Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 17 of 31
Found at i:3978647 original size:6 final size:6
Alignment explanation
Indices: 3978638--3978672 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3978628 AAATATCATA
*
3978638 ATTTAT ATTTAT ATTTAT ATTTATT ATTAAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTA-T ATTTAT ATTT
3978673 TTATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:3978653 original size:12 final size:13
Alignment explanation
Indices: 3978638--3978676 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
3978628 AAATATCATA
3978638 ATTTATATTTA-T
1 ATTTATATTTATT
3978650 ATTTATATTTATT
1 ATTTATATTTATT
*
3978663 ATTAATATTT-TT
1 ATTTATATTTATT
3978675 AT
1 AT
3978677 AATTTTAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTATATTTATT
Found at i:3979012 original size:13 final size:13
Alignment explanation
Indices: 3978996--3979021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3978986 AATTATAAAT
3978996 TATATATATATAA
1 TATATATATATAA
3979009 TATATATATATAA
1 TATATATATATAA
3979022 ATTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATATATATAA
Found at i:3979032 original size:15 final size:14
Alignment explanation
Indices: 3978976--3979032 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
3978966 AATAGGTATC
*
3978976 ATATTAATT-TAAT
1 ATATAAATTATAAT
3978989 -TATAAATTAT-AT
1 ATATAAATTATAAT
3979001 ATATATAA-TATATAT
1 ATATA-AATTATA-AT
3979016 ATATAAATTAATAAT
1 ATATAAATT-ATAAT
3979031 AT
1 AT
3979033 TATTATTAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
12 9 0.25
13 8 0.22
14 4 0.11
15 12 0.33
16 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATAAATTATAAT
Found at i:3979483 original size:7 final size:7
Alignment explanation
Indices: 3979471--3979497 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3979461 GCTGTCAGGA
3979471 TGCCAGT
1 TGCCAGT
3979478 TGCCAGT
1 TGCCAGT
3979485 TGCCAGT
1 TGCCAGT
3979492 TGCCAG
1 TGCCAG
3979498 AGGTCTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (7 bp):
TGCCAGT
Found at i:3980003 original size:11 final size:9
Alignment explanation
Indices: 3979977--3980010 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3979967 AAATATTTTG
3979977 ATTTTTAAT
1 ATTTTTAAT
3979986 ATTTTTAAT
1 ATTTTTAAT
*
3979995 ATTTTT-TT
1 ATTTTTAAT
3980003 ATTTTTAA
1 ATTTTTAA
3980011 ATTATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:3981187 original size:27 final size:27
Alignment explanation
Indices: 3981129--3981186 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
3981119 AATAATAAGA
* *
3981129 ATTTTAATTTTATCCTTAAAATTTTAT
1 ATTTTAATTTTATACATAAAATTTTAT
*
3981156 ATTTTAATTTTA-ACATAAAATTTTTT
1 ATTTTAATTTTATACATAAAATTTTAT
3981182 ATTTT
1 ATTTT
3981187 TTTAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTTAATTTTATACATAAAATTTTAT
Found at i:3981806 original size:20 final size:17
Alignment explanation
Indices: 3981779--3981817 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 17
3981769 AATATTTTTT
3981779 TAAAATTAATAATAATAAA
1 TAAAATTAAT-ATAA-AAA
3981798 TAAATATTAATATAAAAA
1 TAAA-ATTAATATAAAAA
3981816 TA
1 TA
3981818 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTAATATAAAAA
Found at i:3982438 original size:22 final size:21
Alignment explanation
Indices: 3982417--3982461 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
3982407 GAAGATTAAT
*
3982417 TTAATATATTATTTATAATAA
1 TTAATATATTAATTATAATAA
3982438 -T--TATATTAATTATAATAA
1 TTAATATATTAATTATAATAA
3982456 TTAATA
1 TTAATA
3982462 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
18 16 0.80
19 1 0.05
20 1 0.05
21 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATATTAATTATAATAA
Found at i:3982441 original size:9 final size:9
Alignment explanation
Indices: 3982429--3982463 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3982419 AATATATTAT
3982429 TTATAATAA
1 TTATAATAA
*
3982438 TTATATTAA
1 TTATAATAA
3982447 TTATAATAA
1 TTATAATAA
3982456 TTAATAAT
1 TT-ATAAT
3982464 TTTTTTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTATAATAA
Found at i:3982444 original size:18 final size:18
Alignment explanation
Indices: 3982421--3982458 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3982411 ATTAATTTAA
*
3982421 TATATTATTTATAATAAT
1 TATATTAATTATAATAAT
3982439 TATATTAATTATAATAAT
1 TATATTAATTATAATAAT
3982457 TA
1 TA
3982459 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTAATTATAATAAT
Found at i:3983602 original size:26 final size:26
Alignment explanation
Indices: 3983573--3983622 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3983563 TGAACCAATG
* *
3983573 GTGATTTGAAGATG-AAGATTTAAAAC
1 GTGATTTCAACATGCAAG-TTTAAAAC
3983599 GTGATTTCAACATGCAAGTTTAAA
1 GTGATTTCAACATGCAAGTTTAAA
3983623 TTTTAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (26 bp):
GTGATTTCAACATGCAAGTTTAAAAC
Found at i:3992448 original size:26 final size:26
Alignment explanation
Indices: 3992384--3992448 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
3992374 TCTTAATCAA
3992384 TTAATA-AAAAAA-TTTATTTAAATT
1 TTAATATAAAAAATTTTATTTAAATT
** * * *
3992408 CAAATTTAAATAAATTTTATTTTATTT
1 TTAATATAAA-AAATTTTATTTAAATT
3992435 TTAATATAAAAAAT
1 TTAATATAAAAAAT
3992449 ATTAATAGCA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
24 3 0.10
25 3 0.10
26 7 0.23
27 17 0.57
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATAAAAAATTTTATTTAAATT
Found at i:4003774 original size:14 final size:14
Alignment explanation
Indices: 4003738--4003777 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4003728 GGCAAAAACA
*
4003738 TATATATACATACC
1 TATATATATATACC
**
4003752 TATATATATATATT
1 TATATATATATACC
4003766 TATATATATATA
1 TATATATATATA
4003778 GATGTGCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATATATATACC
Found at i:4004562 original size:15 final size:15
Alignment explanation
Indices: 4004542--4004582 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
4004532 TGCAGGGTTT
4004542 GACCTATGCAGAAGA
1 GACCTATGCAGAAGA
4004557 GACCTATGCAGAAGA
1 GACCTATGCAGAAGA
4004572 GACCTAATGCA
1 GACCT-ATGCA
4004583 TGCAGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (15 bp):
GACCTATGCAGAAGA
Found at i:4008176 original size:12 final size:12
Alignment explanation
Indices: 4008152--4008189 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4008142 TCAAAACAAG
4008152 ATGATAA-AGATA
1 ATGATAATA-ATA
4008164 ATGATAATAATA
1 ATGATAATAATA
*
4008176 ATAATAATAATA
1 ATGATAATAATA
4008188 AT
1 AT
4008190 TAATTCTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 23 0.96
13 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGATAATAATA
Found at i:4014781 original size:3 final size:3
Alignment explanation
Indices: 4014773--4014798 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4014763 TTTCTTGACC
4014773 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
4014799 GCTTCTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4014816 original size:2 final size:2
Alignment explanation
Indices: 4014809--4014841 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4014799 GCTTCTTAAT
4014809 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4014842 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4014846 original size:2 final size:2
