Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 19 of 32
Found at i:3007885 original size:34 final size:33
Alignment explanation
Indices: 3007842--3007907 Score: 123
Period size: 34 Copynumber: 2.0 Consensus size: 33
3007832 AAAAATAGGA
3007842 ACAAAAATGTTAGCTCAATAGTTTTTCTCTCTT
1 ACAAAAATGTTAGCTCAATAGTTTTTCTCTCTT
3007875 ACAAACAATGTTAGCTCAATAGTTTTTCTCTCT
1 ACAAA-AATGTTAGCTCAATAGTTTTTCTCTCT
3007908 AATATCACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (33 bp):
ACAAAAATGTTAGCTCAATAGTTTTTCTCTCTT
Found at i:3008750 original size:17 final size:16
Alignment explanation
Indices: 3008727--3008766 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3008717 AATATATTAA
3008727 AATATAATATAAAATAT
1 AATATAATATAAAA-AT
* *
3008744 TATATAATTTAAAAAT
1 AATATAATATAAAAAT
3008760 AATATAA
1 AATATAA
3008767 ATTATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:3009067 original size:13 final size:14
Alignment explanation
Indices: 3009046--3009078 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3009036 TTATTCAATC
*
3009046 ATAAATAAAAAAA-
1 ATAAGTAAAAAAAG
3009059 ATAAGTAAAAAAAG
1 ATAAGTAAAAAAAG
3009073 ATAAGT
1 ATAAGT
3009079 TTTAAGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
ATAAGTAAAAAAAG
Found at i:3010152 original size:20 final size:20
Alignment explanation
Indices: 3010078--3010152 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 20
3010068 ATTTATTTGG
*
3010078 TAAATTTAATT-TAAATTGAAT
1 TAAATTTAATTAT-AATT-ATT
3010099 T-AATTTAAGTTA-AATT-TT
1 TAAATTTAA-TTATAATTATT
*
3010117 TAATATTT-ATAAATAATTATT
1 TAA-ATTTAAT-TATAATTATT
3010138 TAAATTTAATTATAA
1 TAAATTTAATTATAA
3010153 AAATATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 17
0.68 0.05 0.27
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 27 0.63
21 10 0.23
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TAAATTTAATTATAATTATT
Found at i:3010196 original size:13 final size:13
Alignment explanation
Indices: 3010170--3010216 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3010160 TAATTATTAA
3010170 TATAAAATAATTT
1 TATAAAATAATTT
*
3010183 TATAATAT-ATTT
1 TATAAAATAATTT
*
3010195 T-TAATATAATTGT
1 TATAAAATAATT-T
3010208 TATAAAATA
1 TATAAAATA
3010217 CGTATGGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 8 0.28
13 9 0.31
14 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TATAAAATAATTT
Found at i:3010605 original size:27 final size:30
Alignment explanation
Indices: 3010575--3010633 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
3010565 AAATTTTTAA
*
3010575 AATATTC-AATAAT-AAAATCCT-TTAATT
1 AATATTCTAATAATGAAAAACCTGTTAATT
*
3010602 AATATTCTAATGATGAAAAACCTGTTAATT
1 AATATTCTAATAATGAAAAACCTGTTAATT
3010632 AA
1 AA
3010634 CTGATAGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 5 0.19
29 7 0.26
30 8 0.30
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (30 bp):
AATATTCTAATAATGAAAAACCTGTTAATT
Found at i:3010782 original size:2 final size:2
Alignment explanation
Indices: 3010775--3010830 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3010765 TTTACAGTCA
3010775 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
3010817 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3010831 GTATGTCCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3011032 original size:25 final size:25
Alignment explanation
Indices: 3010990--3011038 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3010980 TTATATAATT
3010990 TTATATGTTATTAATAAATTAAATAA
1 TTATATGTTATTAATAAA-TAAATAA
*
3011016 TTATAT-TTATTAGTAAATAAATA
1 TTATATGTTATTAATAAATAAATA
3011039 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
TTATATGTTATTAATAAATAAATAA
Found at i:3011150 original size:22 final size:20
Alignment explanation
Indices: 3011104--3011160 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
3011094 TACTAGATCC
* *
3011104 ATTATCAATATATAATTATAT
1 ATTAT-AATATATAAATATAA
3011125 ATTAGTAATATATCAAATATAA
1 ATTA-TAATATAT-AAATATAA
3011147 ATTATATATATATA
1 ATTATA-ATATATA
3011161 TTTAAGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTATAATATATAAATATAA
Found at i:3011234 original size:2 final size:2
Alignment explanation
Indices: 3011227--3011254 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3011217 AATATTTATC
3011227 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
3011255 GGATATGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3011718 original size:21 final size:22
Alignment explanation
Indices: 3011689--3011731 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3011679 AAAGCTCGTA
3011689 AAATATTTTTATATT-AATTTT
1 AAATATTTTTATATTCAATTTT
*
3011710 AAATTTTTTTATATTCAATTTT
1 AAATATTTTTATATTCAATTTT
3011732 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
AAATATTTTTATATTCAATTTT
Found at i:3012347 original size:19 final size:19
Alignment explanation
Indices: 3012311--3012348 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3012301 TATTTAATAA
3012311 TAAAAATATTTTAATATTAG
1 TAAAAATATTTT-ATATTAG
3012331 TAAAAATAATTTT-TATTA
1 TAAAAAT-ATTTTATATTA
3012349 AATTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAAAATATTTTATATTAG
Found at i:3012506 original size:27 final size:27
Alignment explanation
Indices: 3012418--3012506 Score: 63
Period size: 28 Copynumber: 3.2 Consensus size: 27
3012408 AATTTAATTC
* * *
3012418 AATTTATAAATATTTTATTATGAT-TATA
1 AATTTATTAATA-ATTATTATAATATA-A
* * ** *
3012446 AATTTTTTAAGTAAATATTATTTTATTA
1 AATTTATTAA-TAATTATTATAATATAA
*
3012474 AGTTTATTAATAATTATTATAATATAA
1 AATTTATTAATAATTATTATAATATAA
3012501 AATTTA
1 AATTTA
3012507 AATTAAAATA
Statistics
Matches: 45, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
27 18 0.40
28 24 0.53
29 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
AATTTATTAATAATTATTATAATATAA
Found at i:3012552 original size:3 final size:3
Alignment explanation
Indices: 3012539--3012575 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3012529 AATTAAACCT
* *
3012539 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3012576 CAATTCTCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3012945 original size:4 final size:4
Alignment explanation
Indices: 3012936--3012980 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
3012926 AAAGAAAAAT
* * * *
3012936 AAAG AAAG AAAG AAAG AAAG AAAG AGAG AGAG AGAG AGAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
3012981 GAGAGTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3012981 original size:12 final size:12
Alignment explanation
Indices: 3012938--3012985 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3012928 AGAAAAATAA
*
3012938 AGAAAGAAAGAA
1 AGAAAGAAAGAG
3012950 AGAAAGAAAGAG
1 AGAAAGAAAGAG
* *
3012962 AGAGAGAGAGAG
1 AGAAAGAAAGAG
*
3012974 AGAAAGAGAGAG
1 AGAAAGAAAGAG
3012986 TCAACCGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAGAG
Found at i:3017696 original size:2 final size:2
Alignment explanation
Indices: 3017689--3017714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3017679 TTATTATACC
3017689 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
3017715 GTACACACAC
