Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 174 of 313
Found at i:54087556 original size:4 final size:4
Alignment explanation
Indices: 54087547--54087579 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
54087537 TAAGCATCAC
54087547 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
54087580 TACAACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:54089829 original size:7 final size:7
Alignment explanation
Indices: 54089791--54089828 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
54089781 AGAGTAGTGA
54089791 GTGGAGG
1 GTGGAGG
54089798 GTGGAGG
1 GTGGAGG
54089805 GTGGAGG
1 GTGGAGG
54089812 GTGGAGG
1 GTGGAGG
*
54089819 GTGAAGG
1 GTGGAGG
54089826 GTG
1 GTG
54089829 ATTTGGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (7 bp):
GTGGAGG
Found at i:54092804 original size:107 final size:103
Alignment explanation
Indices: 54092541--54092804 Score: 288
Period size: 101 Copynumber: 2.5 Consensus size: 103
54092531 AAAAATTTAC
* * * * *
54092541 TTATTTTTTATTTTTAAATTTTTTAATATTTAAAAATTATTTCTGAAAA-CTCCTAAAACTCTTT
1 TTATTTTATATTTTTAAATTTTTTAACATTT-AAAATTATTTTTGAAAATCT-CTAAAACTCGTG
* * **
54092605 CCCATGTTAGTGGTGTTTTAAGGAGGTATATAAATATTTT
64 CCCATGTTAATGGTCTTTTAAGGAGACATATAAATATTTT
* *
54092645 TTATTTTAT-TTTATT---TTTATTTACCATTTAAAATTATTTTTGAAAATCTCTAAAGCT-GTG
1 TTATTTTATATTT-TTAAATTT-TTTAACATTTAAAATTATTTTTGAAAATCTCTAAAACTCGTG
* *
54092705 CCTCGTGTTAATGGTCTTTTAATGAGACATATAAATATTTTTT
64 CC-CATGTTAATGGTCTTTTAAGGAGACATATAAATA--TTTT
54092748 TATATTTTATATTTTTAAATTCTTTTAACATTTAAAATTATTTTTGAAAATCTCTAA
1 T-TATTTTATATTTTTAAATT-TTTTAACATTTAAAATTATTTTTGAAAATCTCTAA
54092805 CGGTCGCATA
Statistics
Matches: 134, Mismatches: 14, Indels: 21
0.79 0.08 0.12
Matches are distributed among these distances:
100 3 0.02
101 54 0.40
102 10 0.07
103 8 0.06
104 20 0.15
105 3 0.02
107 35 0.26
108 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.52
Consensus pattern (103 bp):
TTATTTTATATTTTTAAATTTTTTAACATTTAAAATTATTTTTGAAAATCTCTAAAACTCGTGCC
CATGTTAATGGTCTTTTAAGGAGACATATAAATATTTT
Found at i:54101947 original size:23 final size:23
Alignment explanation
Indices: 54101920--54101965 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54101910 AAAAATAAGT
54101920 ATAAAAATACATGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
54101943 ATAAAAATACATGGTATTGGATA
1 ATAAAAATACATGGTATTGGATA
54101966 TTTACATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (23 bp):
ATAAAAATACATGGTATTGGATA
Found at i:54105994 original size:12 final size:12
Alignment explanation
Indices: 54105963--54106012 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
54105953 TCCTTCTGCT
54105963 TCATCACATTCCA
1 TCATC-CATTCCA
54105976 T-ATCCATGT-CA
1 TCATCCAT-TCCA
54105987 TCATCCATTCCA
1 TCATCCATTCCA
54105999 TCATCCATTTCCA
1 TCATCCA-TTCCA
54106012 T
1 T
54106013 ACTCTCATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.21
12 19 0.58
13 7 0.21
ACGTcount: A:0.26, C:0.36, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATCCATTCCA
Found at i:54107725 original size:15 final size:15
Alignment explanation
Indices: 54107705--54107755 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
54107695 ACAAAACGAT
54107705 AACGTAAGTGACTAA
1 AACGTAAGTGACTAA
*
54107720 AACGTAA-T-ACTTCA
1 AACGTAAGTGAC-TAA
*
54107734 AACATAAGTGACTAA
1 AACGTAAGTGACTAA
*
54107749 AATGTAA
1 AACGTAA
54107756 ATTGAGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
AACGTAAGTGACTAA
Found at i:54110355 original size:9 final size:9
Alignment explanation
Indices: 54110341--54110457 Score: 135
Period size: 9 Copynumber: 12.6 Consensus size: 9
54110331 TTTGGTTAAA
54110341 AATTACCCG
1 AATTACCCG
54110350 AATTACCCG
1 AATTACCCG
*
54110359 ACTTACCCG
1 AATTACCCG
*
54110368 ACTTACCCG
1 AATTACCCG
*
54110377 AATTACCCA
1 AATTACCCG
*
54110386 AATTACTCG
1 AATTACCCG
*
54110395 AATTACCCAAA
1 AATTACCC--G
*
54110406 AATTACCCA
1 AATTACCCG
54110415 AATTACCCG
1 AATTACCCG
*
54110424 AATTACCCACA
1 AATTA-CC-CG
54110435 AATTACCCG
1 AATTACCCG
54110444 AATTACCCG
1 AATTACCCG
54110453 AATTA
1 AATTA
54110458 AATCACTACA
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
9 76 0.81
10 4 0.04
11 14 0.15
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:54110415 original size:29 final size:29
Alignment explanation
Indices: 54110402--54110457 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
54110392 TCGAATTACC
54110402 CAAAAATTACCCAAATTACCCGAATTACC
1 CAAAAATTACCCAAATTACCCGAATTACC
* *
54110431 CACAAATTACCCGAATTACCCGAATTA
1 CAAAAATTACCCAAATTACCCGAATTA
54110458 AATCACTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.21
Consensus pattern (29 bp):
CAAAAATTACCCAAATTACCCGAATTACC
Found at i:54110486 original size:17 final size:17
Alignment explanation
Indices: 54110453--54110561 Score: 69
Period size: 17 Copynumber: 6.1 Consensus size: 17
54110443 GAATTACCCG
*
54110453 AATT-AAATCACTACAT
1 AATTAAAATCATTACAT
*
54110469 AATTAAAAGCATTACAT
1 AATTAAAATCATTACAT
* *
54110486 AAATCTTTAAATCACTACAT
1 -AA--TTAAAATCATTACAT
54110506 AATTAAAA-CTATTACAT
1 AATTAAAATC-ATTACAT
** *
54110523 AAGTTTTTGAATCACTACAT
1 AA---TTAAAATCATTACAT
*
54110543 AATTAAAAACATTACAT
1 AATTAAAATCATTACAT
54110560 AA
1 AA
54110562 GTCTTGAATT
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
16 5 0.07
17 36 0.51
18 2 0.03
19 2 0.03
20 24 0.34
21 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.33
Consensus pattern (17 bp):
AATTAAAATCATTACAT
Found at i:54110501 original size:37 final size:36
Alignment explanation
Indices: 54110455--54110566 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 36
54110445 ATTACCCGAA
*
54110455 TTAAATCACTACATAATTAAAAGCATTACATAAATCT
1 TTAAATCACTACATAATTAAAA-CATTACATAAGTCT
*
54110492 TTAAATCACTACATAATTAAAACTATTACATAAGTTT
1 TTAAATCACTACATAATTAAAAC-ATTACATAAGTCT
*
54110529 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTAAATCACTACATAATT-AAAACATTACATAAGTCT
54110566 T
1 T
54110567 GAATTAACAC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.01
37 63 0.91
38 5 0.07
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (36 bp):
TTAAATCACTACATAATTAAAACATTACATAAGTCT
Found at i:54110506 original size:20 final size:18
Alignment explanation
Indices: 54110455--54110507 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
54110445 ATTACCCGAA
54110455 TTAAATCACTACAT-AAT
1 TTAAATCACTACATAAAT
* * *
54110472 TAAAAGCATTACATAAATCT
1 TTAAATCACTACATAAA--T
54110492 TTAAATCACTACATAA
1 TTAAATCACTACATAA
54110508 TTAAAACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
20 14 0.52
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAATCACTACATAAAT
Found at i:54113094 original size:15 final size:16
Alignment explanation
Indices: 54113061--54113099 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
54113051 GGGCCTTGAT
54113061 ATTATAATGATGAAAA
1 ATTATAATGATGAAAA
54113077 ATTATAATGATG-AAA
1 ATTATAATGATGAAAA
54113092 ATTATAAT
1 ATTATAAT
54113100 ATTAGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (16 bp):
ATTATAATGATGAAAA
Found at i:54113350 original size:25 final size:25
Alignment explanation
Indices: 54113317--54113364 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
54113307 TTTATATATG
*
54113317 CTGGTTGTGTAAAGAAATTTGTACA
1 CTGGATGTGTAAAGAAATTTGTACA
54113342 CTGGATGTGTAAAGAAATTTGTA
1 CTGGATGTGTAAAGAAATTTGTA
54113365 AGTAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (25 bp):
CTGGATGTGTAAAGAAATTTGTACA
Found at i:54116066 original size:32 final size:32
Alignment explanation
Indices: 54116023--54116137 Score: 144
Period size: 32 Copynumber: 3.6 Consensus size: 32
54116013 TTTTAAAGGA
*
54116023 ATATTT-TTATCATTTAACAAAATTAAAGTTG
1 ATATTTGTTATCATTTCACAAAATTAAAGTTG
*
54116054 ATATTTGTTATCATTTCACAAAATTGAAGTTG
1 ATATTTGTTATCATTTCACAAAATTAAAGTTG
* * ** *
54116086 TTATTTGGTA-CAATTTCACAAAACGAAAGGTG
1 ATATTTGTTATC-ATTTCACAAAATTAAAGTTG
54116118 ATATTTGTTATCATTTCACA
1 ATATTTGTTATCATTTCACA
54116138 GAACCATGCA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
31 7 0.10
32 63 0.89
33 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (32 bp):
ATATTTGTTATCATTTCACAAAATTAAAGTTG
Found at i:54120692 original size:18 final size:18
Alignment explanation
Indices: 54120661--54120699 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54120651 TCACGTCAAC
54120661 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATT-TA
*
54120680 AAAT-ATTTTAAAATTTA
1 AAATAATTTAAAAATTTA
54120697 AAA
1 AAA
54120700 AATCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTTAAAAATTTA
Found at i:54120700 original size:18 final size:19