Alignment explanation
Indices: 4014841--4014873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4014831 TCTCTCTCTC
4014841 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 T
4014874 GTAGGCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4016074 original size:19 final size:19
Alignment explanation
Indices: 4016038--4016088 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
4016028 ATATATTAAA
* *
4016038 AATAAAATATTAAATTAATT
1 AATAAAA-AATAATTTAATT
*
4016058 ATTAAAAAATAATTTAATT
1 AATAAAAAATAATTTAATT
4016077 AATAAAAAATAA
1 AATAAAAAATAA
4016089 AATTAAATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAAAAAATAATTTAATT
Found at i:4016092 original size:16 final size:17
Alignment explanation
Indices: 4016053--4016094 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
4016043 AATATTAAAT
*
4016053 TAATTATTAAAAAATAA
1 TAATTAATAAAAAATAA
4016070 TTTAATTAATAAAAAATAA
1 --TAATTAATAAAAAATAA
4016089 -AATTAA
1 TAATTAA
4016095 ATCGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
19 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATTAATAAAAAATAA
Found at i:4020452 original size:15 final size:16
Alignment explanation
Indices: 4020432--4020472 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4020422 ATTACATGCA
4020432 TATAAATTTT-AAAAT
1 TATAAATTTTGAAAAT
*
4020447 TATAAATATTTGATAAT
1 TATAAAT-TTTGAAAAT
4020464 TA-AAATTTT
1 TATAAATTTT
4020473 TAAACATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATAAATTTTGAAAAT
Found at i:4021308 original size:23 final size:24
Alignment explanation
Indices: 4021257--4021309 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
4021247 TAAAATGTTA
*
4021257 TATTTTAATTTTTATTTATCTAAT
1 TATTTTAATTTTTAATTATCTAAT
* *
4021281 T-TTTTTATTTTTAATTAT-TTAT
1 TATTTTAATTTTTAATTATCTAAT
4021303 TATTTTA
1 TATTTTA
4021310 TAATTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.17
23 19 0.79
24 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TATTTTAATTTTTAATTATCTAAT
Found at i:4021313 original size:18 final size:16
Alignment explanation
Indices: 4021264--4021317 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
4021254 TTATATTTTA
4021264 ATTTTTATTTATCTAATT
1 ATTTTTATTT-T-TAATT
4021282 -TTTTTATTTTTAATT
1 ATTTTTATTTTTAATT
4021297 ATTTATTATTTTATAATT
1 ATTT-TTATTTT-TAATT
4021315 ATT
1 ATT
4021318 ATTGATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.15
16 4 0.12
17 16 0.48
18 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTATTTTTAATT
Found at i:4021320 original size:17 final size:17
Alignment explanation
Indices: 4021254--4021317 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 17
4021244 AATTAAAATG
4021254 TTATATTTTAATT-TTTA
1 TTAT-TTTTAATTATTTA
* *
4021271 TT-TATCTAATT-TTT-
1 TTATTTTTAATTATTTA
4021285 TTATTTTTAATTATTTA
1 TTATTTTTAATTATTTA
4021302 TTATTTTATAATTATT
1 TTATTTT-TAATTATT
4021318 ATTGATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.05
15 16 0.41
16 4 0.10
17 9 0.23
18 8 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTTAATTATTTA
Found at i:4021931 original size:18 final size:18
Alignment explanation
Indices: 4021908--4021950 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4021898 GCACAATATT
4021908 TTTATTTTAAAATTTTT-A
1 TTTATTTT-AAATTTTTAA
*
4021926 TTTA-TTTGAATTTTTAA
1 TTTATTTTAAATTTTTAA
4021943 TTTATTTT
1 TTTATTTT
4021951 TTTTATCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
17 8 0.36
18 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTAAATTTTTAA
Found at i:4021939 original size:16 final size:17
Alignment explanation
Indices: 4021918--4021949 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4021908 TTTATTTTAA
4021918 AATTTTT-ATTTATTTG
1 AATTTTTAATTTATTTG
4021934 AATTTTTAATTTATTT
1 AATTTTTAATTTATTT
4021950 TTTTTATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
AATTTTTAATTTATTTG
Found at i:4021987 original size:16 final size:16
Alignment explanation
Indices: 4021905--4021992 Score: 64
Period size: 16 Copynumber: 5.6 Consensus size: 16
4021895 TTAGCACAAT
*
4021905 ATTTTTA-TT-TTAAA
1 ATTTTTATTTATTATA
4021919 ATTTTTATTTATT-TGA
1 ATTTTTATTTATTAT-A
4021935 ATTTTTAATTTATT-T-
1 ATTTTT-ATTTATTATA
*
4021950 -TTTTTATCCTTCATTATT
1 ATTTTTAT--TT-ATTATA
4021968 ATTTTTATTTATTATA
1 ATTTTTATTTATTATA
4021984 A-TTTTATTT
1 ATTTTTATTT
4021993 GAAAATAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
13 2 0.03
14 12 0.19
15 12 0.19
16 18 0.29
17 11 0.18
19 7 0.11
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (16 bp):
ATTTTTATTTATTATA
Found at i:4022065 original size:21 final size:21
Alignment explanation
Indices: 4022039--4022082 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4022029 AATCTAATTA
4022039 ATAATAATTTAT-TATGTATTT
1 ATAAT-ATTTATATATGTATTT
* *
4022060 ATAATATTTTTATATTTATTT
1 ATAATATTTATATATGTATTT
4022081 AT
1 AT
4022083 TTATTTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATAATATTTATATATGTATTT
Found at i:4024914 original size:2 final size:2
Alignment explanation
Indices: 4024907--4024936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4024897 TCTAAGAATA
4024907 AT AT 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 AT AT
4024937 CAGACAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4027132 original size:2 final size:2
Alignment explanation
Indices: 4027125--4027171 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4027115 TCAACTTGTC
4027125 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
4027167 AT AT A
1 AT AT A
4027172 AAGTTCATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4028584 original size:38 final size:38
Alignment explanation
Indices: 4028487--4028639 Score: 209
Period size: 38 Copynumber: 4.1 Consensus size: 38
4028477 CACCAGCCAC
* * * * *
4028487 CAGCCACCGGCCAATTCCAAATTGAATTCTTTAATCGT
1 CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGT
* *
4028525 CAG-CGCCGGCCAATTTCAAATTGAATTCTCTAGCCGT
1 CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGT
*
4028562 CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAGCCGT
1 CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGT
* *
4028600 CAGTCGCCAGTCAATTTCAAATTGAATTCTCTAACCGT
1 CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGT
4028638 CA
1 CA
4028640 ACTAATTCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
37 32 0.30
38 73 0.70
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28
Consensus pattern (38 bp):
CAGCCGCCAGCCAATTTCAAATTGAATTCTCTAACCGT
Found at i:4032692 original size:66 final size:66
Alignment explanation
Indices: 4032610--4032743 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
4032600 AAATGCAACT
4032610 TCGTCACAAATAGGAGATCCTTCATCTTGCTTCTCCATATGTGGTAATTCGTACCATTTAAGCTA
1 TCGTCACAAATAGGAGATCCTTCATCTTGCTTCTCCATATGTGGTAATTCGTACCATTTAAGCTA
4032675 A
66 A
4032676 TCGTCACAAATAGGAGATCCTTCATCTTGCTTCTCCATATGTGGTAATTCGTACCATTTAAGCTA
1 TCGTCACAAATAGGAGATCCTTCATCTTGCTTCTCCATATGTGGTAATTCGTACCATTTAAGCTA
4032741 A
66 A
4032742 TC
1 TC
4032744 ATTTTGCTCG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (66 bp):
TCGTCACAAATAGGAGATCCTTCATCTTGCTTCTCCATATGTGGTAATTCGTACCATTTAAGCTA
A
