Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 5 of 14
Found at i:579874 original size:17 final size:17
Alignment explanation
Indices: 579848--579887 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
579838 TTTGTCGTAC
579848 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
* *
579865 ATATTTAATATTAATAT
1 ATATTAAATATAAATAT
579882 AT-TTAA
1 ATATTAA
579888 TTTTTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:579895 original size:13 final size:15
Alignment explanation
Indices: 579863--579914 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
579853 AAATATAAAT
579863 ATATATTTAATATTA
1 ATATATTTAATATTA
* *
579878 ATATATTTAATTTTT
1 ATATATTTAATATTA
*
579893 ATATATTTAAAATATA
1 ATATATTTAATAT-TA
579909 ATATAT
1 ATATAT
579915 CTATACTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
15 24 0.77
16 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATTTAATATTA
Found at i:580109 original size:2 final size:2
Alignment explanation
Indices: 580096--580130 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
580086 ATATAAATTT
*
580096 TA TA TA TT 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 TA TA TA TA T
580131 TTTCGTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:581032 original size:37 final size:37
Alignment explanation
Indices: 580967--581053 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 37
580957 TTTTTCTGTA
** *
580967 AATATTTATAATTGGTATTTATCGTAATTTA-TCGTAAT
1 AATATTTAT-ATTAATATTTATCATAA-TTAGTCGTAAT
*
581005 AATATTTATATTAATATTTATTATAATTAGTCGTAAT
1 AATATTTATATTAATATTTATCATAATTAGTCGTAAT
581042 AATATTTATATT
1 AATATTTATATT
581054 TATACCCGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.07
37 32 0.73
38 9 0.20
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (37 bp):
AATATTTATATTAATATTTATCATAATTAGTCGTAAT
Found at i:581622 original size:13 final size:13
Alignment explanation
Indices: 581604--581628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
581594 TCAAATTTAA
581604 ATATTATATTATC
1 ATATTATATTATC
581617 ATATTATATTAT
1 ATATTATATTAT
581629 GGGAATTAAT
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:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTATATTATC
Found at i:583219 original size:18 final size:17
Alignment explanation
Indices: 583171--583248 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 17
583161 GGTGTGTTAG
*
583171 TAAATTTTATTATTCATA
1 TAAATTTTAATATT-ATA
583189 -AGATATTTT-ATATTAATA
1 TA-A-ATTTTAATATT-ATA
583207 TAAATTTTAATATT-T-
1 TAAATTTTAATATTATA
*
583222 TAATAATTT-ATATTATA
1 TAA-ATTTTAATATTATA
583239 TAAATTTTAA
1 TAAATTTTAA
583249 AATATTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
15 8 0.17
16 10 0.21
17 10 0.21
18 14 0.29
19 6 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TAAATTTTAATATTATA
Found at i:583244 original size:15 final size:15
Alignment explanation
Indices: 583195--583245 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
583185 CATAAGATAT
583195 TTTATATTAATATAAA
1 TTTATATT-ATATAAA
*
583211 TTTTAATATTTTA-ATAA
1 -TTT-ATATTATATA-AA
583228 TTTATATTATATAAA
1 TTTATATTATATAAA
583243 TTT
1 TTT
583246 TAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 12 0.41
16 5 0.17
17 7 0.24
18 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:583244 original size:32 final size:34
Alignment explanation
Indices: 583191--583267 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
583181 TATTCATAAG
*
583191 ATAT-TTTATATTAATATAAATTTTAATAT-TTT
1 ATATATTTATATTAATATAAATTTTAAAATATTT
583223 A-ATAATTTATATT-ATATAAATTTTAAAATATTT
1 ATAT-ATTTATATTAATATAAATTTTAAAATATTT
583256 ATATATTTATAT
1 ATATATTTATAT
583268 CCGTATGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 2 0.05
32 16 0.40
33 20 0.50
34 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
ATATATTTATATTAATATAAATTTTAAAATATTT
Found at i:584209 original size:16 final size:17
Alignment explanation
Indices: 584167--584209 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
584157 TTTAATATTT
584167 ATAAAACTTT-TAATTAA
1 ATAAAA-TTTATAATTAA
584184 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
584199 ATAAAATTTAT
1 ATAAAATTTAT
584210 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:585160 original size:12 final size:11
Alignment explanation
Indices: 585135--585185 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
585125 AATATACAAA
585135 AAATAAAAATAT
1 AAATAAAAA-AT
585147 AACATAAAAAAT
1 AA-ATAAAAAAT
* *
585159 AATTAAAATAT
1 AAATAAAAAAT
585170 -AATATAAAAAT
1 AAATA-AAAAAT
585181 AAATA
1 AAATA
585186 TGACACGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.09
11 12 0.38
12 10 0.31
13 7 0.22
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:585170 original size:23 final size:22
Alignment explanation
Indices: 585132--585185 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
585122 TTAAATATAC
585132 AAAAAATAAAAATATAACATAA
1 AAAAAATAAAAATATAACATAA
* *
585154 AAAATAATTAAAATATAATATAA
1 AAAA-AATAAAAATATAACATAA
585177 AAATAAATA
1 AAA-AAATA
585186 TGACACGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 22 0.81
24 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATAAAAATATAACATAA
Found at i:585178 original size:22 final size:22
Alignment explanation
Indices: 585125--585182 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
585115 TACTACTTTA
585125 AATATACAAAA-AATAAAAATAT
1 AATATA-AAAATAATAAAAATAT
* *
585147 AACATAAAAAATAATTAAAATAT
1 AATAT-AAAAATAATAAAAATAT
585170 AATATAAAAATAA
1 AATATAAAAATAA
585183 ATATGACACG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (22 bp):
AATATAAAAATAATAAAAATAT
Found at i:585409 original size:2 final size:2
Alignment explanation
Indices: 585402--585443 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
585392 CATGAAAATA
585402 AT AT AT AT AT AT AT AT A- AT AT GA- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
585443 A
1 A
585444 AAAATATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.92
3 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:585564 original size:11 final size:11
Alignment explanation
Indices: 585534--585564 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
585524 TTTTTTTCTT
585534 TCTTTCTTTTC
1 TCTTTCTTTTC
585545 TCTTT-TTTTC
1 TCTTTCTTTTC
585555 TCTTTCTTTT
1 TCTTTCTTTT
585565 TCGGCTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTCTTTTC
Found at i:589104 original size:20 final size:20
Alignment explanation
Indices: 589054--589100 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
589044 GATTAATTTT
*
589054 ATATTTATTATTTTATAAAA
1 ATATTTATTATGTTATAAAA
*
589074 ATATATTATTATGTTA-AACA
1 ATAT-TTATTATGTTATAAAA
589094 ATATTTA
1 ATATTTA
589101 ATTAATTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 11 0.46
21 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATATTTATTATGTTATAAAA
Found at i:590548 original size:16 final size:17
Alignment explanation
Indices: 590524--590557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
590514 AATATTTATA
590524 TAAAAATA-TAATTTTT
1 TAAAAATATTAATTTTT
