Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 15 of 24
Found at i:1955099 original size:12 final size:12
Alignment explanation
Indices: 1955084--1955108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1955074 AAAAATTATC
1955084 AATTTAATTTTT
1 AATTTAATTTTT
1955096 AATTTAATTTTT
1 AATTTAATTTTT
1955108 A
1 A
1955109 TTTTTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTAATTTTT
Found at i:1957443 original size:2 final size:2
Alignment explanation
Indices: 1957436--1957464 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1957426 GAGTTCAACT
1957436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1957465 TAATTTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1958315 original size:16 final size:17
Alignment explanation
Indices: 1958290--1958323 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1958280 ATTATAATTA
*
1958290 AATTTTAATAAG-TAAT
1 AATTTAAATAAGTTAAT
1958306 AATTTAAATAAGTTAAT
1 AATTTAAATAAGTTAAT
1958323 A
1 A
1958324 TAAAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTTAAATAAGTTAAT
Found at i:1958508 original size:5 final size:5
Alignment explanation
Indices: 1958498--1958525 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1958488 TTTAATATCA
1958498 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
1958526 GAGTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1968305 original size:129 final size:131
Alignment explanation
Indices: 1968160--1968397 Score: 304
Period size: 129 Copynumber: 1.8 Consensus size: 131
1968150 ATTTTTTCTT
* * ** **
1968160 AAAAAAAAATTATTTATTTATGTTTTTGTTAATTTTTT-ATATGTTTTAAATATTATAAATTTAT
1 AAAAAAAAATTATTTA--TATGTCTTTGTTAATTTTTTCACACATTCAAAATATTATAAATTTAT
* * * * *
1968224 ATATA-TTTTACGTTTTAATAATTTGTTTTATTTATATATTGATATGTTCATGTATAAATAAAAA
64 ATAAATTTTTACATATTAATAATTTATTTTATATATATATTGATATGTTCATGTATAAATAAAAA
1968288 ATG
129 ATG
*
1968291 AAAAAAAAA-T-TTTATATGTCTTTGTTAATTTTTTCGCACATTCAAAATATTATAAATTTATAT
1 AAAAAAAAATTATTTATATGTCTTTGTTAATTTTTTCACACATTCAAAATATTATAAATTTATAT
* *
1968354 AAATTTTTACATATTAATATTTTATTTTATATATATTTTGATAT
66 AAATTTTTACATATTAATAATTTATTTTATATATATATTGATAT
1968398 TTTCTTATAT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
127 19 0.21
128 24 0.26
129 38 0.42
130 1 0.01
131 9 0.10
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (131 bp):
AAAAAAAAATTATTTATATGTCTTTGTTAATTTTTTCACACATTCAAAATATTATAAATTTATAT
AAATTTTTACATATTAATAATTTATTTTATATATATATTGATATGTTCATGTATAAATAAAAAAT
G
Found at i:1968400 original size:19 final size:19
Alignment explanation
Indices: 1968376--1968429 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1968366 ATTAATATTT
1968376 TATTTTATATATATTTTGA
1 TATTTTATATATATTTTGA
*
1968395 TATTTTCT-TATATTTATGA
1 TATTTTATATATATTT-TGA
1968414 T-TGTTTATAT-TATTTT
1 TAT-TTTATATATATTTT
1968430 TGAAGTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 9 0.30
19 20 0.67
20 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.67
Consensus pattern (19 bp):
TATTTTATATATATTTTGA
Found at i:1972919 original size:14 final size:14
Alignment explanation
Indices: 1972900--1972926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1972890 TTTAAGTATA
1972900 AAATATAAAAATAT
1 AAATATAAAAATAT
1972914 AAATATAAAAATA
1 AAATATAAAAATA
1972927 ATTTTTAAAT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATAAAAATAT
Found at i:1974759 original size:7 final size:7
Alignment explanation
Indices: 1974747--1974919 Score: 82
Period size: 7 Copynumber: 23.1 Consensus size: 7
1974737 GAATTATACG
