT-GCAGCGTTTGTGATA
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT-TTTTAGCGGCGTTTGTG-GA
39888432 AAAGCG-C-C-GCCATGG
64 AAAGCGCCGCAGCCATGG
*
39888447 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGGTTTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTT
39888505 ATTTCTAAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.03
79 56 0.47
84 1 0.01
85 50 0.42
86 8 0.07
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (81 bp):
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTTGTGGAAA
AGCGCCGCAGCCATGG
Found at i:39889014 original size:25 final size:26
Alignment explanation
Indices: 39888986--39889038 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
39888976 AAAATTAAAA
* *
39888986 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTAATTTCATTTCTT
* *
39889011 ATTTTTGTATTTTAATTTTATTTCTT
1 ATTTTAGTATTTTAATTTCATTTCTT
39889037 AT
1 AT
39889039 AATTTGGTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (26 bp):
ATTTTAGTATTTTAATTTCATTTCTT
Found at i:39889021 original size:19 final size:18
Alignment explanation
Indices: 39888985--39889038 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
39888975 TAAAATTAAA
39888985 AATTTTAGTGTTTTTATTTC
1 AATTTTA-T-TTTTTATTTC
* *
39889005 ATTTTTATTTTTGTATTTT
1 AATTTTATTTTT-TATTTC
*
39889024 AATTTTATTTCTTAT
1 AATTTTATTTTTTAT
39889039 AATTTGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (18 bp):
AATTTTATTTTTTATTTC
Found at i:39889527 original size:56 final size:51
Alignment explanation
Indices: 39889461--39889612 Score: 164
Period size: 50 Copynumber: 2.9 Consensus size: 51
39889451 GAATGAGATA
* * **
39889461 CCATCTAAGACCATGTCAGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA-G--ATGAGAGGTC
*
39889517 CCATGTAAGACCATGTCTGGGACATGGCGTTGGC-ACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGTC
** * *
39889567 CCCCGTAAGACCATGTCTGGGACATGGCATGGGC-ACCGATATGAGA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGA
39889613 ACTCCTAAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 51 0.59
52 1 0.01
53 3 0.03
56 31 0.36
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (51 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGTC
Found at i:39889565 original size:50 final size:50
Alignment explanation
Indices: 39889507--39889612 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
39889497 TATTGAGGTT
* * *
39889507 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* *
39889557 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
39889607 ATGAGA
1 ATGAGA
39889613 ACTCCTAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:39889809 original size:20 final size:20
Alignment explanation
Indices: 39889764--39889816 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
39889754 AAAAATTAAA
*
39889764 AATTTTAGAGTTTTTATATTT
1 AATTTT-GATTTTTTATATTT
*
39889785 CATTTTGATTTTTGTAT-TTT
1 AATTTTGATTTTT-TATATTT
*
39889805 AATTTTAATTTT
1 AATTTTGATTTT
39889817 AATTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (20 bp):
AATTTTGATTTTTTATATTT
Found at i:39890532 original size:22 final size:22
Alignment explanation
Indices: 39890479--39890535 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39890469 ACCCCTGAAA