*
590540 TAAATATATTAATTTTT
1 TAAAAATATTAATTTTT
590557 T
1 T
590558 TTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAAATATTAATTTTT
Found at i:597368 original size:1 final size:1
Alignment explanation
Indices: 597362--597391 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
597352 ATACAAATTT
597362 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
597392 TGGAAGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:599803 original size:20 final size:20
Alignment explanation
Indices: 599778--599830 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
599768 TTTTTATACC
*
599778 TAATTTAAATTTAAATTATT
1 TAATTTAAATTAAAATTATT
*
599798 TAATTTAAATTAAAATTTTT
1 TAATTTAAATTAAAATTATT
599818 TAATATT-AATTAA
1 TAAT-TTAAATTAA
599831 TAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTTAAATTAAAATTATT
Found at i:599804 original size:14 final size:15
Alignment explanation
Indices: 599780--599809 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
599770 TTTATACCTA
599780 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
599795 ATTT-AATTTAAATT
1 ATTTAAATTTAAATT
599809 A
1 A
599810 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:602240 original size:25 final size:27
Alignment explanation
Indices: 602198--602260 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
602188 AAATTTTTAT
602198 TAATTATATAAATAT-AAAAATAT-TA
1 TAATTATATAAATATAAAAAATATATA
* * *
602223 TAATTATTTAATTTTAAAAAATATATA
1 TAATTATATAAATATAAAAAATATATA
602250 T-ATATATATAA
1 TAAT-TATATAA
602261 TATGTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 12 0.39
26 10 0.32
27 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATTATATAAATATAAAAAATATATA
Found at i:602272 original size:34 final size:34
Alignment explanation
Indices: 602207--602273 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
602197 TTAATTATAT
*
602207 AAATATAAAAATATTATAATTATTTAATTTTAAA
1 AAATATAAAAATATTATAATTATGTAATTTTAAA
* * *
602241 AAATATATATATATATATAA-TATGTATTTTTAA
1 AAATATAAAAATAT-TATAATTATGTAATTTTAA
602274 TATATTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
AAATATAAAAATATTATAATTATGTAATTTTAAA
Found at i:602319 original size:24 final size:24
Alignment explanation
Indices: 602292--602348 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
602282 TGTTAATTAT
*
602292 ATTTAAATATTTTT-AATTTAATAA
1 ATTTAAAT-TTTTTAAATTAAATAA
*
602316 ATTT-AATTTTTTAAAATTAAATTA
1 ATTTAAATTTTTT-AAATTAAATAA
602340 ATTTAAATT
1 ATTTAAATT
602349 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 16 0.57
25 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTAAATTTTTTAAATTAAATAA
Found at i:602338 original size:15 final size:14
Alignment explanation
Indices: 602313--602372 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
602303 TTTAATTTAA
*
602313 TAAATTTAATTTTT
1 TAAATTAAATTTTT
*
602327 TAAAATTAAATTAATT
1 T-AAATTAAATT-TTT
602343 TAAATTAAA--TTT
1 TAAATTAAATTTTT
*
602355 TAAATAAAAATTTTT
1 TAAAT-TAAATTTTT
602370 TAA
1 TAA
602373 TGCATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
12 7 0.19
13 3 0.08
14 1 0.03
15 23 0.62
16 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTAAATTTTT
Found at i:602516 original size:25 final size:24
Alignment explanation
Indices: 602493--602539 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
602483 AATAATTAAT
*
602493 ATTAT-AT-ATTTTAAATATTTTTA
1 ATTATAATAATTTT-AATACTTTTA
602516 ATTATAATAATTTTAATACTTTTA
1 ATTATAATAATTTTAATACTTTTA
602540 TCGAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATAATAATTTTAATACTTTTA
Found at i:603022 original size:25 final size:25
Alignment explanation
Indices: 602994--603044 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
602984 AATTAAATAA
* *
602994 ATTTTTAATTTTTAAAA-TATTTATT
1 ATTTTTAA-TATTAAAATTAATTATT
603019 ATTTTTAATATTAAAATTAATTATT
1 ATTTTTAATATTAAAATTAATTATT
603044 A
1 A
603045 AATATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTAATATTAAAATTAATTATT
Found at i:603065 original size:14 final size:13
Alignment explanation
Indices: 603038--603092 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
603028 ATTAAAATTA
*
603038 ATTAT-TAAATAT
1 ATTATATAAAAAT
603050 ATTTATATAAAAAT
1 A-TTATATAAAAAT
*
603064 ATGATATAAAAAT
1 ATTATATAAAAAT
*
603077 AATATAATAAAAAT
1 ATTAT-ATAAAAAT
603091 AT
1 AT
603093 ATAAATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.03
13 18 0.51
14 16 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
ATTATATAAAAAT
Found at i:603070 original size:13 final size:12
Alignment explanation
Indices: 603053--603095 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 12
603043 TAAATATATT
603053 TATATAAAAATA
1 TATATAAAAATA
603065 TGATATAAAAATAA
1 T-ATATAAAAAT-A
603079 TATAATAAAAATA
1 TAT-ATAAAAATA
603092 TATA
1 TATA
603096 AATATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 16 0.57
14 10 0.36
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:607153 original size:29 final size:29
Alignment explanation
Indices: 607121--607177 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
607111 TTTATGGAAT
607121 GAAATGCTTGAACCTGTTAAGCTGATGAC
1 GAAATGCTTGAACCTGTTAAGCTGATGAC
607150 GAAATGCTTGAACCTGTTAAGCTGATGA
1 GAAATGCTTGAACCTGTTAAGCTGATGA
607178 AATTTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
GAAATGCTTGAACCTGTTAAGCTGATGAC
Found at i:607611 original size:16 final size:16
Alignment explanation
Indices: 607587--607618 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
607577 CCAATTTTAT
607587 ATTAAAAATATTATAA
1 ATTAAAAATATTATAA
*
607603 ATTATAAATATTATAA
1 ATTAAAAATATTATAA
607619 TTCAAACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAAAATATTATAA
Found at i:611834 original size:18 final size:18
Alignment explanation
Indices: 611811--611847 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
611801 ATGAAAAAGT
* *
611811 AATTAAAACATGACATGA
1 AATTAAAAAATAACATGA
611829 AATTAAAAAATAACATGA
1 AATTAAAAAATAACATGA
611847 A
1 A
611848 TATATGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (18 bp):
AATTAAAAAATAACATGA
Found at i:611880 original size:33 final size:32
Alignment explanation
Indices: 611838--611906 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
611828 AAATTAAAAA
* * *
611838 ATAACATGAATATATGAATGTCTCAAAATCTAT
1 ATAACATGAAT-TATCAACGTATCAAAATCTAT
* *
611871 ATAATATGAATTATCAACGTATCAAAATTTAT
1 ATAACATGAATTATCAACGTATCAAAATCTAT
611903 ATAA
1 ATAA
611907 ATATAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (32 bp):
ATAACATGAATTATCAACGTATCAAAATCTAT
Found at i:613487 original size:21 final size:22
Alignment explanation
Indices: 613432--613487 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
613422 TTAATTTTTA
613432 AAATTAAATATAAAAATTAAATT
1 AAATTAAATA-AAAAATTAAATT
** * *
613455 ATTTTTATTAAAAAA-TAAATT
1 AAATTAAATAAAAAATTAAATT
613476 AAATTAAATAAA
1 AAATTAAATAAA
613488 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
23 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTAAATAAAAAATTAAATT
Found at i:613984 original size:24 final size:25