1974747 AATATAA
1 AATATAA
1974754 AATATAA
1 AATATAA
*
1974761 AATATTA
1 AATATAA
*
1974768 AATATAT
1 AATATAA
1974775 AATATAA
1 AATATAA
* **
1974782 CAAGATTTG
1 -AATA-TAA
1974791 AATATAA
1 AATATAA
* *
1974798 ATTTTAA
1 AATATAA
*
1974805 AATTTATAT
1 AA--TATAA
1974814 AATATAA
1 AATATAA
*
1974821 ATTATTAA
1 AATA-TAA
*
1974829 TATATTAA
1 AATA-TAA
1974837 AATTTATATA
1 AA--TATA-A
1974847 AATATAA
1 AATATAA
*
1974854 AATAATTTA
1 AAT-A-TAA
1974863 AATAT-A
1 AATATAA
1974869 AATATAA
1 AATATAA
*
1974876 TATAATAA
1 AAT-ATAA
1974884 AATATATA
1 AATATA-A
1974892 AATAT--
1 AATATAA
1974897 AATATAA
1 AATATAA
1974904 ATATATAA
1 A-ATATAA
*
1974912 ATTATAA
1 AATATAA
1974919 A
1 A
1974920 TGCATAACAA
Statistics
Matches: 126, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
5 5 0.04
6 6 0.05
7 56 0.44
8 41 0.33
9 13 0.10
10 5 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (7 bp):
AATATAA
Found at i:1974776 original size:23 final size:23
Alignment explanation
Indices: 1974748--1974919 Score: 94
Period size: 21 Copynumber: 7.6 Consensus size: 23
1974738 AATTATACGA
1974748 ATATAAAATATAAAATATTAAAT
1 ATATAAAATATAAAATATTAAAT
* **
1974771 ATAT--AATATAACAAGATTTGA-
1 ATATAAAATATAA-AATATTAAAT
* * *
1974792 ATATAAATTTTAAAAT-TTATAT
1 ATATAAAATATAAAATATTAAAT
* *
1974814 AATATAAATTATTAATATATTAAAAT
1 -ATATAAAATA-TAAAATATT-AAAT
* *
1974840 TTATATAAATATAAAATAATTTAA-
1 ATATA-AAATATAAAAT-ATTAAAT
* *
1974864 ATAT-AAATATAATATAATAAA-
1 ATATAAAATATAAAATATTAAAT
1974885 ATATATAAATAT--AATA-TAAAT
1 ATATA-AAATATAAAATATTAAAT
*
1974906 ATATAAATTATAAA
1 ATATAAAATATAAA
1974920 TGCATAACAA
Statistics
Matches: 113, Mismatches: 21, Indels: 31
0.68 0.13 0.19
Matches are distributed among these distances:
20 9 0.08
21 30 0.27
22 19 0.17
23 24 0.21
24 8 0.07
25 13 0.12
26 10 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (23 bp):
ATATAAAATATAAAATATTAAAT
Found at i:1974815 original size:18 final size:18
Alignment explanation
Indices: 1974792--1974849 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1974782 CAAGATTTGA
1974792 ATATAAATTTTAAAATTT
1 ATATAAATTTTAAAATTT
*
1974810 ATAT-AA-TAT-AAA-TT
1 ATATAAATTTTAAAATTT
*
1974824 AT-TAATATATTAAAATTT
1 ATATAA-ATTTTAAAATTT
1974842 ATATAAAT
1 ATATAAAT
1974850 ATAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 4 0.13
16 3 0.10
17 5 0.16
18 10 0.32
19 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAAATTTTAAAATTT
Found at i:1974850 original size:20 final size:21
Alignment explanation
Indices: 1974827--1974913 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 21
1974817 ATAAATTATT
1974827 AATATATTAA-AATTTATATA
1 AATATATTAATAATTTATATA
*
1974847 AATATA-AAATAATTTAAATATA
1 AATATATTAATAATTT--ATATA
**
1974869 AATATAATATAATAAAATATATA
1 AATAT-AT-TAATAATTTATATA
* *
1974892 AATATAAT-ATAA-ATATATA
1 AATATATTAATAATTTATATA
1974911 AAT
1 AAT
1974914 TATAAATGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
19 12 0.21
20 15 0.27
21 1 0.02
22 11 0.20
23 11 0.20
25 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATATTAATAATTTATATA
Found at i:1974851 original size:18 final size:17
Alignment explanation
Indices: 1974792--1974914 Score: 76
Period size: 19 Copynumber: 6.9 Consensus size: 17
1974782 CAAGATTTGA
*
1974792 ATATAAATTTTAAAATTT
1 ATATAAA-TATAAAATTT
1974810 ATAT-AATAT-AAA-TT
1 ATATAAATATAAAATTT
1974824 AT-TAATATATTAAAATTT
1 ATATAA-ATA-TAAAATTT
*
1974842 ATATAAATATAAAA-TA
1 ATATAAATATAAAATTT
* *
1974858 ATTTAAATATAAATATAAT
1 ATATAAATATAAA-AT-TT
*
1974877 ATAATAAAATATATAAATATA