Alignment explanation
Indices: 54120661--54120702 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54120651 TCACGTCAAC
54120661 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTATA
* * *
54120680 AAATATTTTAAAATTTAAA
1 AAATAATTTAAAAATTATA
54120699 AAAT
1 AAAT
54120703 CATAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAAAAATTATA
Found at i:54120712 original size:11 final size:11
Alignment explanation
Indices: 54120696--54120721 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54120686 TTTAAAATTT
54120696 AAAAAATCATA
1 AAAAAATCATA
54120707 AAAAAATCATA
1 AAAAAATCATA
54120718 AAAA
1 AAAA
54120722 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATCATA
Found at i:54122542 original size:45 final size:47
Alignment explanation
Indices: 54122476--54122567 Score: 161
Period size: 45 Copynumber: 2.0 Consensus size: 47
54122466 AGCGTGGCAC
54122476 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
*
54122523 TACTACAC-T-TCCTATTGATTAGTTTCAGGCAATAATAAATGCCAA
1 TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
54122568 ATACGAAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 35 0.80
46 1 0.02
47 8 0.18
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (47 bp):
TACTACACTTCTCCTATTGATTAGTTGCAGGCAATAATAAATGCCAA
Found at i:54134103 original size:5 final size:5
Alignment explanation
Indices: 54134093--54134123 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
54134083 GGTTATAATT
54134093 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
54134124 GCTTTCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:54139685 original size:23 final size:23
Alignment explanation
Indices: 54139636--54139685 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
54139626 ACTTTTTTTG
* ** *
54139636 AGTTATCTCAAATAAGTGTTTCG
1 AGTTAACTCAAATAAGTAATTCA
*
54139659 AGTTAACTCGAATAAGTAATTCA
1 AGTTAACTCAAATAAGTAATTCA
54139682 AGTT
1 AGTT
54139686 TTGAGTTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (23 bp):
AGTTAACTCAAATAAGTAATTCA
Found at i:54139820 original size:9 final size:9
Alignment explanation
Indices: 54139808--54139878 Score: 58
Period size: 9 Copynumber: 8.2 Consensus size: 9
54139798 TTATAAAAAT
54139808 AATTTTTAA
1 AATTTTTAA
*
54139817 AATTTATAA
1 AATTTTTAA
*
54139826 TATTTTTAA
1 AATTTTTAA
*
54139835 AATTTTCAA
1 AATTTTTAA
54139844 AA--TTT-A
1 AATTTTTAA
*
54139850 CATTTTTAA
1 AATTTTTAA
* *
54139859 AATATATAA
1 AATTTTTAA
*
54139868 ATTTTTTAA
1 AATTTTTAA
54139877 AA
1 AA
54139879 AATTATAAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
6 2 0.04
7 2 0.04
8 3 0.07
9 38 0.84
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (9 bp):
AATTTTTAA
Found at i:54139885 original size:19 final size:18
Alignment explanation
Indices: 54139852--54139887 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54139842 AAAATTTACA
*
54139852 TTTTTAAAATATATAAAT
1 TTTTTAAAAAATATAAAT
54139870 TTTTTAAAAAATTATAAA
1 TTTTTAAAAAA-TATAAA
54139888 AAATATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAAATATAAAT
Found at i:54142201 original size:15 final size:16
Alignment explanation
Indices: 54142185--54142228 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
54142175 ATAATTAATT
54142185 AATATTTTTATATTTAA
1 AATA-TTTTATATTTAA
*
54142202 AATCATTTTATATTTTTA
1 AAT-ATTTTATA-TTTAA
54142220 AATATTTTA
1 AATATTTTA
54142229 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTTATATTTAA
Found at i:54142226 original size:17 final size:18
Alignment explanation
Indices: 54142185--54142239 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
54142175 ATAATTAATT
54142185 AATATTTT-TATATTTAA
1 AATATTTTATATATTTAA
*
54142202 AATCATTTTATAT-TTTTA
1 AAT-ATTTTATATATTTAA
*
54142220 AATATTTTAAATATATTAA
1 AATATTTTATATAT-TTAA
54142239 A
1 A
54142240 TGTAGATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 11 0.35
18 13 0.42
19 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTTTATATATTTAA
Found at i:54142229 original size:9 final size:9
Alignment explanation
Indices: 54142185--54142240 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
54142175 ATAATTAATT
54142185 AATATTTT-
1 AATATTTTA
* *
54142193 TATATTTAA
1 AATATTTTA
54142202 AATCATTTTA
1 AAT-ATTTTA
*
54142212 TAT-TTTTA
1 AATATTTTA
54142220 AATATTTTA
1 AATATTTTA
*
54142229 AATATATTA
1 AATATTTTA
54142238 AAT
1 AAT
54142241 GTAGATAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 13 0.34
9 18 0.47
10 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
AATATTTTA
Found at i:54143254 original size:21 final size:21
Alignment explanation
Indices: 54143225--54143279 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
54143215 GATATATCTG
* * *
54143225 TATTTAAATTTTATTTTATTT
1 TATTCAAATTTTAATCTATTT
54143246 TATTCAAATTTTAATCTATTT
1 TATTCAAATTTTAATCTATTT
*
54143267 TTTTC--ATTTTAAT
1 TATTCAAATTTTAAT
54143280 ATTGTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 8 0.27
21 22 0.73
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTCAAATTTTAATCTATTT
Found at i:54146487 original size:43 final size:43
Alignment explanation
Indices: 54146426--54146512 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
54146416 TTTATTCAAG
54146426 TTAGTCTCTAAACTTGATAATGTTCCTATATTGAGATCTAAAC
1 TTAGTCTCTAAACTTGATAATGTTCCTATATTGAGATCTAAAC
54146469 TTAGTCTCTAAACTTGATAATGTTCCTATATTGAGATCTAAAC
1 TTAGTCTCTAAACTTGATAATGTTCCTATATTGAGATCTAAAC
54146512 T
1 T
54146513 CAAGAATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (43 bp):
TTAGTCTCTAAACTTGATAATGTTCCTATATTGAGATCTAAAC
Found at i:54164661 original size:19 final size:18
Alignment explanation
Indices: 54164633--54164668 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54164623 AAGGGAAGAA
54164633 GTAAAAAAAAAACTAAAT
1 GTAAAAAAAAAACTAAAT
*
54164651 GTAATAAAAAAAAGTAAA
1 GTAA-AAAAAAAACTAAA
54164669 AGATGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (18 bp):
GTAAAAAAAAAACTAAAT
Found at i:54165160 original size:25 final size:24
Alignment explanation
Indices: 54165132--54165189 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
54165122 GTTTTTCTTA
**
54165132 AATATTTGTATAATTATTTTTAATT
1 AATATTTACATAA-TATTTTTAATT
*
54165157 AATATTAACATAATATTTTTAATT
1 AATATTTACATAATATTTTTAATT
54165181 ATATATTTA
1 A-ATATTTA
54165190 TTTATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AATATTTACATAATATTTTTAATT
Found at i:54165216 original size:19 final size:19
Alignment explanation
Indices: 54165188--54165224 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54165178 ATTATATATT
*
54165188 TATTTATAAACTTTTTATA
1 TATTTATAAAATTTTTATA
*
54165207 TATTTTTAAAATTTTTAT
1 TATTTATAAAATTTTTAT
54165225 TTCAGTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATAAAATTTTTATA
Found at i:54167945 original size:28 final size:28
Alignment explanation
Indices: 54167886--54167945 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
54167876 AATGTTAATC
* * * *
54167886 TTTCATAGTTTGCCATAAAGGCTTCTTT
1 TTTCATAGTTTGCCACAAAGGCATATTA
54167914 TTTCATAGTTTGCCACAAAGGCATATTA
1 TTTCATAGTTTGCCACAAAGGCATATTA
54167942 TTTC
1 TTTC
54167946 CTGACATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (28 bp):
TTTCATAGTTTGCCACAAAGGCATATTA
Found at i:54169809 original size:17 final size:17
Alignment explanation
Indices: 54169772--54169819 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
54169762 GAATTTATAA
*
54169772 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
54169788 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
54169805 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
54169820 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:54171107 original size:46 final size:46
Alignment explanation
Indices: 54171037--54171218 Score: 292
Period size: 46 Copynumber: 4.0 Consensus size: 46
54171027 CATGGAAAAG
*
54171037 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
54171083 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
54171129 TGTGAAAAGTAGGTATGGTGTTTCAGTGAATAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
54171175 TGTGAAAAATAGGTATGGTATTTCCGTGAAGAAAACCATACTGA
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGA
54171219 TTTATAGCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:54172935 original size:38 final size:38
Alignment explanation
Indices: 54172884--54172976 Score: 141
Period size: 38 Copynumber: 2.4 Consensus size: 38
54172874 CTACTGAGTG
* *
54172884 CATGTTAAGCATGTGTACTACTACTATTAAACAAAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
* **
54172922 CATGTTAAGCATGTCTACGGCTACTATTAAATTAAATA