Alignment explanation
Indices: 613952--614002 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
613942 TTTTTTAAAA
613952 TAAAAAATAAA-ATT-CAATTAAATT
1 TAAAAAATAAATATTAC-ATTAAATT
*
613976 TAAATAATAAATATTACATTAAATT
1 TAAAAAATAAATATTACATTAAATT
614001 TA
1 TA
614003 TATTAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 10 0.42
25 13 0.54
26 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAAAATAAATATTACATTAAATT
Found at i:615436 original size:11 final size:11
Alignment explanation
Indices: 615424--615465 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
615414 TTTTAAATTT
615424 AATTTTTATTTA
1 AATTTTTA-TTA
615436 AA-TTTTATTA
1 AATTTTTATTA
* *
615446 AATATTTAATA
1 AATTTTTATTA
615457 AATTTTTAT
1 AATTTTTAT
615466 ATTTAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 5 0.20
11 18 0.72
12 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTTATTA
Found at i:615588 original size:17 final size:16
Alignment explanation
Indices: 615566--615597 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
615556 TTAATACATA
615566 AAAATAAAATAATTTAT
1 AAAATAAAAT-ATTTAT
615583 AAAATAAAATATTTA
1 AAAATAAAATATTTA
615598 AAATTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAAAATATTTAT
Found at i:619696 original size:2 final size:2
Alignment explanation
Indices: 619691--619727 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
619681 TTAATGGGTT
*
619691 TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
619728 TTGTTTTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:620507 original size:18 final size:19
Alignment explanation
Indices: 620456--620508 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
620446 GATTTAAATT
* *
620456 TTTATTTATAAGTGAAAAA
1 TTTATTTTTAAATGAAAAA
620475 TTATAATTATTTAAAT-AAAAA
1 TT-T-ATT-TTTAAATGAAAAA
620496 TTTATTTTTAAAT
1 TTTATTTTTAAAT
620509 TTTTTATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 2 0.07
21 10 0.34
22 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTATTTTTAAATGAAAAA
Found at i:623683 original size:4 final size:4
Alignment explanation
Indices: 623674--623708 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
623664 TCTGTTACAT
* *
623674 ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
623709 TATGTATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:625881 original size:2 final size:2
Alignment explanation
Indices: 625874--625899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
625864 TCAATTTTTG
625874 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
625900 TGAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:626329 original size:20 final size:19
Alignment explanation
Indices: 626305--626355 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
626295 TATAATTTTA
626305 AATTATTATATAAATATAT
1 AATTATTATATAAATATAT
* *
626324 GTATTA-AATATAAA-ATAT
1 -AATTATTATATAAATATAT
626342 AATTATTAT-TAAAT
1 AATTATTATATAAAT
626356 TTAAAATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 8 0.32
18 6 0.24
19 7 0.28
20 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTATTATATAAATATAT
Found at i:626637 original size:12 final size:12
Alignment explanation
Indices: 626620--626644 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
626610 TATAAAATAT
626620 TTAATTTTAAAA
1 TTAATTTTAAAA
626632 TTAATTTTAAAA
1 TTAATTTTAAAA
626644 T
1 T
626645 AAAAATGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:636399 original size:16 final size:16
Alignment explanation
Indices: 636355--636411 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
636345 AAATTTAGTT
* *
636355 TATTTAATTAATATAA
1 TATTTAATAAATTTAA
636371 TTATTTTAA-AAATTTAA
1 -TA-TTTAATAAATTTAA
636388 TATTTAATAAATTTAA
1 TATTTAATAAATTTAA
*
636404 AATTTAAT
1 TATTTAAT
636412 TCTTTCTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 5 0.14
16 17 0.49
17 8 0.23
18 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTAATAAATTTAA
Found at i:637406 original size:2 final size:2
Alignment explanation
Indices: 637399--637425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
637389 TCAACATTTC
637399 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 A
637426 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:638054 original size:13 final size:14
Alignment explanation
Indices: 638018--638054 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
638008 AAATCTTTTA
638018 AAAACATAA-TATT
1 AAAACATAATTATT
*
638031 AAAAGATAATTATT
1 AAAACATAATTATT
638045 AAAA-ATAATT
1 AAAACATAATT
638055 TTTTATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAACATAATTATT
Found at i:639218 original size:17 final size:18
Alignment explanation
Indices: 639196--639234 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
639186 TTATAAAAAT
* *
639196 AATATTTTAAATATAA-A
1 AATATTTAAAAAATAATA
639213 AATATTTAAAAAATAATA
1 AATATTTAAAAAATAATA
639231 AATA
1 AATA
639235 AAAAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATTTAAAAAATAATA
Found at i:639230 original size:14 final size:14
Alignment explanation
Indices: 639185--639242 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
639175 TTTTTTGAAT
639185 TTTATAAAAATAATA
1 TTTA-AAAAATAATA
*
639200 TTTTAAATATAAAAATA
1 -TTTAAA-A-AATAATA
639217 TTTAAAAAATAATA
1 TTTAAAAAATAATA
**
639231 AATAAAAAATAA
1 TTTAAAAAATAA
639243 ATACCAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 11 0.31
17 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TTTAAAAAATAATA
Found at i:639256 original size:26 final size:24
Alignment explanation
Indices: 639226--639287 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
639216 ATTTAAAAAA
*
639226 TAATAAATAAAAAATAAATACCAAT
1 TAATAAATAAAAAA-AAATACAAAT
*
639251 TAAATAAA-ACTAAAAAAAATTCAAAT
1 T-AATAAATA--AAAAAAAATACAAAT
639277 TAATAAATAAA
1 TAATAAATAAA
639288 TTTATAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 2 0.06
25 8 0.26
26 16 0.52
27 5 0.16
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (24 bp):
TAATAAATAAAAAAAAATACAAAT
Found at i:639448 original size:3 final size:3
Alignment explanation
Indices: 639442--639475 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
639432 TCCATACTAC
639442 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
639476 TTGGATTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:639949 original size:14 final size:14
Alignment explanation
Indices: 639927--639963 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
639917 TATTTTATTA
639927 TTATTTTTAAAATT
1 TTATTTTTAAAATT
* *
639941 TTATATTTAATATT
1 TTATTTTTAAAATT
639955 TTATTTTTA
1 TTATTTTTA
639964 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTTTAAAATT
Found at i:640132 original size:23 final size:23
Alignment explanation
Indices: 640099--640167 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
640089 AACTGATTAG
*
640099 TTTAATAATAAAAATTATTTATA
1 TTTAATTATAAAAATTATTTATA
* *
640122 TTTAATTATAAAAA-TATATAAA
1 TTTAATTATAAAAATTATTTATA
640144 TATTAA-TATAAAAATAATATTTAT
1 T-TTAATTATAAAAAT--TATTTAT
640168 GAAGTGTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 15 0.41