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:3021022 original size:16 final size:16
Alignment explanation
Indices: 3021003--3021040 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3020993 GAATTTTAAA
*
3021003 TAAATTTTTATAAATT
1 TAAATTTTAATAAATT
*
3021019 TAAA-TTTAATTAATT
1 TAAATTTTAATAAATT
3021034 TAAATTT
1 TAAATTT
3021041 ATATTTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTTAATAAATT
Found at i:3021029 original size:21 final size:21
Alignment explanation
Indices: 3020997--3021058 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3020987 TTAATTGAAT
* *
3020997 TTTAAA-TAAATTTTTATAAA
1 TTTAAATTTAATTATTATAAA
3021017 TTTAAATTTAATTAATT-TAAA
1 TTTAAATTTAATT-ATTATAAA
* *
3021038 TTTATATTTAATCATTATAAA
1 TTTAAATTTAATTATTATAAA
3021059 ATATTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.26
21 24 0.69
22 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAATTTAATTATTATAAA
Found at i:3021092 original size:35 final size:34
Alignment explanation
Indices: 3021032--3021097 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
3021022 ATTTAATTAA
*
3021032 TTTAAATTTATATTTAATCATTATAAAATATTTTC
1 TTTAAATTTATATTTAATAATTAT-AAATATTTTC
3021067 TTTAAATTTA-ATTATAA-AATATATAAATATT
1 TTTAAATTTATATT-TAATAAT-TATAAATATT
3021098 AATAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 12 0.43
35 16 0.57
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (34 bp):
TTTAAATTTATATTTAATAATTATAAATATTTTC
Found at i:3021114 original size:21 final size:21
Alignment explanation
Indices: 3021067--3021117 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3021057 AAATATTTTC
3021067 TTTAAATTTAATTATAAAATA
1 TTTAAATTTAATTATAAAATA
*
3021088 TATAAATATTAA-TA-AAAATA
1 TTTAAAT-TTAATTATAAAATA
3021108 TTTTAAATTT
1 -TTTAAATTT
3021118 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.31
21 14 0.54
22 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATTTAATTATAAAATA
Found at i:3021404 original size:2 final size:2
Alignment explanation
Indices: 3021397--3021428 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3021387 GTTGGACGTG
3021397 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3021429 GAGCACAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3021683 original size:24 final size:23
Alignment explanation
Indices: 3021646--3021716 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
3021636 TGATTATTGA
*
3021646 TATAATTTTT-TAAATTAAAAAT
1 TATATTTTTTATAAATTAAAAAT
3021668 TATATTTTATTATAAA-TAAAAAT
1 TATATTTT-TTATAAATTAAAAAT
* *
3021691 TTTATTTTTTAT--ATTTAAAAT
1 TATATTTTTTATAAATTAAAAAT
3021712 TATAT
1 TATAT
3021717 GATTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.02
21 10 0.24
22 11 0.26
23 16 0.38
24 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATTTTTTATAAATTAAAAAT
Found at i:3021688 original size:22 final size:22
Alignment explanation
Indices: 3021650--3021716 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
3021640 TATTGATATA
*
3021650 ATTTTTTA-AATTAAAAATTAT
1 ATTTTTTATAAATAAAAATTAT
*
3021671 ATTTTATTATAAATAAAAATTTT
1 ATTTT-TTATAAATAAAAATTAT
* *
3021694 ATTTTTTAT-ATTTAAAATTAT
1 ATTTTTTATAAATAAAAATTAT
3021715 AT
1 AT
3021717 GATTTAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 16 0.41
22 7 0.18
23 16 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTTATAAATAAAAATTAT
Found at i:3021721 original size:24 final size:23
Alignment explanation
Indices: 3021645--3021721 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 23
3021635 ATGATTATTG
*
3021645 ATATAATTTTTTAAATTAAAAATT
1 ATAT-ATTTTTTATATTAAAAATT
* *
3021669 ATAT-TTTATTATAAATAAAAATT
1 ATATATTTTTTAT-ATTAAAAATT
*
3021692 -T-TATTTTTTATATTTAAAATT
1 ATATATTTTTTATATTAAAAATT
3021713 ATATGATTT
1 ATAT-ATTT
3021722 AAAAGTTCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 9 0.21
22 15 0.36
23 10 0.24
24 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
ATATATTTTTTATATTAAAAATT
Found at i:3022445 original size:3 final size:3
Alignment explanation
Indices: 3022437--3022462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3022427 TTTGATGTAG
3022437 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3022463 AAAATGTATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3023017 original size:3 final size:3
Alignment explanation
Indices: 3023005--3023040 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3022995 TTTCATCTTC
3023005 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3023041 TATTTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3025320 original size:16 final size:16
Alignment explanation
Indices: 3025283--3025320 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3025273 TTTCTAAGCT
3025283 ATAAAAAAAAATTAAA
1 ATAAAAAAAAATTAAA
*
3025299 A-AAAAAAAGAATTCAA
1 ATAAAAAAA-AATTAAA
3025315 ATAAAA
1 ATAAAA
3025321 CTCAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
ATAAAAAAAAATTAAA
Found at i:3028291 original size:23 final size:24
Alignment explanation
Indices: 3028261--3028318 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
3028251 AATGGATATT
*
3028261 TTTTAAAATTAAA-TAATTATAAA
1 TTTTAAAATTAAATTAATTAAAAA
*
3028284 TTTTAAAAATAAATTAATTAAAAA
1 TTTTAAAATTAAATTAATTAAAAA
3028308 TATTTAAAATT
1 T-TTTAAAATT
3028319 TGATACTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 12 0.40
24 10 0.33
25 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTAAAATTAAATTAATTAAAAA
Found at i:3029328 original size:21 final size:22
Alignment explanation
Indices: 3029304--3029344 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3029294 TTATTATTAG
*
3029304 ATTAAAATTTATATA-AAATAT
1 ATTAAAATATATATATAAATAT
3029325 ATTAAAATATATATATAAAT
1 ATTAAAATATATATATAAAT
3029345 TATCGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAAATATATATATAAATAT
Found at i:3029432 original size:26 final size:26
Alignment explanation
Indices: 3029396--3029447 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3029386 TGAGTTTTGG
3029396 CCCTTGGCCGATGTCACTTGGGGTGT
1 CCCTTGGCCGATGTCACTTGGGGTGT
3029422 CCCTTGGCCGATGTCACTTGGGGTGT
1 CCCTTGGCCGATGTCACTTGGGGTGT
3029448 TTTCAGCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.27, G:0.35, T:0.31
Consensus pattern (26 bp):
CCCTTGGCCGATGTCACTTGGGGTGT
Found at i:3029441 original size:14 final size:14
Alignment explanation
Indices: 3029398--3029442 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3029388 AGTTTTGGCC
3029398 CTTGGCCGATGTCA
1 CTTGGCCGATGTCA
* *
3029412 CTTGG--GGTGTCC
1 CTTGGCCGATGTCA
3029424 CTTGGCCGATGTCA
1 CTTGGCCGATGTCA
3029438 CTTGG
1 CTTGG
3029443 GGTGTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.09, C:0.27, G:0.33, T:0.31
Consensus pattern (14 bp):
CTTGGCCGATGTCA
Found at i:3030743 original size:22 final size:21
Alignment explanation
Indices: 3030702--3030741 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3030692 AATAATTTTA
3030702 TTTAAATTTAATTATAAAATT
1 TTTAAATTTAATTATAAAATT
3030723 TTTAAATATTAA-TATAAAA
1 TTTAAAT-TTAATTATAAAA
3030742 ATAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATTTAATTATAAAATT
Found at i:3030745 original size:27 final size:26
Alignment explanation