1 AT-AT-AAATATA-AAAT-TT
1974898 ATATAAATATATAAATT
1 ATATAAATATA-AAATT
1974915 ATAAATGCAT
Statistics
Matches: 85, Mismatches: 8, Indels: 24
0.73 0.07 0.21
Matches are distributed among these distances:
13 1 0.01
14 5 0.06
15 6 0.07
16 16 0.19
17 11 0.13
18 12 0.14
19 17 0.20
20 3 0.04
21 12 0.14
22 2 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:1974853 original size:6 final size:6
Alignment explanation
Indices: 1974842--1974908 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
1974832 ATTAAAATTT
* *
1974842 ATATAA ATATAA A-AT-A ATTTAA ATATAA ATAT-A ATAT-A ATAAAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1974886 TATATAA ATAT-A ATATAA ATATA
1 -ATATAA ATATAA ATATAA ATATA
1974909 TAAATTATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 2 0.04
5 17 0.33
6 28 0.54
7 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:1974906 original size:49 final size:47
Alignment explanation
Indices: 1974747--1974920 Score: 156
Period size: 49 Copynumber: 3.5 Consensus size: 47
1974737 GAATTATACG
* *
1974747 AATATAAAATATA-AAATATTAAATATATAATATAACAAGATTTGAATATA
1 AATATAAAATATATAAATA-TAAATAT-TAATATAATAAAATTT-AA-ATA
* * * *
1974797 AATTTTAAAATTTATATAATATAAATTATTAATATATTAAAATTTATATA
1 AA-TATAAAATATATA-AATATAAA-TATTAATATAATAAAATTTAAATA
*
1974847 AATATAAAATAATTTAAATATAAATA-TAATATAATAAAATATATAAATA
1 AATATAAAAT-ATATAAATATAAATATTAATATAATAAAAT-T-TAAATA
1974896 TAATAT-AAATATATAAATTATAAAT
1 -AATATAAAATATATAAA-TATAAAT
1974921 GCATAACAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
47 13 0.13
48 9 0.09
49 31 0.30
50 15 0.15
51 10 0.10
52 18 0.17
53 7 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (47 bp):
AATATAAAATATATAAATATAAATATTAATATAATAAAATTTAAATA
Found at i:1974920 original size:15 final size:15
Alignment explanation
Indices: 1974815--1974920 Score: 55
Period size: 15 Copynumber: 7.0 Consensus size: 15
1974805 AATTTATATA
*
1974815 ATATAAATTATTAAT
1 ATATAAATTATAAAT
1974830 ATATTAAAATTTATATAA-
1 ATA-T-AAA-TTATA-AAT
* *
1974848 ATATAAAATAATTTAA-
1 ATAT-AAATTA-TAAAT
1974864 ATATAAA-TAT-AAT
1 ATATAAATTATAAAT
*
1974877 ATAATAAAATATATAA-
1 AT-ATAAATTATA-AAT
1974893 ATAT-AA-TATAAAT
1 ATATAAATTATAAAT
1974906 ATATAAATTATAAAT
1 ATATAAATTATAAAT
1974921 GCATAACAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
12 4 0.05
13 11 0.15
14 10 0.14
15 18 0.24
16 11 0.15
17 11 0.15
18 7 0.09
19 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAAATTATAAAT
Found at i:1975128 original size:8 final size:8
Alignment explanation
Indices: 1975117--1975210 Score: 75
Period size: 8 Copynumber: 11.2 Consensus size: 8
1975107 TAATTTCTAT
1975117 TATATTTA
1 TATATTTA
1975125 TATATTTTAA
1 TATA-TTT-A
1975135 TAATATTTA
1 T-ATATTTA
*
1975144 -AAATATTA
1 TATAT-TTA
1975152 TATATTTA
1 TATATTTA
1975160 TATATTTA
1 TATATTTA
*
1975168 TATATTAA
1 TATATTTA
*
1975176 T-TATTTT
1 TATATTTA
1975183 TATATTATA
1 TATATT-TA
*
1975192 TTTATATTA
1 TATAT-TTA
*
1975201 TATAATTA
1 TATATTTA
1975209 TA
1 TA
1975211 ACTTGCATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 8 0.12
8 35 0.51
9 17 0.25
10 6 0.09
11 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:1975149 original size:28 final size:28
Alignment explanation
Indices: 1975093--1975158 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1975083 ATTTTCGCAC
* **
1975093 ATTTA-ATAATTTAATAATTTCTATTAT
1 ATTTATATATTTTAATAATTTCTAAAAT
1975120 ATTTATATATTTTAATAATATT-TAAAAT
1 ATTTATATATTTTAATAAT-TTCTAAAAT
1975148 A-TTATATATTT
1 ATTTATATATTT