Found at i:4033334 original size:38 final size:38
Alignment explanation
Indices: 4033292--4033424 Score: 158
Period size: 38 Copynumber: 3.5 Consensus size: 38
4033282 AGCCACCGAC
* ** * * **
4033292 CAATTCCAAATTGAATTCTCTAGTCGTCAGTTGTCGGT
1 CAATTTCAAATTGAATTCTCTAACCGTCAGTCGCCAAT
4033330 CAATTTCAAATTGAATTCTCTAACCGTCAGTCGCCAAT
1 CAATTTCAAATTGAATTCTCTAACCGTCAGTCGCCAAT
* ** *
4033368 CAATTTCAAATTAAATTCTCTAACCGTCAACCGTCAAT
1 CAATTTCAAATTGAATTCTCTAACCGTCAGTCGCCAAT
*
4033406 CAATTTCAAATTAAATTCT
1 CAATTTCAAATTGAATTCT
4033425 TTAATCATCA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 84 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (38 bp):
CAATTTCAAATTGAATTCTCTAACCGTCAGTCGCCAAT
Found at i:4033717 original size:23 final size:24
Alignment explanation
Indices: 4033634--4033722 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 24
4033624 TGTAATAATA
* *
4033634 ATAAAGTATTTATAT-T-ATTTTT
1 ATAAAATATTTATATATGATATTT
* *
4033656 ATAAGATATTTATATTATTTTATATTT
1 ATAAAATATTTATA-TA--TGATATTT
*
4033683 ATAAAATTTTTA-ATATGATATTT
1 ATAAAATATTTATATATGATATTT
* *
4033706 TTAATATATTTATATAT
1 ATAAAATATTTATATAT
4033723 TTTAGTAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
22 12 0.23
23 17 0.33
24 4 0.08
25 2 0.04
26 2 0.04
27 15 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
ATAAAATATTTATATATGATATTT
Found at i:4033724 original size:19 final size:20
Alignment explanation
Indices: 4033700--4033747 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
4033690 TTTTAATATG
4033700 ATATTTTTAAT-ATATTTAT
1 ATATTTTTAATAATATTTAT
*
4033719 ATA-TTTTAGTAATATTTAT
1 ATATTTTTAATAATATTTAT
4033738 ATTATTTTTA
1 A-TATTTTTA
4033748 TATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 2 0.08
21 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATTTTTAATAATATTTAT
Found at i:4033982 original size:2 final size:2
Alignment explanation
Indices: 4033975--4034001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4033965 GTTTATTTCA
4033975 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
4034002 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4035092 original size:22 final size:22
Alignment explanation
Indices: 4035029--4035099 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
4035019 ATTTTTTAAT
*
4035029 TTTAATTAGATTTATAGTTTAGA
1 TTTAAATAGATTTA-AGTTTAGA
* *
4035052 TTTAAATAGACTCAAGTTTATG-
1 TTTAAATAGATTTAAGTTTA-GA
* *
4035074 TTTAAATAGATTTACGTTTAAA
1 TTTAAATAGATTTAAGTTTAGA
4035096 TTTA
1 TTTA
4035100 TATTTTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 27 0.69
23 12 0.31
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTAAATAGATTTAAGTTTAGA
Found at i:4035121 original size:9 final size:9
Alignment explanation
Indices: 4035107--4035133 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4035097 TTATATTTTA
4035107 TTAAATATT
1 TTAAATATT
4035116 TTAAATATT
1 TTAAATATT
4035125 TTAAATATT
1 TTAAATATT
4035134 AATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAAATATT
Found at i:4036534 original size:19 final size:18
Alignment explanation
Indices: 4036499--4036533 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4036489 GCTATGGGTG
4036499 AGTTTTTGTTTTATTTTC
1 AGTTTTTGTTTTATTTTC
4036517 AGTTTTTGATTTT-TTTT
1 AGTTTTTG-TTTTATTTT
4036534 TTTTTTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.03, G:0.11, T:0.74
Consensus pattern (18 bp):
AGTTTTTGTTTTATTTTC
Found at i:4037314 original size:2 final size:2
Alignment explanation
Indices: 4037307--4037343 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4037297 TTTGTTTGTT
*
4037307 TA TA TA TA TA TA TA TA TA TA TA TA TA TT 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
4037344 CTTGTTATCT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:4039250 original size:14 final size:14
Alignment explanation
Indices: 4039231--4039260 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4039221 TTATTTTTAA
4039231 TAAATTTAAATATT
1 TAAATTTAAATATT
4039245 TAAATTTAAATATT
1 TAAATTTAAATATT
4039259 TA
1 TA
4039261 TAAAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTTAAATATT
Found at i:4039837 original size:2 final size:2
Alignment explanation
Indices: 4039832--4039865 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4039822 ATATATATGT
4039832 AG 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 AG
4039866 TTCTAATGGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4040958 original size:23 final size:22
Alignment explanation
Indices: 4040932--4040974 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4040922 AAGGAGCAAT
4040932 TTTTTGTTAAGAAAAATCGATTG
1 TTTTTGTTAA-AAAAATCGATTG
*
4040955 TTTTTTTTAAAAAAATCGAT
1 TTTTTGTTAAAAAAATCGAT
4040975 CTTTTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (22 bp):
TTTTTGTTAAAAAAATCGATTG
Found at i:4040980 original size:22 final size:22
Alignment explanation
Indices: 4040931--4040980 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4040921 TAAGGAGCAA
4040931 TTTTTTGTTAAGAAAAATCGAT
1 TTTTTTGTTAAGAAAAATCGAT
*
4040953 TGTTTTTTTTAA-AAAAATCGAT
1 T-TTTTTGTTAAGAAAAATCGAT
*
4040975 CTTTTT
1 TTTTTT
4040981 ATGTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 11 0.44
23 9 0.36
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTTTGTTAAGAAAAATCGAT
Found at i:4042648 original size:16 final size:16
Alignment explanation
Indices: 4042627--4042662 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4042617 CATTCGATTT
*
4042627 AATAAATTTAATTTAA
1 AATAAATTAAATTTAA
4042643 AATAAATTAAATTTAA
1 AATAAATTAAATTTAA
4042659 AATA
1 AATA
4042663 TTTTTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATTAAATTTAA
Found at i:4049407 original size:2 final size:2
Alignment explanation
Indices: 4049400--4049437 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4049390 TTTGGCAGCA
4049400 AT AT AT AT AT AT 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 AT AT AT AT AT AT
4049438 TTGAAGTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4049763 original size:20 final size:18
Alignment explanation
Indices: 4049738--4049784 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
4049728 AAAAGATACG
4049738 TTAAAATTTAAATATATTAA
1 TTAAAATTT--ATATATTAA
*
4049758 TTAAAATTTTTATATTAA
1 TTAAAATTTATATATTAA
*
4049776 TTTAAATTT
1 TTAAAATTT
4049785 TTTAAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAAATTTATATATTAA
Found at i:4049788 original size:19 final size:18
Alignment explanation
Indices: 4049750--4049786 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4049740 AAAATTTAAA
4049750 TATATTAATTAAAATTTT
1 TATATTAATTAAAATTTT
*
4049768 TATATTAATTTAAATTTT
1 TATATTAATTAAAATTTT
4049786 T
1 T
4049787 TAAAACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTAATTAAAATTTT
Found at i:4050496 original size:2 final size:2
Alignment explanation
Indices: 4050489--4050529 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4050479 AGGAAGCTTT
4050489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4050530 GCTCTGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4052971 original size:21 final size:21
Alignment explanation
Indices: 4052945--4052985 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4052935 CTATATATCT
