Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 2 of 17
Found at i:92672 original size:32 final size:33
Alignment explanation
Indices: 92585--92678 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 33
92575 TGATTATTTA
* *
92585 AATAT-AATATTAATAAAATAATTAAAATATTATAT
1 AATATAAATATTATTAAAAT--TT-ATATATTATAT
92620 AATATAAATATTATTAAAATTTATATATTATA-
1 AATATAAATATTATTAAAATTTATATATTATAT
*
92652 AATTATTAATA-TATTAAAATTTATATA
1 AA-TATAAATATTATTAAAATTTATATA
92679 AATATAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 18 0.33
33 16 0.30
34 2 0.04
35 5 0.09
36 13 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATATAAATATTATTAAAATTTATATATTATAT
Found at i:92675 original size:18 final size:19
Alignment explanation
Indices: 92621--92688 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 19
92611 ATATTATATA
92621 ATATAAATATTATTAAAATTT
1 ATAT-AATA-TATTAAAATTT
92642 ATAT-AT-TA-T-AAA-TT
1 ATATAATATATTAAAATTT
92656 AT-TAATATATTAAAATTT
1 ATATAATATATTAAAATTT
92674 ATATAA-ATA-TAAAAT
1 ATATAATATATTAAAAT
92689 AATTTACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.02
14 6 0.15
15 5 0.12
16 2 0.05
17 11 0.27
18 7 0.17
19 5 0.12
21 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATATATTAAAATTT
Found at i:92678 original size:27 final size:28
Alignment explanation
Indices: 92586--92681 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 28
92576 GATTATTTAA
* *
92586 ATATAATATTAATAAAATAATTAAAATATT
1 ATATAA-ATTATTAATAT-ATTAAAATATT
*
92616 ATAT-AA-TATAAATATTATTAAAATTTATAT
1 ATATAAATTATTAATA-TATTAAAA--TAT-T
92646 ATTATAAATTATTAATATATTAAAAT-TT
1 A-TATAAATTATTAATATATTAAAATATT
92674 ATATAAAT
1 ATATAAAT
92682 ATAAAATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
27 19 0.35
28 4 0.07
29 5 0.09
30 7 0.13
31 3 0.05
32 10 0.18
33 7 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAAATTATTAATATATTAAAATATT
Found at i:92686 original size:17 final size:17
Alignment explanation
Indices: 92634--92745 Score: 56
Period size: 18 Copynumber: 6.4 Consensus size: 17
92624 TAAATATTAT
*
92634 TAAAATTTATAT-ATTA
1 TAAAATTTATATAAATA
92650 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
92665 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
*
92683 TAAAATAATT-TACAAATAA
1 TAAAAT--TTATATAAAT-A
* *
92702 TTATAATATA-ATAAATA
1 -TAAAATTTATATAAATA
*
92719 TATAAATATAATATAAATA
1 TA-AAAT-TTATATAAATA
92738 TATAAATT
1 TA-AAATT
92746 ATTAAACCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
13 1 0.01
14 5 0.07
15 5 0.07
16 4 0.05
17 13 0.18
18 21 0.28
19 20 0.27
20 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:92689 original size:27 final size:27
Alignment explanation
Indices: 92597--92751 Score: 85
Period size: 27 Copynumber: 5.6 Consensus size: 27
92587 TATAATATTA
92597 ATAAAATA-ATTAAAATATTATAT-AAT
1 ATAAAATATATTAAAAT-TTATATAAAT
*
92623 AT-AAATATTATTAAAATTTATATATTATAA
1 ATAAAATA-TATTAAAATTTATATA--A-AT
*
92653 ATTATTAATATATTAAAATTTATATAAAT
1 A-TA-AAATATATTAAAATTTATATAAAT
*
92682 ATAAAATA-ATTTACAAA-TAAT-TATAAT
1 ATAAAATATA-TTA-AAATTTATATA-AAT
*
92709 ATAATAA-ATA-TATAAATATAATATAAAT
1 ATAA-AATATATTA-AAAT-TTATATAAAT
92737 ATATAAAT-TATTAAA
1 ATA-AAATATATTAAA
92752 CCTATTTTTA
Statistics
Matches: 103, Mismatches: 6, Indels: 38
0.70 0.04 0.26
Matches are distributed among these distances:
25 5 0.05
26 16 0.16
27 26 0.25
28 24 0.23
29 8 0.08
30 3 0.03
31 1 0.01
32 16 0.16
33 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAAAATATATTAAAATTTATATAAAT
Found at i:93709 original size:18 final size:19
Alignment explanation
Indices: 93686--93721 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
93676 AAGCTTGTCA
*
93686 TTAATTT-ATTTTTTTAAT
1 TTAATTTAAATTTTTTAAT
93704 TTAATTTAAATTTTTTAA
1 TTAATTTAAATTTTTTAA
93722 AATTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATTTAAATTTTTTAAT
Found at i:93718 original size:20 final size:19
Alignment explanation
Indices: 93693--93746 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
93683 TCATTAATTT
93693 ATTTTTTTAATTTAATTTAA
1 ATTTTTTTAATTT-ATTTAA
* *
93713 ATTTTTTAAAATTTATTTAC
1 ATTTTTT-TAATTTATTTAA
93733 ATTATATTTTAATT
1 ATT-T-TTTTAATT
93747 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 15 0.54
21 10 0.36
22 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTTAATTTATTTAA
Found at i:93773 original size:16 final size:16
Alignment explanation
Indices: 93696--93777 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 16
93686 TTAATTTATT
*
93696 TTTTTAATTTAATTTAAA
1 TTTTT-ATTAAATTT-AA
*
93714 TTTTT-TAAAATTT-A
1 TTTTTATTAAATTTAA
** *
93728 TTTACATTATATTTTAA
1 TTTTTATTA-AATTTAA
93745 TTACTTT-TTAAATTTAA
1 TT--TTTATTAAATTTAA
93762 TTTTTATTAAATTTAA
1 TTTTTATTAAATTTAA
93778 CATATAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
14 4 0.08
15 5 0.10
16 20 0.41
17 11 0.22
18 8 0.16
19 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTATTAAATTTAA
Found at i:93874 original size:13 final size:15
Alignment explanation
Indices: 93848--93880 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
93838 TGATAAAAAT
93848 TATATAATATATTAA
1 TATATAATATATTAA
93863 TATATAA-A-ATTAA
1 TATATAATATATTAA
93876 TATAT
1 TATAT
93881 TTTATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 1 0.06
15 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAATATATTAA
Found at i:94030 original size:18 final size:17
Alignment explanation
Indices: 93984--94048 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 17
93974 AGTATTATAA
*
93984 TTATATTTA-A-ATATT
1 TTATATTTATATAAATT
93999 TTATATTTATATAAATT
1 TTATATTTATATAAATT
94016 TTGATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
94032 TTATA-TTATA-AAATT
1 TTATATTTATATAAATT
94047 TT
1 TT
94049 TTGATATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 15 0.36
16 4 0.10
17 8 0.19
18 6 0.14
19 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:94036 original size:33 final size:32
Alignment explanation
Indices: 93993--94057 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
93983 ATTATATTTA
*
93993 AATATTTTATATTTATATAAA-TTTTGATATATT
1 AATAATTTATA-TTATA-AAATTTTTGATATATT
94026 AATAATTTATATTATAAAATTTTTTGATATAT
1 AATAATTTATATTATAAAA-TTTTTGATATAT
94058 ATTTATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.10
32 5 0.17
33 21 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
AATAATTTATATTATAAAATTTTTGATATATT
Found at i:94104 original size:21 final size:21
Alignment explanation
Indices: 94079--94122 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
94069 ATTATATTTT
94079 TTAAATGTA-TATTTAAAATTA
1 TTAAATGTACT-TTTAAAATTA
* *
94100 TTAAATTTACTTTTAAATTTA
1 TTAAATGTACTTTTAAAATTA
94121 TT
1 TT
94123 TATTTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAATGTACTTTTAAAATTA
Found at i:94152 original size:16 final size:16
Alignment explanation
Indices: 94099--94153 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
94089 ATTTAAAATT
*
94099 ATTAAATTTACTTTTAA
1 ATTAAA-TTATTTTTAA
* *
94116 ATTTATTTATTTTT--
1 ATTAAATTATTTTTAA
94130 ATCTAAATTATTTTTAA
1 AT-TAAATTATTTTTAA
94147 ATTAAAT
1 ATTAAAT
94154 ATCTTACTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
16 12 0.40
17 6 0.20
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAAATTATTTTTAA
Found at i:94721 original size:3 final size:3