1 CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
54172960 CATGTTAAGCATGTCTA
1 CATGTTAAGCATGTCTA
54172977 TTATTTCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (38 bp):
CATGTTAAGCATGTCTACGACTACTATTAAACAAAATA
Found at i:54173198 original size:22 final size:23
Alignment explanation
Indices: 54173136--54173198 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
54173126 AAAAATAATA
*
54173136 GTGGTTCATCCCCAAATTTTTACTG
1 GTGGTTCATCCTCAAA--TTTACTG
* *
54173161 GTAGTTTAT-CTACAAA-TTACTG
1 GTGGTTCATCCT-CAAATTTACTG
54173183 GTGGTTCATCCTCAAA
1 GTGGTTCATCCTCAAA
54173199 ATGGAATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 17 0.55
23 2 0.06
24 1 0.03
25 11 0.35
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (23 bp):
GTGGTTCATCCTCAAATTTACTG
Found at i:54174880 original size:17 final size:17
Alignment explanation
Indices: 54174849--54174895 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
54174839 ATAGCTTTTA
54174849 TATATATATTTATATTT
1 TATATATATTTATATTT
54174866 TATA-ATATTTAATATTT
1 TATATATATTT-ATATTT
54174883 T-TCATAT-TTTATA
1 TAT-ATATATTTATA
54174896 ACTTATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 10 0.37
17 15 0.56
18 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATATTTATATTT
Found at i:54174891 original size:54 final size:52
Alignment explanation
Indices: 54174796--54174910 Score: 117
Period size: 52 Copynumber: 2.2 Consensus size: 52
54174786 TGTTATATTC
* * *
54174796 ATATATATATATATATTATGTATATTTTATTATCTTTTATTTCATAGCTTTT
1 ATATATATATATATATTATGTATATTTTAATATCTTTTATTTCATAACTTAT
* * *
54174848 ATATATATATTTATATT-T-TATAATATTTAATATTTTTCATATTTTATAACTTAT
1 ATATATATATATATATTATGTAT-AT-TTTAATATCTTT--TATTTCATAACTTAT
*
54174902 ACATATATA
1 ATATATATA
54174911 CACGCATAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
50 3 0.06
51 3 0.06
52 26 0.50
54 20 0.38
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (52 bp):
ATATATATATATATATTATGTATATTTTAATATCTTTTATTTCATAACTTAT
Found at i:54175035 original size:28 final size:27
Alignment explanation
Indices: 54174989--54175046 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
54174979 ATTTTCTTAG
* *
54174989 TTTATATATATATATATACATTTACAT
1 TTTATATACATATACATACATTTACAT
* *
54175016 TTTATAATACATATACATACTTTTATAT
1 TTTAT-ATACATATACATACATTTACAT
54175044 TTT
1 TTT
54175047 TATCTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTATATACATATACATACATTTACAT
Found at i:54178255 original size:3 final size:3
Alignment explanation
Indices: 54178247--54178285 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
54178237 AATATTATGG
54178247 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54178286 AACGCAAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54178575 original size:11 final size:11
Alignment explanation
Indices: 54178559--54178602 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
54178549 AGATTAATTT
54178559 GAATTTTTTTA
1 GAATTTTTTTA
*
54178570 GAATTTTTATA
1 GAATTTTTTTA
54178581 -AGATTTTTTTA
1 GA-ATTTTTTTA
*
54178592 AAATTTTTTTA
1 GAATTTTTTTA
54178603 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (11 bp):
GAATTTTTTTA
Found at i:54178591 original size:13 final size:12
Alignment explanation
Indices: 54178573--54178611 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
54178563 TTTTTTAGAA
54178573 TTTTTATAAGATT
1 TTTTTATAA-ATT
54178586 TTTTTA-AAATT
1 TTTTTATAAATT
54178597 TTTTTATAAAATT
1 TTTTTAT-AAATT
54178610 TT
1 TT
54178612 AATAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TTTTTATAAATT
Found at i:54178611 original size:11 final size:11
Alignment explanation
Indices: 54178560--54178616 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
54178550 GATTAATTTG
* *
54178560 AATTTTTTTAG
1 AATTTTTATAA
54178571 AATTTTTATAA
1 AATTTTTATAA
* *
54178582 GATTTTTTTAA
1 AATTTTTATAA
54178593 AATTTTTTTATAA
1 AA--TTTTTATAA
*
54178606 AATTTTAATAA
1 AATTTTTATAA
54178617 TTACTAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 27 0.73
13 10 0.27
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:54183077 original size:41 final size:41
Alignment explanation
Indices: 54183031--54183114 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
54183021 ATAATTGTTG
54183031 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
*
54183072 ATTGCCTTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
54183113 AT
1 AT
54183115 GCTTCAAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (41 bp):
ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
Found at i:54198033 original size:27 final size:27
Alignment explanation
Indices: 54197971--54198189 Score: 222
Period size: 27 Copynumber: 8.1 Consensus size: 27
54197961 GCTGATTGCC
* * **
54197971 AGGCTGGTGTTCAAATTGCTGCTGACT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
*** *
54197998 AGATTGGTGTTCAAATTGCTGCTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* *
54198025 AGGCCGGTGATCGAATTGCTGCTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * * *
54198052 AGGCCGGTGCTCGAATGGCTGTTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * * *
54198079 AGGCCGGTGTTCGAATGGTTGTTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * *
54198106 AGGCCGGTGATCAAATTGCTGTTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* *
54198133 AGGCCGGTGTTCGAATGGCTGTTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
*
54198160 AGGCCGGTGATCGAATTGCTGCTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
54198187 AGG
1 AGG
54198190 GCAATAGTCG
Statistics
Matches: 166, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 166 1.00
ACGTcount: A:0.15, C:0.16, G:0.38, T:0.31
Consensus pattern (27 bp):
AGGCCGGTGTTCGAATTGCTGCTGGGT
Found at i:54198088 original size:81 final size:81
Alignment explanation
Indices: 54198003--54198189 Score: 275
Period size: 81 Copynumber: 2.3 Consensus size: 81
54197993 TGACTAGATT
* * *
54198003 GGTGTTCAAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
*
54198068 GGCTGTTGGTTAGGCC
66 GGCTGTTGGGTAGGCC
* * * * * *
54198084 GGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCAAATTGCTGTTGGGTAGGCCGGTGTTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
54198149 GGCTGTTGGGTAGGCC
66 GGCTGTTGGGTAGGCC
*
54198165 GGTGATCGAATTGCTGCTGGGTAGG
1 GGTGTTCGAATTGCTGCTGGGTAGG
54198190 GCAATAGTCG
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 91 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (81 bp):
GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
GGCTGTTGGGTAGGCC
Found at i:54198202 original size:54 final size:54
Alignment explanation
Indices: 54198011--54198189 Score: 259
Period size: 54 Copynumber: 3.3 Consensus size: 54
54198001 TTGGTGTTCA
* * * *
54198011 AATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* * * * *
54198065 AATGGCTGTTGGTTAGGCCGGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCA
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* *
54198119 AATTGCTGTTGGGTAGGCCGGTGTTCGAATGGCTGTTGGGTAGGCCGGTGATCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
54198173 AATTGCTGCTGGGTAGG
1 AATTGCTGCTGGGTAGG
54198190 GCAATAGTCG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (54 bp):
AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
Found at i:54202860 original size:33 final size:32
Alignment explanation
Indices: 54202744--54202866 Score: 131
Period size: 33 Copynumber: 3.8 Consensus size: 32
54202734 GCAGTAGTCA
* * * *
54202744 CACCCTCCCCATCAGCTTTTACCTTTTCAACAT
1 CACCCTCCCTAGCAGCTTCTACC-CTTCAACAT
* *
54202777 CACCCTCCCTAACAACTTCTATCCCTTCAACAT
1 CACCCTCCCTAGCAGCTTCTA-CCCTTCAACAT
*
54202810 CACCCT-CTTCAGCAGCTTCTACACCTTCAACAT
1 CACCCTCCCT-AGCAGCTTCTAC-CCTTCAACAT
*
54202843 CACCCTCCCTAGTAGCTTCTACCC
1 CACCCTCCCTAGCAGCTTCTACCC
54202867 CCTCCCTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.07
33 67 0.88
34 4 0.05
ACGTcount: A:0.23, C:0.45, G:0.04, T:0.28
Consensus pattern (32 bp):
CACCCTCCCTAGCAGCTTCTACCCTTCAACAT
Found at i:54202869 original size:21 final size:21
Alignment explanation
Indices: 54202845--54202887 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54202835 TTCAACATCA
*
54202845 CCCTCCCTAGTAGCTTCTACC
1 CCCTCCCTAGTAACTTCTACC
*
54202866 CCCTCCCTAGTAACTTTTACC
1 CCCTCCCTAGTAACTTCTACC
54202887 C
1 C
54202888 ATTCAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.07, T:0.30
Consensus pattern (21 bp):
CCCTCCCTAGTAACTTCTACC
Found at i:54202894 original size:54 final size:54
Alignment explanation
Indices: 54202826--54202953 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
54202816 CTTCAGCAGC
* *