1975159 ATATATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.44
28 17 0.50
29 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTATATATTTTAATAATTTCTAAAAT
Found at i:1975176 original size:41 final size:42
Alignment explanation
Indices: 1975117--1975210 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 42
1975107 TAATTTCTAT
1975117 TATATTTATATATTTTAATAATATTTA-A-AATATTATATATTTA
1 TATATTTATATA-TTTAATAATATTTATATAATATT-TATA-TTA
* * *
1975160 TATATTTATATA-TTAATTATTTTTATATTATATTTATATTA
1 TATATTTATATATTTAATAATATTTATATAATATTTATATTA
*
1975201 TATAATTATA
1 TATATTTATA
1975211 ACTTGCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 23 0.51
42 5 0.11
43 17 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (42 bp):
TATATTTATATATTTAATAATATTTATATAATATTTATATTA
Found at i:1975202 original size:11 final size:11
Alignment explanation
Indices: 1975109--1975203 Score: 71
Period size: 11 Copynumber: 9.2 Consensus size: 11
1975099 TAATTTAATA
*
1975109 ATTTCTATTAT
1 ATTTATATTAT
1975120 ATTTATA-TAT
1 ATTTATATTAT
*
1975130 -TTTA-ATAAT
1 ATTTATATTAT
*
1975139 ATTTA-A-AAT
1 ATTTATATTAT
1975148 ATTATATATT-T
1 ATT-TATATTAT
*
1975159 ATATAT-TTAT
1 ATTTATATTAT
1975169 ATATTA-ATTAT
1 AT-TTATATTAT
*
1975180 TTTTATATTAT
1 ATTTATATTAT
1975191 ATTTATATTAT
1 ATTTATATTAT
1975202 AT
1 AT
1975204 AATTATAACT
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
8 1 0.01
9 14 0.21
10 19 0.28
11 34 0.50
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:1975417 original size:16 final size:18
Alignment explanation
Indices: 1975387--1975420 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1975377 AATTTTTATA
1975387 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
1975405 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
1975421 CATTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:1975522 original size:40 final size:39
Alignment explanation
Indices: 1975474--1975554 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 39
1975464 TTTTATATTG
*
1975474 ATTTAAATTT-ATATTACTTAATATAT-TAAATAATTTTTA
1 ATTTAAATTTAAT-TTAATTAATATATAT-AATAATTTTTA
* *
1975513 ATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTA
1 ATTT-AAATTTAATTTAATTAATATATATAATAATTTTTA
1975553 AT
1 AT
1975555 AAATAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 4 0.11
40 29 0.81
41 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (39 bp):
ATTTAAATTTAATTTAATTAATATATATAATAATTTTTA
Found at i:1975530 original size:28 final size:29
Alignment explanation
Indices: 1975499--1975603 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 29
1975489 ACTTAATATA
1975499 TTAAATAATTTT-TAATTTAAAATTTAAT
1 TTAAATAATTTTATAATTTAAAATTTAAT
* **
1975527 TTAATTAATTTATATAA-TT-ATTTTTAAT
1 TTAAATAATTT-TATAATTTAAAATTTAAT
** *
1975555 AAATAATATTTTTATAAATTTAAAATTTAAAT
1 TTA-AATAATTTTAT-AATTTAAAATTT-AAT
1975587 TTAAAT-A-TTTATAATTT
1 TTAAATAATTTTATAATTT
1975604 TTTATTTTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
28 26 0.45
29 16 0.28
30 5 0.09
31 7 0.12
32 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTAAATAATTTTATAATTTAAAATTTAAT
Found at i:1975571 original size:15 final size:17
Alignment explanation
Indices: 1975540--1975573 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1975530 ATTAATTTAT
1975540 ATAATTATTTTTAATAA
1 ATAATTATTTTTAATAA
1975557 ATAA-TATTTTT-ATAA
1 ATAATTATTTTTAATAA
1975572 AT
1 AT
1975574 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 7 0.41
17 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAATTATTTTTAATAA
Found at i:1975587 original size:13 final size:14
Alignment explanation
Indices: 1975569--1975603 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1975559 AATATTTTTA
1975569 TAAATTTAAA-ATT
1 TAAATTTAAATATT
1975582 TAAATTTAAATATT
1 TAAATTTAAATATT
1975596 TATAATTT
1 TA-AATTT
1975604 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
14 5 0.25
15 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATTTAAATATT
Found at i:1975790 original size:11 final size:11
Alignment explanation
Indices: 1975771--1975890 Score: 58
Period size: 11 Copynumber: 11.3 Consensus size: 11
1975761 TTGATAATTT
*
1975771 TAAATATAATA
1 TAAAAATAATA
1975782 TAAAAATAATA
1 TAAAAATAATA
*
1975793 TAAATATAATA
1 TAAAAATAATA
1975804 T----A-AATA
1 TAAAAATAATA
1975810 TAAAAAT-ATA
1 TAAAAATAATA
* *
1975820 TTAAAAT-TTA
1 TAAAAATAATA
*
1975830 TATAAAT-ATA
1 TAAAAATAATA
**
1975840 TAATATTTTAAATA
1 TAA-A-AAT-AATA
**
1975854 TAATTATAATA
1 TAAAAATAATA
1975865 TAAAAATTAATA
1 TAAAAA-TAATA
*
1975877 TAAATATAATA
1 TAAAAATAATA
1975888 TAA
1 TAA
1975891 TTTTTTAATT
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
6 5 0.06
7 1 0.01
10 21 0.25
11 38 0.45
12 13 0.15
14 6 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:1975797 original size:22 final size:22
Alignment explanation
Indices: 1975771--1975890 Score: 101
Period size: 22 Copynumber: 5.6 Consensus size: 22
1975761 TTGATAATTT
1975771 TAAATATAATATAAAAATAATA
1 TAAATATAATATAAAAATAATA
1975793 TAAATATAATAT--AAAT-ATA
1 TAAATATAATATAAAAATAATA
* * *
1975812 AAAATAT-AT-TAAAATTTATA
1 TAAATATAATATAAAAATAATA
***
1975832 TAAATAT-ATA-ATATTTTAAATA
1 TAAATATAATATA-AAAAT-AATA
*
1975854 TAATTATAATATAAAAATTAATA
1 TAAATATAATATAAAAA-TAATA
1975877 TAAATATAATATAA
1 TAAATATAATATAA
1975891 TTTTTTAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 2 0.03
19 12 0.15
20 16 0.21
21 3 0.04
22 21 0.27
23 21 0.27
24 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATAATATAAAAATAATA
Found at i:1975849 original size:20 final size:20
Alignment explanation
Indices: 1975808--1975865 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1975798 ATAATATAAA
* *
1975808 TATAAAAATATATTAA-AATT
1 TATATAAATATA-TAATATTT
1975828 TATATAAATATATAATATTT
1 TATATAAATATATAATATTT
*
1975848 TAAATATAAT-TATAATAT
1 TATATA-AATATATAATAT
1975866 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATAAATATATAATATTT
Found at i:1976632 original size:2 final size:2
Alignment explanation
Indices: 1976625--1976661 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1976615 AGTACAACCT
1976625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1976662 GTGACATTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1977300 original size:2 final size:2
Alignment explanation
Indices: 1977255--1977283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1977245 TGACTTCTTT
1977255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1977284 TTAGTAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1977400 original size:27 final size:26
Alignment explanation
Indices: 1977370--1977459 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 26
1977360 CCACCATTTA
1977370 TGTTTGTTAAAAATGATGGTTCTTTT
1 TGTTTGTTAAAAATGATGGTTCTTTT
*
1977396 GTGTTT-TTCAAAAATGATGATTCCTTTT
1 -TGTTTGTT-AAAAATGATGGTT-CTTTT
* *
1977424 TGTTTGTAAAAAATGATGG-T-TTGT
1 TGTTTGTTAAAAATGATGGTTCTTTT
1977448 TGTTTGTTAAAA
1 TGTTTGTTAAAA
1977460 TTAATAGCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
24 14 0.25
26 3 0.05
27 32 0.58
28 6 0.11