Alignment explanation
Indices: 94713--94741 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
94703 CAAATAAAAG
94713 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
94742 AAACTTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:94807 original size:5 final size:5
Alignment explanation
Indices: 94797--94832 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
94787 TTAAAAAAAA
94797 TTTAT TTTAT TTTAT TTTA- TTTA- TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
94833 TCTTATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:94838 original size:18 final size:18
Alignment explanation
Indices: 94796--94832 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
94786 CTTAAAAAAA
94796 ATTTATTTTATTTTATTTT
1 ATTTA-TTTATTTTATTTT
94815 ATTTATTTATTTTATTTT
1 ATTTATTTATTTTATTTT
94833 TCTTATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:94843 original size:23 final size:23
Alignment explanation
Indices: 94796--94843 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
94786 CTTAAAAAAA
*
94796 ATTTATTTTATTTTATTTTATTT
1 ATTTATTTTATTTTATCTTATTT
94819 ATTTATTTTATTTT-TCTTATGTT
1 ATTTATTTTATTTTATCTTAT-TT
94842 AT
1 AT
94844 CTTCCTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (23 bp):
ATTTATTTTATTTTATCTTATTT
Found at i:95051 original size:19 final size:20
Alignment explanation
Indices: 95005--95051 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
94995 TAGATATCGA
95005 TTTAATAATTATTATTTAA-
1 TTTAATAATTATTATTTAAT
* *
95024 TTAAATAATATTTTTATTTAAT
1 TTTAAT-A-ATTATTATTTAAT
95046 TTTAAT
1 TTTAAT
95052 TATAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 1 0.05
21 11 0.50
22 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATAATTATTATTTAAT
Found at i:95075 original size:27 final size:27
Alignment explanation
Indices: 95012--95077 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
95002 CGATTTAATA
* *
95012 ATTATTATTTAATTAAATAATATTTTT
1 ATTATTTTTTAATTAAAAAATATTTTT
*
95039 ATT-TAATTTTAATTATAAAAATA-TTTT
1 ATTAT-TTTTTAATTA-AAAAATATTTTT
95066 ATTATTTTTTAA
1 ATTATTTTTTAA
95078 ATAGTGATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 24 0.75
28 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTATTTTTTAATTAAAAAATATTTTT
Found at i:99451 original size:24 final size:24
Alignment explanation
Indices: 99423--99468 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
99413 GATCTGAATT
99423 AAATTATTATTTAAAT-AATTAAAA
1 AAATTATT-TTTAAATAAATTAAAA
*
99447 AAATTATTTTTATATAAATTAA
1 AAATTATTTTTAAATAAATTAA
99469 TTATTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTATTTTTAAATAAATTAAAA
Found at i:99489 original size:39 final size:40
Alignment explanation
Indices: 99419--99510 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 40
99409 ATATGATCTG
99419 AATTAAATT-ATTATTTAAATAATTAAAAAAATTATT-TTT
1 AATTAAATTAATTATTTAAATAATTAAAAAAA-TATTATTT
99458 -ATATAAATTAATTA-TT-AAT-ATTAATATAAAATATTATTT
1 AAT-TAAATTAATTATTTAAATAATTAA-A-AAAATATTATTT
99497 AATTAAACTTAATT
1 AATTAAA-TTAATT
99511 TAAATATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
37 5 0.11
38 10 0.22
39 19 0.41
40 12 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
AATTAAATTAATTATTTAAATAATTAAAAAAATATTATTT
Found at i:99517 original size:39 final size:37
Alignment explanation
Indices: 99422--99529 Score: 96
Period size: 39 Copynumber: 2.8 Consensus size: 37
99412 TGATCTGAAT
99422 TAAATTATTATTTAAATAATTAA-AAAAATTATTTTTATA
1 TAAATTA--ATTTAAAT-ATTAATAAAAATTATTTTTATA
*
99461 TAAATTAATTATTAATATTAATATAAAA-TATTATTTA-A
1 TAAATTAATT-TAAATATTAATA-AAAATTATT-TTTATA
*
99499 TTAAACTTAATTTAAATATAAATAAATAATT
1 -TAAA-TTAATTTAAATATTAATAAA-AATT
99530 TTAAAAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
37 8 0.14
38 12 0.21
39 31 0.53
40 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
TAAATTAATTTAAATATTAATAAAAATTATTTTTATA
Found at i:99836 original size:6 final size:6
Alignment explanation
Indices: 99825--99854 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
99815 TGGAAAATGT
*
99825 CAGAGA CAGAGA CAGAGA CAGTGA CAGAGA
1 CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA
99855 TAGCATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.03
Consensus pattern (6 bp):
CAGAGA
Found at i:100402 original size:2 final size:2
Alignment explanation
Indices: 100395--100439 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
100385 TCTGTACAAT
100395 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
100437 AG A
1 AG A
100440 ATCCTATGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:100733 original size:27 final size:27
Alignment explanation
Indices: 100689--100742 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
100679 TTGATACGTT
*
100689 AATAATTTATATTATATTA-ATTTTAA
1 AATAATTTACATTATATTATATTTTAA
*
100715 AATATATTTACATTTTATTATATTTTAA
1 AATA-ATTTACATTATATTATATTTTAA
100743 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
AATAATTTACATTATATTATATTTTAA
Found at i:103435 original size:2 final size:2
Alignment explanation
Indices: 103428--103452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103418 AATTTAAATG
103428 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
103453 AACCAAACTC
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:104549 original size:33 final size:33
Alignment explanation
Indices: 104486--104552 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
104476 AAATATTTTT
* *
104486 TTATCTTAAATTTAATAGTATCGAAGATGAATA
1 TTATCTTAAATTTAATAGTATCAAAAATGAATA
*
104519 TTATCTCT-AATTTAATAGTATTAAAAATGAATA
1 TTATCT-TAAATTTAATAGTATCAAAAATGAATA
104552 T
1 T
104553 CGTTTTTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (33 bp):
TTATCTTAAATTTAATAGTATCAAAAATGAATA
Found at i:104965 original size:23 final size:23
Alignment explanation
Indices: 104921--104965 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
104911 TATTTTGTCT
*
104921 ATATAAGAAACAAATAATATAAA
1 ATATAAGAAACAAATAACATAAA
*
104944 ATATAATAAA-AAATAAGCATAA
1 ATATAAGAAACAAATAA-CATAA
104966 TGTAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (23 bp):
ATATAAGAAACAAATAACATAAA
Found at i:108580 original size:24 final size:24
Alignment explanation
Indices: 108530--108598 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
108520 AAATTAACTA
* *
108530 TTAAATAAAATAA-TTTTATTTTCT
1 TTAAAT-ATATAATTTTTATTATCT
* *
108554 TTATATATCTAAATTTTTATTAT-T
1 TTAAATATAT-AATTTTTATTATCT
108578 TTAAATATATAATTTTT-TTAT
1 TTAAATATATAATTTTTATTAT
108599 AAACATTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 16 0.43
25 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAAATATATAATTTTTATTATCT
Found at i:109640 original size:26 final size:27
Alignment explanation
Indices: 109606--109656 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
109596 TTAAATATAT
*
109606 TAAATTTTATAATTTAATATTTAAAAA
1 TAAATTTTATAATTAAATATTTAAAAA
*
109633 TAAA-TTTATGATTAAATATTTAAA
1 TAAATTTTATAATTAAATATTTAAA
109657 TTTATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TAAATTTTATAATTAAATATTTAAAAA
Found at i:109825 original size:7 final size:7
Alignment explanation
Indices: 109803--109837 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
109793 TCGAACTAAA
109803 AAAATTT
1 AAAATTT
109810 AAAACTTT
1 AAAA-TTT
109818 AAAATTT