Indices: 3030715--3030765 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3030705 AAATTTAATT
* *
3030715 ATAAAATTTTTAAATATTAATATAAAA
1 ATAAAA-TTTTAAATAATAAAATAAAA
*
3030742 ATAATATTTTAAATAATAAAATAA
1 ATAAAATTTTAAATAATAAAATAA
3030766 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATAAAATTTTAAATAATAAAATAAAA
Found at i:3030762 original size:20 final size:20
Alignment explanation
Indices: 3030739--3030777 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3030729 TATTAATATA
3030739 AAAATAATATTTTAAATAAT
1 AAAATAATATTTTAAATAAT
3030759 AAAATAATATTTTAAATAA
1 AAAATAATATTTTAAATAA
3030778 ATATCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATATTTTAAATAAT
Found at i:3033287 original size:5 final size:5
Alignment explanation
Indices: 3033279--3033313 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
3033269 TTAGGATAGG
3033279 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
3033314 GATTCCAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:3033878 original size:36 final size:36
Alignment explanation
Indices: 3033820--3033915 Score: 95
Period size: 38 Copynumber: 2.6 Consensus size: 36
3033810 TACATGAACC
**
3033820 AAATTAAATTTAAATTGAATTAGTTAATGA-GTTAGA
1 AAATTAAATTTAAATTG-ATTAGAGAATGACGTTAGA
* * *
3033856 GAATTTAATTTAAAATTGATTAGAGATTGACGGTTAGA
1 AAATTAAATTT-AAATTGATTAGAGAATGAC-GTTAGA
*
3033894 AAATTCAATTTGAAATTGATTA
1 AAATTAAATTT-AAATTGATTA
3033916 CGTGGCTAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 18 0.37
37 6 0.12
38 25 0.51
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.39
Consensus pattern (36 bp):
AAATTAAATTTAAATTGATTAGAGAATGACGTTAGA
Found at i:3034301 original size:13 final size:13
Alignment explanation
Indices: 3034283--3034307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3034273 TTATTTTTAC
3034283 TTCTAGAATAGTT
1 TTCTAGAATAGTT
3034296 TTCTAGAATAGT
1 TTCTAGAATAGT
3034308 CTCTCTTGTG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TTCTAGAATAGTT
Found at i:3038641 original size:38 final size:38
Alignment explanation
Indices: 3038599--3038702 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
3038589 GGTTGATGGT
* *
3038599 TAGAGAATTCAATTTGGAATTGGCTGGTAGCTAACGAC
1 TAGAGAATTAAATTTGAAATTGGCTGGTAGCTAACGAC
* * * ** *
3038637 TAGAGAATTTAATTTAAAATT-GATCGGTAGCTAATTAT
1 TAGAGAATTAAATTTGAAATTGGCT-GGTAGCTAACGAC
3038675 TAGAGAATTAAATTTGAAATTGGCTGGT
1 TAGAGAATTAAATTTGAAATTGGCTGGT
3038703 GGCAGGTGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 2 0.04
38 50 0.93
39 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.35
Consensus pattern (38 bp):
TAGAGAATTAAATTTGAAATTGGCTGGTAGCTAACGAC
Found at i:3039138 original size:11 final size:12
Alignment explanation
Indices: 3039122--3039151 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3039112 TCATTTACTT
3039122 TTTTATTTA-TA
1 TTTTATTTATTA
3039133 TTTTATTTATTA
1 TTTTATTTATTA
3039145 TTTTATT
1 TTTTATT
3039152 CACCTCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:3046477 original size:27 final size:27
Alignment explanation
Indices: 3046422--3046478 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3046412 GAAACTAGTT
* * **
3046422 TCATTATCACCATCAGAAATGCAGTAA
1 TCATCATCACCATCAGAAATCCAAAAA
*
3046449 TCATCATCACCATCAGAAGTCCAAAAA
1 TCATCATCACCATCAGAAATCCAAAAA
3046476 TCA
1 TCA
3046479 AGAGAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (27 bp):
TCATCATCACCATCAGAAATCCAAAAA
Found at i:3046656 original size:29 final size:28
Alignment explanation
Indices: 3046623--3046718 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 28
3046613 TTTTCCTTAT
* *
3046623 TACTGCTGCAATTGTTACATCATTGTTAC
1 TACTGCAGCCATTGTTACA-CATTGTTAC
* *
3046652 TACTGCAGCCATTGTTGCACCACTGTTAC
1 TACTGCAGCCATTGTTACA-CATTGTTAC
*
3046681 TACTGCAGCCACTGTTACACAATTGTTAC
1 TACTGCAGCCATTGTTACAC-ATTGTTAC
*
3046710 TACCGCAGC
1 TACTGCAGC
3046719 AAAAATAGGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (28 bp):
TACTGCAGCCATTGTTACACATTGTTAC
Found at i:3046819 original size:2 final size:2
Alignment explanation
Indices: 3046812--3046836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3046802 TCAATTCCAA
3046812 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3046837 TCTCAAAAGA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3049412 original size:21 final size:21
Alignment explanation
Indices: 3049382--3049422 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3049372 ATAATGTAAA
*
3049382 ATAAAAATATACATAATTTAT
1 ATAAAAATATAAATAATTTAT
* *
3049403 ATAAATATATAAATATTTTA
1 ATAAAAATATAAATAATTTA
3049423 AATATTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAAATATAAATAATTTAT
Found at i:3049568 original size:31 final size:31
Alignment explanation
Indices: 3049473--3049568 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
3049463 AAAAATAATA
* *
3049473 AAAATATAAATAAGTT-TAATA-ATTATATTT
1 AAAATATATATAA-TTATAATATAATATATTT
* * *
3049503 AAAATATATATAATTTTATATTATAAAATTTTT
1 AAAATATATATAA--TTATAATATAATATATTT
*
3049536 AAAATATATATTAA-TATAATATCATATATTT
1 AAAATATATA-TAATTATAATATAATATATTT
3049567 AA
1 AA
3049569 TATTTTATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
30 12 0.23
31 17 0.33
32 4 0.08
33 16 0.31
34 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
AAAATATATATAATTATAATATAATATATTT
Found at i:3049574 original size:55 final size:55
Alignment explanation
Indices: 3049515--3049618 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
3049505 AATATATATA
*
3049515 ATTTTATATTATAAAATTTTTA-AAATATATATTAATATAA-TATCATATATTTAAT
1 ATTTTATA-TATAAAATTTATATAAATATATATTAATATAACTAT-ATATATTTAAT
* * * *
3049570 ATTTTATATATTATATTTATATAATTATATATTCATATAACTATATATA
1 ATTTTATATATAAAATTTATATAAATATATATTAATATAACTATATATA
3049619 AAATTATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 10 0.24
55 29 0.69
56 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (55 bp):
ATTTTATATATAAAATTTATATAAATATATATTAATATAACTATATATATTTAAT
Found at i:3049577 original size:14 final size:15
Alignment explanation
Indices: 3049559--3049608 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
3049549 ATATAATATC
3049559 ATATATTTAATATTT
1 ATATATTTAATATTT
3049574 -TATATATT-ATATTT
1 ATATAT-TTAATATTT
* *
3049588 ATATAATTATATATTC
1 ATATATTTA-ATATTT
3049604 ATATA
1 ATATA
3049609 ACTATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 13 0.45
15 6 0.21
16 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATTTAATATTT
Found at i:3049597 original size:21 final size:21
Alignment explanation
Indices: 3049560--3049607 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3049550 TATAATATCA
*
3049560 TATATTTAATATTTTATATAT
1 TATATTTAATATATTATATAT
3049581 TATATTT-ATATAATTATATAT
1 TATATTTAATAT-ATTATATAT
3049602 TCATAT
1 T-ATAT
3049608 AACTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTAATATATTATATAT
Found at i:3049607 original size:16 final size:15
Alignment explanation
Indices: 3049509--3049617 Score: 62
Period size: 16 Copynumber: 7.0 Consensus size: 15
3049499 ATTTAAAATA
*
3049509 TATATAATTTTATAT
1 TATATAATTATATAT
* * *
3049524 TATAAAATT-TTTAA
1 TATATAATTATATAT
* *
3049538 AATATATATTAATATAA