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (26 bp):
TGTTTGTTAAAAATGATGGTTCTTTT
Found at i:1981944 original size:27 final size:27
Alignment explanation
Indices: 1981914--1982018 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
1981904 TAAAAGCCAC
*
1981914 CCTTTGTGTTTGTCAAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
*
1981941 CCTTTGTATTTGTCAAAAATAGTGGTT
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
* * * * *
1981968 CTTTTTTGTTTGT-AAAAAAAATGGTG
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
* *
1981994 GC-TTGTTGTTTGTCAAAATTAGTGG
1 CCTTTG-TGTTTGTCAAAAATAGTGG
1982019 CTAATTTTTA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
25 2 0.03
26 17 0.27
27 43 0.69
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATAGTGGTT
Found at i:1983790 original size:43 final size:43
Alignment explanation
Indices: 1983742--1983828 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
1983732 AGTGTCTTCG
*
1983742 TAATCTTGACTGACTTTTTATAAATGG-TTAA-GTTCCACATTTT
1 TAATCTTGACCGAC-TTTTATAAATGGTTTAACG-TCCACATTTT
*
1983785 TAATCTTGACCGACTTTTGTAAATGGTTTAACGTCCACATTTT
1 TAATCTTGACCGACTTTTATAAATGGTTTAACGTCCACATTTT
1983828 T
1 T
1983829 TTTTTTGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 11 0.28
43 28 0.70
44 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (43 bp):
TAATCTTGACCGACTTTTATAAATGGTTTAACGTCCACATTTT
Found at i:1984111 original size:25 final size:26
Alignment explanation
Indices: 1984078--1984130 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1984068 ATTTAAATTT
1984078 AATTATAAATATTAATATAAA-AATA
1 AATTATAAATATTAATATAAATAATA
* * *
1984103 AATTTTAAATATTATTTTAAATAATA
1 AATTATAAATATTAATATAAATAATA
1984129 AA
1 AA
1984131 ATAATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTATAAATATTAATATAAATAATA
Found at i:1985131 original size:17 final size:18
Alignment explanation
Indices: 1985099--1985133 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1985089 ATTTGACAAT
1985099 TTAAATAAAAATATTAAA
1 TTAAATAAAAATATTAAA
1985117 TTAAATAAAAA-ATTAAA
1 TTAAATAAAAATATTAAA
1985134 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATAAAAATATTAAA
Found at i:1985151 original size:10 final size:11
Alignment explanation
Indices: 1985114--1985150 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
1985104 TAAAAATATT
1985114 AAATTAAATAAA
1 AAATTAAA-AAA
1985126 AAATTAAAAAAA
1 AAATT-AAAAAA
1985138 AAATTAAAAAA
1 AAATTAAAAAA
1985149 AA
1 AA
1985151 TGTATCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 13 0.54
13 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:1986693 original size:18 final size:19
Alignment explanation
Indices: 1986665--1986703 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1986655 TTATTTAAAT
1986665 TTAATTATAAAAATATATA
1 TTAATTATAAAAATATATA
*
1986684 TTAA-TATAAAAATATTTA
1 TTAATTATAAAAATATATA
1986702 TT
1 TT
1986704 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATTATAAAAATATATA
Found at i:1986709 original size:20 final size:18
Alignment explanation
Indices: 1986664--1986710 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
1986654 TTTATTTAAA
1986664 TTTAATTATAAAAATATAT
1 TTTAA-TATAAAAATATAT
*
1986683 ATTAATATAAAAATATTTAT
1 TTTAATATAAAAATA--TAT
1986703 TTTAATAT
1 TTTAATAT
1986711 TTTGATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 4 0.17
20 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATATAAAAATATAT
Found at i:1986991 original size:2 final size:2
Alignment explanation