1 AAAATTT
109825 AAAATTT
1 AAAATTT
109832 AAAATT
1 AAAATT
109838 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:109834 original size:14 final size:15
Alignment explanation
Indices: 109803--109837 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
109793 TCGAACTAAA
109803 AAAATTTAAAACTTT
1 AAAATTTAAAACTTT
109818 AAAATTTAAAA-TTT
1 AAAATTTAAAACTTT
109832 AAAATT
1 AAAATT
109838 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTAAAACTTT
Found at i:112244 original size:22 final size:22
Alignment explanation
Indices: 112201--112250 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
112191 AAAATATTAA
*
112201 AAATAATTTTAAATTAATATTT
1 AAATATTTTTAAATTAATATTT
*
112223 ATATATTTTTATAATTAA-ATTT
1 AAATATTTTTA-AATTAATATTT
112245 AAATAT
1 AAATAT
112251 AAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATTTTTAAATTAATATTT
Found at i:112289 original size:17 final size:17
Alignment explanation
Indices: 112243--112290 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
112233 ATAATTAAAT
112243 TTAAATATAAAATTTATTA
1 TTAAAT-TAAAATTTA-TA
*
112262 TTAAATAAAAATTTA-A
1 TTAAATTAAAATTTATA
112278 TTAAGATTAAAAT
1 TTAA-ATTAAAAT
112291 AATTCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
18 8 0.31
19 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAATTAAAATTTATA
Found at i:112879 original size:14 final size:14
Alignment explanation
Indices: 112860--112886 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
112850 CAACGTAAAA
112860 AAAAAAAAAATCAG
1 AAAAAAAAAATCAG
112874 AAAAAAAAAATCA
1 AAAAAAAAAATCA
112887 TAGTAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.07, G:0.04, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAATCAG
Found at i:118375 original size:30 final size:30
Alignment explanation
Indices: 118299--118412 Score: 72
Period size: 30 Copynumber: 3.7 Consensus size: 30
118289 TTATTGATCA
*
118299 AATTAAAAATATTTTTTATTAATTTAAATT
1 AATTAAAAATATTTTTAATTAATTTAAATT
* **
118329 AATTTATTATGA-TTTTAATTGATATTT-AA-T
1 AATTAAAAAT-ATTTTTAATT-A-ATTTAAATT
* * *
118359 AATTAAAAATATTTTTATTTATATATAATTATA
1 AATTAAAAATATTTTTAATTA-ATTTAA--ATT
*
118392 AAATAAAAATATTTTTTAATT
1 AATTAAAAATA-TTTTTAATT
118413 TTTATTAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
29 6 0.10
30 30 0.48
31 4 0.06
32 5 0.08
33 10 0.16
34 8 0.13
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTAAAAATATTTTTAATTAATTTAAATT
Found at i:118402 original size:33 final size:34
Alignment explanation
Indices: 118362--118426 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
118352 ATTTAATAAT
118362 TAAAAATA-TTTTT-ATTTATATATAATTATAAAA
1 TAAAAATATTTTTTAATTTATAT-TAATTATAAAA
*
118395 TAAAAATATTTTTTAATTTTTATTAATTATAA
1 TAAAAATATTTTTTAATTTATATTAATTATAA
118427 GTAATATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 8 0.28
34 14 0.48
35 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TAAAAATATTTTTTAATTTATATTAATTATAAAA
Found at i:122989 original size:2 final size:2
Alignment explanation
Indices: 122984--123032 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
122974 TAAAACCACA
*
122984 AT AT AT AC 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
123026 AT AT AT A
1 AT AT AT A
123033 CTTTGCAGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:128049 original size:24 final size:25
Alignment explanation
Indices: 128022--128068 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
128012 ATATATATTA
128022 AAATGTTAAT-TATTT-ATATTTAAT
1 AAATGTTAATAT-TTTAATATTTAAT
*
128046 AAATTTTAATATTTTAATATTTA
1 AAATGTTAATATTTTAATATTTA
128069 TATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AAATGTTAATATTTTAATATTTAAT
Found at i:128078 original size:18 final size:18
Alignment explanation
Indices: 128055--128092 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
128045 TAAATTTTAA
*
128055 TATTTTAATAT-TTATAT
1 TATTTTTATATATTATAT
*
128072 TATTTTTTTATATTATAT
1 TATTTTTATATATTATAT
128090 TAT
1 TAT
128093 ACTTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTATATATTATAT
Found at i:128325 original size:23 final size:23
Alignment explanation
Indices: 128282--128325 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
128272 TATGATATAA
* *
128282 ATATATAAATAATATTTTAATTT
1 ATATATAAATAAGATTATAATTT
128305 ATATAATAAAT-AGATTATAAT
1 ATAT-ATAAATAAGATTATAAT
128326 ATGTAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATATAAATAAGATTATAATTT
Found at i:128353 original size:21 final size:21
Alignment explanation
Indices: 128329--128371 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
128319 TTATAATATG
**
128329 TAATAATTTATATAAATATAA
1 TAATAATAAATATAAATATAA
* *
128350 TAATTATAAATATAATTATAA
1 TAATAATAAATATAAATATAA
128371 T
1 T
128372 TTATAAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATAAATATAAATATAA
Found at i:128357 original size:15 final size:15
Alignment explanation
Indices: 128303--128365 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
128293 ATATTTTAAT
128303 TTATATAATA-AATAGA
1 TTATA-AATATAATA-A
*
128319 TTATAATATGTAATAA
1 TTATAA-ATATAATAA
128335 TTTATATAAATATAATAA
1 --T-TATAAATATAATAA
128353 TTATAAATATAAT
1 TTATAAATATAAT
128366 TATAATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
15 13 0.32
16 9 0.22
17 4 0.10
18 9 0.22
19 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TTATAAATATAATAA
Found at i:128381 original size:15 final size:16
Alignment explanation
Indices: 128299--128381 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 16
128289 AATAATATTT
* *
128299 TAATTTATATAATAAA
1 TAATTTATAAAATTAA
*
128315 TAGA-TTATAATATGTAA
1 TA-ATTTATAAAAT-TAA
128332 TAATTTATATAAATATAA
1 TAATTTATA-AAAT-TAA
*
128350 TAA-TTATAAATATAATTA
1 TAATTTATAAA-AT--TAA
128368 TAATTTATAAAATT
1 TAATTTATAAAATT
128382 GATATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
16 13 0.24
17 17 0.31
18 17 0.31
19 7 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTATAAAATTAA
Found at i:130198 original size:22 final size:22
Alignment explanation
Indices: 130160--130203 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
130150 AATTAAATAT
*
130160 TATTAAGTTAAATATATTTTTA
1 TATTAAGTTAAATATATATTTA
*
130182 TATTAA-TTAATTAATATATTTA
1 TATTAAGTTAAAT-ATATATTTA
130204 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTAAGTTAAATATATATTTA
Found at i:133539 original size:42 final size:38
Alignment explanation
Indices: 133471--133567 Score: 99
Period size: 41 Copynumber: 2.5 Consensus size: 38
133461 AGTAAAAATT
**
133471 TTAATATTTAAATAA-TTTAATTTAATTTAAATTAT-TA
1 TTAATATAAAAATAATTTTAATTTAATTT-AATTATATA
*
133508 TTTATATAATAAAAATAATTTTTATTCTAATTTAATTATATA
1 -TTA-AT-ATAAAAATAATTTTAATT-TAATTTAATTATATA
*
133550 TTAATATGAAAATAATTT
1 TTAATATAAAAATAATTT
133568 ATTAATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
38 3 0.06
39 14 0.28
40 10 0.20
41 15 0.30
42 8 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (38 bp):
TTAATATAAAAATAATTTTAATTTAATTTAATTATATA
Found at i:133569 original size:37 final size:37
Alignment explanation
Indices: 133470--133570 Score: 98
Period size: 40 Copynumber: 2.6 Consensus size: 37
133460 GAGTAAAAAT
**
133470 TTTAATATTTAAATAATTTAATTTAATTTAAATTATTA
1 TTTAATATAAAAATAATTT-ATTTAATTTAAATTATTA
133508 TTTATATAATAAAAATAATTTTTATTCTAATTT-AATTA-TA