1 TATATA-ATT-ATATAT
3049555 TATCATATATT-TAATAT
1 TAT-ATA-ATTAT-ATAT
*
3049572 TTTATATATTATAT-T
1 TATATA-ATTATATAT
3049587 TATATAATTATATAT
1 TATATAATTATATAT
*
3049602 TCATATAACTATATAT
1 T-ATATAATTATATAT
3049618 AAAATTATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
14 14 0.19
15 19 0.25
16 23 0.31
17 12 0.16
18 7 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATAATTATATAT
Found at i:3052545 original size:29 final size:29
Alignment explanation
Indices: 3052512--3052569 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3052502 ATTTTAGATA
3052512 GTTTTCTGATAGAAGAAAGGGAGGGCATT
1 GTTTTCTGATAGAAGAAAGGGAGGGCATT
*
3052541 GTTTTCTGATATAAGAAAGGGAGGGCATT
1 GTTTTCTGATAGAAGAAAGGGAGGGCATT
3052570 ACTGGTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (29 bp):
GTTTTCTGATAGAAGAAAGGGAGGGCATT
Found at i:3053740 original size:2 final size:2
Alignment explanation
Indices: 3053733--3053766 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3053723 ATTATTAATT
3053733 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
3053767 AGTAAAGGTA
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:3057503 original size:29 final size:27
Alignment explanation
Indices: 3057450--3057504 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
3057440 TATATAATAT
*
3057450 AATTTATTATAAAAATATATTATTTAA
1 AATTTATTATAAAAATATATAATTTAA
3057477 AATTTATTTAATAAAAAT-TAATAATTTA
1 AATTTA-TT-ATAAAAATAT-ATAATTTA
3057505 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 3 0.12
29 15 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTTATTATAAAAATATATAATTTAA
Found at i:3057509 original size:18 final size:17
Alignment explanation
Indices: 3057482--3057516 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3057472 TTTAAAATTT
3057482 ATTTAATAAAAATTAATA
1 ATTTAAT-AAAATTAATA
*
3057500 ATTTATTAAAATTAATA
1 ATTTAATAAAATTAATA
3057517 TAAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAATAAAATTAATA
Found at i:3057874 original size:22 final size:22
Alignment explanation
Indices: 3057809--3057889 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
3057799 TTAATTTAAA
** *
3057809 AATTTAAATTATTAAATAAATTA
1 AATTTAAA-TATTTTATAAATTT
3057832 AATTTAAATA--TTATAATATTT
1 AATTTAAATATTTTATAA-ATTT
3057853 AATTTAAATATTTTATAAATTT
1 AATTTAAATATTTTATAAATTT
3057875 AA-TTAAAT-TTTTATA
1 AATTTAAATATTTTATA
3057890 CTTAATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.21
21 19 0.37
22 8 0.15
23 14 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTAAATATTTTATAAATTT
Found at i:3057940 original size:6 final size:6
Alignment explanation
Indices: 3057931--3058115 Score: 54
Period size: 6 Copynumber: 31.0 Consensus size: 6
3057921 AAATAACTTT
* **
3057931 AATTTA AATTTA AACTTA AATTTA CACATAAA TAATTT- AATTTAA AATTT-
1 AATTTA AATTTA AATTTA AATTTA -A-ATTTA -AATTTA AATTT-A AATTTA
* * *
3057981 AATTT- AATTTT AA-TAA AATTT- AATTAA AATTT- --TTTAAA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A AATTTA
* ** * *
3058025 ACTTTTA TTTTATA AATTTTA AAATAA AATTT- AA-TTA AATTTA AA-TTA
1 A-ATTTA AATT-TA AA-TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
3058073 AATTTTTA AATTTA AATATTA AA--TA TATTTA AATTAA AATTTA
1 AA--TTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA
3058116 TTATTAAACT
Statistics
Matches: 132, Mismatches: 24, Indels: 46
0.65 0.12 0.23
Matches are distributed among these distances:
3 3 0.02
4 5 0.04
5 31 0.23
6 56 0.42
7 23 0.17
8 14 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:3057990 original size:22 final size:22
Alignment explanation
Indices: 3057963--3058115 Score: 70
Period size: 21 Copynumber: 6.9 Consensus size: 22
3057953 TACACATAAA
3057963 TAATTTAATTTAAAATTTAATT
1 TAATTTAATTTAAAATTTAATT
3057985 TAATTTTAA--TAAAATTTAATT
1 TAA-TTTAATTTAAAATTTAATT
*
3058006 AAAATTT--TTTAAAAATTTAACTTT
1 -TAATTTAATTT-AAAATTTAA--TT
* **
3058030 TATTTTATAAATTTTAAAATAAAATT
1 TA-ATT-T-AA-TTTAAAATTTAATT
* *
3058056 TAATTAAATTT-AAATTAAATT
1 TAATTTAATTTAAAATTTAATT
* * *
3058077 T--TTAAATTTAAATATTAAATA
1 TAATTTAATTTAAA-ATTTAATT
*
3058098 T-ATTTAAATTAAAATTTA
1 TAATTTAATTTAAAATTTA
3058116 TTATTAAACT
Statistics
Matches: 103, Mismatches: 12, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
19 8 0.08
20 2 0.02
21 38 0.37
22 26 0.25
23 8 0.08
24 4 0.04
25 3 0.03
26 4 0.04
28 7 0.07
29 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTAATTTAAAATTTAATT
Found at i:3058001 original size:33 final size:33
Alignment explanation
Indices: 3057908--3058012 Score: 92
Period size: 38 Copynumber: 3.1 Consensus size: 33
3057898 ATATTTTATT
*
3057908 TTTAA-TTAATTTTAA-ATAACTTTAATTT-AAA
1 TTTAATTTAATTTTAATA-AAATTTAATTTAAAA
* *
3057939 TTTAAACTTAAATTTACACATAAATAATTTAATTTAAAA
1 TTT-AA-TTTAATTT-TA-AT-AA-AATTTAATTTAAAA
3057978 TTTAATTTAATTTTAATAAAATTTAA-TTAAAA
1 TTTAATTTAATTTTAATAAAATTTAATTTAAAA
3058010 TTT
1 TTT
3058013 TTTAAAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
31 3 0.05
32 11 0.18
33 7 0.12
34 8 0.13
35 3 0.05
36 2 0.03
37 8 0.13
38 12 0.20
39 6 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.49
Consensus pattern (33 bp):
TTTAATTTAATTTTAATAAAATTTAATTTAAAA
Found at i:3058040 original size:43 final size:44
Alignment explanation
Indices: 3057974--3058056 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
3057964 AATTTAATTT
*
3057974 AAAATTTAATTTAATTTTAATAAAATTT-AATTAAAATTTTTTA
1 AAAATTTAATTTAATTTTAATAAAATTTAAAATAAAATTTTTTA
* *
3058017 AAAATTTAACTTTTATTTT-ATAAATTTTAAAATAAAATTT
1 AAAATTTAA-TTTAATTTTAATAAAATTTAAAATAAAATTT
3058057 AATTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 17 0.49
44 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (44 bp):
AAAATTTAATTTAATTTTAATAAAATTTAAAATAAAATTTTTTA
Found at i:3058065 original size:43 final size:42
Alignment explanation
Indices: 3057964--3058115 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 42
3057954 ACACATAAAT
*
3057964 AATTTAATTTAAAATTTAATTTAATTTTAATAAAATTT-AATTAA
1 AATTTAA-TTAAAATTTAATTTAATTTT-AT-AAATTTAAAATAA
* *
3058008 AATTT-TTTAAAAATTTAACTTTTATTTTATAAATTTTAAAATAA
1 AATTTAATT-AAAATTTAA-TTTAATTTTATAAA-TTTAAAATAA
*
3058052 AATTTAATT-AAATTTAAATTAAATTTT-TAAATTTAAATATTAAA
1 AATTTAATTAAAATTT-AATTTAATTTTATAAATTTAAA-A-T-AA
3058096 TATATTTAAATTAAAATTTA
1 -A-ATTT-AATTAAAATTTA
3058116 TTATTAAACT
Statistics
Matches: 89, Mismatches: 6, Indels: 23
0.75 0.05 0.19
Matches are distributed among these distances:
41 6 0.07
42 10 0.11
43 28 0.31
44 27 0.30
45 3 0.03
46 4 0.04
47 5 0.06
48 6 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
AATTTAATTAAAATTTAATTTAATTTTATAAATTTAAAATAA
Found at i:3058083 original size:42 final size:43
Alignment explanation
Indices: 3058031--3058113 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
3058021 TTTAACTTTT
* *
3058031 ATTTTATAAATTTTAAA-ATAAAATTTAATTAAATTTAAATTAA
1 ATTTTATAAA-TTTAAATATAAAATATAATTAAATTAAAATTAA
* *
3058074 ATTTT-TAAATTTAAATATTAAATATATTTAAATTAAAATT
1 ATTTTATAAATTTAAATATAAAATATAATTAAATTAAAATT
3058114 TATTATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 6 0.17
42 24 0.69
43 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (43 bp):