*
4052945 TAATTTTGAGACATTCAAAAA
1 TAATTTTGAGACACTCAAAAA
*
4052966 TAATTTTGAGATACTCAAAA
1 TAATTTTGAGACACTCAAAA
4052986 GTCACCGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
TAATTTTGAGACACTCAAAAA
Found at i:4053196 original size:19 final size:19
Alignment explanation
Indices: 4053148--4053199 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4053138 TTATAAGTTC
*
4053148 TATTTTAATATTTAAAAAA
1 TATTTTAATATTAAAAAAA
**
4053167 TATTAAAATATTAAAAAAA
1 TATTTTAATATTAAAAAAA
*
4053186 TATTTTTATATTAA
1 TATTTTAATATTAA
4053200 TATTTTTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTTAATATTAAAAAAA
Found at i:4053203 original size:14 final size:15
Alignment explanation
Indices: 4053184--4053218 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
4053174 ATATTAAAAA
4053184 AATATTTTTAT-ATT
1 AATATTTTTATAATT
4053198 AATATTTTTATAATT
1 AATATTTTTATAATT
4053213 AA-ATTT
1 AATATTT
4053219 AAATATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATATTTTTATAATT
Found at i:4053491 original size:43 final size:43
Alignment explanation
Indices: 4053427--4053526 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
4053417 AAAATGAGAA
* * *
4053427 ACAGATTTATATTCTTAACGTTATATTGGATTTATATGGAAAT
1 ACAGATTTATATTCATAACGTTAAATTGGATTTATAAGGAAAT
* *
4053470 ACAGATTTATATTCATGACGTTAAATTGGCTTTATAAGGAAAT
1 ACAGATTTATATTCATAACGTTAAATTGGATTTATAAGGAAAT
4053513 ACAGATTTATATTC
1 ACAGATTTATATTC
4053527 TTAAGATGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (43 bp):
ACAGATTTATATTCATAACGTTAAATTGGATTTATAAGGAAAT
Found at i:4053634 original size:59 final size:53
Alignment explanation
Indices: 4053536--4053647 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 53
4053526 CTTAAGATGA
*
4053536 GGTTTTGCTTTCTGTTCTTAACGTTACTTTACATGGAAACGAAATTAAAGCTT
1 GGTTTTGCTTCCTGTTCTTAACGTTACTTTACATGGAAACGAAATTAAAGCTT
4053589 GGTTTTGCTTCCTGTTCTTAACGTTAAATTGGCTTTACATGGAAACGAAATTAAAGCTT
1 GGTTTTGCTTCCTGTTCTTAACGTT--A----CTTTACATGGAAACGAAATTAAAGCTT
4053648 TCTAAGGTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
53 24 0.46
55 1 0.02
59 27 0.52
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (53 bp):
GGTTTTGCTTCCTGTTCTTAACGTTACTTTACATGGAAACGAAATTAAAGCTT
Found at i:4054221 original size:3 final size:3
Alignment explanation
Indices: 4054213--4054252 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4054203 ATCAAATTGC
4054213 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4054253 CTCAAATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4057846 original size:21 final size:21
Alignment explanation
Indices: 4057820--4057928 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
4057810 AAAACTATTA
*
4057820 CAAAATTATATTAAAAGTTAC
1 CAAAATTATATTAAAAGTTAT
* *
4057841 CAAAA-TATATCAAAAGTTTT
1 CAAAATTATATTAAAAGTTAT
* *
4057861 TAAAATTATATTAATAGTTAT
1 CAAAATTATATTAAAAGTTAT
* * *
4057882 TAAAATTATA-TCAATGATTAT
1 CAAAATTATATTAAAAG-TTAT
* *
4057903 TAAAATTATATTAAATGTTAT
1 CAAAATTATATTAAAAGTTAT
*
4057924 AAAAA
1 CAAAA
4057929 ATTGTCAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 19 0.26
21 49 0.67
22 5 0.07
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
CAAAATTATATTAAAAGTTAT
Found at i:4057866 original size:41 final size:42
Alignment explanation
Indices: 4057821--4057922 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
4057811 AAACTATTAC
*
4057821 AAAATTATATTAAAAGTTACCAAAA-TATATCAAA-AGTTTTT
1 AAAATTATATTAAAAGTTACCAAAATTATATCAAAGA-TTATT
* ** *
4057862 AAAATTATATTAATAGTTATTAAAATTATATCAATGATTATT
1 AAAATTATATTAAAAGTTACCAAAATTATATCAAAGATTATT
*
4057904 AAAATTATATTAAATGTTA
1 AAAATTATATTAAAAGTTA
4057923 TAAAAAATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 22 0.42
42 29 0.56
43 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (42 bp):
AAAATTATATTAAAAGTTACCAAAATTATATCAAAGATTATT
Found at i:4057927 original size:41 final size:41
Alignment explanation
Indices: 4057821--4057927 Score: 121
Period size: 41 Copynumber: 2.6 Consensus size: 41
4057811 AAACTATTAC
* * *
4057821 AAAATTATATTAAAAGTTACCAAAATATATCAAAAGTTTTT
1 AAAATTATATTAAATGTTACTAAAATATATCAAAAGTTATT
* *
4057862 AAAATTATATT-AATAGTTATTAAAATTATATC-AATGATTATT
1 AAAATTATATTAAAT-GTTACTAAAA-TATATCAAAAG-TTATT
4057904 AAAATTATATTAAATGTTA-TAAAA
1 AAAATTATATTAAATGTTACTAAAA
4057928 AATTGTCAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
40 2 0.04
41 27 0.47
42 25 0.44
43 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (41 bp):
AAAATTATATTAAATGTTACTAAAATATATCAAAAGTTATT
Found at i:4057948 original size:32 final size:30
Alignment explanation
Indices: 4057904--4057962 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
4057894 AATGATTATT
* *
4057904 AAAATTATATTAAATGTTATAAAAAATTGTC
1 AAAATAATATTAAAGGTTA-AAAAAATTGTC
*
4057935 AAAATAATAATTAAAGGTTAAAATAATT
1 AAAATAAT-ATTAAAGGTTAAAAAAATT
4057963 ATATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (30 bp):
AAAATAATATTAAAGGTTAAAAAAATTGTC
Found at i:4057992 original size:20 final size:21
Alignment explanation
Indices: 4057967--4058012 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4057957 ATAATTATAT
* *
4057967 AAAATTGTA-TAAAGGTTATC
1 AAAATTATATTAAAGATTATC
*
4057987 AAAATTATATTAAATATTATC
1 AAAATTATATTAAAGATTATC
4058008 AAAAT
1 AAAAT
4058013 GTAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (21 bp):
AAAATTATATTAAAGATTATC
Found at i:4058012 original size:41 final size:42
Alignment explanation
Indices: 4057821--4058012 Score: 119
Period size: 42 Copynumber: 4.6 Consensus size: 42
4057811 AAACTATTAC
* * *
4057821 AAAATTATATTAAA-AGTTACCAAAA-TATATCAAAAGTTTTT
1 AAAATTATATTAAATA-TTATCAAAATTATATCAAAAATTATT
* **
4057862 AAAATTATATT-AATAGTTATTAAAATTATATCAATGATTATT
1 AAAATTATATTAAATA-TTATCAAAATTATATCAAAAATTATT
* * * * *
4057904 AAAATTATATTAAATGTTATAAAAAAT-TGTCAAAATAATAATT
1 AAAATTATATTAAATATTATCAAAATTATATC-AAA-AATTATT
* * * * * ** *
4057947 AAAGGTTAAAATAATTA-TAT-AAAATTGTAT-AAAGGTTATC
1 AAA-ATTATATTAAATATTATCAAAATTATATCAAAAATTATT
4057987 AAAATTATATTAAATATTATCAAAAT
1 AAAATTATATTAAATATTATCAAAAT
4058013 GTAAAAAAAT
Statistics
Matches: 114, Mismatches: 28, Indels: 18
0.71 0.17 0.11
Matches are distributed among these distances:
39 9 0.08
40 11 0.10
41 31 0.27
42 39 0.34
43 16 0.14
44 8 0.07
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (42 bp):
AAAATTATATTAAATATTATCAAAATTATATCAAAAATTATT
Found at i:4058091 original size:21 final size:21
Alignment explanation
Indices: 4058067--4058142 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
4058057 ATATTGAAAA
4058067 TTACCAAAATTATTTCATAGG
1 TTACCAAAATTATTTCATAGG
* *
4058088 TTACTAAAATTATATCCAGTA--
1 TTACCAAAATTAT-TTCA-TAGG
* *
4058109 TTACCAAAA-TAATTAATAGG
1 TTACCAAAATTATTTCATAGG
*
4058129 TTATCAAAGATTAT
1 TTACCAAA-ATTAT
4058143 AAAAACTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 9 0.22
21 21 0.51
22 5 0.12
23 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (21 bp):
TTACCAAAATTATTTCATAGG
Found at i:4058163 original size:21 final size:21
Alignment explanation
Indices: 4058130--4058232 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
4058120 ATTAATAGGT
4058130 TATC-AAAGATTATAAAAACTA
1 TATCAAAAG-TTATAAAAACTA