1 TTTA-AT-ATAAAAATAA--TTTATT-TAATTTAAATTATTA
*
133548 TATTAATATGAAAATAATTTATT
1 T-TTAATATAAAAATAATTTATT
133571 AATATTATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
37 6 0.11
38 4 0.07
39 11 0.20
40 13 0.24
41 11 0.20
42 9 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTAATATAAAAATAATTTATTTAATTTAAATTATTA
Found at i:134613 original size:2 final size:2
Alignment explanation
Indices: 134606--134645 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
134596 TCTGTCATAC
134606 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
134646 GCAGGAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137967 original size:8 final size:8
Alignment explanation
Indices: 137956--138025 Score: 70
Period size: 8 Copynumber: 8.9 Consensus size: 8
137946 CCCCATCTCC
137956 CTTTCTAT
1 CTTTCTAT
* *
137964 CTTTATCT
1 CTTTCTAT
**
137972 CTTTCTCC
1 CTTTCTAT
137980 CTTTCTAT
1 CTTTCTAT
*
137988 CTTTCTCT
1 CTTTCTAT
*
137996 CTTTCT-C
1 CTTTCTAT
138003 CTTTCTAT
1 CTTTCTAT
*
138011 CTTTCTCT
1 CTTTCTAT
138019 CTTTCTA
1 CTTTCTA
138026 CCTGTATCCC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
7 6 0.12
8 44 0.88
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (8 bp):
CTTTCTAT
Found at i:137977 original size:16 final size:16
Alignment explanation
Indices: 137951--138025 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
137941 CCCTTCCCCA
*
137951 TCTCCCTTTCTATCTT
1 TCTCTCTTTCTATCTT
* **
137967 TATCTCTTTCTCCCTT
1 TCTCTCTTTCTATCTT
* *
137983 TCTATCTTTCTCTCTT
1 TCTCTCTTTCTATCTT
137999 TCTC-CTTTCTATCTT
1 TCTCTCTTTCTATCTT
138014 TCTCTCTTTCTA
1 TCTCTCTTTCTA
138026 CCTGTATCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
15 14 0.29
16 35 0.71
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.59
Consensus pattern (16 bp):
TCTCTCTTTCTATCTT
Found at i:138009 original size:23 final size:24
Alignment explanation
Indices: 137951--138024 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
137941 CCCTTCCCCA
*
137951 TCTCCCTTTCTATCTTTATCTCTT
1 TCTCCCTTTCTATCTTTCTCTCTT
137975 TCTCCCTTTCTATCTTTCTCTCTT
1 TCTCCCTTTCTATCTTTCTCTCTT
137999 TCT-CCTTTCTATCTTTCTCTCTT
1 TCTCCCTTTCTATCTTTCTCTCTT
138022 TCT
1 TCT
138025 ACCTGTATCC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 23 0.47
24 26 0.53
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.59
Consensus pattern (24 bp):
TCTCCCTTTCTATCTTTCTCTCTT
Found at i:140224 original size:81 final size:79
Alignment explanation
Indices: 140119--140272 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 79
140109 ATTGATGATT
* * * **
140119 ATAGATTTAAGATTCGAATCTCAACATTTGTAATTCATTTTTTTATGTATACATACAATCACC-T
1 ATAGATATAAGATTCGAATCTCAACATTTATAATTC---CTTTTATACATACATACAATCACCTT
*
140183 TTAATAGATGATATTTG
63 TTAAGAGATGATATTTG
*
140200 ATAGATATAAGATTTGAATCTCAACATTTATAATTCCTTTTATACATACATACAATCACCTTTTA
1 ATAGATATAAGATTCGAATCTCAACATTTATAATTCCTTTTATACATACATACAATCACCTTTTA
140265 AGAGATGA
66 AGAGATGA
140273 GTCGATGACA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 21 0.32
79 11 0.17
81 33 0.51
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (79 bp):
ATAGATATAAGATTCGAATCTCAACATTTATAATTCCTTTTATACATACATACAATCACCTTTTA
AGAGATGATATTTG
Found at i:141878 original size:2 final size:2
Alignment explanation
Indices: 141871--141905 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
141861 GAAGCAGGTA
141871 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
141906 CTTGATTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:142650 original size:27 final size:27
Alignment explanation
Indices: 142616--142696 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
142606 ACCACCCATT
142616 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
142643 TGTTTGTCAAAAATGGTAGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* * *
142671 TATTTGTCAAATATGGAGGCTTATTT
1 TGTTTGTCAAAAATGGTGG-TTATTT
142697 ATTTGTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.02
27 20 0.44
28 21 0.47
29 2 0.04
30 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:142671 original size:28 final size:27
Alignment explanation
Indices: 142616--142686 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
142606 ACCACCCATT
*
142616 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTAGTTATTTTG
142643 TGTTTGTCAAAAATGGTAGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTAGTTAT--TTTG
* *
142671 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
142687 AGGCTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTAGTTATTTTG
Found at i:147241 original size:28 final size:27
Alignment explanation
Indices: 147188--147277 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 27
147178 CACCCATTTG
147188 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTCAAAAATGGTGGTTATTTTGTA
147215 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGGTTAT--TTTGTA
* *
147243 TTTGTCAAATATGGAGGCTTA--TT-TA
1 TTTGTCAAAAATGGTGG-TTATTTTGTA
147268 TTTGTCAAAA
1 TTTGTCAAAA
147278 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 19 0.34
28 21 0.38
29 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTGTA
Found at i:148700 original size:17 final size:19
Alignment explanation
Indices: 148680--148720 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
148670 TTAATTTGAT
148680 TTAAAATAAT-T-TTTTAA
1 TTAAAATAATATATTTTAA
*
148697 TTAAAATAATATATTTTAT
1 TTAAAATAATATATTTTAA
148716 TTAAA
1 TTAAA
148721 TTTAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATATTTTAA
Found at i:148741 original size:21 final size:21
Alignment explanation
Indices: 148717--148756 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
148707 ATATTTTATT
148717 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
148738 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
148757 ATTTTTAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:148931 original size:18 final size:17
Alignment explanation
Indices: 148898--148953 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
148888 GAATATCTAT
148898 ATTTAAAATAAAAATTAAA
1 ATTTAAAAT-AAAATT-AA
* *
148917 ATTTTAAGTAAAATTAA
1 ATTTAAAATAAAATTAA
148934 ATTTAAAATAAAATTTAA
1 ATTTAAAATAAAA-TTAA
148952 AT
1 AT
148954 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 13 0.41
18 12 0.38
19 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTTAAAATAAAATTAA
Found at i:149387 original size:20 final size:21
Alignment explanation
Indices: 149330--149388 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
149320 ACGAGATTGG
*
149330 ATTAATTTTTAAAATTT-TTTT
1 ATTAA-TTTAAAAATTTATTTT
**
149351 ATTAAATTTAATGATTTATTTT
1 ATT-AATTTAAAAATTTATTTT
149373 ATT-ATTTAAAAATTTA
1 ATTAATTTAAAAATTTA
149389 AAAATTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.35
21 11 0.35
22 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTAATTTAAAAATTTATTTT
Found at i:149441 original size:26 final size:27
Alignment explanation
Indices: 149390--149441 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
149380 AAAAATTTAA
*
149390 AAATTTTAATAATATATTTTTATAATT
1 AAATTTTAATAATATATTTATATAATT
149417 AAATTTTAA-AATATATATTAT-TAAT
1 AAATTTTAATAATATAT-TTATATAAT
149442 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATTTTAATAATATATTTATATAATT
Found at i:149778 original size:23 final size:23
Alignment explanation