23 17 0.46
25 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAATTATAAAAATTATTTATA
Found at i:640469 original size:15 final size:15
Alignment explanation
Indices: 640449--640503 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
640439 TATTTAATTT
640449 TTTAAATTT-TTTAAA
1 TTTAAATTTATTT-AA
640464 TTTAAATTTATTTAA
1 TTTAAATTTATTTAA
*
640479 TTT--ATTTA-AT-A
1 TTTAAATTTATTTAA
640490 TTTAAATTTATTTA
1 TTTAAATTTATTTA
640504 TTTTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 4 0.12
12 1 0.03
13 10 0.30
14 1 0.03
15 14 0.42
16 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAATTTATTTAA
Found at i:640478 original size:33 final size:30
Alignment explanation
Indices: 640441--640525 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
640431 ATAGGATATA
*
640441 TTTAATTT-TTTAAATTTTTTAAATTTAAATTTA
1 TTTAATTTATTT-AA-TATTTAAATTT--ATTTA
640474 TTTAATTTATTTAATATTTAAATTTATTTA
1 TTTAATTTATTTAATATTTAAATTTATTTA
* * *
640504 TTT-TTTTATTTATTATTAAAAT
1 TTTAATTTATTTAATATTTAAAT
640526 ATTAATATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 16 0.34
30 8 0.17
32 10 0.21
33 10 0.21
34 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTAATTTATTTAATATTTAAATTTATTTA
Found at i:640480 original size:9 final size:9
Alignment explanation
Indices: 640439--640517 Score: 59
Period size: 9 Copynumber: 9.4 Consensus size: 9
640429 GGATAGGATA
640439 TATTTAATT
1 TATTTAATT
640448 T-TTTAAATT
1 TATTT-AATT
640457 T-TTTAA--
1 TATTTAATT
640463 -ATTTAAATT
1 TATTT-AATT
640472 TATTTAATT
1 TATTTAATT
640481 TATTTAA--
1 TATTTAATT
640488 TATTTAAATT
1 TATTT-AATT
640498 TATTT-ATT
1 TATTTAATT
*
640506 T-TTTTATT
1 TATTTAATT
640514 TATT
1 TATT
640518 ATTAAAATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
6 3 0.05
7 10 0.17
8 15 0.25
9 22 0.37
10 9 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTAATT
Found at i:640499 original size:17 final size:16
Alignment explanation
Indices: 640472--640517 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
640462 AATTTAAATT
640472 TATTTAATTTATTTAA
1 TATTTAATTTATTTAA
*
640488 TATTTAAATTTATTTAT
1 TATTT-AATTTATTTAA
* *
640505 TTTTTTATTTATT
1 TATTTAATTTATT
640518 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTAATTTATTTAA
Found at i:640666 original size:40 final size:40
Alignment explanation
Indices: 640620--640719 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
640610 TTTAAGTATA
* *
640620 AAATTTAGATATTTAAATTTATTAT-TCATATAAATAAAAT
1 AAATTTAGATATATAAATTTATTATCT-ACATAAATAAAAT
* * * *
640660 AAATTTAAATATCTAAATCTATTATCTACATAATTAAAAT
1 AAATTTAGATATATAAATTTATTATCTACATAAATAAAAT
640700 AAATTTAGATA-ATAAATTTA
1 AAATTTAGATATATAAATTTA
640720 CATATTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 7 0.14
40 43 0.84
41 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (40 bp):
AAATTTAGATATATAAATTTATTATCTACATAAATAAAAT
Found at i:641630 original size:17 final size:17
Alignment explanation
Indices: 641578--641646 Score: 60
Period size: 17 Copynumber: 4.3 Consensus size: 17
641568 AATTTTTATT
641578 TATTATAATTA-ATTTAA
1 TATTATAATTATA-TTAA
641595 TA--AT-ATT-TATT-A
1 TATTATAATTATATTAA
641607 TATTTATAATTATATTAA
1 TA-TTATAATTATATTAA
*
641625 TATTATATTTATATTAA
1 TATTATAATTATATTAA
*
641642 AATTA
1 TATTA
641647 ATTGCAATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
12 3 0.07
13 2 0.05
14 4 0.09
15 4 0.09
16 3 0.07
17 24 0.56
18 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATAATTATATTAA
Found at i:641631 original size:11 final size:11
Alignment explanation
Indices: 641602--641640 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
641592 TAATAATATT
641602 TATTATATTTA
1 TATTATATTTA
*
641613 TAATTATATTAA
1 T-ATTATATTTA
641625 TATTATATTTA
1 TATTATATTTA
641636 TATTA
1 TATTA
641641 AAATTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTATATTTA
Found at i:641646 original size:23 final size:23
Alignment explanation
Indices: 641602--641648 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
641592 TAATAATATT
*
641602 TATTATATTTATAATTATATTAA
1 TATTATATTTATAATTAAATTAA
641625 TATTATATTTAT-ATTAAAATTAA
1 TATTATATTTATAATT-AAATTAA
641648 T
1 T
641649 TGCAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATATTTATAATTAAATTAA
Found at i:641984 original size:16 final size:15
Alignment explanation
Indices: 641963--641996 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
641953 AATAAATGTG
641963 TTAAATATAAATATAT
1 TTAAATATAAATAT-T
*
641979 TTAAATATGAATATT
1 TTAAATATAAATATT
641994 TTA
1 TTA
641997 GGAGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAATATAAATATT
Found at i:646298 original size:19 final size:19
Alignment explanation
Indices: 646255--646301 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
646245 TATTAATCTC
*
646255 ATATTAGATA-AAAAAAAT
1 ATATTATATATAAAAAAAT
* *
646273 TTA-TATATATAAATAAAT
1 ATATTATATATAAAAAAAT
646291 ATATTATATAT
1 ATATTATATAT
646302 CTTATTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATTATATATAAAAAAAT
Found at i:646663 original size:10 final size:11
Alignment explanation
Indices: 646648--646676 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
646638 AAATTAGATT
646648 ATAATTTAAAA
1 ATAATTTAAAA
646659 A-AATTTAAAA
1 ATAATTTAAAA
646669 ATAATTTA
1 ATAATTTA
646677 TTTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATTTAAAA
Found at i:646700 original size:33 final size:34
Alignment explanation
Indices: 646646--646711 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
646636 TTAAATTAGA
646646 TTATAATTTAAAAAAATTTAAAA-ATAATTTATT
1 TTATAATTTAAAAAAATTTAAAATATAATTTATT
* * *
646679 TTATTATTT-AAATAATATTAAAATATATTTTAT
1 TTATAATTTAAAAAAAT-TTAAAATATAATTTAT
646712 ATTAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.21
33 14 0.50
34 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTATAATTTAAAAAAATTTAAAATATAATTTATT
Found at i:646721 original size:18 final size:17
Alignment explanation
Indices: 646693--646735 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
646683 TATTTAAATA
646693 ATATT-AAAATATATTTT
1 ATATTAAAAATAT-TTTT
646710 ATATTAAAAATATTTTT
1 ATATTAAAAATATTTTT
646727 ATAATTAAA
1 AT-ATTAAA
646736 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTAAAAATATTTTT
Found at i:646736 original size:16 final size:17
Alignment explanation
Indices: 646693--646735 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
646683 TATTTAAATA
646693 ATATTAAAATATATTTT
1 ATATTAAAATATATTTT
646710 ATATTAAAA-ATATTTTT
1 ATATTAAAATATA-TTTT
646727 ATAATTAAA
1 AT-ATTAAA
646736 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTAAAATATATTTT
Found at i:646759 original size:26 final size:29
Alignment explanation
Indices: 646714--646767 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
646704 TATTTTATAT
646714 TAAAAATATTTTTATAATTAAAT-TTAAA
1 TAAAAATATTTTTATAATTAAATATTAAA
*
646742 TAAAAA-A-TTTTATTATTAAATATTAA
1 TAAAAATATTTTTATAATTAAATATTAA
646768 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 13 0.54
27 5 0.21