54202826 TTCTACACC-TTCAACATCACCCTCCCTAGTAGCTTCTACCCCCTCCCTAGTAACT
1 TTCTAC-CCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCA-TAACT
* * * * * *
54202881 TT-TACCCATTCAACAACACCCTCCTTAGCAGTTTGTACCCCCTCCCCATCAGT
1 TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
54202934 TTCTACCCATTCAACATCAC
1 TTCTACCCATTCAACATCAC
54202954 ACTCTCCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
53 7 0.11
54 53 0.85
55 2 0.03
ACGTcount: A:0.23, C:0.42, G:0.05, T:0.29
Consensus pattern (54 bp):
TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
Found at i:54209571 original size:134 final size:134
Alignment explanation
Indices: 54209326--54210022 Score: 731
Period size: 134 Copynumber: 5.2 Consensus size: 134
54209316 TAAGTAAAAG
* * * * * *
54209326 GTCGTGATCGTAAATCAGCGAACTGATTAAGTGGAGTCGCGATTGTAAATCAACGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * * *
54209391 AAAGTGGTCATGATCGTAAATCGATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
54209456 GATA
131 GACA
* * * *
54209460 GTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCGACCGTAAATCGATGAACTCTTTTT
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * *
54209525 GAAGTGTTTATGATCGTAAATCAATAAACTGAAGCTGTAATTGTAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
54209590 GATA
131 GACA
* * * * *
54209594 GTCGTGATCGTAAATCAGCTAACTGTTTAAGTGGAGTTGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * *
54209659 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
54209724 GACA
131 GACA
* ** * * * * *
54209728 GTTGTGATTATAAATCAGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTG-TCAAACTCTTT
1 GTCGTGATCGTAAATCAGCGAACT-GTTTAAGTGGAGTCGCGATCGTAAATCGAT-GAACTCTTT
* * * *
54209791 ATAAAGTGTTCATGATCGTAAATCAATGAACT-AAAATCGTAATAGTAAATCATCGAGCTTTAAA
64 ATGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAA
54209855 AATGACA
128 AATGACA
* * * * *
54209862 GTCATGATCGTAAATCAGCGAATTGTTTTAGTGGAGT-GTTGATCGTAAATCGACGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCG-CGATCGTAAATCGATGAACTCTTTA
* * * * * * * * *
54209926 TGAAGTGTTTACGATTGTAAATTAACGAACTTAA-ATCGTGATTGTAAATCAACAAGCTTTAAAA
65 TGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAAA
54209990 ATGACA
129 ATGACA
* * *
54209996 ATCAG-GATTGTAAATCAACGAACTGTT
1 GTC-GTGATCGTAAATCAGCGAACTGTT
54210023 AGAAAATCGA
Statistics
Matches: 470, Mismatches: 85, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
133 6 0.01
134 461 0.98
135 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (134 bp):
GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
GACA
Found at i:54210050 original size:39 final size:39
Alignment explanation
Indices: 54210005--54210080 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
54209995 AATCAGGATT
* *
54210005 GTAAATCAACGAACTGTTAGAAAATCGAATGTCGTGATC
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
** * *
54210044 GTAAATCAGTGGACTGTAAGAAAGTCGAAGGTCGTGA
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGA
54210081 CTGTATTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (39 bp):
GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
Found at i:54232323 original size:23 final size:23
Alignment explanation
Indices: 54232253--54232338 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
54232243 CCTGATCAAT
54232253 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
54232274 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
54232294 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
54232317 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
54232339 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.16
21 23 0.42
23 23 0.42
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:54232335 original size:44 final size:41
Alignment explanation
Indices: 54232253--54232339 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
54232243 CCTGATCAAT
* *
54232253 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
54232294 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
54232338 AT
1 AT
54232340 CGGCAAAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.25
43 1 0.03
44 18 0.45
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:54232714 original size:16 final size:17
Alignment explanation
Indices: 54232693--54232724 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54232683 TAATAATAGT
54232693 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
54232709 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
54232725 GCTTGTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:54236402 original size:16 final size:17
Alignment explanation
Indices: 54236374--54236409 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
54236364 TTAGAATTGG
*
54236374 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
54236391 ATTGAG-AAATTAATTA
1 ATTGAGAAAATTAATTA
54236407 ATT
1 ATT
54236410 TAAATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:54243506 original size:24 final size:24
Alignment explanation
Indices: 54243474--54243522 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
54243464 CAAGTAGGAG
* *
54243474 TTGTGTTACTCTTTGTAGGGAGCA
1 TTGTCTTACTCTTTGTAGAGAGCA
*
54243498 TTGTCTTACTGTTTGTAGAGAGCA
1 TTGTCTTACTCTTTGTAGAGAGCA
54243522 T
1 T
54243523 CAAAAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (24 bp):
TTGTCTTACTCTTTGTAGAGAGCA
Found at i:54248003 original size:22 final size:24
Alignment explanation
Indices: 54247977--54248020 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54247967 GAAAAATATT
54247977 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
54247999 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
54248021 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:54248228 original size:16 final size:16
Alignment explanation
Indices: 54248207--54248248 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
54248197 AATAATTTGA
*
54248207 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
54248223 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
54248239 TAGTTTTAAT
1 TAATTTTAAT
54248249 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:54248232 original size:22 final size:23
Alignment explanation
Indices: 54248222--54248277 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
54248212 TTACTAACAA
* * *
54248222 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
54248244 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
54248267 TTAATTTTAAT
1 TTAATTTTAAT
54248278 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:54248539 original size:28 final size:27
Alignment explanation
Indices: 54248508--54248577 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
54248498 AAATAAAAAA
*
54248508 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
54248536 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
54248563 TTACCAAAATATATA
1 TTACCAAAATATATA
54248578 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.61
28 10 0.26
29 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:54248689 original size:4 final size:4
Alignment explanation
Indices: 54248682--54248817 Score: 72
Period size: 4 Copynumber: 34.0 Consensus size: 4
54248672 AATAGGGAGG
* * * *
54248682 GAAA GAAA GAAA GAAA GGAAT GAAT GAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
** *
54248730 GAAA GAAA -AGG GAAG GAGAA GAGAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
*
54248775 GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
54248818 AGGAAAGGAG
Statistics
Matches: 109, Mismatches: 11, Indels: 24
0.76 0.08 0.17
Matches are distributed among these distances:
3 19 0.17
4 65 0.60
5 22 0.20
6 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:54248762 original size:41 final size:39
Alignment explanation
Indices: 54248708--54248890 Score: 184
Period size: 41 Copynumber: 4.7 Consensus size: 39
54248698 GGAATGAATG
* * *
54248708 AGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGA
1 AGAGAAAAAAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGA
54248749 AGAGAAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGA
1 AGAGAAAAAAAAG-AA-AAAGAAGAAGAAAAGGAAAGGAGA
*
54248790 AGA-AAAAAGAAAGAAAGAAGGA-AAGAAAAGGAAAGGAGA
1 AGAGAAAAA-AAAGAAA-AAGAAGAAGAAAAGGAAAGGAGA
* *
54248829 AGAGAAGAGAAAAA-AAAAAGAAGAAGAAGAGGGAA-G-GA
1 AGAGAA-A-AAAAAGAAAAAGAAGAAGAAAAGGAAAGGAGA
54248867 AG-GAAAAAAAAGAAAAA-AA-AAGAA
1 AGAGAAAAAAAAGAAAAAGAAGAAGAA
54248891 TTTTTTTTTT
Statistics
Matches: 126, Mismatches: 7, Indels: 25
0.80 0.04 0.16
Matches are distributed among these distances:
34 5 0.04
35 7 0.06
36 6 0.05
37 3 0.02
38 4 0.03
39 26 0.21
40 26 0.21
41 38 0.30
42 5 0.04