Indices: 1986979--1987013 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1986969 TCAAAATTTC
*
1986979 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1987014 ACTCGTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1987589 original size:2 final size:2
Alignment explanation
Indices: 1987582--1987608 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1987572 ATGCCAATTT
1987582 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
1987609 GTGTGTATGC
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:1988501 original size:28 final size:27
Alignment explanation
Indices: 1988470--1988523 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1988460 ATATCCATAC
1988470 AAAT-AAAAAAATATGAAAATAAAATATT
1 AAATGAAAAAAA-ATG-AAATAAAATATT
* *
1988498 AAATGCAAAGAAATGAAATAAAATAT
1 AAATGAAAAAAAATGAAATAAAATAT
1988524 GCATCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 7 0.30
29 5 0.22
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (27 bp):
AAATGAAAAAAAATGAAATAAAATATT
Found at i:1992419 original size:2 final size:2
Alignment explanation
Indices: 1992412--1992437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1992402 TTAGAGTGAC
1992412 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
1992438 TCATATAAAG
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:1996450 original size:3 final size:3
Alignment explanation
Indices: 1996444--1996494 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
1996434 TCCTACTATT
*
1996444 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1996492 ATA
1 ATA
1996495 GCAATTTGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1998917 original size:24 final size:24
Alignment explanation
Indices: 1998886--1998931 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1998876 TTTAAAATAA
*
1998886 TTTAAATTTAAATAATTTAAAAGT
1 TTTAAATTAAAATAATTTAAAAGT
1998910 TTTAAATTAAAATAATTTAAAA
1 TTTAAATTAAAATAATTTAAAA
1998932 TTAAATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTAAATTAAAATAATTTAAAAGT
Found at i:1999250 original size:20 final size:19
Alignment explanation
Indices: 1999214--1999259 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1999204 ATATTTTATT
*
1999214 TAAATTTTATTACTAAAATA
1 TAAATTTTAATACTAAAA-A
1999234 TAAATATTTAATA-TAAAAA
1 TAAAT-TTTAATACTAAAAA
1999253 T-AATTTT
1 TAAATTTT
1999260 TTATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 2 0.08
20 10 0.42
21 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTTTAATACTAAAAA
Found at i:1999313 original size:22 final size:22
Alignment explanation
Indices: 1999283--1999324 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1999273 TTTAAAATTT
*
1999283 TAATTAAATTTATAA-ATTAAAA
1 TAATGAAATTTA-AATATTAAAA
1999305 TAATGAAATTTAAATATTAA
1 TAATGAAATTTAAATATTAA
1999325 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATGAAATTTAAATATTAAAA
Found at i:2003203 original size:24 final size:23
Alignment explanation
Indices: 2003158--2003205 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
2003148 TATATATTCA
2003158 TATTATATTTATATTATTTTTTG
1 TATTATATTTATATTATTTTTTG
2003181 TATTATATTTTATATT-TTATTTTG
1 TATTATA-TTTATATTATT-TTTTG
2003205 T
1 T
2003206 GTTCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTATATTTATATTATTTTTTG
Found at i:2004920 original size:17 final size:17
Alignment explanation
Indices: 2004900--2004935 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2004890 ATATTTAACA
* *
2004900 TAAAAATATTATTTTTT
1 TAAAAAAATTATATTTT
2004917 TAAAAAAATTATATTTT
1 TAAAAAAATTATATTTT
2004934 TA