28 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAAATATTTTTATAATTAAATATTAAA
Found at i:646949 original size:20 final size:20
Alignment explanation
Indices: 646926--646980 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
646916 TTTAAATGTG
*
646926 TTATTATTATTTTTATTATA
1 TTATTATTATTTTTATTAAA
* *
646946 TTATT-TTATATTTAGTAAA
1 TTATTATTATTTTTATTAAA
646965 TATATTA-TATTTTTAT
1 T-TATTATTATTTTTAT
646981 AACGTTCTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTATTATTTTTATTAAA
Found at i:647842 original size:2 final size:2
Alignment explanation
Indices: 647835--647884 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
647825 TTTAAATCGT
647835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
647874 TA TA AA TA TA T
1 TA TA TA TA TA T
647885 TAAAATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:648823 original size:15 final size:15
Alignment explanation
Indices: 648786--648826 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
648776 TAAAAATAAT
*
648786 ATTTAATAAATTTAAA
1 ATTT-ATAAATCTAAA
648802 A--TATAAATCTAAA
1 ATTTATAAATCTAAA
648815 ATTTATAAATCT
1 ATTTATAAATCT
648827 TTTTCTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
15 9 0.41
16 1 0.05
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTATAAATCTAAA
Found at i:649336 original size:18 final size:17
Alignment explanation
Indices: 649303--649370 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 17
649293 TATTAAAAAT
649303 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
649320 ATTTTGATATATT-TAT-A
1 ATTTT-ATAT-TTATATAA
*
649337 A-TTTATA-TTATATAG
1 ATTTTATATTTATATAA
649352 ATTTTCATTTATTTATATA
1 ATTTT-A--TATTTATATA
649371 TTCATATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 2 0.05
14 3 0.07
15 4 0.10
16 6 0.15
17 8 0.20
18 7 0.17
19 4 0.10
20 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:649356 original size:32 final size:33
Alignment explanation
Indices: 649301--649378 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
649291 CTTATTAAAA
*
649301 ATAT-TTTATATTTATATAAATTTTGATATATTT
1 ATATATTTATA-TTATATAAATTTTCATATATTT
* *
649334 ATA-ATTTATATTATATAGATTTTCATTTATTT
1 ATATATTTATATTATATAAATTTTCATATATTT
*
649366 ATATATTCATATT
1 ATATATTTATATT
649379 TTTTTCATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 22 0.56
33 17 0.44
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (33 bp):
ATATATTTATATTATATAAATTTTCATATATTT
Found at i:649663 original size:14 final size:15
Alignment explanation
Indices: 649638--649671 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
649628 ATTATTTAAA
*
649638 ATATTAAATATTTTT
1 ATATTAAATATTTAT
649653 ATATT-AATATTTAT
1 ATATTAAATATTTAT
649667 ATATT
1 ATATT
649672 TTATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTAAATATTTAT
Found at i:649663 original size:21 final size:23
Alignment explanation
Indices: 649637--649690 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
649627 TATTATTTAA
649637 AATATTAAATAT-TTTTAT-ATT
1 AATATTAAATATATTTTATAATT
*
649658 AATATT-TATATATTTTATAATT
1 AATATTAAATATATTTTATAATT
649680 AA-ATTTAAATA
1 AATA-TTAAATA
649691 AAAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 7 0.26
23 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTAAATATATTTTATAATT
Found at i:649726 original size:16 final size:17
Alignment explanation
Indices: 649696--649730 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
649686 AAATAAAAAA
*
649696 TTATAATTTTTATTATT
1 TTATAATTTTAATTATT
649713 TTAT-ATTTTAATTATT
1 TTATAATTTTAATTATT
649729 TT
1 TT
649731 CAGATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATAATTTTAATTATT
Found at i:651360 original size:18 final size:18
Alignment explanation
Indices: 651337--651403 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
651327 AATAATATAA
*
651337 ATTTTTAAAAAATCGATT
1 ATTTTTAAAAAATCAATT
651355 ATTTTTAAAAAATATCAATT
1 ATTTTT-AAAAA-ATCAATT
* *
651375 -TTTTTTAAAAAT-TATAT
1 ATTTTTAAAAAATCAAT-T
651392 ATTTTTAAAAAA
1 ATTTTTAAAAAA
651404 ATGATTTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.05
17 3 0.07
18 20 0.49
19 10 0.24
20 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTTTTAAAAAATCAATT
Found at i:651379 original size:20 final size:19
Alignment explanation
Indices: 651337--651405 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
651327 AATAATATAA
*
651337 ATTTTT-AAAAAATCGATT
1 ATTTTTAAAAAAATCAATT
651355 ATTTTTAAAAAATATCAATT
1 ATTTTTAAAAAA-ATCAATT
* *
651375 -TTTTT-TAAAAAT-TATAT
1 ATTTTTAAAAAAATCAAT-T
651392 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
651406 GATTTTTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
16 2 0.05
17 3 0.07
18 15 0.36
19 16 0.38
20 6 0.14
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (19 bp):
ATTTTTAAAAAAATCAATT
Found at i:651432 original size:37 final size:37
Alignment explanation
Indices: 651316--651441 Score: 100
Period size: 37 Copynumber: 3.4 Consensus size: 37
651306 AATCTAAATC
* * *
651316 TTATTATTAATAATAATAT-AAATTTT-TAAAAAATCGA
1 TTATTTTTAA-AA-AATATCAATTTTTCTAAAAAATTGA
* *
651353 TTATTTTTAAAAAATATCAATTTTTTTTAAAAATT-A
1 TTATTTTTAAAAAATATCAATTTTTCTAAAAAATTGA
*
651389 TATATTTTTAAAAAA-AT-GATTTTTCTAAAAGAGATTGA
1 T-TATTTTTAAAAAATATCAATTTTTCTAAAA-A-ATTGA
651427 TTATTTATGTAAAAA
1 TTATTT-T-TAAAAA
651442 TTTAAATAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
35 15 0.20
36 13 0.18
37 37 0.50
38 3 0.04
39 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (37 bp):
TTATTTTTAAAAAATATCAATTTTTCTAAAAAATTGA
Found at i:652024 original size:35 final size:35
Alignment explanation
Indices: 651932--652026 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 35
651922 TTTAAAATTT
* *
651932 ATATTTTTATTTATAAAATTATAAAATATTAAAAAA
1 ATATTTTTATTT-TTAAATAATAAAATATTAAAAAA
* *
651968 ATTATTTATATATATTT--ATAATTAAAT-TTAAATAAA
1 A-TATTT-T-TATTTTTAAATAATAAAATATTAAA-AAA
652004 ATATTTTTATTTTTAAATAATAA
1 ATATTTTTATTTTTAAATAATAA
652027 TTAAATTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 16 0.34
36 13 0.28
37 5 0.11
38 2 0.04
39 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATATTTTTATTTTTAAATAATAAAATATTAAAAAA
Found at i:652963 original size:19 final size:18
Alignment explanation
Indices: 652939--652978 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
652929 AGATTTAATA
652939 ATTTATATATTATTATCAT
1 ATTTATATATTATTAT-AT
*
652958 ATTTATATATTTTTATAT
1 ATTTATATATTATTATAT
652976 ATT
1 ATT
652979 ATAATCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATATATTATTATAT
Found at i:653266 original size:23 final size:21
Alignment explanation
Indices: 653240--653285 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
653230 TAATTTATTA
653240 ATAAAAATGTAATTATAAAATAT
1 ATAAAAAT-TAA-TATAAAATAT
*
653263 ATAAATATTAATATAAAATAT
1 ATAAAAATTAATATAAAATAT
653284 AT
1 AT
653286 TTTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 3 0.14
23 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAAATTAATATAAAATAT
Found at i:653302 original size:32 final size:34
Alignment explanation
Indices: 653235--653311 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 34