43 6 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (39 bp):
AGAGAAAAAAAAGAAAAAGAAGAAGAAAAGGAAAGGAGA
Found at i:54248820 original size:34 final size:35
Alignment explanation
Indices: 54248715--54248821 Score: 103
Period size: 35 Copynumber: 3.0 Consensus size: 35
54248705 ATGAGAGGAA
* * * * *
54248715 AGAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGAA-G
1 AGAAA-AAAAAGAAAGAAAGAAGA-GAAAAGAAAAGG
*
54248751 AGAAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGG
1 AGAAAAAAAAGAAAGAAAGAAG-AGAAAAGAAAAGG
54248787 AGAAGAAAAAAGAAAGAAAGAAG-G-AAAGAAAAGG
1 AGAA-AAAAAAGAAAGAAAGAAGAGAAAAGAAAAGG
54248821 A
1 A
54248822 AAGGAGAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
34 10 0.16
35 22 0.36
36 11 0.18
37 18 0.30
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (35 bp):
AGAAAAAAAAGAAAGAAAGAAGAGAAAAGAAAAGG
Found at i:54248828 original size:80 final size:81
Alignment explanation
Indices: 54248713--54248886 Score: 239
Period size: 80 Copynumber: 2.1 Consensus size: 81
54248703 GAATGAGAGG
*
54248713 AAAGAAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGAAGAGAA-AAAAAAGAAAGAAAGAAGAAGA
1 AAAGAAAG-AAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAAAAAA-AAA-AAAGAAGAAGA
54248777 AAAGGAAAGG-A-GAAGAAA
63 AAAGGAAAGGAAGGAA-AAA
* *
54248795 AAAGAAAG-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAAAAAGAAGAAGAAGA
1 AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAAAAAAAAAAAAGAAGAAGAAAA
*
54248859 GGGAAGGAAGGAAAAA
66 GGAAAGGAAGGAAAAA
*
54248875 AAAGAAAAAAAA
1 AAAGAAAGAAAA
54248887 AGAATTTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
79 19 0.23
80 45 0.54
81 11 0.13
82 8 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (81 bp):
AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAAAAAAAAAAAAGAAGAAGAAAA
GGAAAGGAAGGAAAAA
Found at i:54253831 original size:515 final size:515
Alignment explanation
Indices: 54252860--54253890 Score: 2062
Period size: 515 Copynumber: 2.0 Consensus size: 515
54252850 TGCCACGACT
54252860 CCATTGTGCTCAACCATTGTCGGAAAGATGTGTTTGTCTGCCCCTCCATGTCACTCTCAAGTTGG
1 CCATTGTGCTCAACCATTGTCGGAAAGATGTGTTTGTCTGCCCCTCCATGTCACTCTCAAGTTGG
54252925 ATCATTCTTTGCCGGAAAATATGTGGCTCTAACTCGTACGCTGCATACGTATTAACGAAAAATAA
66 ATCATTCTTTGCCGGAAAATATGTGGCTCTAACTCGTACGCTGCATACGTATTAACGAAAAATAA
54252990 GTTCTAGTAAGTCGATAACATCAAACATTACAACTTATATTGAAAAGATAAGGTTATCATTTACC
131 GTTCTAGTAAGTCGATAACATCAAACATTACAACTTATATTGAAAAGATAAGGTTATCATTTACC
54253055 CATTGCCACGACTTGTCTCTTCCAGTCTGCATTCTTATAATCTTTATGGAAGTTAGACACAATGT
196 CATTGCCACGACTTGTCTCTTCCAGTCTGCATTCTTATAATCTTTATGGAAGTTAGACACAATGT
54253120 GACAAATACAGTAAACAGATCTCCACGGCACACCGAAACGCCTAATAGCTGCAATTAAACCCTTC
261 GACAAATACAGTAAACAGATCTCCACGGCACACCGAAACGCCTAATAGCTGCAATTAAACCCTTC
54253185 CCTCTATCGGAGATGATGCAAATCTTATCGTTCCTAATAACATATCTCCGCATATTTGTGAGGAA
326 CCTCTATCGGAGATGATGCAAATCTTATCGTTCCTAATAACATATCTCCGCATATTTGTGAGGAA
54253250 GAATTCCCAAGACTCCATGTTCTCTTTATCTACGATAGTAAATGCTATCGGGAGCACATTTCTGT
391 GAATTCCCAAGACTCCATGTTCTCTTTATCTACGATAGTAAATGCTATCGGGAGCACATTTCTGT
54253315 TACCGCCTTGAGCAACTGCAAGAAGCAGTATCTGTGTATATTTTCCATACAGCCAGGTCC
456 TACCGCCTTGAGCAACTGCAAGAAGCAGTATCTGTGTATATTTTCCATACAGCCAGGTCC
54253375 CCATTGTGCTCAACCATTGTCGGAAAGATGTGTTTGTCTGCCCCTCCATGTCACTCTCAAGTTGG
1 CCATTGTGCTCAACCATTGTCGGAAAGATGTGTTTGTCTGCCCCTCCATGTCACTCTCAAGTTGG
54253440 ATCATTCTTTGCCGGAAAATATGTGGCTCTAACTCGTACGCTGCATACGTATTAACGAAAAATAA
66 ATCATTCTTTGCCGGAAAATATGTGGCTCTAACTCGTACGCTGCATACGTATTAACGAAAAATAA
54253505 GTTCTAGTAAGTCGATAACATCAAACATTACAACTTATATTGAAAAGATAAGGTTATCATTTACC
131 GTTCTAGTAAGTCGATAACATCAAACATTACAACTTATATTGAAAAGATAAGGTTATCATTTACC
54253570 CATTGCCACGACTTGTCTCTTCCAGTCTGCATTCTTATAATCTTTATGGAAGTTAGACACAATGT
196 CATTGCCACGACTTGTCTCTTCCAGTCTGCATTCTTATAATCTTTATGGAAGTTAGACACAATGT
54253635 GACAAATACAGTAAACAGATCTCCACGGCACACCGAAACGCCTAATAGCTGCAATTAAACCCTTC
261 GACAAATACAGTAAACAGATCTCCACGGCACACCGAAACGCCTAATAGCTGCAATTAAACCCTTC
54253700 CCTCTATCGGAGATGATGCAAATCTTATCGTTCCTAATAACATATCTCCGCATATTTGTGAGGAA
326 CCTCTATCGGAGATGATGCAAATCTTATCGTTCCTAATAACATATCTCCGCATATTTGTGAGGAA
54253765 GAATTCCCAAGACTCCATGTTCTCTTTATCTACGATAGTAAATGCTATCGGGAGCACATTTCTGT
391 GAATTCCCAAGACTCCATGTTCTCTTTATCTACGATAGTAAATGCTATCGGGAGCACATTTCTGT
54253830 TACCGCCTTGAGCAACTGCAAGAAGCAGTATCTGTGTATATTTTCCATACAGCCAGGTCC
456 TACCGCCTTGAGCAACTGCAAGAAGCAGTATCTGTGTATATTTTCCATACAGCCAGGTCC
54253890 C
1 C
54253891 ATCCACCTGC
Statistics
Matches: 516, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
515 516 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (515 bp):
CCATTGTGCTCAACCATTGTCGGAAAGATGTGTTTGTCTGCCCCTCCATGTCACTCTCAAGTTGG
ATCATTCTTTGCCGGAAAATATGTGGCTCTAACTCGTACGCTGCATACGTATTAACGAAAAATAA
GTTCTAGTAAGTCGATAACATCAAACATTACAACTTATATTGAAAAGATAAGGTTATCATTTACC
CATTGCCACGACTTGTCTCTTCCAGTCTGCATTCTTATAATCTTTATGGAAGTTAGACACAATGT
GACAAATACAGTAAACAGATCTCCACGGCACACCGAAACGCCTAATAGCTGCAATTAAACCCTTC
CCTCTATCGGAGATGATGCAAATCTTATCGTTCCTAATAACATATCTCCGCATATTTGTGAGGAA
GAATTCCCAAGACTCCATGTTCTCTTTATCTACGATAGTAAATGCTATCGGGAGCACATTTCTGT
TACCGCCTTGAGCAACTGCAAGAAGCAGTATCTGTGTATATTTTCCATACAGCCAGGTCC
Found at i:54254809 original size:18 final size:18
Alignment explanation
Indices: 54254786--54254830 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54254776 ATCCCAATGA
54254786 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
54254804 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
54254822 TCACCACCA
1 TCGCCACCA
54254831 ACCATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:54255687 original size:3 final size:3
Alignment explanation
Indices: 54255679--54255713 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54255669 TCTTAATACT
54255679 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
54255714 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:54255988 original size:27 final size:27
Alignment explanation
Indices: 54255958--54256015 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
54255948 CCAATCAGTA
*
54255958 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
54255985 TGGCACCATTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
54256012 TGGC
1 TGGC
54256016 GTGACCAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.22
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGCCAT
Found at i:54256134 original size:27 final size:27
Alignment explanation
Indices: 54256078--54256146 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
54256068 TTTGTTTTTG
*
54256078 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAGTAT
*
54256105 ATATTTTTTGGTAAATAAAAAAAAGT-T
1 ATATATTTTGGTAAAT-AAAAAAAGTAT
*
54256132 ATAACATTTTGGTAA
1 AT-ATATTTTGGTAA
54256147 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAAGTAT
Found at i:54256141 original size:28 final size:27
Alignment explanation
Indices: 54256082--54256146 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
54256072 TTTTTGATAT
*
54256082 ATTTTGGTAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
54256109 TTTTTGGTAAATAAAAAAAAGTTATA-AC
1 ATTTTGGTAAAT-AAAAAAA-TTATATAC
54256137 ATTTTGGTAA
1 ATTTTGGTAA
54256147 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.33
28 17 0.52
29 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:54257605 original size:25 final size:23
Alignment explanation
Indices: 54257522--54257601 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
54257512 ATATATATAA
54257522 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
54257545 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
54257568 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
*
54257591 AAAAAATATAT
1 AAAATATATAT
54257602 ATTTAATATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATATATATTTGATTAAAAAT
Found at i:54260382 original size:18 final size:20
Alignment explanation
Indices: 54260358--54260400 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
54260348 TTTATTTGTT
*
54260358 TTATTATAATAATATAATATA
1 TTATTAT-ATAATAAAATATA
54260379 TTATTATATAATAAAATATA
1 TTATTATATAATAAAATATA
54260399 TT
1 TT
54260401 TACTCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTATATAATAAAATATA
Found at i:54261487 original size:6 final size:6
Alignment explanation
Indices: 54261438--54261468 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
54261428 ACTATTAAAT
54261438 TAAAAA TAAAAA TAAAAA TAAAAA TAGAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA
54261469 GATCAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:54266685 original size:27 final size:26
Alignment explanation
Indices: 54266654--54266849 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 26