Indices: 149743--149786 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
149733 AAATTATAAA
149743 TATTATAATTTAAATTTTAAATT
1 TATTATAATTTAAATTTTAAATT
*
149766 TATTA-AATATTAATTTTTAAA
1 TATTATAAT-TTAAATTTTAAA
149787 AATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATAATTTAAATTTTAAATT
Found at i:150476 original size:19 final size:17
Alignment explanation
Indices: 150457--150490 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
150447 GGTCTAAATT
*
150457 ATTA-TTTAAGTAAAAA
1 ATTATTTTAAATAAAAA
150473 ATTATTTTAAATAAAAA
1 ATTATTTTAAATAAAAA
150490 A
1 A
150491 ATAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTATTTTAAATAAAAA
Found at i:152264 original size:2 final size:2
Alignment explanation
Indices: 152257--152288 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
152247 CAAAATCAAC
152257 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
152289 TTCTTTAGGC
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:153289 original size:17 final size:17
Alignment explanation
Indices: 153263--153307 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
153253 TTTGAACTCG
153263 AATATAAATATAAATTA
1 AATATAAATATAAATTA
* * *
153280 CATTTAAATATAAGTTA
1 AATATAAATATAAATTA
153297 AATATAAATAT
1 AATATAAATAT
153308 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AATATAAATATAAATTA
Found at i:155106 original size:2 final size:2
Alignment explanation
Indices: 155099--155125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155089 TTTCAAGTAT
155099 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
155126 TTATGAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156528 original size:2 final size:2
Alignment explanation
Indices: 156521--156569 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
156511 GCTGCTTAAC
*
156521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
156563 AT AT AT A
1 AT AT AT A
156570 AAAGGAGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:156952 original size:20 final size:21
Alignment explanation
Indices: 156918--156959 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
156908 TTGTAAATGA
*
156918 TTATTAAAAAGTAAATATTTG
1 TTATTAAAAAGTAAAAATTTG
*
156939 TTATT-AAAATTAAAAATTTG
1 TTATTAAAAAGTAAAAATTTG
156959 T
1 T
156960 AGAGAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TTATTAAAAAGTAAAAATTTG
Found at i:159739 original size:19 final size:20
Alignment explanation
Indices: 159715--159752 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
159705 CTCAATATAA
159715 AATTTTTTATTT-TATTTTT
1 AATTTTTTATTTATATTTTT
159734 AATTTTTTATTTATATTTT
1 AATTTTTTATTTATATTTT
159753 AAATAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
AATTTTTTATTTATATTTTT
Found at i:161933 original size:15 final size:17
Alignment explanation
Indices: 161909--162041 Score: 60
Period size: 19 Copynumber: 7.2 Consensus size: 17
161899 TTGGCTTGAA
161909 ATATTATATATT-TTAAT
1 ATATT-TATATTATTAAT
161926 A-ATTTATATTATATTAAT
1 ATATTTATA-T-TATTAAT
*
161944 ATATTTATATTACATTTAT
1 ATATTTATATT--ATTAAT
*
161963 AAATTTTATTATTATTTAA-
1 ATA-TTTA-TATTA-TTAAT
*
161982 ATTATTT-T-TTAATAAT
1 A-TATTTATATTATTAAT
161998 ATATTTATATTTTATTATAT
1 ATATTTATA--TTATTA-AT
*
162018 CATATTTAAAATTATTAAAT
1 -ATATTT-ATATTATT-AAT
162038 ATAT
1 ATAT
162042 ATTAATTAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 36
0.68 0.05 0.27
Matches are distributed among these distances:
15 12 0.13
16 9 0.10
17 4 0.04
18 7 0.08
19 28 0.31
20 17 0.19
21 11 0.12
22 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTATATTATTAAT
Found at i:161951 original size:19 final size:19
Alignment explanation
Indices: 161912--162025 Score: 82
Period size: 19 Copynumber: 6.2 Consensus size: 19
161902 GCTTGAAATA
*
161912 TTATA-TATTTTAATA-AT
1 TTATATTATATTAATATAT
161929 TTATATTATATTAATATAT
1 TTATATTATATTAATATAT
* * *
161948 TTATATTACATTTATAAAT
1 TTATATTATATTAATATAT
161967 TT-TATTATTATTTAA-ATTAT
1 TTATATTA-TA-TTAATA-TAT
161987 TT-T-TTA-A-TAATATAT
1 TTATATTATATTAATATAT
*
162002 TTATATTTTATTATATCATAT
1 TTATATTATATTA-AT-ATAT
162023 TTA
1 TTA
162026 AAATTATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
15 8 0.10
16 2 0.03
17 8 0.10
18 15 0.19
19 27 0.35
20 10 0.13
21 7 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTATATTAATATAT
Found at i:162046 original size:20 final size:20
Alignment explanation
Indices: 162009--162046 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
161999 TATTTATATT
*
162009 TTATTATATCATATTTAAAA
1 TTATTAAATCATATTTAAAA
162029 TTATTAAAT-ATATATTAA
1 TTATTAAATCATAT-TTAA
162047 TTAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAATCATATTTAAAA
Found at i:164081 original size:25 final size:27
Alignment explanation
Indices: 164023--164083 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 27
164013 ATTAATTATA
*
164023 TAAATTA-ATTAAATTAAAATATATTT
1 TAAATTATTTTAAATTAAAATATATTT
164049 TAAA-TATTTTAAA-TAAAAT-TATTT
1 TAAATTATTTTAAATTAAAATATATTT
164073 TAAATTATTTT
1 TAAATTATTTT
164084 TATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 9 0.28
25 14 0.44
26 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAATTATTTTAAATTAAAATATATTT
Found at i:165919 original size:27 final size:29
Alignment explanation
Indices: 165885--165952 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 29
165875 AATTTGATTC
*
165885 ATATTAATTATATTTAAAAAAAT-TATAA
1 ATATTAATTATAATTAAAAAAATATATAA
* *
165913 AT-TTAATT-TAATTATAAAATTATATAA
1 ATATTAATTATAATTAAAAAAATATATAA
165940 ATATTAATTATAA
1 ATATTAATTATAA
165953 ATATAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.29
27 13 0.38
28 8 0.24
29 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATTAATTATAATTAAAAAAATATATAA
Found at i:165951 original size:13 final size:13
Alignment explanation
Indices: 165920--165956 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
165910 TAAATTTAAT
165920 TTAATTATAAA-A
1 TTAATTATAAATA
165932 TT-A-TATAAATA
1 TTAATTATAAATA
165943 TTAATTATAAATA
1 TTAATTATAAATA
165956 T
1 T
165957 AAATATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.27
11 4 0.18
12 3 0.14
13 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTATAAATA
Found at i:165996 original size:12 final size:12
Alignment explanation
Indices: 165979--166004 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
165969 TTAATATTTT
165979 AATAATATAATA
1 AATAATATAATA
165991 AATAATATAATA
1 AATAATATAATA
166003 AA
1 AA
166005 ATAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATATAATA
Found at i:166216 original size:16 final size:16
Alignment explanation
Indices: 166195--166234 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
166185 CCCCCCCCCC
166195 CAAAAGAAAAGGAAAA
1 CAAAAGAAAAGGAAAA
* *
166211 CAAAAGAAAATGAACA
1 CAAAAGAAAAGGAAAA
166227 -AAAAGAAA
1 CAAAAGAAA
166235 TGGGTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.75, C:0.07, G:0.15, T:0.03
Consensus pattern (16 bp):
CAAAAGAAAAGGAAAA
Found at i:168859 original size:17 final size:15
Alignment explanation
Indices: 168832--168888 Score: 62
Period size: 14 Copynumber: 3.7 Consensus size: 15
168822 TGAAGATCTC
168832 ATTTCATTATTTATTAT
1 ATTT-ATTATTTA-TAT
* *
168849 ATTATATTATTAAAAT
1 ATT-TATTATTTATAT
168865 ATTTA-TATTTATAT
1 ATTTATTATTTATAT
168879 ATTTATTATT
1 ATTTATTATT