ATTTTATAAATTTAAATATAAAATATAATTAAATTAAAATTAA
Found at i:3058094 original size:13 final size:12
Alignment explanation
Indices: 3057931--3058115 Score: 54
Period size: 11 Copynumber: 15.5 Consensus size: 12
3057921 AAATAACTTT
3057931 AATTTAAATTTA
1 AATTTAAATTTA
*
3057943 AACTTAAATTTA
1 AATTTAAATTTA
**
3057955 CACATAAATAATTT-
1 -A-ATTTA-AATTTA
3057969 AATTTAAAATTT-
1 AATTT-AAATTTA
*
3057981 AATTT-AATTTT
1 AATTTAAATTTA
*
3057992 AA-TAAAATTT-
1 AATTTAAATTTA
*
3058002 AATTAAAATTT-
1 AATTTAAATTTA
3058013 --TTTAAAAATTTA
1 AATTT--AAATTTA
* **
3058025 ACTTTTATTTTATA
1 A-ATTTAAATT-TA
* *
3058039 AATTTTAAAATAA
1 AA-TTTAAATTTA
3058052 AATTT-AA-TTA
1 AATTTAAATTTA
3058062 AATTTAAA-TTA
1 AATTTAAATTTA
3058073 AATTTTTAAATTTA
1 AA--TTTAAATTTA
3058087 AATATTAAA--TA
1 AAT-TTAAATTTA
* *
3058098 TATTTAAATTAA
1 AATTTAAATTTA
3058110 AATTTA
1 AATTTA
3058116 TTATTAAACT
Statistics
Matches: 132, Mismatches: 19, Indels: 44
0.68 0.10 0.23
Matches are distributed among these distances:
9 2 0.02
10 20 0.15
11 34 0.26
12 33 0.25
13 20 0.15
14 15 0.11
15 8 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTTAAATTTA
Found at i:3058103 original size:23 final size:21
Alignment explanation
Indices: 3058037--3058113 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
3058027 TTTTATTTTA
* *
3058037 TAAATTTTAAAATAAAATTTAAT
1 TAAA-TTTAAAATTAAA-TTATT
3058060 TAAATTT-AAATTAAATT-TT
1 TAAATTTAAAATTAAATTATT
3058079 TAAATTTAAATATTAAATATATT
1 TAAATTTAAA-ATTAAAT-TATT
3058102 TAAA-TTAAAATT
1 TAAATTTAAAATT
3058114 TATTATTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.17
20 4 0.08
21 17 0.35
22 9 0.19
23 10 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATTTAAAATTAAATTATT
Found at i:3058106 original size:36 final size:34
Alignment explanation
Indices: 3058037--3058115 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 34
3058027 TTTTATTTTA
*
3058037 TAAATTTTAAAATAAAATTTAATTAAATTTAAAT
1 TAAATTTTAAAATAAAATTTAAATAAATTTAAAT
* * *
3058071 TAAATTTTTAAATTTAAATATTAAATATATTTAAAT
1 TAAA-TTTTAAAATAAAAT-TTAAATAAATTTAAAT
*
3058107 TAAAATTTA
1 TAAATTTTA
3058116 TTATTAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 4 0.11
35 16 0.42
36 18 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
TAAATTTTAAAATAAAATTTAAATAAATTTAAAT
Found at i:3062760 original size:2 final size:2
Alignment explanation
Indices: 3062753--3062784 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3062743 ATGTCTTTGT
3062753 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3062785 ATGCTTGAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3065301 original size:18 final size:16
Alignment explanation
Indices: 3065275--3065321 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
3065265 ATGTATAAAA
3065275 AAATA-ATTAAAATAT
1 AAATATATTAAAATAT
*
3065290 AATATGATATTAATATAT
1 AA-AT-ATATTAAAATAT
*
3065308 AAATATTTTAAAAT
1 AAATATATTAAAAT
3065322 TTTTATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 10 0.38
17 3 0.12
18 11 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATATATTAAAATAT
Found at i:3065335 original size:16 final size:16
Alignment explanation
Indices: 3065316--3065380 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
3065306 ATAAATATTT
3065316 TAAAATTTTTATAATA
1 TAAAATTTTTATAATA
*
3065332 T-AAATTATTAATAA-A
1 TAAAATT-TTTATAATA
*
3065347 TAAAAATTTATATAAATA
1 T-AAAATTTTTAT-AATA
3065365 TAAAATATTTTA-AATA
1 TAAAAT-TTTTATAATA
3065381 AGATTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
15 7 0.18
16 14 0.36
17 12 0.31
18 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTTTTATAATA
Found at i:3065355 original size:32 final size:32
Alignment explanation
Indices: 3065317--3065396 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
3065307 TAAATATTTT
* *
3065317 AAAATTTTTAT-AATATAAATTATTAATAAATA
1 AAAATTTATATAAATATAAAATATT-ATAAATA
*
3065349 AAAATTTATATAAATATAAAATATTTTAAAT-
1 AAAATTTATATAAATATAAAATATTATAAATA
*
3065380 AAGA-TTATATAAATATA
1 AAAATTTATATAAATATA
3065397 TGAATTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.30
31 3 0.07
32 15 0.35
33 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (32 bp):
AAAATTTATATAAATATAAAATATTATAAATA
Found at i:3065369 original size:17 final size:17
Alignment explanation
Indices: 3065316--3065370 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
3065306 ATAAATATTT
*
3065316 TAAAATTTTTAT-AATA
1 TAAAATTTATATAAATA
*
3065332 TAAATTATTA-ATAAATA
1 TAAAAT-TTATATAAATA
3065349 -AAAATTTATATAAATA
1 TAAAATTTATATAAATA
3065365 TAAAAT
1 TAAAAT
3065371 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 3 0.09
16 18 0.56
17 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3075410 original size:39 final size:41
Alignment explanation
Indices: 3075331--3075411 Score: 96
Period size: 39 Copynumber: 2.0 Consensus size: 41
3075321 AATTGATGGT
*
3075331 TTTATTCATAAATAAATAAATATATTTTTATATAGATATAA
1 TTTATTCATAAATAAATAAATATATTTTTAGATAGATATAA
* * *
3075372 TTTA-TCA-AAATATATAAATATCTATTTT-GATAGTTATAA
1 TTTATTCATAAATAAATAAATATAT-TTTTAGATAGATATAA
3075411 T
1 T
3075412 ATTTAACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 24 0.69
40 7 0.20
41 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (41 bp):
TTTATTCATAAATAAATAAATATATTTTTAGATAGATATAA
Found at i:3075453 original size:28 final size:26
Alignment explanation
Indices: 3075413--3075470 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3075403 AGTTATAATA
* *
3075413 TTTAACAAATAATATTAAAAGATATTTT
1 TTTAACAAAT-A-ATTAAAAAATATTAT
*
3075441 TTTAATAAATAATTAAAAAATATTAT
1 TTTAACAAATAATTAAAAAATATTAT
3075467 TTTA
1 TTTA
3075471 CAATTATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 17 0.63
27 1 0.04
28 9 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTAACAAATAATTAAAAAATATTAT
Found at i:3078727 original size:8 final size:8
Alignment explanation
Indices: 3078714--3078746 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3078704 TGCCACTTTC
3078714 TTTTTCTT
1 TTTTTCTT
3078722 TTTTTCTT
1 TTTTTCTT
3078730 TTTTT-TT
1 TTTTTCTT
*
3078737 TTTTTGTT
1 TTTTTCTT
3078745 TT
1 TT
3078747 ATACTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3078740 original size:14 final size:14
Alignment explanation
Indices: 3078710--3078739 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3078700 CAGTTGCCAC
3078710 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
3078724 TTTCTTTTT-TTTT
1 TTTCTTTTTCTTTT
3078737 TTT
1 TTT
3078740 TTGTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:3097184 original size:2 final size:2
Alignment explanation
Indices: 3097177--3097202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3097167 TTGATAAATA
3097177 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
3097203 TTCTGATTTA
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:3105771 original size:2 final size:2
Alignment explanation
Indices: 3105764--3105800 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3105754 CCTATGGTAT
3105764 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3105801 ATTATAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3111159 original size:21 final size:21