54266644 TATAACAGTT
*
54266654 ATTTTATCCTATGGGGATATTTCGGTC
1 ATTTTACCCTATGGGG-TATTTCGGTC
* * *
54266681 ATTTTACCCTATCAGGGCATTTTGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
54266708 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
54266735 ATTTTACCCTATGGAGGTATTTCGATC
1 ATTTTACCCTATGG-GGTATTTCGGTC
* *
54266762 ATTTTACCCTATGAGGGTGTTTTGGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
* * *
54266789 ATTTTACCCTATGGGATATTTTGGTT
1 ATTTTACCCTATGGGGTATTTCGGTC
*
54266815 ATTTTACCCTATAGGGGTATTTCGGTT
1 ATTTTACCCTAT-GGGGTATTTCGGTC
54266842 ATTTTACC
1 ATTTTACC
54266850 TTAATTTAGG
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 24 0.16
27 118 0.81
28 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:54266764 original size:81 final size:79
Alignment explanation
Indices: 54266636--54266849 Score: 277
Period size: 81 Copynumber: 2.7 Consensus size: 79
54266626 CATTTCATCT
** *
54266636 CCTA-GGGGTATAACAGTTATTTTATCCTATGGGGATATTTCGGTCATTTTACCCTATCAGGGCA
1 CCTATGGGGTATTTCAGTTATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCTATCAGGGCA
54266700 TTTTGGTCATTTTAC
65 TTTTGGTCATTTTAC
* * * *
54266715 CCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTCGATCATTTTACCCTATGAGGGT
1 CCTAT-GGGGTATTTCAGTTATTTTACCCTATGG-GGTATTTCGGTCATTTTACCCTATCAGGGC
*
54266780 GTTTTGGTCATTTTAC
64 ATTTTGGTCATTTTAC
* ** *
54266796 CCTATGGGATATTTTGGTTATTTTACCCTATAGGGGTATTTCGGTTATTTTACC
1 CCTATGGGGTATTTCAGTTATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
54266850 TTAATTTAGG
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
79 4 0.03
80 40 0.34
81 71 0.61
82 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.43
Consensus pattern (79 bp):
CCTATGGGGTATTTCAGTTATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATCAGGGCAT
TTTGGTCATTTTAC
Found at i:54273072 original size:37 final size:37
Alignment explanation
Indices: 54273022--54273237 Score: 115
Period size: 37 Copynumber: 5.8 Consensus size: 37
54273012 TTCAAAGTAA
54273022 TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
1 TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
* * *
54273059 TAAATTGGCACCCAGTGCCTCATTGA--AACA-C-ACCAG
1 TAAATTGACACCCAGTGTCTCATCGACTAA-ATCGA--AG
* * * * *
54273095 T---TTGGCATCCAGTG-CGTCATCGAATAATTCAAAG
1 TAAATTGACACCCAGTGTC-TCATCGACTAAATCGAAG
* * *
54273129 TAATAAATTGACACCCAGTGTCTCATTGGCTAAACCGAAG
1 ---TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
* * * * * *
54273169 TAAATTGGCACCTAGTGTCTTATTGAATTAATCCGAAG
1 TAAATTGACACCCAGTGTCTCATCGACTAAAT-CGAAG
*
54273207 TAACAAATTGACACCCAGTGTCTCACCGACT
1 T---AAATTGACACCCAGTGTCTCATCGACT
54273238 CGAAGTCGAA
Statistics
Matches: 133, Mismatches: 27, Indels: 34
0.69 0.14 0.18
Matches are distributed among these distances:
32 1 0.01
33 18 0.14
34 3 0.02
35 6 0.05
36 5 0.04
37 49 0.37
38 6 0.05
40 23 0.17
41 22 0.17
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (37 bp):
TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
Found at i:54273168 original size:110 final size:110
Alignment explanation
Indices: 54272974--54273195 Score: 374
Period size: 110 Copynumber: 2.0 Consensus size: 110
54272964 GATCCAACCA
54272974 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
1 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
*
54273039 TCTCATCGACTAAATCGAAGTAAATTGGCACCCAGTGCCTCATTG
66 TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
54273084 AAACACACCAGTTTGGCATCC-AGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
1 AAACACACCAGTTTGGCA-CCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
* * * * *
54273148 GTCTCATTGGCTAAACCGAAGTAAATTGGCACCTAGTGTCTTATTG
65 GTCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
54273194 AA
1 AA
54273196 TTAATCCGAA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
110 103 0.98
111 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (110 bp):
AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
Found at i:54273227 original size:41 final size:39
Alignment explanation
Indices: 54273126--54273231 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 39
54273116 GAATAATTCA
*
54273126 AAGTAATAAATTGACACCCAGTGTCTCATTGGCTAAACCG
1 AAGTAA-AAATTGACACCCAGTGTCTCATTGACTAAACCG
* * * * *
54273166 AAGT--AAATTGGCACCTAGTGTCTTATTGAATTAATCCG
1 AAGTAAAAATTGACACCCAGTGTCTCATTG-ACTAAACCG
54273204 AAGTAACAAATTGACACCCAGTGTCTCA
1 AAGTAA-AAATTGACACCCAGTGTCTCA
54273232 CCGACTCGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 21 0.40
38 10 0.19
40 4 0.08
41 18 0.34
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (39 bp):
AAGTAAAAATTGACACCCAGTGTCTCATTGACTAAACCG
Found at i:54274157 original size:19 final size:16
Alignment explanation
Indices: 54274108--54274178 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
54274098 TAATTTTTCC
54274108 TTCTTTCTTT-TC--T
1 TTCTTTCTTTCTCTAT
*
54274121 TTCTTT-TTCTCCCTAT
1 TTCTTTCTT-TCTCTAT
54274137 TTCGTTTGGCTTTCTCTAT
1 TTC-TTT--CTTTCTCTAT
54274156 TTCTTTCTTTCTCT-T
1 TTCTTTCTTTCTCTAT
54274171 TCTCTTTC
1 T-TCTTTC
54274179 CTTTTTCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
12 2 0.04
13 7 0.15
14 1 0.02
15 2 0.04
16 18 0.38
17 3 0.06
18 3 0.06
19 9 0.19
20 2 0.04
ACGTcount: A:0.03, C:0.27, G:0.04, T:0.66
Consensus pattern (16 bp):
TTCTTTCTTTCTCTAT
Found at i:54274187 original size:17 final size:16
Alignment explanation
Indices: 54274146--54274188 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
54274136 TTTCGTTTGG
54274146 CTTTCTCTATT-TCTTT
1 CTTTCTCT-TTCTCTTT
54274162 CTTTCTCTTTCTCTTT
1 CTTTCTCTTTCTCTTT
*
54274178 CCTTTTTCTTT
1 -CTTTCTCTTT
54274189 TTAGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTCTCTTTCTCTTT
Found at i:54283147 original size:15 final size:15
Alignment explanation
Indices: 54283127--54283161 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
54283117 AGCAGAAAGA
54283127 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
54283142 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
54283157 TTCCT
1 TTCCT
54283162 GCCTAGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (15 bp):
TTCCTCATGAAGTAT
Found at i:54292095 original size:18 final size:18
Alignment explanation
Indices: 54292072--54292117 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
54292062 GGCAACCCAC
54292072 ATTTATTTTCATTTA-GTA
1 ATTTATTTT-ATTTATGTA
*
54292090 ATTTATTTTATTTATTTA
1 ATTTATTTTATTTATGTA
54292108 ATTTAATTTT
1 ATTT-ATTTT
54292118 GAATTCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATTTTATTTATGTA
Found at i:54292464 original size:20 final size:22
Alignment explanation
Indices: 54292418--54292464 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
54292408 AAATGACCAA
*
54292418 GAAAGAAAAAGAAGGAAAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
54292440 G--AGAAAAA-AAAG-AAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
54292458 GAAAGAA
1 GAAAGAA
54292465 TGGCTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 11 0.50
22 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAGAAAGAAAAAAG
Found at i:54297644 original size:16 final size:16
Alignment explanation
Indices: 54297619--54297662 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
54297609 CCGATATAAT
* * *
54297619 AAATTATTTATTTTTA
1 AAATTTTTTAATTTAA
54297635 AAATTTTTTAATTTAA
1 AAATTTTTTAATTTAA
54297651 AAATATTTTTAA
1 AAAT-TTTTTAA
54297663 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTTTAATTTAA
Found at i:54297666 original size:11 final size:11
Alignment explanation
Indices: 54297650--54297712 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
54297640 TTTTAATTTA
54297650 AAAATATTTTT
1 AAAATATTTTT
54297661 AAAATACTTTTT
1 AAAATA-TTTTT
54297673 ---A-A-TTTT
1 AAAATATTTTT
54297679 AAAATATTTTT
1 AAAATATTTTT
54297690 AAAATATTTTT
1 AAAATATTTTT
54297701 AAAATACTTTTT
1 AAAATA-TTTTT
54297713 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 2 0.04
10 1 0.02
11 27 0.60
12 10 0.22
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:54297690 original size:17 final size:18
Alignment explanation
Indices: 54297657--54297691 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54297647 TTAAAAATAT
54297657 TTTTAAAATACTTTTTAA
1 TTTTAAAATACTTTTTAA
54297675 TTTTAAAATA-TTTTTAA
1 TTTTAAAATACTTTTTAA
54297692 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATACTTTTTAA
Found at i:54297696 original size:40 final size:41
Alignment explanation
Indices: 54297642--54297760 Score: 145
Period size: 40 Copynumber: 2.9 Consensus size: 41
54297632 TTAAAATTTT
*