168889 AAATTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.35
15 6 0.18
16 5 0.15
17 10 0.29
18 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTATTTATAT
Found at i:168936 original size:31 final size:32
Alignment explanation
Indices: 168843--168936 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 32
168833 TTTCATTATT
* *
168843 TATTATATTATATTATT-AA-AAT-ATTTATA
1 TATTATATTTTATTATTAAATAATAATTTAAA
* **
168872 T-TTATATATTTATTATTAAAT-TTAAATAAAAA
1 TATTATAT-TTTATTATTAAATAAT-AATTTAAA
168904 TATTAT-TTTTATTATTAAATAATAATTTAAA
1 TATTATATTTTATTATTAAATAATAATTTAAA
168935 TA
1 TA
168937 GAATAAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
28 6 0.12
29 9 0.18
30 3 0.06
31 21 0.42
32 7 0.14
33 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTATATTTTATTATTAAATAATAATTTAAA
Found at i:171513 original size:15 final size:15
Alignment explanation
Indices: 171493--171521 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
171483 ATCTTGAATT
171493 TATATATATTATATA
1 TATATATATTATATA
171508 TATATATATTATAT
1 TATATATATTATAT
171522 TGTTACCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATTATATA
Found at i:177258 original size:16 final size:16
Alignment explanation
Indices: 177237--177277 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
177227 TTTAATATTT
*
177237 ATAATTGATATTTATC
1 ATAATTAATATTTATC
*
177253 ATAATTAATATTTATT
1 ATAATTAATATTTATC
177269 ATAATTAAT
1 ATAATTAAT
177278 TGAAACGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
ATAATTAATATTTATC
Found at i:182170 original size:19 final size:19
Alignment explanation
Indices: 182129--182184 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
182119 TTTGGTAATA
*
182129 ATTTATTATATTTAATTTG
1 ATTTATTATATTTAAATTG
*
182148 ATTTATTATTTTATAAATT-
1 ATTTATTATATT-TAAATTG
*
182167 ATTTA-AATATTTATAATT
1 ATTTATTATATTTA-AATT
182185 ATTCAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 8 0.26
19 16 0.52
20 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTATTATATTTAAATTG
Found at i:182186 original size:18 final size:19
Alignment explanation
Indices: 182157--182192 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
182147 GATTTATTAT
*
182157 TTTATAAATTATTTAAATA
1 TTTATAAATTATTCAAATA
182176 TTTAT-AATTATTCAAAT
1 TTTATAAATTATTCAAAT
182193 TGAATGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATAAATTATTCAAATA
Found at i:182633 original size:22 final size:22
Alignment explanation
Indices: 182591--182633 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
182581 TTTTTAATAT
*
182591 ATAAAATAAATTATAATTTAAG
1 ATAAAATAAAGTATAATTTAAG
182613 ATAAAATAAAGTA-AATATTAA
1 ATAAAATAAAGTATAAT-TTAA
182634 TATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
ATAAAATAAAGTATAATTTAAG
Found at i:184445 original size:30 final size:31
Alignment explanation
Indices: 184389--184446 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
184379 TTTAATTATA
**
184389 AAAATAATATTTTAATAATATTACAAATAAT
1 AAAATAATATTTTAATAATAACACAAATAAT
184420 AAAATAA-ATTTTAA-AATCAACACAAAT
1 AAAATAATATTTTAATAAT-AACACAAAT
184447 TTAACTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 14 0.58
31 7 0.29
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (31 bp):
AAAATAATATTTTAATAATAACACAAATAAT
Found at i:184833 original size:21 final size:21
Alignment explanation
Indices: 184782--184838 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
184772 ATCATGGTGA
**
184782 TTATATATTTATAA-TCGTAAT
1 TTATAT-TTTATAATTAATAAT
*
184803 TTAAATTTTTATAATTAATAAT
1 TTATA-TTTTATAATTAATAAT
*
184825 TTATATTTTTTAAT
1 TTATATTTTATAAT
184839 AAATTGTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATATTTTATAATTAATAAT
Found at i:184879 original size:26 final size:26
Alignment explanation
Indices: 184849--184905 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
184839 AAATTGTGAT
*
184849 ATATATTTAT-TTTATAATAAAATATA
1 ATATATTTATGATTATAAT-AAATATA
*
184875 TTATATTTATGATTATAATAAATATA
1 ATATATTTATGATTATAATAAATATA
184901 ATATA
1 ATATA
184906 ATTAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATATTTATGATTATAATAAATATA
Found at i:185581 original size:174 final size:172
Alignment explanation
Indices: 185317--185738 Score: 450
Period size: 172 Copynumber: 2.4 Consensus size: 172
185307 AGAATGTCAA
* * * *** * * *
185317 TATATATTTT-TTTGAGACTTATTATTTCATAATTTTTTAACTTAGTTAGTATATTTTATTCTTA
1 TATATTTTTTCTTTGAGACTTATTATTTTATAA-TTTTTAACCTAAAAAATAAATTTTATTATTA
** * *
185381 AAATATCTAAAATTATTTTGTAAATATTTAAAAAATTTTAAAATGTAAAATTATGTAAGACGAAT
65 AAATATCTAAAATTATCATGTAAATATTTAAAAAATTTTAAAATCT-AAATTA-GTAAAACGAA-
* * *
185446 TTTTTAC-ATTTA-AGAAACTGT-TACTTTAATATAAAAATG-TT-AATT
127 TTTTT-CGA-CTAGAGAAACTATCTAATTTAATAT-AAAA-GCTTCAATT
*
185491 TATATTTTTTCTTTGAGACTTATTATTTTATAATTTTTAACCTAAAAAATACATTTTATTATTAA
1 TATATTTTTTCTTTGAGACTTATTATTTTATAATTTTTAACCTAAAAAATAAATTTTATTATTAA
* * *
185556 AATATATAAAATTCTGCAT-TAAATATTTAAAAAATTTTAAAATCTAAATTAGTAAAATGAATTT
66 AATATCTAAAATTAT-CATGTAAATATTTAAAAAATTTTAAAATCTAAATTAGTAAAACGAATTT
* *
185620 TTCGACTAGAGATACTATCGTAATTTAATATGAAAGCTTCAATT
130 TTCGACTAGAGAAACTATC-TAATTTAATATAAAAGCTTCAATT
* *
185664 TATA-TTTTTCTTTTAGACTTAATATTTCT-TAATTTTTAA-CTCAAAAAATAAATTTTATTATT
1 TATATTTTTTCTTTGAGACTTATTATTT-TATAATTTTTAACCT-AAAAAATAAATTTTATTATT
185726 AAAATATCTAAAA
64 AAAATATCTAAAA
185739 AAATTAAGAA
Statistics
Matches: 213, Mismatches: 25, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
170 3 0.01
171 16 0.08
172 75 0.35
173 25 0.12
174 72 0.34
175 22 0.10
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (172 bp):
TATATTTTTTCTTTGAGACTTATTATTTTATAATTTTTAACCTAAAAAATAAATTTTATTATTAA
AATATCTAAAATTATCATGTAAATATTTAAAAAATTTTAAAATCTAAATTAGTAAAACGAATTTT
TCGACTAGAGAAACTATCTAATTTAATATAAAAGCTTCAATT
Found at i:186168 original size:22 final size:20
Alignment explanation
Indices: 186135--186178 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
186125 TTTATTATTA
186135 AAATATCTAAAATTATTTTGT
1 AAATATCTAAAATT-TTTTGT
* *
186156 AAATATTTAAAAATTTTT-T
1 AAATATCTAAAATTTTTTGT
186175 AAAT
1 AAAT
186179 GTAAAGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATATCTAAAATTTTTTGT
Found at i:186803 original size:21 final size:21
Alignment explanation
Indices: 186778--186819 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
186768 ATTTTAATAT
186778 TTTTAAATA-TTTATTAGTTAA
1 TTTTAAATATTTTATTA-TTAA
*
186799 TTTTAGATATTTTATTATTAA
1 TTTTAAATATTTTATTATTAA
186820 AATTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTAAATATTTTATTATTAA
Found at i:186811 original size:39 final size:38
Alignment explanation
Indices: 186742--186817 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 38
186732 TTCTTAAGTA
186742 TAAATATTTATTTTATATAATTTTGAATTTTAATATTTT
1 TAAATATTTA-TTTATATAATTTTGAATTTTAATATTTT
*
186781 TAAATATTTA-TTAGT-TAATTTTAGATATTTTATTATT
1 TAAATATTTATTTA-TATAATTTT-GA-ATTTTAATATT
186818 AAAATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 10 0.30
38 3 0.09
39 20 0.61
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (38 bp):
TAAATATTTATTTATATAATTTTGAATTTTAATATTTT
Found at i:186825 original size:22 final size:21
Alignment explanation
Indices: 186779--186825 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
186769 TTTTAATATT
*
186779 TTTAAATATTTATTAGTTAAT