Alignment explanation
Indices: 3111135--3111180 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3111125 GCAAATATAT
3111135 CAAAAAAAATAATAAATGTAA
1 CAAAAAAAATAATAAATGTAA
** *
3111156 CAAATCATATAATAAATGTAA
1 CAAAAAAAATAATAAATGTAA
3111177 CAAA
1 CAAA
3111181 TCATCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (21 bp):
CAAAAAAAATAATAAATGTAA
Found at i:3111181 original size:21 final size:21
Alignment explanation
Indices: 3111143--3111184 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3111133 ATCAAAAAAA
3111143 ATAATAAATGTAACAAATCAT
1 ATAATAAATGTAACAAATCAT
3111164 ATAATAAATGTAACAAATCAT
1 ATAATAAATGTAACAAATCAT
3111185 CTGACACCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (21 bp):
ATAATAAATGTAACAAATCAT
Found at i:3116206 original size:26 final size:27
Alignment explanation
Indices: 3116176--3116231 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3116166 TGGAAAATTT
*
3116176 TTAATATTTATA-AATATTTAA-TTAAA
1 TTAATAATTATATAA-ATTTAAGTTAAA
3116202 TTAATAATTATATAAATTTAAGTTAAA
1 TTAATAATTATATAAATTTAAGTTAAA
3116229 TTA
1 TTA
3116232 TTAAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAATAATTATATAAATTTAAGTTAAA
Found at i:3117209 original size:27 final size:27
Alignment explanation
Indices: 3117178--3117240 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
3117168 TATAATATGA
3117178 ATATAAAAATATTA-AAAATTATAAAT
1 ATATAAAAATATTATAAAATTATAAAT
* * *
3117204 ATTATATAAAT-TTATAATATTTTAAAT
1 A-TATAAAAATATTATAAAATTATAAAT
3117231 A-ATAAAAATA
1 ATATAAAAATA
3117241 CAAAAAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
25 7 0.23
26 4 0.13
27 19 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAAAAATATTATAAAATTATAAAT
Found at i:3117220 original size:19 final size:19
Alignment explanation
Indices: 3117153--3117236 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 19
3117143 AATATTAAAA
* *
3117153 ATATAAATAAATAAATATA
1 ATATAAATATATAAATATT
* *
3117172 ATATGAATATAAAAATATT
1 ATATAAATATATAAATATT
3117191 A-A-AAAT-TATAAATATT
1 ATATAAATATATAAATATT
*
3117207 ATATAAATTTAT-AATATT
1 ATATAAATATATAAATATT
3117225 -T-TAAATA-ATAAA
1 ATATAAATATATAAA
3117237 AATACAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.04
16 17 0.31
17 5 0.09
18 11 0.20
19 19 0.35
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
ATATAAATATATAAATATT
Found at i:3125679 original size:16 final size:16
Alignment explanation
Indices: 3125658--3125690 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3125648 CCAAGGAACT
3125658 GTACTACATTAGGATG
1 GTACTACATTAGGATG
3125674 GTACTACATTAGGATG
1 GTACTACATTAGGATG
3125690 G
1 G
3125691 CGCAACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (16 bp):
GTACTACATTAGGATG
Found at i:3130256 original size:22 final size:23
Alignment explanation
Indices: 3130231--3130275 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3130221 ACATTTCGGG
*
3130231 ATCTTCAA-TTTAGAGAGATACA
1 ATCTTCAAGTTCAGAGAGATACA
3130253 ATCTTCAAGTTCAGAGAGATACA
1 ATCTTCAAGTTCAGAGAGATACA
3130276 GCATATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (23 bp):
ATCTTCAAGTTCAGAGAGATACA
Found at i:3132759 original size:42 final size:41
Alignment explanation
Indices: 3132693--3132775 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
3132683 TCAACAATGG
3132693 AAAAGAAGCTGGATACCCACTAATCCATTCAAAGTTCAAACAT
1 AAAAGAAGCTGGATACCCACTAATCCATTC-AA-TTCAAACAT
*
3132736 AAAAGAAGCT-GATACCCATTAATCCATTCAATTCAAACAT
1 AAAAGAAGCTGGATACCCACTAATCCATTCAATTCAAACAT
3132776 CACTCAGTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 9 0.23
41 2 0.05
42 18 0.46
43 10 0.26
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (41 bp):
AAAAGAAGCTGGATACCCACTAATCCATTCAATTCAAACAT
Found at i:3135166 original size:42 final size:39
Alignment explanation
Indices: 3135120--3135230 Score: 98
Period size: 42 Copynumber: 2.7 Consensus size: 39
3135110 TAATATTTAT
*
3135120 TATTTAAAATTAATAAAAAATTTAAAAATATATTTTTATTAA
1 TATTTAAAATTAATAAAAAATTTAAAAA-ATA-TTTTA-AAA
* * * *
3135162 TATTTATATTTTATAATTAAATTTAAAAAATATTTTAAAA
1 TATTTAAAATTAATAA-AAAATTTAAAAAATATTTTAAAA
3135202 TA-TTAAATATTAAATAAAACTAATTTAAA
1 TATTTAAA-ATT-AATAAAA--AATTTAAA
3135231 TTTATAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
39 4 0.07
40 7 0.13
41 9 0.16
42 24 0.44
43 11 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (39 bp):
TATTTAAAATTAATAAAAAATTTAAAAAATATTTTAAAA
Found at i:3135180 original size:20 final size:17
Alignment explanation
Indices: 3135148--3135186 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 17
3135138 AATTTAAAAA
3135148 TATATTTTTATTAATATT
1 TATATTTTTATTAA-ATT
3135166 TATATTTTATAATTAAATT
1 TATATTTT-T-ATTAAATT
3135185 TA
1 TA
3135187 AAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTTATTAAATT
Found at i:3135263 original size:48 final size:48
Alignment explanation
Indices: 3135178--3135276 Score: 107
Period size: 48 Copynumber: 2.1 Consensus size: 48
3135168 TATTTTATAA
3135178 TTAAATTTAAAAAATATTTTAAAATATTAAATATTAAATAAAACT-AAT
1 TTAAATTTAAAAAATATTTTAAAATATTAAATATTAAA-AAAACTAAAT
* * *
3135226 TTAAATTTATAAAAAATATATTTATAA-CTT-AAT-TTAAAAAAATTAAAT
1 TTAAA-TT-TAAAAAATAT-TTTAAAATATTAAATATTAAAAAAACTAAAT
3135274 TTA
1 TTA
3135277 TCAAACTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
47 5 0.11
48 16 0.36
49 5 0.11
50 12 0.27
51 6 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (48 bp):
TTAAATTTAAAAAATATTTTAAAATATTAAATATTAAAAAAACTAAAT
Found at i:3135734 original size:17 final size:17
Alignment explanation
Indices: 3135714--3135747 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3135704 AAATTATTTT
* *
3135714 ATTATTTAAAATATTAA
1 ATTATTAAAAAAATTAA
3135731 ATTATTAAAAAAATTAA
1 ATTATTAAAAAAATTAA
3135748 TTTTTATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTAAAAAAATTAA
Found at i:3137480 original size:21 final size:20
Alignment explanation
Indices: 3137451--3137501 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
3137441 TTTATATTTT
*
3137451 ATTATTTAATATTATTATA-AA
1 ATTAATTAAT-TT-TTATATAA
3137472 ATTAATTAATTTTTATATAA
1 ATTAATTAATTTTTATATAA
3137492 ATTAA-TAATT
1 ATTAATTAATT
3137502 GAGTTAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAATTAATTTTTATATAA
Found at i:3140540 original size:19 final size:19
Alignment explanation
Indices: 3140516--3140553 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3140506 AGATTGTCAG
3140516 AATTTAATACTTGATGTTA
1 AATTTAATACTTGATGTTA
3140535 AATTTAATACTTGATGTTA
1 AATTTAATACTTGATGTTA
3140554 TCATCTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (19 bp):
AATTTAATACTTGATGTTA
Found at i:3143961 original size:6 final size:6
Alignment explanation
Indices: 3143947--3143984 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3143937 AAACCAGAAA
* *
3143947 GGAT-G GGATTG GGATGG GGATGG GGATGG GGATTG GGA
1 GGATGG GGATGG GGATGG GGATGG GGATGG GGATGG GGA
3143985 CCGGGTTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (6 bp):
GGATGG
Found at i:3143972 original size:12 final size:12
Alignment explanation
Indices: 3143947--3143984 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3143937 AAACCAGAAA