653225 ATTATTAATT
*
653235 TATTAATA-AAAATGTAATTATAAAATATATAAA
1 TATTAATATAAAATATAATTATAAAATATATAAA
* * *
653268 TATTAATATAAAATAT-ATT-TTAAATATTTTAA
1 TATTAATATAAAATATAATTATAAAATATATAAA
*
653300 TATTAAAATAAA
1 TATTAATATAAA
653312 TTTATAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 21 0.55
33 11 0.29
34 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (34 bp):
TATTAATATAAAATATAATTATAAAATATATAAA
Found at i:653739 original size:23 final size:22
Alignment explanation
Indices: 653699--653747 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
653689 ATTTTAATTT
*
653699 TAAATTTATTTAATTTATTATCA
1 TAAATTTATTTAATTTA-TATAA
*
653722 TAAATTTA-TTATTATTATATAA
1 TAAATTTATTTAAT-TTATATAA
653744 TAAA
1 TAAA
653748 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTTATTTAATTTATATAA
Found at i:653986 original size:14 final size:16
Alignment explanation
Indices: 653956--653989 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
653946 TTTAAAAAAA
653956 TTAATATTTATATTTT
1 TTAATATTTATATTTT
653972 TTAATA-TTA-ATTTT
1 TTAATATTTATATTTT
653986 TTAA
1 TTAA
653990 AAAATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 3 0.17
16 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATATTTATATTTT
Found at i:654210 original size:19 final size:18
Alignment explanation
Indices: 654186--654223 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
654176 TTAATATATT
654186 AATAATATATAAAT-TTAAA
1 AATAAT-TA-AAATATTAAA
654205 AATAATTAAAATATTAAA
1 AATAATTAAAATATTAAA
654223 A
1 A
654224 TATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAATTAAAATATTAAA
Found at i:654257 original size:19 final size:19
Alignment explanation
Indices: 654194--654257 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
654184 TTAATAATAT
*
654194 ATAAATTTAAAAATA-ATTA
1 ATAAA-TTAAAAATATTTTA
654213 A-AATATT-AAAATATTTTA
1 ATAA-ATTAAAAATATTTTA
* **
654231 TTTTATTAAAAATATTTTA
1 ATAAATTAAAAATATTTTA
654250 ATAAATTA
1 ATAAATTA
654258 TTATAATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 18 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTAAAAATATTTTA
Found at i:654328 original size:18 final size:20
Alignment explanation
Indices: 654302--654341 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
654292 ATATTATCAA
654302 TATATTAAATATAAA-TTTT
1 TATATTAAATATAAACTTTT
654321 TATA-TAAATATAAACTTTT
1 TATATTAAATATAAACTTTT
654340 TA
1 TA
654342 AAAATACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTAAATATAAACTTTT
Found at i:654724 original size:19 final size:20
Alignment explanation
Indices: 654690--654730 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
654680 CACTTTCATC
654690 TAATTGAAACTTAAATTTATT
1 TAATTGAAACTTAAA-TTATT
654711 TAATT-AAA-TTAAATTATT
1 TAATTGAAACTTAAATTATT
654729 TA
1 TA
654731 TTCATTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 3 0.15
21 5 0.25
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATTGAAACTTAAATTATT
Found at i:655087 original size:15 final size:15
Alignment explanation
Indices: 655067--655096 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
655057 GTTTAATATC
*
655067 ACTATATATATATTA
1 ACTATAAATATATTA
655082 ACTATAAATATATTA
1 ACTATAAATATATTA
655097 TTGTTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ACTATAAATATATTA
Found at i:658461 original size:20 final size:20
Alignment explanation
Indices: 658436--658475 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
658426 AAATGTCATA
658436 GCATGTTTAAATCGCATGAG
1 GCATGTTTAAATCGCATGAG
658456 GCATGTTTAAATCGCATGAG
1 GCATGTTTAAATCGCATGAG
658476 TCCGGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
GCATGTTTAAATCGCATGAG
Found at i:659269 original size:84 final size:84
Alignment explanation
Indices: 659156--659323 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 84
659146 GACTATTTGC
* *
659156 TACTTTGTAACCCATTCAATTGTTGTTACATGGTAGAAATAATGCAATACTAAGAATTTGTA-CT
1 TACTTTGTAACCCATTCAATTGTTGTTACATGGTAGAAATAATACAATACCAAGAATTTGTATC-
659220 TTCTTATCTAAAGCTTTGTT
65 TTCTTATCTAAAGCTTTGTT
*
659240 TACTTTGTAATCCATTCAATTGTTGTTACATGGTAGAAATAATACAATACCAAGAATTTGTATCT
1 TACTTTGTAACCCATTCAATTGTTGTTACATGGTAGAAATAATACAATACCAAGAATTTGTATCT
659305 TCTTATCTAAAGCTTTGTT
66 TCTTATCTAAAGCTTTGTT
659324 CTGAGTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
84 79 0.99
85 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (84 bp):
TACTTTGTAACCCATTCAATTGTTGTTACATGGTAGAAATAATACAATACCAAGAATTTGTATCT
TCTTATCTAAAGCTTTGTT
Found at i:659389 original size:14 final size:14
Alignment explanation
Indices: 659367--659399 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
659357 TGTTGAATAC
*
659367 GTGTATAGATTTGG
1 GTGTGTAGATTTGG
659381 GTGTGTAGATTTGG
1 GTGTGTAGATTTGG
659395 GTGTG
1 GTGTG
659400 AGTATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (14 bp):
GTGTGTAGATTTGG
Found at i:659838 original size:41 final size:41
Alignment explanation
Indices: 659782--659863 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
659772 TCAAATATGC
* * *
659782 GTTATTCGATATGTTACTTATACTCGAGGTGAGTGTTGAAT
1 GTTACTCGATATGTTACTCACACTCGAGGTGAGTGTTGAAT
* **
659823 GTTACTCGATATGTTAGTCACGTTCGAGGTGAGTGTTGAAT
1 GTTACTCGATATGTTACTCACACTCGAGGTGAGTGTTGAAT
659864 ATGGTATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (41 bp):
GTTACTCGATATGTTACTCACACTCGAGGTGAGTGTTGAAT
Found at i:659927 original size:116 final size:116
Alignment explanation
Indices: 659738--660165 Score: 383
Period size: 116 Copynumber: 3.7 Consensus size: 116
659728 TGAATTTGGA
* * * * * *** *
659738 TGAGTGTCG-ATATGTTA-TTCATGTTAATTAAACTTCAAATATGCGTTATTCGATATGTTACTT
1 TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTA-TT
* * * *
659801 -ATACTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAGTCACGTTCGAGG
65 CACATTTGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCGAGG
659852 TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTC
1 TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTC
* * * * * ** * *
659917 ACGTTTGAGGTGAGTGGTG-A--TTAC-GGTATTTCATGTTACTTAAATTTG-GA
66 ACATTTGAGGTGAGTGTTGAATGTTACTCG-A--T-ATGTTAATCACGTTCGAGG
* * * * * * * ** *
659967 CGAGTG-TCAATATGTTA-TTCATATTAATTAAACTTCAAATACGCGTTATTCGATATGTTACTT
1 TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTA-TT
* * *
660030 -ATATTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCAAGG
65 CACATTTGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCGAGG
** *
660081 TGAGCATTGAATACGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTC
1 TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTC
660146 ACATTTGAGGTGAGTGTTGA
66 ACATTTGAGGTGAGTGTTGA
660166 TTATAGTATT
Statistics
Matches: 240, Mismatches: 58, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
112 1 0.00
113 66 0.28
114 25 0.10
115 27 0.11
116 120 0.50
117 1 0.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (116 bp):
TGAGTGTTGAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTC
ACATTTGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCGAGG
Found at i:660131 original size:229 final size:229
Alignment explanation
Indices: 659730--660202 Score: 820
Period size: 229 Copynumber: 2.1 Consensus size: 229
659720 GGATAACATG
* * *
659730 AATTTGGATGAGTGTCGATATGTTATTCATGTTAATTAAACTTCAAATATGCGTTATTCGATATG
1 AATTTGGATGAGTGTCAATATGTTATTCATATTAATTAAACTTCAAATACGCGTTATTCGATATG
* * **
659795 TTACTTATACTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAGTCACGTTCGAGGTGAGTGTT
66 TTACTTATACTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCAAGGTGAGCATT
* *
659860 GAATATGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTCACGTTTGA
131 GAATACGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTCACATTTGA
*
659925 GGTGAGTGGTGATTACGGTATTTCATGTTACTTA
196 GGTGAGTGGTGATTACAGTATTTCATGTTACTTA
*
659959 AATTTGGACGAGTGTCAATATGTTATTCATATTAATTAAACTTCAAATACGCGTTATTCGATATG
1 AATTTGGATGAGTGTCAATATGTTATTCATATTAATTAAACTTCAAATACGCGTTATTCGATATG
*
660024 TTACTTATATTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCAAGGTGAGCATT
66 TTACTTATACTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCAAGGTGAGCATT
660089 GAATACGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTCACATTTGA
131 GAATACGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTCACATTTGA
* *
660154 GGTGAGTGTTGATTATAGTATTTCATGTTACTTA
196 GGTGAGTGGTGATTACAGTATTTCATGTTACTTA
660188 AATTTGGATGAGTGT
1 AATTTGGATGAGTGT
660203 TGAGCACAGG
Statistics
Matches: 229, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
229 229 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.40
Consensus pattern (229 bp):
AATTTGGATGAGTGTCAATATGTTATTCATATTAATTAAACTTCAAATACGCGTTATTCGATATG
TTACTTATACTCGAGGTGAGTGTTGAATGTTACTCGATATGTTAATCACGTTCAAGGTGAGCATT
GAATACGGTATTTCATGTTACTTGAACTTCGAATACATGTTACTCGATATGTTATTCACATTTGA
GGTGAGTGGTGATTACAGTATTTCATGTTACTTA
Found at i:661272 original size:22 final size:23
Alignment explanation
Indices: 661247--661299 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
661237 TTAATTAAAT
661247 TTAAATAAAAAT-ATTATTTTAA
1 TTAAATAAAAATAATTATTTTAA
*
661269 TT-AATAAATAATAATTTTTTTAA
1 TTAAATAAA-AATAATTATTTTAA
661292 --AAATAAAA
1 TTAAATAAAA
661300 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAATAAAAATAATTATTTTAA
Found at i:661536 original size:16 final size:16
Alignment explanation
Indices: 661507--661553 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
661497 CAATAATTTT
661507 AAATATTA-TATAAAA
1 AAATATTATTATAAAA
*
661522 AAATTTTATTATAAAA
1 AAATATTATTATAAAA
*
661538 AAATATTATTTTAAAA
1 AAATATTATTATAAAA
661554 TTATTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATTATTATAAAA
Found at i:661788 original size:41 final size:41
Alignment explanation
Indices: 661707--661799 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
661697 TTTAATTAAG
* *
661707 TTTAAATAAATATTTTAATAAATAATTTAATTGAATTATTA
1 TTTATATAAATATTTTAATAAATAATTTAATTGAAATATTA
* ** *
661748 TTTATATAAATATTTTTATTTA-AATTTAATTATAAATATTA
1 TTTATATAAATATTTTAATAAATAATTTAATT-GAAATATTA
*
661789 -ATATATAAATA
1 TTTATATAAATA
661800 AATTTTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 19 0.43
41 25 0.57
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (41 bp):
TTTATATAAATATTTTAATAAATAATTTAATTGAAATATTA
Found at i:661795 original size:14 final size:14
Alignment explanation
Indices: 661750--661799 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
661740 AATTATTATT
**
661750 TATATAAATATTTT
1 TATATAAATATTAA
*
661764 TATTTAAAT-TTAA
1 TATATAAATATTAA
661777 T-TATAAATATTAA
1 TATATAAATATTAA
661790 TATATAAATA
1 TATATAAATA
661800 AATTTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 6 0.20
13 8 0.27
14 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATATTAA
Found at i:661822 original size:12 final size:13
Alignment explanation
Indices: 661766--661827 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 13
661756 AATATTTTTA
661766 TTTAAAT-TTAAT
1 TTTAAATATTAAT
*
661778 TATAAATATTAAT
1 TTTAAATATTAAT
*
661791 ATATAAATA--AAT
1 -TTTAAATATTAAT
*
661803 TTTTAATATT-AT
1 TTTAAATATTAAT
*
661815 TTTAAATAATAAT
1 TTTAAATATTAAT
661828 ATAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 6 0.15
12 19 0.47
13 7 0.17
14 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAATATTAAT
Found at i:662264 original size:23 final size:21
Alignment explanation
Indices: 662227--662278 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
662217 TTTTTTAATG
*
662227 AAAAAAATAAGATAAGTTTCAA
1 AAAAAAATAAAATAA-TTTCAA
*
662249 AAATAAAATAAAATAATTTCTA
1 AAA-AAAATAAAATAATTTCAA
662271 AAAAAAAT
1 AAAAAAAT
662279 TAATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 11 0.41
23 11 0.41
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAAAAATAAAATAATTTCAA
Found at i:662677 original size:2 final size:2
Alignment explanation
Indices: 662670--662708 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
662660 TCATAGGCTT
662670 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
662709 TGCTTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:663223 original size:3 final size:3
Alignment explanation
Indices: 663215--663261 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
663205 CCTTTTTTAA
* *
663215 AAT AAT AAT TA- AAT AAT ACTT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
663260 AA
1 AA
663262 CAGATTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.92
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:663634 original size:11 final size:12
Alignment explanation
Indices: 663617--663655 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
663607 AAATTATTTA
*
663617 AAATAATATTAT
1 AAATAATATAAT
663629 -AATAATATAAT
1 AAATAATATAAT
*
663640 AAATAATAAAAT
1 AAATAATATAAT
663652 AAAT
1 AAAT
663656 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAATATAAT
Found at i:663845 original size:21 final size:23
Alignment explanation
Indices: 663817--663872 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
663807 AAAAAATATT
663817 TATT-TAAAT-TTAAT-TATAAAA
1 TATTATAAATATTAATATA-AAAA
663838 TA-TATAAATATTAATATAAAAA
1 TATTATAAATATTAATATAAAAA
663860 TATTATAAATATT
1 TATTATAAATATT
663873 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.03
21 7 0.23
22 11 0.35
23 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAAATATTAATATAAAAA
Found at i:663870 original size:23 final size:23
Alignment explanation
Indices: 663817--663872 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
663807 AAAAAATATT
663817 TATT-TAAAT-TTAATTATAAAA
1 TATTATAAATATTAATTATAAAA
663838 TA-TATAAATATTAA-TATAAAAA
1 TATTATAAATATTAATTAT-AAAA
663860 TATTATAAATATT
1 TATTATAAATATT
663873 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.03
21 10 0.32
22 10 0.32
23 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAAATATTAATTATAAAA
Found at i:669074 original size:24 final size:21
Alignment explanation
Indices: 669041--669092 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 21
669031 ATGATAAAAA
669041 AATAAAAATAATATATATTATAT
1 AATAAAAATAATATA-A-TATAT
669064 ACATAAAAATAATATAATATAT
1 A-ATAAAAATAATATAATATAT