*
4058151 TATCAAAAGTTATCAAACACTA
1 TATCAAAAGTTAT-AAAAACTA
* * *
4058173 TTAT-AAATGTTATCAAAATTA
1 -TATCAAAAGTTATAAAAACTA
* * * *
4058194 TATTAAAAGTCATCAAAATTA
1 TATCAAAAGTTATAAAAACTA
*
4058215 TATCAAAAGTTACAAAAA
1 TATCAAAAGTTATAAAAA
4058233 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 3 0.04
21 42 0.63
22 19 0.28
23 3 0.04
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (21 bp):
TATCAAAAGTTATAAAAACTA
Found at i:4058520 original size:12 final size:12
Alignment explanation
Indices: 4058503--4058538 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
4058493 CAAAATTGTT
4058503 AAAATTATATTA
1 AAAATTATATTA
4058515 AAAATTATATTA
1 AAAATTATATTA
4058527 AAAATTATATTA
1 AAAATTATATTA
4058539 TATTTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTATATTA
Found at i:4058546 original size:24 final size:26
Alignment explanation
Indices: 4058503--4058565 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
4058493 CAAAATTGTT
*
4058503 AAAATTATATTAAAAATTATA-T-TA
1 AAAATTATATTATAAATTATACTATA
**
4058527 AAAATTATATTATATTTTATACTATA
1 AAAATTATATTATAAATTATACTATA
4058553 AAATATTAT-TTAT
1 AAA-ATTATATTAT
4058566 TTATAGTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 18 0.55
25 1 0.03
26 9 0.27
27 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATTATATTATAAATTATACTATA
Found at i:4058887 original size:21 final size:21
Alignment explanation
Indices: 4058863--4058965 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 21
4058853 TACATCAATG
*
4058863 TTATTAAAATTATATTAAAAG
1 TTATTAAAATTATATTAAAAA
*
4058884 TTATT-AAATTCATATAAAAAA
1 TTATTAAAATT-ATATTAAAAA
* * *
4058905 TTATCAAAA-CATATTTAAAA
1 TTATTAAAATTATATTAAAAA
* *
4058925 TTACTAAAATCATATTAAAAA
1 TTATTAAAATTATATTAAAAA
4058946 TTATTATATATATTATATTA
1 TTATTA-A-A-ATTATATTA
4058966 TATAAAAATA
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 20 0.31
21 32 0.49
22 4 0.06
23 1 0.02
24 8 0.12
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (21 bp):
TTATTAAAATTATATTAAAAA
Found at i:4059167 original size:22 final size:20
Alignment explanation
Indices: 4059126--4059177 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
4059116 TTTCATAACC
*
4059126 AAAAAATTTATGAAAGGTTA
1 AAAAAATTTATGAAACGTTA
*
4059146 AAAAAATTCATATTAAACGTTA
1 AAAAAATT--TATGAAACGTTA
**
4059168 TCAAAATTTA
1 AAAAAATTTA
4059178 CATAGAAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAAATTTATGAAACGTTA
Found at i:4059282 original size:21 final size:21
Alignment explanation
Indices: 4059243--4059379 Score: 111
Period size: 21 Copynumber: 6.5 Consensus size: 21
4059233 CATACATGAC
*
4059243 CAAAATTATATAAAAAAATTAT
1 CAAAATTATAT-TAAAAATTAT
*
4059265 CAATATTATATTAAAAATTAT
1 CAAAATTATATTAAAAATTAT
* *
4059286 TAAAATTATATTAAAAATCAT
1 CAAAATTATATTAAAAATTAT
*
4059307 CAAAATTATA-TAAAAAGCTATT
1 CAAAATTATATTAAAAA-TTA-T
*
4059329 C-AAATCATATTAAAGAA-TAT
1 CAAAATTATATTAAA-AATTAT
* * *
4059349 TAAAATCATA-TAAAAACTAT
1 CAAAATTATATTAAAAATTAT
* *
4059369 TAAAATCATAT
1 CAAAATTATAT
4059380 CAGATGTTAT
Statistics
Matches: 98, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.02
20 24 0.24
21 54 0.55
22 16 0.16
23 2 0.02
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.34
Consensus pattern (21 bp):
CAAAATTATATTAAAAATTAT
Found at i:4059315 original size:42 final size:40
Alignment explanation
Indices: 4059256--4059379 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 40
4059246 AATTATATAA
* * *
4059256 AAAAATTATCAATATTATATTAAAAATTATTAAAATTATATT
1 AAAAA-TATCAAAATTATA-TAAAAACTATTAAAATCATATT
*
4059298 AAAAATCATCAAAATTATATAAAAAGCTATTCAAATCATATT
1 AAAAAT-ATCAAAATTATATAAAAA-CTATTAAAATCATATT
* *
4059340 AAAGAATATTAAAATCATATAAAAACTATTAAAATCATAT
1 AAA-AATATCAAAATTATATAAAAACTATTAAAATCATAT
4059380 CAGATGTTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
41 21 0.29
42 48 0.67
43 3 0.04
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (40 bp):
AAAAATATCAAAATTATATAAAAACTATTAAAATCATATT
Found at i:4059354 original size:63 final size:63
Alignment explanation
Indices: 4059243--4059364 Score: 160
Period size: 63 Copynumber: 1.9 Consensus size: 63
4059233 CATACATGAC
* *
4059243 CAAAATTATATAAAAAAATTATCAATATTATATTAAAAATTATTAAAATTATATTAAAAATCAT
1 CAAAATTATATAAAAAAATTATCAATATCATATTAAAAATTATTAAAATCATA-TAAAAATCAT
**
4059307 CAAAATTATAT-AAAAAGCTATTCAA-ATCATATTAAAGAA-TATTAAAATCATATAAAAA
1 CAAAATTATATAAAAAAATTA-TCAATATCATATTAAA-AATTATTAAAATCATATAAAAA
4059365 CTATTAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
62 6 0.12
63 29 0.56
64 17 0.33
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (63 bp):
CAAAATTATATAAAAAAATTATCAATATCATATTAAAAATTATTAAAATCATATAAAAATCAT
Found at i:4059395 original size:41 final size:42
Alignment explanation
Indices: 4059283--4059398 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
4059273 TATTAAAAAT
* * *
4059283 TATTAAAATTATATTAAA-AATCATCAAAATTATATAAAAAGC
1 TATTAAAATCATATCAAAGAAT-ATCAAAATCATATAAAAAGC
* * *
4059325 TATTCAAATCATATTAAAGAATATTAAAATCATATAAAAA-C
1 TATTAAAATCATATCAAAGAATATCAAAATCATATAAAAAGC
* *
4059366 TATTAAAATCATATCAGATG-TTATCAAAATCAT
1 TATTAAAATCATATCA-AAGAATATCAAAATCAT
4059399 TCCTAAAGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 26 0.41
42 34 0.54
43 3 0.05
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (42 bp):
TATTAAAATCATATCAAAGAATATCAAAATCATATAAAAAGC
Found at i:4060009 original size:19 final size:20
Alignment explanation
Indices: 4059965--4060010 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
4059955 CTAATATTTC
*
4059965 ATTAATTTAATAAGAAAATTA
1 ATTAA-TTAAGAAGAAAATTA
*
4059986 A-TAATTAAGAATAAAA-TA
1 ATTAATTAAGAAGAAAATTA
4060004 ATTAATT
1 ATTAATT
4060011 TAGTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.14
19 15 0.68
20 3 0.14
21 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
ATTAATTAAGAAGAAAATTA
Found at i:4062975 original size:14 final size:15
Alignment explanation
Indices: 4062943--4062996 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 15
4062933 TTTAATAAAT
4062943 TATTTTTA-AATTAA
1 TATTTTTATAATTAA
4062957 TATTTTTATAATTAA
1 TATTTTTATAATTAA
* *
4062972 -ATTTATATAA-AAA
1 TATTTTTATAATTAA
*
4062985 TAATTTTATAAT
1 TATTTTTATAAT
4062997 AAATGAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 25 0.76
15 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTTTATAATTAA
Found at i:4062975 original size:28 final size:28
Alignment explanation
Indices: 4062920--4063000 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
4062910 CCCATTTTAC
*
4062920 TATATAAAAATATTTTAATAAATT--ATT
1 TATATAAAAATATTTTTAT-AATTAAATT
4062947 T-T-TAAATTAATATTTTTATAATTAAATT
1 TATATAAA--AATATTTTTATAATTAAATT
*
4062975 TATATAAAAATAATTTTATAA-TAAAT
1 TATATAAAAATATTTTTATAATTAAAT
4063001 GAATAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
25 4 0.09
26 5 0.11
27 16 0.35
28 16 0.35
29 1 0.02
30 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATATAAAAATATTTTTATAATTAAATT
Found at i:4063000 original size:15 final size:15
Alignment explanation
Indices: 4062913--4063000 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 15
4062903 CTCGAAACCC
4062913 ATTTTACTATATAAA-A
1 ATTTTA-TA-ATAAATA
*
4062929 ATATTT-TAATAAATT