3143947 GGAT-GGGATTG
1 GGATGGGGATTG
*
3143958 GGATGGGGATGG
1 GGATGGGGATTG
3143970 GGATGGGGATTG
1 GGATGGGGATTG
3143982 GGA
1 GGA
3143985 CCGGGTTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (12 bp):
GGATGGGGATTG
Found at i:3146573 original size:13 final size:13
Alignment explanation
Indices: 3146555--3146582 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3146545 GTCATGTTTG
3146555 TACGTTATGCGTT
1 TACGTTATGCGTT
3146568 TACGTTATGCGTT
1 TACGTTATGCGTT
3146581 TA
1 TA
3146583 TGGGTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.46
Consensus pattern (13 bp):
TACGTTATGCGTT
Found at i:3149945 original size:2 final size:2
Alignment explanation
Indices: 3149938--3149991 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
3149928 GTCTTCTTCC
* *
3149938 AT AT AT AT AC AT GT -T 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
3149979 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3149992 ACAAACAGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3157890 original size:37 final size:37
Alignment explanation
Indices: 3157844--3157931 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 37
3157834 ACTCATAAAT
3157844 ATAATATTTAAATA-TTATTAAATTTAAAA-TTTA-ATTTA
1 ATAA-ATTTAAATATTTATT---TTTAAAATTTTATATTTA
* *
3157882 ATTAATTTATATATTTATTTTTAAAATTTTATATTTA
1 ATAAATTTAAATATTTATTTTTAAAATTTTATATTTA
*
3157919 ATAAAATTAAATA
1 ATAAATTTAAATA
3157932 AATTATCCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
35 7 0.17
36 4 0.10
37 23 0.55
38 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
ATAAATTTAAATATTTATTTTTAAAATTTTATATTTA
Found at i:3157897 original size:22 final size:22
Alignment explanation
Indices: 3157847--3157920 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 22
3157837 CATAAATATA
3157847 ATATTTAAATATT-ATTAAATTTA-
1 ATATTT-AAT-TTAATT-AATTTAT
*
3157870 AAATTTAATTTAATTAATTTAT
1 ATATTTAATTTAATTAATTTAT
*
3157892 ATATTTATTTTTAA--AATTT-T
1 ATATTTA-ATTTAATTAATTTAT
3157912 ATATTTAAT
1 ATATTTAAT
3157921 AAAATTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.02
20 8 0.18
21 13 0.30
22 12 0.27
23 10 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTAATTTAATTAATTTAT
Found at i:3160430 original size:2 final size:2
Alignment explanation
Indices: 3160425--3160452 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3160415 CAACACACAA
3160425 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
3160453 GTTCTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3166804 original size:26 final size:26
Alignment explanation
Indices: 3166754--3166805 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3166744 TTTTAAATAA
**
3166754 AAAATTCTTATTATTTTCATAATTTT
1 AAAATTCTTATTATTTAAATAATTTT
3166780 AAAATT-TTATTATTTAAATATATTTT
1 AAAATTCTTATTATTTAAATA-ATTTT
3166806 TTCAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
AAAATTCTTATTATTTAAATAATTTT
Found at i:3169862 original size:2 final size:2
Alignment explanation
Indices: 3169857--3169887 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3169847 ACAGTTATAT
*
3169857 AC AC AC AC AC AC AC GC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3169888 TGGAAGGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3181512 original size:3 final size:3
Alignment explanation
Indices: 3181504--3181577 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
3181494 ATATCAATAC
* * *
3181504 AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3181552 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3181578 ACGACTGAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3185532 original size:18 final size:18
Alignment explanation
Indices: 3185501--3185545 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
3185491 TTTGATTACG
3185501 ATATAAATATATATGATATAA
1 ATAT-AATATATAT-A-ATAA
*
3185522 ATATAATATATTTAATAA
1 ATATAATATATATAATAA
3185540 ATATAA
1 ATATAA
3185546 AATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 8 0.35
21 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAATATATATAATAA
Found at i:3185545 original size:24 final size:20
Alignment explanation
Indices: 3185518--3185565 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3185508 TATATATGAT
*
3185518 ATAAATATAATA-T-ATTTA
1 ATAAATATAAAATTAATTTA
3185536 ATAAATATAAAATTAATTTA
1 ATAAATATAAAATTAATTTA
*
3185556 ATTAATATAA
1 ATAAATATAA
3185566 TACAATGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
20 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAATATAAAATTAATTTA
Found at i:3186066 original size:32 final size:32
Alignment explanation
Indices: 3186025--3186091 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
3186015 ATCATGCTAC
*
3186025 AAAATTTTAATTACGAATATATTATGTATACT
1 AAAATTTTAATTACGAACATATTATGTATACT
* *
3186057 AAAATTTTAATTATGAACATATTATGTATATT
1 AAAATTTTAATTACGAACATATTATGTATACT
3186089 AAA
1 AAA
3186092 TGTATTGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (32 bp):
AAAATTTTAATTACGAACATATTATGTATACT
Found at i:3186067 original size:80 final size:80
Alignment explanation
Indices: 3185977--3186139 Score: 263
Period size: 80 Copynumber: 2.0 Consensus size: 80
3185967 ATAACGTGCC
* *
3185977 AAAATGTTAATTACGAATATATTATGTATACTAAATGTATCATGCTACAAAATTTTAATTACGAA
1 AAAATGTTAATTACGAACATATTATGTATACTAAATGTATCATGCTACAAAATTTTAATTACAAA
3186042 TATATTATGTATACT
66 TATATTATGTATACT
* * * **
3186057 AAAATTTTAATTATGAACATATTATGTATATTAAATGTATTGTGCTACAAAATTTTAATTACAAA
1 AAAATGTTAATTACGAACATATTATGTATACTAAATGTATCATGCTACAAAATTTTAATTACAAA
3186122 TATATTATGTATACT
66 TATATTATGTATACT
3186137 AAA
1 AAA
3186140 TGTATCGTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (80 bp):
AAAATGTTAATTACGAACATATTATGTATACTAAATGTATCATGCTACAAAATTTTAATTACAAA
TATATTATGTATACT
Found at i:3186114 original size:48 final size:48
Alignment explanation
Indices: 3186057--3186151 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
3186047 TATGTATACT
** * *
3186057 AAAATTTTAATTATGAACATATTATGTATATTAAATGTATTGTGCTAC
1 AAAATTTTAATTACAAACATATTATGTATACTAAATGTATCGTGCTAC
*
3186105 AAAATTTTAATTACAAATATATTATGTATACTAAATGTATCGTGCTA
1 AAAATTTTAATTACAAACATATTATGTATACTAAATGTATCGTGCTA
3186152 ATTATATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (48 bp):
AAAATTTTAATTACAAACATATTATGTATACTAAATGTATCGTGCTAC
Found at i:3189205 original size:24 final size:26
Alignment explanation
Indices: 3189173--3189231 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
3189163 ATTAAATTAA
3189173 TTTTTAATATCAACAT-AA-TTA-AAT
1 TTTTTAATAT-AACATAAATTTATAAT
*
3189197 TTTTTAATATAATATAAATTTATAAT
1 TTTTTAATATAACATAAATTTATAAT
3189223 TTTTTAATA
1 TTTTTAATA
3189232 AAATTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.13
24 12 0.39
25 3 0.10
26 12 0.39
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTTAATATAACATAAATTTATAAT
Found at i:3189524 original size:30 final size:29
Alignment explanation
Indices: 3189485--3189542 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
3189475 TATCAAAAAA
* *
3189485 TAATAAATAAAATTATTAATAATTATATT
1 TAATAAATAAAATTATTAAAAATAATATT
*
3189514 TAATATAATAATATTATTAAAAATAATAT
1 TAATA-AATAAAATTATTAAAAATAATAT