*
39890479 CCTTAAA-CCCTAAATCTTTAAC
1 CCTTAAACCCCT-AATCTATAAC
* *
39890501 TCTT-AACCCCTAATGTATAAC
1 CCTTAAACCCCTAATCTATAAC
39890522 CCTTAAACCCCTAA
1 CCTTAAACCCCTAA
39890536 CCCCTAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (22 bp):
CCTTAAACCCCTAATCTATAAC
Found at i:39890600 original size:15 final size:14
Alignment explanation
Indices: 39890565--39890602 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
39890555 AACCCTTAAT
39890565 TAAAT-CATAATCC
1 TAAATCCATAATCC
*
39890578 TTAATCCATAATCCC
1 TAAATCCATAAT-CC
39890593 TAAATCCATA
1 TAAATCCATA
39890603 TATACTCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 6 0.29
15 11 0.52
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATCCATAATCC
Found at i:39890873 original size:23 final size:24
Alignment explanation
Indices: 39890838--39890905 Score: 97
Period size: 23 Copynumber: 2.9 Consensus size: 24
39890828 ATAGTCTTTT
*
39890838 AATTTTTCCATGTGTTTTATTTCA
1 AATTTTTCTATGTGTTTTATTTCA
39890862 AA-TTTTCTATGTGTTTTATTTCA
1 AATTTTTCTATGTGTTTTATTTCA
39890885 AATTATTTCTA--TGTTTTATTT
1 AATT-TTTCTATGTGTTTTATTT
39890906 TTTTCTGAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 32 0.78
24 3 0.07
25 6 0.15
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (24 bp):
AATTTTTCTATGTGTTTTATTTCA
Found at i:39890954 original size:16 final size:15
Alignment explanation
Indices: 39890916--39890970 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
39890906 TTTTCTGAAG
39890916 ATTTTAAAT-ATTCA
1 ATTTTAAATAATTCA
**
39890930 ATTAGAAATAAGTTCA
1 ATTTTAAATAA-TTCA
39890946 ATTTTAAATAATT-A
1 ATTTTAAATAATTCA
*
39890960 A-TATAAATAAT
1 ATTTTAAATAAT
39890971 AAACCAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
15 3 0.09
16 13 0.38
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTTTAAATAATTCA
Found at i:39891044 original size:41 final size:40
Alignment explanation
Indices: 39890997--39891372 Score: 265
Period size: 41 Copynumber: 9.2 Consensus size: 40
39890987 AATATTTTTT
* *
39890997 GCGGCGCTTTAAAAAGAACGACTCTAAAACCCCGAGCATTA
1 GCGGCGCTTTTAAAA-AACGCCTCTAAAACCCCGAGCATTA
* * * *
39891038 GTGGCGCTTTCTCAAAAATGCCAT-TAAAACCCCGACCATTA
1 GCGGCGCTTT-TAAAAAACGCC-TCTAAAACCCCGAGCATTA
* * *
39891079 GCGGCGCTTTTTAGAAAACGCCGCTAAAACCTCGAGCATTA
1 GCGGCGC-TTTTAAAAAACGCCTCTAAAACCCCGAGCATTA
* *
39891120 GCGGCGCTTCTTAAAAAATG-CTGCTAAAACCCAGAGCATTA
1 GCGGCGCTT-TTAAAAAACGCCT-CTAAAACCCCGAGCATTA
** * * *
39891161 GTAGCGCTTTAACAAAAACGCCGCTAAAACCCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* ** * * **
39891202 GCGACGCTTCCACAAAAACGCCGCTTAAACCTTGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* * * *
39891243 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACGCCTCTAAAACCCCGAGCATTA
* ** * *
39891284 GCGGTGCTTCCACAAAAACGTCGT-TAAAA-CCAGAGCATTA
1 GCGGCGCTTTTA-AAAAACG-CCTCTAAAACCCCGAGCATTA
* * ** * *
39891324 GCGGCGCTTTATCAAAAACACAGCTAAAACTCCGATCATTA
1 GCGGCGCTTT-TAAAAAACGCCTCTAAAACCCCGAGCATTA
*
39891365 GCGACGCT
1 GCGGCGCT
39891373 AATCCAAAAA
Statistics
Matches: 271, Mismatches: 52, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.00
40 35 0.13
41 226 0.83
42 9 0.03