1 AT-TTTATAATAAATA
*
4062944 ATTTT-TAAATTAATA
1 ATTTTAT-AATAAATA
*
4062959 TTTTTATAATTAAAT-
1 ATTTTATAA-TAAATA
*
4062974 -TTATATAA-AAATA
1 ATTTTATAATAAATA
4062987 ATTTTATAATAAAT
1 ATTTTATAATAAAT
4063001 GAATAAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.07
14 23 0.40
15 20 0.35
16 7 0.12
17 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTATAATAAATA
Found at i:4066000 original size:2 final size:2
Alignment explanation
Indices: 4065993--4066026 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4065983 TACTTTTCAC
4065993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4066027 CACTCATTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4066188 original size:27 final size:26
Alignment explanation
Indices: 4066135--4066210 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 26
4066125 TTTATTATTT
* *
4066135 TATTTAAATTTTTATATTTA-AATAAA
1 TATTTTAATTTTT-TATTTATATTAAA
4066161 T-TTTTAACTTTTTTATTTATATTCAAA
1 TATTTTAA-TTTTTTATTTATATT-AAA
*
4066188 TAATTTTAATTTTTAATTTATAT
1 T-ATTTTAATTTTTTATTTATAT
4066211 CGGAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 11 0.26
26 8 0.19
27 4 0.10
28 13 0.31
29 6 0.14
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTTTAATTTTTTATTTATATTAAA
Found at i:4066193 original size:30 final size:30
Alignment explanation
Indices: 4066145--4066257 Score: 124
Period size: 30 Copynumber: 3.8 Consensus size: 30
4066135 TATTTAAATT
*
4066145 TTTATATTTAAATAAATTTTTAACTTTTTTA
1 TTTATATTCAAATAAATTTTTAA-TTTTTTA
*
4066176 TTTATATTCAAAT-AA-TTTTAATTTTTAA
1 TTTATATTCAAATAAATTTTTAATTTTTTA
* * *
4066204 TTTATA-TCGGAATAAATTTTTAATCTTCTA
1 TTTATATTC-AAATAAATTTTTAATTTTTTA
* *
4066234 TTCATATCCAAATAAATTTTTAAT
1 TTTATATTCAAATAAATTTTTAAT
4066258 ATAAATCAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.03
28 15 0.22
29 8 0.12
30 31 0.45
31 13 0.19
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTATATTCAAATAAATTTTTAATTTTTTA
Found at i:4066773 original size:2 final size:2
Alignment explanation
Indices: 4066766--4066797 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4066756 TAAATATAAA
4066766 AT AT AT 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 AT AT AT
4066798 CATTCCTTCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4067403 original size:15 final size:16
Alignment explanation
Indices: 4067377--4067406 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4067367 AGATGTGAAT
4067377 ATAGATTTAAGTTATG
1 ATAGATTTAAGTTATG
4067393 ATAGA-TTAAGTTAT
1 ATAGATTTAAGTTAT
4067407 ATTTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (16 bp):
ATAGATTTAAGTTATG
Found at i:4067932 original size:22 final size:24
Alignment explanation
Indices: 4067898--4067941 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
4067888 AAATTTTAAA
4067898 TTTTAATATTTATAATTTTTTTAT
1 TTTTAATATTTATAATTTTTTTAT
4067922 TTTTAA-A-TTATAATTTTTTT
1 TTTTAATATTTATAATTTTTTT
4067942 GTACTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTAATATTTATAATTTTTTTAT
Found at i:4068810 original size:2 final size:2
Alignment explanation
Indices: 4068803--4068835 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4068793 TACTGCCTGA
4068803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4068836 AATACATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4069229 original size:21 final size:21
Alignment explanation
Indices: 4069205--4069260 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4069195 GTGATCTCAA
4069205 TATAATTTTATAATTATTATT
1 TATAATTTTATAATTATTATT
4069226 TATAA-TTT-TAATT-TTATT
1 TATAATTTTATAATTATTATT
* *
4069244 AATATTTATTATAATTA
1 TATAATT-TTATAATTA
4069261 ATCATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 5 0.17
21 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATAATTTTATAATTATTATT
Found at i:4069237 original size:27 final size:27
Alignment explanation
Indices: 4069207--4069259 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4069197 GATCTCAATA
4069207 TAATTTTA-TAAT-TATTATTTATAATTT
1 TAATTTTATTAATAT-TTA-TTATAATTT
4069234 TAATTTTATTAATATTTATTATAATT
1 TAATTTTATTAATATTTATTATAATT
4069260 AATCATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 16 0.67
28 7 0.29
29 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TAATTTTATTAATATTTATTATAATTT
Found at i:4069288 original size:30 final size:29
Alignment explanation
Indices: 4069246--4069309 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
4069236 ATTTTATTAA
* *
4069246 TATTTATTATAATTAATCAT-AATATTATT
1 TATTTATTATAATT-ATAATAAATACTATT
4069275 TATTTATTTATAATTATAATAAATACTATT
1 TATTTA-TTATAATTATAATAAATACTATT
4069305 TATTT
1 TATTT
4069310 GCAAGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTTATTATAATTATAATAAATACTATT
Found at i:4071625 original size:11 final size:11
Alignment explanation
Indices: 4071609--4071649 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4071599 GTTTAAATTT
4071609 AAAATATATTA
1 AAAATATATTA
*
4071620 AAAATAT-TAA
1 AAAATATATTA
4071630 AAAAT-TAATTA
1 AAAATAT-ATTA
4071641 AAAATATAT
1 AAAATATAT
4071650 GATAATCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 1 0.04
10 7 0.28
11 16 0.64
12 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATATATTA
Found at i:4073279 original size:3 final size:3
Alignment explanation
Indices: 4073271--4073299 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4073261 ATTAATCCTC
4073271 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4073300 TATTTACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4073626 original size:13 final size:13
Alignment explanation
Indices: 4073610--4073634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4073600 TACAAAAACC
4073610 AAGAAAAAAAAAA
1 AAGAAAAAAAAAA
4073623 AAGAAAAAAAAA
1 AAGAAAAAAAAA
4073635 TCAGTTGATG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAA
Found at i:4073891 original size:5 final size:5
Alignment explanation
Indices: 4073881--4073908 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4073871 GAAGCACTTT
4073881 GAGAA GAGAA GAGAA GAGAA GAGAA GAG
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAG
4073909 TGCAGTATAT
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:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:4074231 original size:17 final size:17
Alignment explanation
Indices: 4074211--4074244 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4074201 TTTCAAAAAG
*
4074211 AAAAGTAATTAAGTTAAA
1 AAAAG-AATTAACTTAAA
4074229 AAAAGAATTAACTTAA
1 AAAAGAATTAACTTAA
4074245 GAATTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAAGAATTAACTTAAA
Found at i:4077236 original size:57 final size:57
Alignment explanation
Indices: 4077116--4077258 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 57
4077106 TATAGTGAAC
* *
4077116 TTGAAAAAGCAATGATGAACTT--AAAAAAGCAAGGTGTTTGAAAAGATAATAAAGAA
1 TTGAAAAAGCAATGGTGAACTTGAAAAAAAG-AAGGTGTCTGAAAAGATAATAAAGAA
* *
4077172 TTGAAAAAAGCAATGGTGAACTTGAAAAAAAG-AGGTGTCTGAAAAGGTAATAAAGAGC
1 TTG-AAAAAGCAATGGTGAACTTGAAAAAAAGAAGGTGTCTGAAAAGATAATAAAGA-A
*
4077230 TT-AAAAAG-ATTATAGTGAACTTGAAAAAA
1 TTGAAAAAGCA--ATGGTGAACTTGAAAAAA
4077259 CAATGATGAG
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
55 1 0.01
56 9 0.12