669086 AATAAAA
1 AATAAAA
669093 TACGTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.21
22 6 0.21
23 2 0.07
24 14 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAAAATAATATAATATAT
Found at i:669314 original size:15 final size:16
Alignment explanation
Indices: 669291--669323 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
669281 TGAAAAATCT
669291 TTTATTTTAAAAAATA
1 TTTATTTTAAAAAATA
*
669307 TTTA-TTTAAAAATTA
1 TTTATTTTAAAAAATA
669322 TT
1 TT
669324 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATTTTAAAAAATA
Found at i:669400 original size:21 final size:21
Alignment explanation
Indices: 669357--669403 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
669347 TAATATAATA
669357 ATATATATTAATTTTATATTT
1 ATATATATTAATTTTATATTT
669378 ATATATTATATAATTTT-TA-TT
1 ATATA-TAT-TAATTTTATATTT
669399 ATATA
1 ATATA
669404 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATATTAATTTTATATTT
Found at i:669597 original size:36 final size:39
Alignment explanation
Indices: 669542--669649 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 39
669532 AGAAAAATAA
* * *
669542 TATAAATA-AATTTAAATAATTT-TAA-ACTA-TTTATT
1 TATAAATATAATATAAATAATTTAAAATAATATTTTATT
669577 TATAAATATAATATAAATAATTTAAAATTAATATTTTATT
1 TATAAATATAATATAAATAATTTAAAA-TAATATTTTATT
* *
669617 T-TAAATATAATATAAATAAATAAAAATAATATT
1 TATAAATATAATATAAATAATTTAAAATAATATT
669650 AATATTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
35 8 0.13
36 13 0.21
37 2 0.03
38 7 0.11
39 26 0.41
40 7 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (39 bp):
TATAAATATAATATAAATAATTTAAAATAATATTTTATT
Found at i:670364 original size:2 final size:2
Alignment explanation
Indices: 670357--670390 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
670347 TTGTTTGTTT
670357 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
670391 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:670395 original size:2 final size:2
Alignment explanation
Indices: 670390--670428 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
670380 ATATATATAT
670390 AG AG AG AG AG 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 AG AG AG AG AG A
670429 TTTGTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:672330 original size:19 final size:20
Alignment explanation
Indices: 672293--672330 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
672283 TTTAAATTTT
*
672293 ATAAAAGTATATATATTAAA
1 ATAAAAATATATATATTAAA
*
672313 ATAAAAATA-ATATTTTAA
1 ATAAAAATATATATATTAA
672331 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
ATAAAAATATATATATTAAA
Found at i:673570 original size:21 final size:21
Alignment explanation
Indices: 673531--673570 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
673521 AAGCAAAAAG
* * *
673531 AAAAAAGTGTACTATATATTT
1 AAAAAAGTGCAATACATATTT
673552 AAAAAAGTGCAATACATAT
1 AAAAAAGTGCAATACATAT
673571 ATGTTACGTA
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:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAAGTGCAATACATATTT
Found at i:674223 original size:34 final size:37
Alignment explanation
Indices: 674184--674254 Score: 112
Period size: 34 Copynumber: 2.0 Consensus size: 37
674174 GATGTAAATA
*
674184 TAATAAAATATATAAATAT-A-ATAAATATAT-AATT
1 TAATAAAATATAAAAATATAATATAAATATATGAATT
674218 TAATAAAATATAAAAATATAATATAAATATATGAATT
1 TAATAAAATATAAAAATATAATATAAATATATGAATT
674255 ATTAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 18 0.55
35 1 0.03
36 10 0.30
37 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (37 bp):
TAATAAAATATAAAAATATAATATAAATATATGAATT
Found at i:674249 original size:8 final size:8
Alignment explanation
Indices: 674178--674242 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
674168 AAATATGATG
674178 TAAATATAA
1 TAAATAT-A
674187 TAAAATATA
1 T-AAATATA
674196 TAAATATAA
1 TAAATAT-A
674205 TAAATATA
1 TAAATATA
*
674213 T-AATTTAA
1 TAAATAT-A
674221 TAAA-ATA
1 TAAATATA
*
674228 TAAAAATA
1 TAAATATA
674236 T-AATATA
1 TAAATATA
674243 AATATATGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 14 0.29
8 15 0.31
9 13 0.27
10 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAATATA
Found at i:674821 original size:26 final size:25
Alignment explanation
Indices: 674776--674834 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
674766 TTAATAAAAA
* **
674776 TTAAATTTTATTTTTATGTTTAGTT
1 TTAAATTTGATTTTTATGTTTAAAT
674801 TTAAATTTGATTATTTATGTTTAAAT
1 TTAAATTTGATT-TTTATGTTTAAAT
674827 TTAAATTT
1 TTAAATTT
674835 AATAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.63
Consensus pattern (25 bp):
TTAAATTTGATTTTTATGTTTAAAT
Found at i:674842 original size:26 final size:26
Alignment explanation
Indices: 674788--674842 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
674778 AAATTTTATT
** * *
674788 TTTATGTTTAGTTTTAAATTTGATTA
1 TTTATGTTTAAATTTAAATTTAATAA
674814 TTTATGTTTAAATTTAAATTTAATAA
1 TTTATGTTTAAATTTAAATTTAATAA
674840 TTT
1 TTT
674843 TTTAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (26 bp):
TTTATGTTTAAATTTAAATTTAATAA
Found at i:674930 original size:32 final size:29
Alignment explanation
Indices: 674857--674931 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 29
674847 ATATTAAATA
* *
674857 AAAAATAAAATAAAAAATTTAATTAAATTT
1 AAAAAT-AATTAAAAAATTTAAATAAATTT
* *
674887 ATAAATTATTAAAAAATATTAAAATATAATTT
1 AAAAATAATTAAAAAAT-TT-AAATA-AATTT
674919 AAAAATAATTAAA
1 AAAAATAATTAAA
674932 TCAAAGTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 9 0.25
30 7 0.19
31 4 0.11
32 16 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAATAATTAAAAAATTTAAATAAATTT
Found at i:677381 original size:26 final size:27
Alignment explanation
Indices: 677352--677417 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 27
677342 TTTAAGGATA
677352 AAAAATTATTATAAAAT-TTAAATTTT
1 AAAAATTATTATAAAATATTAAATTTT
* **
677378 AAAAA-T-TTATTAAATATTATTTTTT
1 AAAAATTATTATAAAATATTAAATTTT
*
677403 AAAAATAATTATAAA
1 AAAAATTATTATAAA
677418 TAATCACATG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.25
25 13 0.41
26 5 0.16
27 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAAATTATTATAAAATATTAAATTTT
Found at i:677384 original size:15 final size:17
Alignment explanation
Indices: 677354--677386 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
677344 TAAGGATAAA
677354 AAATTATTATAAAATTT
1 AAATTATTATAAAATTT
677371 AAATT-TTA-AAAATTT
1 AAATTATTATAAAATTT
677386 A
1 A
677387 TTAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTATTATAAAATTT
Found at i:679058 original size:17 final size:17
Alignment explanation
Indices: 679025--679091 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
679015 TAATTTTTTA
679025 AAAATTTTATAATAATATT
1 AAAA-TTTAT-ATAATATT
679044 AAAATTTATATAATA-T
1 AAAATTTATATAATATT
** *
679060 AAATATTTA-A-CGTGTT
1 AAA-ATTTATATAATATT
679076 AAAATTTATATAATAT
1 AAAATTTATATAATAT
679092 ATATCATTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 6 0.16
16 10 0.26
17 13 0.34
18 5 0.13
19 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAATTTATATAATATT
Done.