1 TTTAAATATTTATTAGTTAAA
*
186800 TTTAGATATTTTATTA-TTAAAA
1 TTTAAATA-TTTATTAGTT-AAA
186822 TTTA
1 TTTA
186826 TTTATTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAAATATTTATTAGTTAAA
Found at i:187968 original size:2 final size:2
Alignment explanation
Indices: 187963--187996 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
187953 GAAGACACAC
187963 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
187997 GAAGGTGCGG
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:188231 original size:27 final size:26
Alignment explanation
Indices: 188190--188276 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
188180 AACTTAAAAG
188190 TAAATTT-TTTAATTTTTATTTATCAAA
1 TAAATTTATTT-ATTTTTATTTAT-AAA
188217 TAAATTTATTTATTTATT-TTTA-AAA
1 TAAATTTATTTATTT-TTATTTATAAA
* **
188242 TAAAAATTATTTATAGTTA-TTATTAAA
1 T-AAATTTATTTATTTTTATTTA-TAAA
188269 TAAATTTA
1 TAAATTTA
188277 ATGATAGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
25 9 0.18
26 17 0.34
27 19 0.38
28 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
TAAATTTATTTATTTTTATTTATAAA
Found at i:188516 original size:14 final size:15
Alignment explanation
Indices: 188499--188531 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
188489 TATAATTAAA
188499 TTTAAT-AAAATTAT
1 TTTAATAAAAATTAT
188513 TTTAATAAAAATTAT
1 TTTAATAAAAATTAT
188528 TTTA
1 TTTA
188532 TTATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATAAAAATTAT
Found at i:189178 original size:19 final size:20
Alignment explanation
Indices: 189141--189187 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
189131 AAATACGTTG
189141 TTTTATATTTATTATAATAT
1 TTTTATATTTATTATAATAT
189161 TTTTATATTTATTA-AATAT
1 TTTTATATTTATTATAATAT
*
189180 ATTTATAT
1 TTTTATAT
189188 ATTAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATATTTATTATAATAT
Found at i:189190 original size:17 final size:18
Alignment explanation
Indices: 189142--189201 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
189132 AATACGTTGT
*
189142 TTTATATTTATTATAATATT
1 TTTATA-TTATTA-AATATA
189162 TTTATATTTATTAAATATA
1 TTTATA-TTATTAAATATA
189181 TTTATA-TATTAAATTATA
1 TTTATATTATTAAA-TATA
189199 TTT
1 TTT
189202 TTTTAAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
17 7 0.18
18 7 0.18
19 11 0.29
20 13 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATTATTAAATATA
Found at i:189564 original size:121 final size:121
Alignment explanation
Indices: 189350--189590 Score: 403
Period size: 121 Copynumber: 2.0 Consensus size: 121
189340 TCTTTATAAG
* * * *
189350 GATTTCATGCTTTTGACGTAAATGTGACGTCCATGTGCAGGGCACTGTGGATTTGCCTTGCTTAC
1 GATTTCATGCTTTTGACATAAATGTGACGTCCATGGGCAGGGCACTGTAGATGTGCCTTGCTTAC
189415 CACCCGAAATATGTCCTGCTGGGGGGAAGAAGAGGAAAGAAAGGAGAAAGGGAGGT
66 CACCCGAAATATGTCCTGCTGGGGGGAAGAAGAGGAAAGAAAGGAGAAAGGGAGGT
*
189471 GATTTCATGCTTTTGACATAAATGTGCCGTCCATGGGCAGGGCACTGTAGATGTGCCTTGCTTAC
1 GATTTCATGCTTTTGACATAAATGTGACGTCCATGGGCAGGGCACTGTAGATGTGCCTTGCTTAC
* *
189536 CACCCGAAATGTGTCCTGCAT-GGGGGAAGAAGAGGAAAGAGAGGAGAAAGGGAGG
66 CACCCGAAATATGTCCTGC-TGGGGGGAAGAAGAGGAAAGAAAGGAGAAAGGGAGG
189591 AAAAAGAAGA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
121 111 0.99
122 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (121 bp):
GATTTCATGCTTTTGACATAAATGTGACGTCCATGGGCAGGGCACTGTAGATGTGCCTTGCTTAC
CACCCGAAATATGTCCTGCTGGGGGGAAGAAGAGGAAAGAAAGGAGAAAGGGAGGT
Found at i:190360 original size:23 final size:23
Alignment explanation
Indices: 190334--190379 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
190324 TTAAAAAATT
*
190334 ATTAAAATATTAA-AAAAATTATA
1 ATTAAAATA-AAATAAAAATTATA
*
190357 ATTAAATTAAAATAAAAATTATA
1 ATTAAAATAAAATAAAAATTATA
190380 TTTTAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTAAAATAAAATAAAAATTATA
Found at i:190934 original size:20 final size:20
Alignment explanation
Indices: 190903--190955 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
190893 ACAAAATATT
190903 TTTAAAAT--TAATATGATA
1 TTTAAAATAATAATATGATA
*
190921 TTTAAAATAATAATATTATA
1 TTTAAAATAATAATATGATA
*
190941 -TTAAGTATAATAATA
1 TTTAA-AATAATAATA
190956 AATAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.27
19 4 0.13
20 18 0.60
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTAAAATAATAATATGATA
Found at i:191755 original size:24 final size:24
Alignment explanation
Indices: 191704--191765 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 24
191694 ATATTAAAAA
*
191704 ATTATTTTAT-A-TAAAATTATAT
1 ATTATTTTATAATTAAAATTAAAT
*
191726 A-T-TTTTATAATTAAATTTAAAT
1 ATTATTTTATAATTAAAATTAAAT
191748 ATTATTTT-TGAATTAAAA
1 ATTATTTTAT-AATTAAAA
191766 AATTTCATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 6 0.19
21 2 0.06
22 11 0.34
23 2 0.06
24 11 0.34
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTATTTTATAATTAAAATTAAAT
Found at i:195021 original size:20 final size:20
Alignment explanation
Indices: 194995--195049 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
194985 ATATAAAAAT
194995 AATTTTTATATTAATATTTA
1 AATTTTTATATTAATATTTA
*
195015 TATTTTTATAATTAA-ATTTA
1 AATTTTTAT-ATTAATATTTA
*
195035 AATTTAT-TATTAATA
1 AATTTTTATATTAATA
195050 AATAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.17
19 2 0.07
20 18 0.60
21 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTTATATTAATATTTA
Found at i:195372 original size:18 final size:19
Alignment explanation
Indices: 195321--195374 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
195311 TATTAAAATA
* *
195321 ATATTAAATATAATAATTTT
1 ATATTAAATTTAA-ATTTTT
195341 ATATTAATATTTAAATTTTT
1 ATATTAA-ATTTAAATTTTT
195361 A-ATTAAATTTAAAT
1 ATATTAAATTTAAAT
195375 AAGGTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.26
19 5 0.16
20 13 0.42
21 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTAAATTTAAATTTTT
Found at i:195916 original size:16 final size:17
Alignment explanation
Indices: 195879--195923 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
195869 AAATATATAA
195879 ATTTATTTATT--ATTT
1 ATTTATTTATTAAATTT
*
195894 ATTTATTTTTTAAATTT
1 ATTTATTTATTAAATTT
195911 -TTTATTTATTAAA
1 ATTTATTTATTAAA
195924 AAATGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATTTATTAAATTT
Found at i:196005 original size:20 final size:19
Alignment explanation
Indices: 195973--196039 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
195963 TAATTTTAAT
195973 ATATAAAA-ATTTATATAA
1 ATATAAAATATTTATATAA
*
195991 ATATAAAATATTTTAAATATA
1 ATATAAAATA-TTTATATA-A
* *
196012 AT-TATAATA-TTATAAAA
1 ATATAAAATATTTATATAA
*
196029 ATAAAAAATAT
1 ATATAAAATAT
196040 ACAAATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
17 3 0.08
18 18 0.47
19 1 0.03
20 13 0.34
21 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAAATATTTATATAA
Found at i:196009 original size:16 final size:15
Alignment explanation
Indices: 195964--196012 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 15
195954 GTTGATGCGT
195964 AATTTTAATATATAAA
1 AATTTTAA-ATATAAA
195980 AATTTATATAAATATAAA
1 AA-TT-T-TAAATATAAA
195998 ATATTTTAAATATAA
1 A-ATTTTAAATATAA
196013 TTATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 11 0.38
19 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAAATATAAA
Found at i:196077 original size:17 final size:17
Alignment explanation