57 57 0.75
58 2 0.03
59 7 0.09
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.22
Consensus pattern (57 bp):
TTGAAAAAGCAATGGTGAACTTGAAAAAAAGAAGGTGTCTGAAAAGATAATAAAGAA
Found at i:4077237 original size:77 final size:77
Alignment explanation
Indices: 4077156--4077313 Score: 176
Period size: 77 Copynumber: 2.1 Consensus size: 77
4077146 AAGGTGTTTG
* * *
4077156 AAAAGATAATAAAGAA-TTGAAAAAAGCAATGGTGAACTTGAAAAA-AAGAGGTGTCTGAAAAGG
1 AAAAGATAATAAAGAACTTGAAAAAA-CAATGATGAACTT-AAAAAGAAGAAGTGTCTGAAAAGA
4077219 TAATAAAGAGCTTA
64 TAATAAAGAGCTTA
* ** * * * *
4077233 AAAAGATTATAGTGAACTTGAAAAAACAATGATGAGCTTAAAAAGACGAAGTGTTTTAAAAGATA
1 AAAAGATAATAAAGAACTTGAAAAAACAATGATGAACTTAAAAAGAAGAAGTGTCTGAAAAGATA
* *
4077298 ATGAAGAGTTTA
66 ATAAAGAGCTTA
4077310 AAAA
1 AAAA
4077314 AACAATGGTG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
76 5 0.07
77 53 0.79
78 9 0.13
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (77 bp):
AAAAGATAATAAAGAACTTGAAAAAACAATGATGAACTTAAAAAGAAGAAGTGTCTGAAAAGATA
ATAAAGAGCTTA
Found at i:4077313 original size:20 final size:20
Alignment explanation
Indices: 4077253--4077336 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
4077243 AGTGAACTTG
* *
4077253 AAAAAACAATGATGAGCTTA
1 AAAAAACAATGAAGAGTTTA
* * *
4077273 AAAAGAC---GAAGTGTTTT
1 AAAAAACAATGAAGAGTTTA
* *
4077290 AAAAGATAATGAAGAGTTTA
1 AAAAAACAATGAAGAGTTTA
**
4077310 AAAAAACAATGGTGAGTTTA
1 AAAAAACAATGAAGAGTTTA
4077330 AAAAAAC
1 AAAAAAC
4077337 GAGGTGCTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
17 12 0.24
20 37 0.76
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.23
Consensus pattern (20 bp):
AAAAAACAATGAAGAGTTTA
Found at i:4077314 original size:57 final size:57
Alignment explanation
Indices: 4077228--4077372 Score: 166
Period size: 57 Copynumber: 2.5 Consensus size: 57
4077218 GTAATAAAGA
* ** * * *
4077228 GCTTAAAAAGATTATAGTGAACTTGAAAAAACAATGATGAGCTTAAAAAGACGAAGT
1 GCTTAAAAAGATAATACAGAGCTTAAAAAAACAATGATGAGCTTAAAAAAACGAAGT
* * * * * *
4077285 GTTTTAAAAGATAATGA-AGAGTTTAAAAAAACAATGGTGAGTTTAAAAAAACGAGGT
1 GCTTAAAAAGATAAT-ACAGAGCTTAAAAAAACAATGATGAGCTTAAAAAAACGAAGT
4077342 GCTTAAAAAGATAATACAGAGCTTAAAAAAA
1 GCTTAAAAAGATAATACAGAGCTTAAAAAAA
4077373 TTATAGTGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
56 1 0.01
57 70 0.97
58 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (57 bp):
GCTTAAAAAGATAATACAGAGCTTAAAAAAACAATGATGAGCTTAAAAAAACGAAGT
Found at i:4077351 original size:134 final size:134
Alignment explanation
Indices: 4077106--4077412 Score: 433
Period size: 134 Copynumber: 2.3 Consensus size: 134
4077096 GTAATAGAAC
*
4077106 TATAGTGAACTTGAAAAAGCAATGATGAACTTAAAAAAGCAAGGTGTTTGAAAAGATAATAAAGA
1 TATAGTGAACTTGAAAAAGCAATGATGAGCTTAAAAAAGCAAGGTGTTTGAAAAGATAATAAAGA
* * *
4077171 ATTGAAAAAAGCAATGGTGAACTTGAAAAAAAGAGGTGTCTGAAAAGGTAATAAAGAGCTTAAAA
66 ATTGAAAAAAACAATGGTGAACTTGAAAAAAAGAGGTGTCTAAAAAGATAATAAAGAGCTTAAAA
*
4077236 AGAT
131 AAAT
* * *
4077240 TATAGTGAACTTGAAAAAACAATGATGAGCTT-AAAAAGACGAA-GTGTTTTAAAAGATAATGAA
1 TATAGTGAACTTGAAAAAGCAATGATGAGCTTAAAAAAG-C-AAGGTGTTTGAAAAGATAATAAA
* * * * *
4077303 GAGTTTAAAAAAACAATGGTG-AGTTTAAAAAAACGAGGTG-CTTAAAAAGATAATACAGAGCTT
64 GAATTGAAAAAAACAATGGTGAACTTGAAAAAAA-GAGGTGTC-TAAAAAGATAATAAAGAGCTT
4077366 AAAAAAAT
127 AAAAAAAT
4077374 TATAGTGAACTTGAAAAAGCAATGATGAGCTTAAAAAAG
1 TATAGTGAACTTGAAAAAGCAATGATGAGCTTAAAAAAG
4077413 TGAAGTTTAT
Statistics
Matches: 154, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
133 17 0.11
134 129 0.84
135 8 0.05
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (134 bp):
TATAGTGAACTTGAAAAAGCAATGATGAGCTTAAAAAAGCAAGGTGTTTGAAAAGATAATAAAGA
ATTGAAAAAAACAATGGTGAACTTGAAAAAAAGAGGTGTCTAAAAAGATAATAAAGAGCTTAAAA
AAAT
Found at i:4077391 original size:57 final size:58
Alignment explanation
Indices: 4077253--4077392 Score: 135
Period size: 57 Copynumber: 2.4 Consensus size: 58
4077243 AGTGAACTTG
* * * *
4077253 AAAAAACAAT-GATGAGCTT-AAAAAGACGAAGTGTTTTAAAAGATAATGAAGAGTTTA
1 AAAAAACAATAG-TGAACTTAAAAAAGACGAAGTGCTTAAAAAGATAATGAAGAGCTTA
* ** *
4077310 AAAAAACAATGGTGAGTTTAAAAAA-ACGAGGTGCTTAAAAAGATAAT-ACAGAGCTTA
1 AAAAAACAATAGTGAACTTAAAAAAGACGAAGTGCTTAAAAAGATAATGA-AGAGCTTA
** *
4077367 AAAAAATTATAGTGAACTTGAAAAAG
1 AAAAAACAATAGTGAACTTAAAAAAG
4077393 CAATGATGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.01
57 61 0.90
58 6 0.09
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (58 bp):
AAAAAACAATAGTGAACTTAAAAAAGACGAAGTGCTTAAAAAGATAATGAAGAGCTTA
Found at i:4078638 original size:13 final size:14
Alignment explanation
Indices: 4078613--4078641 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4078603 AAAACAAAAA
4078613 TAAATATTTAAATT
1 TAAATATTTAAATT
4078627 TAAATA-TTAAATT
1 TAAATATTTAAATT
4078640 TA
1 TA
4078642 GGGTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATATTTAAATT
Found at i:4079011 original size:3 final size:3
Alignment explanation
Indices: 4078997--4079036 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
4078987 AGCTCTAAGC
4078997 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4079037 AAGACCAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4080775 original size:14 final size:14
Alignment explanation
Indices: 4080756--4080786 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4080746 TTGCCTATTG
4080756 AAAGCTTAAGAAGC
1 AAAGCTTAAGAAGC
4080770 AAAGCTTAAGAAGC
1 AAAGCTTAAGAAGC
4080784 AAA
1 AAA
4080787 ACCGAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (14 bp):
AAAGCTTAAGAAGC
Found at i:4087156 original size:19 final size:20
Alignment explanation
Indices: 4087115--4087155 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4087105 ATTGCATGTC
4087115 TTATTTTGTAAAATTAATTT
1 TTATTTTGTAAAATTAATTT
*
4087135 TTATTTTTTAAATATT-ATTT
1 TTATTTTGTAAA-ATTAATTT
4087155 T
1 T
4087156 AAAAACTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTGTAAAATTAATTT
Found at i:4087407 original size:21 final size:21
Alignment explanation
Indices: 4087382--4087421 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4087372 AATTTAACGT
4087382 AAATTATTATTTA-TTAATTAA
1 AAATTATT-TTTATTTAATTAA
4087403 AAATTATTTTTATTTAATT
1 AAATTATTTTTATTTAATT
4087422 TAATTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTATTTTTATTTAATTAA
Found at i:4087766 original size:17 final size:17
Alignment explanation
Indices: 4087744--4087869 Score: 64
Period size: 17 Copynumber: 7.3 Consensus size: 17
4087734 TAATATCTCA
*
4087744 TATATTTATATTTTATT
1 TATATTTATATTATATT
4087761 TATA-TTATAATTATATT
1 TATATTTAT-ATTATATT
*
4087778 TATGATATTATA-TATTACT
1 TAT-AT-TTATATTA-TATT
* *
4087797 AATAATTTA-AATATATT
1 TAT-ATTTATATTATATT
*
4087814 AATTATTTATATTATA-T
1 TA-TATTTATATTATATT
* * *
4087831 AATTTTTGATA-TATTTT
1 TATATTT-ATATTATATT
**
4087848 TATATTTATATCGTATT
1 TATATTTATATTATATT
4087865 TATAT
1 TATAT
4087870 CATATTTAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.16
17 45 0.53
18 14 0.16
19 8 0.09
20 4 0.05
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TATATTTATATTATATT
Found at i:4087810 original size:25 final size:26
Alignment explanation
Indices: 4087757--4087857 Score: 72
Period size: 27 Copynumber: 4.0 Consensus size: 26
4087747 ATTTATATTT