3189543 ATAAACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TAATAAATAAAATTATTAAAAATAATATT
Found at i:3190732 original size:33 final size:33
Alignment explanation
Indices: 3190692--3190766 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
3190682 TTGATTCGGT
*
3190692 GCAGCAGCAACACCACCACCACCAACAACAACA
1 GCAGCAGCAACACCACCACCAACAACAACAACA
3190725 GCAGCAGCAACACCACCACCAACAACAACAACA
1 GCAGCAGCAACACCACCACCAACAACAACAACA
3190758 GCAGCAGCA
1 GCAGCAGCA
3190767 GCAGCAGCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.45, C:0.43, G:0.12, T:0.00
Consensus pattern (33 bp):
GCAGCAGCAACACCACCACCAACAACAACAACA
Found at i:3190761 original size:30 final size:30
Alignment explanation
Indices: 3190696--3190763 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
3190686 TTCGGTGCAG
* * *
3190696 CAGCAACACCACCACCACCAACAACAACAG
1 CAGCAGCAACACCACCACCAACAACAACAA
3190726 CAGCAGCAACACCACCACCAACAACAACAA
1 CAGCAGCAACACCACCACCAACAACAACAA
3190756 CAGCAGCA
1 CAGCAGCA
3190764 GCAGCAGCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.47, C:0.44, G:0.09, T:0.00
Consensus pattern (30 bp):
CAGCAGCAACACCACCACCAACAACAACAA
Found at i:3194871 original size:61 final size:61
Alignment explanation
Indices: 3194795--3194914 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
3194785 TCTGTGACAG
*
3194795 TAAGAAGGGGTTCATGCAGCAACTTTTCTCATGTTCTTTAGTTCATAACTCTCATCTCATA
1 TAAGAAGGGATTCATGCAGCAACTTTTCTCATGTTCTTTAGTTCATAACTCTCATCTCATA
3194856 TAAGAAGGGATTCATGCAGCAACTTTTCTCATGTTCTTTAGTTCATAACTCTCATCTCA
1 TAAGAAGGGATTCATGCAGCAACTTTTCTCATGTTCTTTAGTTCATAACTCTCATCTCA
3194915 GTATGGTCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (61 bp):
TAAGAAGGGATTCATGCAGCAACTTTTCTCATGTTCTTTAGTTCATAACTCTCATCTCATA
Found at i:3201950 original size:29 final size:29
Alignment explanation
Indices: 3201900--3201965 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 29
3201890 GTGTAAAAAA
* *
3201900 TTTAAAACAATAATACTCTGATAATATAT
1 TTTAAAATAATAATACTCTGATAATAAAT
* * * *
3201929 TTTAAAATGATAATATTTTGATATTAAAT
1 TTTAAAATAATAATACTCTGATAATAAAT
*
3201958 TTAAAAAT
1 TTTAAAAT
3201966 TAGCAGTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTAAAATAATAATACTCTGATAATAAAT
Found at i:3204804 original size:2 final size:2
Alignment explanation
Indices: 3204799--3204842 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3204789 ATATATATAT
3204799 AG AG AG AG 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 AG AG AG AG
3204841 AG
1 AG
3204843 GACATTATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3207214 original size:17 final size:17
Alignment explanation
Indices: 3207192--3207225 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3207182 ACATCAGTAA
3207192 TTTTTTCTCCTTTTTCT
1 TTTTTTCTCCTTTTTCT
* *
3207209 TTTTTTTTTCTTTTTCT
1 TTTTTTCTCCTTTTTCT
3207226 GCGTGTGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCTCCTTTTTCT
Found at i:3211561 original size:31 final size:31
Alignment explanation
Indices: 3211509--3211576 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
3211499 AATAAACAAG
*
3211509 ATTATTTATTTATACCATATTTATATATTGT
1 ATTATTTATTTATACCATATTTAAATATTGT
* * *
3211540 ATTATATTATTT-TATCGTATTTAAATATTTT
1 ATTAT-TTATTTATACCATATTTAAATATTGT
3211571 A-TATTT
1 ATTATTT
3211577 TTATAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 3 0.09
31 21 0.66
32 6 0.19
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (31 bp):
ATTATTTATTTATACCATATTTAAATATTGT
Found at i:3213345 original size:20 final size:22
Alignment explanation
Indices: 3213320--3213359 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3213310 CGTAATCGTG
3213320 TATATA-ATAATTTT-AAAAAA
1 TATATATATAATTTTGAAAAAA
*
3213340 TATATATATCATTTTGAAAA
1 TATATATATAATTTTGAAAA
3213360 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (22 bp):
TATATATATAATTTTGAAAAAA
Found at i:3213920 original size:22 final size:21
Alignment explanation
Indices: 3213895--3213961 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
3213885 TAATATTTAA
3213895 TAATTAAAAAATTATTTAAATT
1 TAATTAAAAAA-TATTTAAATT
* *
3213917 TAATTATAAAATATATAAATAT
1 TAATTAAAAAATATTTAAAT-T
*
3213939 T-ATTATAAAAAAATTTTAAATT
1 TAATTA-AAAAATA-TTTAAATT
3213961 T
1 T
3213962 TTTATTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 12 0.32
22 19 0.51
23 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAAAAAATATTTAAATT
Found at i:3213943 original size:21 final size:22
Alignment explanation
Indices: 3213895--3213948 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3213885 TAATATTTAA
* *
3213895 TAATTAAAAAATTATTTAAATT
1 TAATTATAAAATTATATAAATT
3213917 TAATTATAAAA-TATATAAATAT
1 TAATTATAAAATTATATAAAT-T
3213939 T-ATTATAAAA
1 TAATTATAAAA
3213949 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTATAAAATTATATAAATT
Found at i:3213958 original size:23 final size:23
Alignment explanation
Indices: 3213884--3213961 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 23
3213874 TCAGGTTAAA
* *
3213884 TTAATATTTAATAATTAAAAAATTAT
1 TTAA-ATTTAATTA-TAAAAAAAT-T
*
3213910 TTAAATTTAATTAT-AAAATA-T
1 TTAAATTTAATTATAAAAAAATT
*
3213931 ATAAATATT-ATTATAAAAAAATT
1 TTAAAT-TTAATTATAAAAAAATT
3213954 TTAAATTT
1 TTAAATTT
3213962 TTTATTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 11 0.26
22 9 0.21
23 10 0.23
24 1 0.02
25 8 0.19
26 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAATTTAATTATAAAAAAATT
Found at i:3226461 original size:17 final size:17
Alignment explanation
Indices: 3226439--3226480 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3226429 TTAATGATAA
3226439 AATATTAAATT-TTATAT
1 AATATTAAATTATTA-AT
3226456 AATATT-AATTATTAAT
1 AATATTAAATTATTAAT
3226472 -ATATTAAAT
1 AATATTAAAT
3226481 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTAAATTATTAAT
Found at i:3226566 original size:13 final size:13
Alignment explanation
Indices: 3226524--3226569 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3226514 ATAAAATTTT
*
3226524 AAATTAATTAATA
1 AAATTATTTAATA
* *
3226537 AATTTATTTTAAAA
1 AAATTA-TTTAATA
3226551 AAATTATTTAATA
1 AAATTATTTAATA
3226564 AAATTA
1 AAATTA
3226570 ATATATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTATTTAATA
Found at i:3226579 original size:27 final size:27
Alignment explanation
Indices: 3226524--3226581 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3226514 ATAAAATTTT
* * *
3226524 AAATTAATTAATAAATTTATTTTAAAA
1 AAATTAATTAATAAAATTAATATAAAA
*
3226551 AAATTATTTAATAAAATTAATATATAAA
1 AAATTAATTAATAAAATTAATATA-AAA
3226579 AAA
1 AAA
3226582 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATTAATTAATAAAATTAATATAAAA
Found at i:3226665 original size:24 final size:24
Alignment explanation
Indices: 3226638--3226697 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
3226628 AATTTATTTT
3226638 TATTTAAAT-TTAATTATAAAAATA
1 TATTTAAATATTAA-TATAAAAATA
3226662 TATTT-AATATTAATATAAAAATA
1 TATTTAAATATTAATATAAAAATA
*
3226685 AATTTATAATATT
1 TATTTA-AATATT
3226698 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 17 0.53
24 9 0.28
25 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTTAAATATTAATATAAAAATA
Done.