Indices: 196055--196089 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
196045 TACATAAATC
196055 ATATTTTA-TATATTAAA
1 ATATTTTATTAT-TTAAA
196072 ATATTTTATTATTTAAA
1 ATATTTTATTATTTAAA
196089 A
1 A
196090 AATATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTTATTATTTAAA
Found at i:196118 original size:25 final size:24
Alignment explanation
Indices: 196056--196130 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 24
196046 ACATAAATCA
196056 TATTTTATATATTAAAATATTTTAT
1 TATTTTA-ATATTAAAATATTTTAT
* *
196081 TATTTAAAAAATATTAAAATATTATTTT
1 TATTT---TAATATTAAAATATT-TTAT
* *
196109 TATTTTAATATTTATATATTTT
1 TATTTTAATATTAAAATATTTT
196131 TATAATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.05
25 17 0.41
27 13 0.32
28 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTAATATTAAAATATTTTAT
Found at i:196143 original size:22 final size:22
Alignment explanation
Indices: 196103--196144 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
196093 ATTAAAATAT
*
196103 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTATA
196125 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
196145 AATAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:196173 original size:25 final size:26
Alignment explanation
Indices: 196070--196173 Score: 72
Period size: 25 Copynumber: 4.0 Consensus size: 26
196060 TTATATATTA
* *
196070 AAATATTTTATTATTTAAAAAATATT
1 AAATATTTTATTATTTAAATAATAAT
* * * *
196096 AAAATATTATTTTTATTTTAATATTTAT
1 -AAATATT-TTATTATTTAAATAATAAT
* * *
196124 ATAT-TTTTA-TAATTAAAT-TTAAAT
1 AAATATTTTATTATTTAAATAAT-AAT
196148 AAATATTTTATTA-TTAAATAATAAT
1 AAATATTTTATTATTTAAATAATAAT
196173 A
1 A
196174 TAAATCAAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
23 2 0.03
24 12 0.20
25 17 0.29
26 5 0.08
27 10 0.17
28 13 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATATTTTATTATTTAAATAATAAT
Found at i:196787 original size:32 final size:32
Alignment explanation
Indices: 196691--196788 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 32
196681 ATATATTTTA
*
196691 TTATATTATAATTATATTTAAAATAATTTATAT-T
1 TTATATTAT-ATAAT-TTTAAAAT-ATTTATATAT
* * *
196725 TT-T-TTATA-AATTTTAATATGTTAATA-AT
1 TTATATTATATAATTTTAAAATATTTATATAT
196753 TTATATTATATAATTTTAAAATATTTATATAT
1 TTATATTATATAATTTTAAAATATTTATATAT
196785 TTAT
1 TTAT
196789 GTAATATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.15
29 8 0.15
30 7 0.13
31 16 0.31
32 10 0.19
33 1 0.02
34 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TTATATTATATAATTTTAAAATATTTATATAT
Found at i:196817 original size:60 final size:60
Alignment explanation
Indices: 196686--196828 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
196676 TATTTATATA
* * *
196686 TTTTATTATATTATAATTATATTTAAAATAATTTATATTTTTTTATAAATTTTAATATGTT
1 TTTTATTATATTAT-ATAATATTTAAAATAATTTATATATTTATATAAATTTTAATATGTT
** * *
196747 AATAATTTATATTATATAAT-TTTAAAAT-ATTTATATATTTATGTAATATTTTAATAAAT-TT
1 TTTTA-TTATATTATATAATATTTAAAATAATTTATATATTTATATAA-ATTTTAAT--ATGTT
196808 TTTTATTATATTTATATAATA
1 TTTTATTATA-TTATATAATA
196829 AATATTATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
59 15 0.23
60 21 0.32
61 19 0.29
62 11 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (60 bp):
TTTTATTATATTATATAATATTTAAAATAATTTATATATTTATATAAATTTTAATATGTT
Found at i:197264 original size:27 final size:29
Alignment explanation
Indices: 197234--197305 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 29
197224 TAATATGAAT
197234 TATAAAATATATTAAAATTT-A-TATAA-A
1 TATAAAATATATT-AAATTTGATTATAACA
*
197261 TATAAAATAT-TTAAATTTGATTATAACG
1 TATAAAATATATTAAATTTGATTATAACA
197289 TAATAAAATATA-TAAAT
1 T-ATAAAATATATTAAAT
197306 ATGACATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
25 6 0.15
26 3 0.08
27 15 0.38
28 1 0.03
29 14 0.36
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
TATAAAATATATTAAATTTGATTATAACA
Found at i:198039 original size:26 final size:25
Alignment explanation
Indices: 197992--198052 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
197982 AAATGCCATG
*
197992 ATTATTTAATAATTTATGTATT-TA
1 ATTATTTTATAATTTATGTATTATA
* *
198016 TATTATGTTTATAATTTTTTTATTATA
1 -ATTAT-TTTATAATTTATGTATTATA
198043 ATTATATTTA
1 ATTAT-TTTA
198053 AAATGATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 23 0.77
27 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTATTTTATAATTTATGTATTATA
Found at i:198134 original size:11 final size:11
Alignment explanation
Indices: 198120--198153 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
198110 TAACAAATTT
198120 TTATATTTATA
1 TTATATTTATA
198131 TTATATTTATA
1 TTATATTTATA
* *
198142 TTTTTTTTATA
1 TTATATTTATA
198153 T
1 T
198154 AACATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTTATA
Found at i:198520 original size:2 final size:2
Alignment explanation
Indices: 198513--198575 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
198503 AATCTGAAAG
* * * *
198513 AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT GT 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
* * * *
198555 AT GT AT GT AT GT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
198576 GTTCATCTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (2 bp):
AT
Found at i:198552 original size:24 final size:24
Alignment explanation
Indices: 198520--198575 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
198510 AAGATATATA
198520 TATATATATATATGTATGTATGTG
1 TATATATATATATGTATGTATGTG
198544 TATATATATATATGTATGTATGTG
1 TATATATATATATGTATGTATGTG
198568 TATATATA
1 TATATATA
198576 GTTCATCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (24 bp):
TATATATATATATGTATGTATGTG
Found at i:198575 original size:20 final size:20
Alignment explanation
Indices: 198524--198562 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
198514 TATATATATA
*
198524 TATATATATGTATGTATGTG
1 TATATATATATATGTATGTG
198544 TATATATATATATGTATGT
1 TATATATATATATGTATGT
198563 ATGTGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
TATATATATATATGTATGTG
Found at i:198820 original size:23 final size:25
Alignment explanation
Indices: 198787--198844 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
198777 ATTTAAAAAT
* *
198787 TATATTTATA-TATTTAAATTTTGA
1 TATATTTATATTATATAAATTTTAA
198811 TA-ATTTATATTATATAAATTTTAA
1 TATATTTATATTATATAAATTTTAA
198835 TATATTTATA
1 TATATTTATA
198845 ATAATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 7 0.23
24 16 0.53
25 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATTTATATTATATAAATTTTAA
Found at i:198853 original size:34 final size:31
Alignment explanation
Indices: 198760--198889 Score: 91
Period size: 31 Copynumber: 4.3 Consensus size: 31
198750 ATTTATATTT
*
198760 TTTATATATTATAAATTATTTA-AA-AATTATA
1 TTTATAAATT-TAAA-TATTTATAATAATTATA
*
198791 TTTATATATTTAAAT-TTTGATAAT--TTATA
1 TTTATAAATTTAAATATTT-ATAATAATTATA
198820 TTATATAAATTTTAATATATTTATAATAATTATA
1 TT-TATAAA-TTTAA-ATATTTATAATAATTATA
* * *
198854 -TT-TAAA-TTAATTTTTTATTAT-ATTATA
1 TTTATAAATTTAAATATTTATAATAATTATA
198881 TTTA-AAATT
1 TTTATAAATT
198890 ATCCGTTCAC
Statistics
Matches: 83, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
27 6 0.07
28 16 0.19
29 14 0.17
30 11 0.13
31 19 0.23
32 8 0.10
33 4 0.05
34 5 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
TTTATAAATTTAAATATTTATAATAATTATA
Done.