*
4087757 TATTTATATTATAATTATATTTATGA
1 TATTTATATTATAATTATATTTATAA
4087783 TATTATATATTACTAA-TA-ATTTA-AA
1 TATT-TATATTA-TAATTATATTTATAA
4087808 TATATTA-ATTAT--TTATATTATATAA
1 TAT-TTATATTATAATTATATT-TATAA
* **
4087833 TTTTTGATA-TATTTTTATATTTATA
1 TATTT-ATATTATAATTATATTTATA
4087858 TCGTATTTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
22 2 0.03
23 4 0.06
24 8 0.13
25 14 0.23
26 15 0.24
27 16 0.26
28 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTTATATTATAATTATATTTATAA
Found at i:4088818 original size:16 final size:16
Alignment explanation
Indices: 4088770--4088829 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
4088760 ATAGAGAATT
*
4088770 TAAATATTCAATAT-A
1 TAAATATTAAATATAA
*
4088785 T-AATGTTAAA-AGTAAA
1 TAAATATTAAATA-T-AA
4088801 TAAATATTAAATATAA
1 TAAATATTAAATATAA
*
4088817 TAAATATTTAATA
1 TAAATATTAAATA
4088830 AAAATATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 1 0.03
14 8 0.22
15 1 0.03
16 16 0.44
17 9 0.25
18 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATATTAAATATAA
Found at i:4089636 original size:2 final size:2
Alignment explanation
Indices: 4089629--4089653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4089619 TTACAGTCTC
4089629 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 A
4089654 ATTTCCCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4090785 original size:2 final size:2
Alignment explanation
Indices: 4090780--4090821 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4090770 AAATTTTTTA
4090780 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
4090822 CAAGAGACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4091703 original size:16 final size:18
Alignment explanation
Indices: 4091679--4091715 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
4091669 ACATAATTGC
4091679 TTTTCTTTTTT-C-TTTT
1 TTTTCTTTTTTGCATTTT
*
4091695 TTTTTTTTTTTGCATTTT
1 TTTTCTTTTTTGCATTTT
4091713 TTT
1 TTT
4091716 AAAGATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTCTTTTTTGCATTTT
Found at i:4093575 original size:6 final size:6
Alignment explanation
Indices: 4093532--4093573 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
4093522 TGGTGATGAA
* * *
4093532 GAAGAA GAAGAA GAAGAT GAAGAT GAAGAT GAAGAT AAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
4093574 AATGGCTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.12
Consensus pattern (6 bp):
GAAGAT
Found at i:4099124 original size:14 final size:16
Alignment explanation
Indices: 4099107--4099138 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4099097 TTTAATTTTA
4099107 TTTA-TTAA-AAATAT
1 TTTATTTAATAAATAT
4099121 TTTATTTAATAAATAT
1 TTTATTTAATAAATAT
4099137 TT
1 TT
4099139 AAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 4 0.25
16 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATTTAATAAATAT
Found at i:4099148 original size:14 final size:14
Alignment explanation
Indices: 4099129--4099168 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4099119 ATTTTATTTA
4099129 ATAAATATTTAAAT
1 ATAAATATTTAAAT
**
4099143 ATAAATATAAAAAT
1 ATAAATATTTAAAT
4099157 ATAAAT-TTTAAA
1 ATAAATATTTAAA
4099169 AAATATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATATTTAAAT
Found at i:4099157 original size:26 final size:26
Alignment explanation
Indices: 4099129--4099182 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
4099119 ATTTTATTTA
4099129 ATAAATATTTAAATATAA-ATATAAAAAT
1 ATAAAT-TTTAAA-A-AATATATAAAAAT
4099157 ATAAATTTTAAAAAATATATAAAAAT
1 ATAAATTTTAAAAAATATATAAAAAT
4099183 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.08
26 11 0.44
27 6 0.24
28 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAATTTTAAAAAATATATAAAAAT
Found at i:4105770 original size:34 final size:34
Alignment explanation
Indices: 4105728--4105838 Score: 111
Period size: 34 Copynumber: 3.2 Consensus size: 34
4105718 CATTATCTCC
4105728 TATCATATTTATTATATTATATTATAATTAATAAA
1 TATCATATTTATTATATTATATTATAATTAA-AAA
* * *
4105763 TAT-ATATTAATATATATTA-ATTATATTTAAACA
1 TATCATATTTAT-TATATTATATTATAATTAAAAA
* *
4105796 TATCAT-TTTATTATATTATTTTTATATTTATAAAA
1 TATCATATTTATTATATTA-TATTATAATTA-AAAA
*
4105831 TATTATAT
1 TATCATAT
4105839 ATTCATGTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
32 7 0.11
33 9 0.14
34 28 0.44
35 18 0.29
36 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (34 bp):
TATCATATTTATTATATTATATTATAATTAAAAA
Found at i:4114163 original size:13 final size:13
Alignment explanation
Indices: 4114147--4114176 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4114137 TTTTTTTTAA
4114147 ATATTTATATTTG
1 ATATTTATATTTG
4114160 ATATTTATATTTG
1 ATATTTATATTTG
4114173 ATAT
1 ATAT
4114177 ATATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:4114188 original size:10 final size:11
Alignment explanation
Indices: 4114152--4114189 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
4114142 TTTAAATATT
4114152 TATATTTGATA
1 TATATTTGATA
4114163 TTTATATTTGATA
1 --TATATTTGATA
4114176 TATATTT-ATA
1 TATATTTGATA
4114186 TATA
1 TATA
4114190 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.28
11 7 0.28
13 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (11 bp):
TATATTTGATA
Found at i:4114479 original size:11 final size:13
Alignment explanation
Indices: 4114448--4114487 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
4114438 AACTTGAATT
4114448 ATTATTTATAATA
1 ATTATTTATAATA
*
4114461 ATT-TTT-TAAAA
1 ATTATTTATAATA
4114472 ATTATTTAT-ATA
1 ATTATTTATAATA
4114484 ATTA
1 ATTA
4114488 AATTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 7 0.30
12 12 0.52
13 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATTTATAATA
Found at i:4114493 original size:27 final size:28
Alignment explanation
Indices: 4114444--4114507 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
4114434 TAATAACTTG
* *
4114444 AATTATTATTTATAAT-AATTTTTTAAA
1 AATTATTATATATAATAAATTTTATAAA
4114471 AATTATT-TATATAATTAAATTTTAATAAA
1 AATTATTATATATAA-TAAATTTT-ATAAA
4114500 AATT-TTAT
1 AATTATTAT
4114508 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 6 0.19
27 8 0.26
28 8 0.26
29 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AATTATTATATATAATAAATTTTATAAA
Found at i:4114764 original size:2 final size:2
Alignment explanation
Indices: 4114757--4114790 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4114747 GTTAAAACTC
4114757 AT AT AT AT 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 AT AT AT AT
4114791 CGGAATTTCC
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):
AT
Found at i:4115426 original size:3 final size:3
Alignment explanation
Indices: 4115418--4115453 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4115408 ACGAGACATT
*
4115418 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4115454 CCTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:4119020 original size:2 final size:2
Alignment explanation
Indices: 4119009--4119054 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4118999 TATCTGTCAC
4119009 AT AT -T AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
4119050 AT AT A
1 AT AT A
4119055 CTTTTTATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.