54297642 TTAATTTAAAAATATTTTTAAAATACTTTTTAATTTTAAAA
1 TTAATTTTAAAATATTTTTAAAATACTTTTTAATTTTAAAA
* **
54297683 -TATTTTTAAAATATTTTTAAAATACTTTTT--TTAAAAAAAA
1 TTAATTTTAAAATATTTTTAAAATACTTTTTAATT--TTAAAA
*
54297723 TTAATTTTAAAATATTTTAAAAATACTTTTTAAATTTT
1 TTAATTTTAAAATATTTTTAAAATACTTTTT-AATTTT
54297761 TTTTAATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 2 0.03
40 32 0.50
41 28 0.44
44 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (41 bp):
TTAATTTTAAAATATTTTTAAAATACTTTTTAATTTTAAAA
Found at i:54297770 original size:40 final size:39
Alignment explanation
Indices: 54297629--54297756 Score: 139
Period size: 41 Copynumber: 3.2 Consensus size: 39
54297619 AAATTATTTA
** *
54297629 TTTTTAAAATTTTTTAATTTAAAAATATTTTTAAAATAC
1 TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
** * *
54297668 TTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATAC
1 TTTTTAAAATT-AATTAATTTTAAAATATTTTTAAAATAC
** *
54297708 TTTTTTTAAAAAAAATTAATTTTAAAATATTTTAAAAATAC
1 --TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
54297749 TTTTTAAA
1 TTTTTAAA
54297757 TTTTTTTTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 17 0.24
40 23 0.32
41 25 0.35
42 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
Found at i:54298103 original size:19 final size:18
Alignment explanation
Indices: 54298074--54298123 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
54298064 TTAATTCAAC
54298074 TTTTGGAATTTTTATAAATA
1 TTTT-GAATTTTTA-AAATA
*
54298094 TTTTGAA-TTTTAAAATT
1 TTTTGAATTTTTAAAATA
54298111 TATTTGAATTTTT
1 T-TTTGAATTTTT
54298124 TGTTGAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 11 0.41
19 7 0.26
20 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
TTTTGAATTTTTAAAATA
Found at i:54298589 original size:30 final size:30
Alignment explanation
Indices: 54298553--54298612 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
54298543 CCTAAGATCA
54298553 GTATCGGATGTAAAAGCTAATTAAGGCATT
1 GTATCGGATGTAAAAGCTAATTAAGGCATT
54298583 GTATCGGATGTAAAAGCTAATTAAGGCATT
1 GTATCGGATGTAAAAGCTAATTAAGGCATT
54298613 AACAGCCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
GTATCGGATGTAAAAGCTAATTAAGGCATT
Found at i:54299788 original size:19 final size:20
Alignment explanation
Indices: 54299743--54299825 Score: 89
Period size: 20 Copynumber: 4.1 Consensus size: 20
54299733 ATTTTAAATT
*
54299743 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAA-AT-TATTTTG-AA
*
54299766 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
54299785 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
54299804 TTTTTGAAAATTATTTTAAA
1 TTTTTAAAAATTATTTTGAA
54299824 TT
1 TT
54299826 ATTTTTGTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
18 8 0.15
19 11 0.21
20 25 0.47
22 1 0.02
23 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:54299824 original size:10 final size:10
Alignment explanation
Indices: 54299733--54299830 Score: 51
Period size: 10 Copynumber: 9.5 Consensus size: 10
54299723 ATCTCAGAAA
54299733 ATTTTAAATT
1 ATTTTAAATT
*
54299743 TTTTTAAAATAT
1 ATTTT-AAAT-T
54299755 AAATTTTGAAATT
1 --ATTTT-AAATT
54299768 -TTTATAAA-T
1 ATTT-TAAATT
*
54299777 ATTTTGAATT
1 ATTTTAAATT
**
54299787 -TTAAAAATT
1 ATTTTAAATT
*
54299796 ATTTTGAATT
1 ATTTTAAATT
*
54299806 -TTTGAAAATT
1 ATTT-TAAATT
54299816 ATTTTAAATT
1 ATTTTAAATT
54299826 ATTTT
1 ATTTT
54299831 TGTAATTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
9 13 0.20
10 34 0.52
11 8 0.12
12 1 0.02
13 1 0.02
14 8 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:54303139 original size:27 final size:27
Alignment explanation
Indices: 54303085--54303200 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
54303075 AATAACGATC
* * *
54303085 ATTTTACCCTTC-GGGGTATTTCGATA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* ** *
54303111 ATTTTACTCATTTAGAGTATTTCGGTA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* *
54303138 ATTTTTCCCATCAAGGGTATTTCAGTA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* *
54303165 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCATCAAGGGTATTTCGGTA
54303192 ATTTTACCC
1 ATTTTACCC
54303201 TAAAGGGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
26 9 0.12
27 64 0.88
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (27 bp):
ATTTTACCCATCAAGGGTATTTCGGTA
Found at i:54303209 original size:27 final size:27
Alignment explanation
Indices: 54303127--54303209 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
54303117 CTCATTTAGA
* *
54303127 GTATTTCGGTAATTTTTCCCATCAA-GG
1 GTATTTCGGTAATTTTACCC-TAAAGGG
* **
54303154 GTATTTCAGTAATTTTACCC-ATCGAGG
1 GTATTTCGGTAATTTTACCCTAAAG-GG
*
54303181 GTATTTCGGTCATTTTACCCTAAAGGG
1 GTATTTCGGTAATTTTACCCTAAAGGG
54303208 GT
1 GT
54303210 CTCGGTGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 42 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACCCTAAAGGG
Found at i:54307975 original size:10 final size:11
Alignment explanation
Indices: 54307949--54307973 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54307939 ACACCTAATT
54307949 AAAATTAAAAA
1 AAAATTAAAAA
54307960 AAAATTAAAAA
1 AAAATTAAAAA
54307971 AAA
1 AAA
54307974 TTGAACCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:54308052 original size:2 final size:2
Alignment explanation
Indices: 54308045--54308076 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54308035 ATCGAAAGAA
54308045 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
54308077 TAGACAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54308296 original size:14 final size:14
Alignment explanation
Indices: 54308243--54308296 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
54308233 TGTTTAGGGT
54308243 TTTTGAGTTTGGGGA
1 TTTTGA-TTTGGGGA
* * *
54308258 TTTAGGATTTTGGGT
1 TTT-TGATTTGGGGA
54308273 TTTTGAATTTGGGGA
1 TTTTG-ATTTGGGGA
54308288 TTTTGATTT
1 TTTTGATTT
54308297 AAGGTTGTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 5 0.16
15 24 0.77
16 2 0.06
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (14 bp):
TTTTGATTTGGGGA
Found at i:54308296 original size:29 final size:30
Alignment explanation
Indices: 54308256--54308319 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
54308246 TGAGTTTGGG
*
54308256 GATTTAGGATTTTGGGTTTTTGAATTTGGG
1 GATTTAGGATTTAGGGTTTTTGAATTTGGG
* * * *
54308286 GATTT-TGATTTAAGGTTGTCGAATTTGGG
1 GATTTAGGATTTAGGGTTTTTGAATTTGGG
54308315 GATTT
1 GATTT
54308320 GGGCTAGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (30 bp):
GATTTAGGATTTAGGGTTTTTGAATTTGGG
Found at i:54308397 original size:30 final size:29
Alignment explanation
Indices: 54308349--54308405 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
54308339 TGGGGATTTG
* ** *
54308349 TTTAGGGTTTTTTGATTTTAGGGATTTTCA
1 TTTAAGGTTTTTAAATTTT-GGAATTTTCA
54308379 TTTAAGGTTTTTAAATTTTGGAATTTT
1 TTTAAGGTTTTTAAATTTTGGAATTTT
54308406 TGTTTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (29 bp):
TTTAAGGTTTTTAAATTTTGGAATTTTCA
Found at i:54316409 original size:5 final size:5
Alignment explanation
Indices: 54316401--54316428 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54316391 TAACTTTTCT
54316401 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
54316429 ATCAAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:54317230 original size:160 final size:161
Alignment explanation
Indices: 54316954--54317272 Score: 419
Period size: 160 Copynumber: 2.0 Consensus size: 161
54316944 GGTGAGGGTC
* * *
54316954 ACAATAGAAGATCATGCATTCAACCTAACACAACTGGATCACAAATATATCATTAACACTTTTTC
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCATAAACACTTTTTC
* * * * *
54317019 ACTATCAAGTTCTTAAATATTTAAGTCTAATTTGGGGTTTTACAATTTTTTT-TCTCAGTCTGGT
66 ACTATCAAGTTCTAAAATATTTAAATCTAATTTAGGGTTTGACAATTTTTTTGTCTCAGTCTAGT
54317083 ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
131 ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
* **
54317114 ACAACAGAAGATCATGCAATCAACCTACCACAACTGGATCACAGGTATAT-AGTAAACACTTTTT
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCA-TAAACACTTTTT
* * ***
54317178 TACTGTCAAGTT-TCAAAATATTTAAATCTAATTTAGGGTTGTGATTTTTTTTTTGTCTCAGTCT
65 CACTATCAAGTTCT-AAAATATTTAAATCTAATTTAGGGTT-TGACAATTTTTTTGTCTCAGTCT
* * *
54317242 AGTATGAGTGCAAGAACTAGAAGCCAAAAAA
128 AGTACGAGTACAAGAACTAAAAGCCAAAAAA
54317273 GGATGGTATA
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
159 2 0.01
160 89 0.65
161 9 0.07
162 36 0.26
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (161 bp):
ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCATAAACACTTTTTC
ACTATCAAGTTCTAAAATATTTAAATCTAATTTAGGGTTTGACAATTTTTTTGTCTCAGTCTAGT
ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
Found at i:54319364 original size:17 final size:17
Alignment explanation
Indices: 54319325--54319366 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54319315 TAAAAGCAAA
*
54319325 TTTTATTAAATTGTTTT
1 TTTTATAAAATTGTTTT
*
54319342 TGTTATAAAATT-TTTGT
1 TTTTATAAAATTGTTT-T
54319359 TTTTATAA
1 TTTTATAA
54319367 TTTCAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTTATAAAATTGTTTT
Found at i:54324584 original size:41 final size:42
Alignment explanation
Indices: 54324508--54324603 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
54324498 ATACACCGGT
* * *
54324508 TTAAGCCTGCTAGACTTATAGTCCGAATTTATTTCACCGGCA
1 TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
* * *
54324550 TTAAGCCTGCTAGACGTAAAGTCTGAA-TGGTTTCACTGGCA
1 TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
**
54324591 ACAAGCCTGCTAG
1 TTAAGCCTGCTAG
54324604 GTACTGAGCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 22 0.48
42 24 0.52
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
Found at i:54329276 original size:24 final size:24
Alignment explanation
Indices: 54329249--54329300 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54329239 TTAGTAAGTC
*
54329249 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54329273 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54329297 AAAT
1 AAAT
54329301 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:54331451 original size:18 final size:18
Alignment explanation
Indices: 54331428--54331463 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54331418 ACAATGGTCT
54331428 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
54331446 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
54331464 CTATATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
AGCAATTTTGATTTGACC
Found at i:54335725 original size:30 final size:30
Alignment explanation
Indices: 54335691--54335759 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
54335681 AGTTTCATTT
** *
54335691 CAGTCACTCAAC-TTTCGAAAAGTTACAAAA
1 CAGTCACT-AACGTTTAAAAAAGTGACAAAA
54335721 CAGTCACTAACGTTTTAAAAAAGTGACAAAA
1 CAGTCACTAACG-TTTAAAAAAGTGACAAAA
*
54335752 TAGTCACT
1 CAGTCACT
54335760 GATTAACAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 8 0.24
31 22 0.67
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (30 bp):
CAGTCACTAACGTTTAAAAAAGTGACAAAA
Found at i:54335819 original size:21 final size:20
Alignment explanation
Indices: 54335791--54335832 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
54335781 TGTTAACGGG
54335791 ACCACTGACATGGCAAGTTA
1 ACCACTGACATGGCAAGTTA
**
54335811 ACCAGCTGATGTGGCAAGTTA
1 ACCA-CTGACATGGCAAGTTA
54335832 A
1 A
54335833 TTTGCCACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (20 bp):
ACCACTGACATGGCAAGTTA
Found at i:54336315 original size:12 final size:12
Alignment explanation
Indices: 54336298--54336362 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
54336288 ATTTAGAGTT
54336298 ATTTTGATTTCG
1 ATTTTGATTTCG
54336310 ATTTTGA-TTCTG
1 ATTTTGATTTC-G
54336322 A-TTT-ATTTCG
1 ATTTTGATTTCG
** *
54336332 ATTTCAATTTAG
1 ATTTTGATTTCG
*
54336344 ATTTTGATTTCA
1 ATTTTGATTTCG
54336356 ATTTTGA
1 ATTTTGA
54336363 AACACTCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 3 0.07
11 11 0.26
12 29 0.67
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.57
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:54336336 original size:28 final size:28
Alignment explanation
Indices: 54336296--54336353 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
54336286 TTATTTAGAG
* * *
54336296 TTATTTTGATTTCGATTTTGATTCTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
*
54336324 TTATTTCGATTTCAATTTAGATTTTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
54336352 TT
1 TT
54336354 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (28 bp):
TTATTTCGATTTCAATTTAGATTCTGAT
Found at i:54336400 original size:12 final size:12
Alignment explanation
Indices: 54336379--54336413 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54336369 CACTGGTTCT
*
54336379 GATTTTGATTTC
1 GATTTAGATTTC
*
54336391 GATTTCGATTTC
1 GATTTAGATTTC
54336403 GATTTAGATTT
1 GATTTAGATTT
54336414 TGGTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (12 bp):
GATTTAGATTTC
Found at i:54336406 original size:18 final size:18
Alignment explanation
Indices: 54336379--54336413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54336369 CACTGGTTCT
* *
54336379 GATTTTGATTTCGATTTC
1 GATTTCGATTTAGATTTC
54336397 GATTTCGATTTAGATTT
1 GATTTCGATTTAGATTT
54336414 TGGTTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (18 bp):
GATTTCGATTTAGATTTC
Found at i:54336677 original size:20 final size:22
Alignment explanation
Indices: 54336637--54336677 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
54336627 TTACCTTCTA
54336637 TATTGTACTAGTTATTATCTGT
1 TATTGTACTAGTTATTATCTGT
*
54336659 TATTGT-CTA-TTATTGTCTG
1 TATTGTACTAGTTATTATCTG
54336678 CCATGTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (22 bp):
TATTGTACTAGTTATTATCTGT
Found at i:54338648 original size:28 final size:28
Alignment explanation
Indices: 54338611--54338665 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
54338601 AAGTGTTTTT
*
54338611 TAATATGCATGCAGTGAGTATTTTTTAA
1 TAATATGCATGCAGTGACTATTTTTTAA
* *
54338639 TAATATGCATGTAGTGACTTTTTTTTA
1 TAATATGCATGCAGTGACTATTTTTTA
54338666 GGTGTGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (28 bp):
TAATATGCATGCAGTGACTATTTTTTAA
Found at i:54339369 original size:21 final size:21
Alignment explanation
Indices: 54339343--54339394 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
54339333 CAAGTGGTTG
* *
54339343 CCCCAACTCAGCAA-CAGGCTA
1 CCCCAACTCAGCAAGAAAG-TA
*
54339364 CCCCAAATCAGCAAGAAAGTA
1 CCCCAACTCAGCAAGAAAGTA
54339385 CCCCAACTCA
1 CCCCAACTCA
54339395 ACAGGCTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAAAGTA
Found at i:54339883 original size:22 final size:23
Alignment explanation
Indices: 54339832--54339876 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54339822 CTTCTCTTCT
*
54339832 AACATATGAGAATTGAAAAAATA
1 AACATGTGAGAATTGAAAAAATA
*
54339855 AACATGTGAGAATT-AAGAAATA
1 AACATGTGAGAATTGAAAAAATA
54339877 CAAATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (23 bp):
AACATGTGAGAATTGAAAAAATA
Found at i:54341212 original size:29 final size:30
Alignment explanation
Indices: 54341170--54341227 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
54341160 AATGAAAATT
54341170 TAAATACTTCAATTT-TAGTATAGAAATTGA
1 TAAATACTTCAATTTATAGTATA-AAATTGA
* *
54341200 TAAATA-TTGAATTTATATTATAAAATTG
1 TAAATACTTCAATTTATAGTATAAAATTG
54341228 TTTAGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (30 bp):
TAAATACTTCAATTTATAGTATAAAATTGA
Found at i:54349544 original size:26 final size:26
Alignment explanation
Indices: 54349506--54349558 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
54349496 GTCATGTTGA
*
54349506 TGGAATTGCCTCTCCGACGAGAGAGG
1 TGGAATTGACTCTCCGACGAGAGAGG
*
54349532 TGGAATTGACTCTCCGGCGAGAGAGG
1 TGGAATTGACTCTCCGACGAGAGAGG
54349558 T
1 T
54349559 TAACGGGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (26 bp):
TGGAATTGACTCTCCGACGAGAGAGG
Found at i:54353743 original size:18 final size:17
Alignment explanation
Indices: 54353720--54353754 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54353710 TACTGCTTTC
*
54353720 TTGTTGTTTTTTATTGTT
1 TTGTTGATTTTT-TTGTT
54353738 TTGTTGATTTTTTTGTT
1 TTGTTGATTTTTTTGTT
54353755 GTTTTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (17 bp):
TTGTTGATTTTTTTGTT
Found at i:54357772 original size:42 final size:42
Alignment explanation
Indices: 54357713--54357799 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
54357703 ATTAAATTTG
54357713 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
1 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
54357755 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
1 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
54357797 AAT
1 AAT
54357800 GAACTCAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (42 bp):
AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
Found at i:54360957 original size:19 final size:20
Alignment explanation
Indices: 54360915--54360957 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
54360905 TCATGCTTTC
*
54360915 TATTCACATTTTCATATTCA
1 TATTCACATTTTCATAATCA
54360935 -ATTCACATTTTCA-AATCA
1 TATTCACATTTTCATAATCA
54360953 TATTC
1 TATTC
54360958 CACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATTTTCATAATCA
Done.