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (40 bp):
GCGGCGCTTTTAAAAAACGCCTCTAAAACCCCGAGCATTA
Found at i:39891137 original size:82 final size:81
Alignment explanation
Indices: 39890997--39891372 Score: 359
Period size: 82 Copynumber: 4.6 Consensus size: 81
39890987 AATATTTTTT
* * * * * * * *
39890997 GCGGCGCTTT-AAAAAGAACGACTCTAAAACCCCGAGCATTAGTGGCGCTTTCTCAAAAATGCCA
1 GCGGCGCTTTCACAAA-AACGCCGCTAAAA-CCCGAGCATTAGCGGCGCTTCCACAAAAACGCCG
* *
39891061 TTAAAACCCCGACCATTA
64 TTAAAACCCAGAGCATTA
* * * * *
39891079 GCGGCGCTTTTTA-GAAAACGCCGCTAAAACCTCGAGCATTAGCGGCGCTTCTTA-AAAAATGCT
1 GCGGCGC-TTTCACAAAAACGCCGCTAAAACC-CGAGCATTAGCGGCGCTTC-CACAAAAACGCC
*
39891142 GCTAAAACCCAGAGCATTA
63 GTTAAAACCCAGAGCATTA
** * *
39891161 GTAGCGCTTTAACAAAAACGCCGCTAAAACCCAGAGCATTAGCGACGCTTCCACAAAAACGCCGC
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCC-GAGCATTAGCGGCGCTTCCACAAAAACGCCG-
**
39891226 TT-AAACCTTGAGCATTA
64 TTAAAACCCAGAGCATTA
* * *
39891243 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTAGCGGTGCTTCCACAAAAACGTCGT
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCC-GAGCATTAGCGGCGCTTCCACAAAAACGCCGT
39891308 TAAAA-CCAGAGCATTA
65 TAAAACCCAGAGCATTA
* * * *
39891324 GCGGCGCTTT-ATCAAAAACACAGCTAAAACTCCGATCATTAGCGACGCT
1 GCGGCGCTTTCA-CAAAAACGCCGCTAAAAC-CCGAGCATTAGCGGCGCT
39891373 AATCCAAAAA
Statistics
Matches: 245, Mismatches: 38, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
80 1 0.00
81 57 0.23
82 180 0.73
83 6 0.02
84 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (81 bp):
GCGGCGCTTTCACAAAAACGCCGCTAAAACCCGAGCATTAGCGGCGCTTCCACAAAAACGCCGTT
AAAACCCAGAGCATTA
Found at i:39891220 original size:123 final size:122
Alignment explanation
Indices: 39890997--39891392 Score: 406
Period size: 123 Copynumber: 3.2 Consensus size: 122
39890987 AATATTTTTT
* * * * * * *
39890997 GCGGCGCTTT-AAAAAGAACGACTCTAAAACCCCGAGCATTAGTGGCGCTTTCTCAAAAATGCCA
1 GCGGCGCTTTCACAAA-AACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCG
* * **
39891061 TTAAAACCCCGACCATTAGCGGCGCTTTTTAGAAAACGCCGCTAAAACCTCGAGCATTA
65 TTAAAACCCAGAGCATTAGCGGCGCTTTACA-AAAACGCCGCTAAAACCTCGAGCATTA
* * * * *
39891120 GCGGCGCTTCTTA-AAAAATGCTGCTAAAACCCAGAGCATTAGTAGCGCTTTAACAAAAACGCCG
1 GCGGCGCTT-TCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCG
* * * * *
39891184 CTAAAACCCAGAGCATTAGCGACGCTTCCACAAAAACGCCGCTTAAACCTTGAGCATTA
65 TTAAAACCCAGAGCATTAGCGGCGCTT-TACAAAAACGCCGCTAAAACCTCGAGCATTA
* * * * *
39891243 GCGGCGCTTTCACAAAAACGCCGCTGAAACCCAGAGCATTAGCGGTGCTTCCACAAAAACGTCGT
1 GCGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGT
* * *
39891308 TAAAA-CCAGAGCATTAGCGGCGCTTTATCAAAAACACAGCTAAAA-CTCCGATCATTA
66 TAAAACCCAGAGCATTAGCGGCGCTTTA-CAAAAACGCCGCTAAAACCT-CGAGCATTA
* * *
39891365 GCGACGCTAATC-CAAAAACGCCACTAAA
1 GCGGCGCT-TTCACAAAAACGCCGCTAAA
39891393 GCCATCGAAG
Statistics
Matches: 225, Mismatches: 41, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
121 3 0.01
122 63 0.28
123 153 0.68
124 5 0.02
125 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (122 bp):
GCGGCGCTTTCACAAAAACGCCGCTAAAACCCAGAGCATTAGTGGCGCTTTCACAAAAACGCCGT
TAAAACCCAGAGCATTAGCGGCGCTTTACAAAAACGCCGCTAAAACCTCGAGCATTA
Done.