1 TA
2004936 CCGATATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAAAAATTATATTTT
Found at i:2005932 original size:15 final size:15
Alignment explanation
Indices: 2005910--2005950 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
2005900 AAATATTATT
2005910 ATAA-AAAATTTTAA
1 ATAATAAAATTTTAA
2005924 ATAATAAAATTTTAA
1 ATAATAAAATTTTAA
*
2005939 ATATTAAAATTT
1 ATAATAAAATTT
2005951 ATTATTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAAATTTTAA
Found at i:2006856 original size:10 final size:10
Alignment explanation
Indices: 2006841--2006874 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2006831 ATGTCATAAA
2006841 AATTAAAATT
1 AATTAAAATT
2006851 AATTAAAAATT
1 AATT-AAAATT
*
2006862 AAATAAAATT
1 AATTAAAATT
2006872 AAT
1 AAT
2006875 ATTTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATTAAAATT
Found at i:2010489 original size:23 final size:23
Alignment explanation
Indices: 2010446--2010489 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2010436 TACACTTTAT
* *
2010446 TAAGATAACATGGAAGTGAATTA
1 TAAGAAAACATGGAAGAGAATTA
2010469 TAAGAAAACA-GGTAAGAGAAT
1 TAAGAAAACATGG-AAGAGAAT
2010490 AAAAGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (23 bp):
TAAGAAAACATGGAAGAGAATTA
Found at i:2017247 original size:24 final size:24
Alignment explanation
Indices: 2017188--2017248 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
2017178 TCCATCATTT
* * *
2017188 AATTAA-TAAAAAAATTTATTTAA
1 AATTAATTATAAAAATTAATATAA
*
2017211 ATTTAATTATAAAAATTAATATAA
1 AATTAATTATAAAAATTAATATAA
* *
2017235 AATTAGTTTTAAAA
1 AATTAATTATAAAA
2017249 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTAATTATAAAAATTAATATAA
Found at i:2019342 original size:33 final size:33
Alignment explanation
Indices: 2019305--2019508 Score: 138
Period size: 33 Copynumber: 6.2 Consensus size: 33
2019295 TAATCAAAGA
* *
2019305 TTCCTCACCTAAGGTTGTGGGACTGGTTGGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
* * * * *
2019338 TTCCTCACCCAAGGTTTTAGGATTGGCTAGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
* * * * * *
2019371 TTCCTCATCTAATGTTGAGGTAATAGTTGGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
* * * * * **
2019404 TACCTCAACCAAAGCTGTGGGAATAGCCGGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
* * * *
2019437 TTCCTCACCCAAGATTTTAGGATTGGTTGGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
** * * * *
2019470 TTCCTCGTCCGATGTTGTGGTAATAGTTGGAGT
1 TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
2019503 TTCCTC
1 TTCCTC
2019509 GGCCGAAGTT
Statistics
Matches: 124, Mismatches: 47, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
33 124 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (33 bp):
TTCCTCACCCAAGGTTGTGGGAATGGTTGGAGT
Found at i:2019375 original size:66 final size:66
Alignment explanation
Indices: 2019305--2019475 Score: 153
Period size: 66 Copynumber: 2.6 Consensus size: 66
2019295 TAATCAAAGA
* * * * * * * *
2019305 TTCCTCACCTAAGGTTGTGGGACTGGTTGGAGTTTCCTCACCCAAGGTTTTAGGATTGGCTAGAG
1 TTCCTCACCTAAGGTTGTGGGAATGGTTGGAGTTTCCTCAACCAAAGCTGTAGGAATAGCCAGAG
2019370 T
66 T
* * * * * * * *
2019371 TTCCTCATCTAATGTTGAGGTAATAGTTGGAGTTACCTCAACCAAAGCTGTGGGAATAGCCGGAG
1 TTCCTCACCTAAGGTTGTGGGAATGGTTGGAGTTTCCTCAACCAAAGCTGTAGGAATAGCCAGAG
2019436 T
66 T
* * * * *
2019437 TTCCTCACCCAAGATTTTAGGATTGGTTGGAGTTTCCTC
1 TTCCTCACCTAAGGTTGTGGGAATGGTTGGAGTTTCCTC
2019476 GTCCGATGTT
Statistics
Matches: 78, Mismatches: 27, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (66 bp):
TTCCTCACCTAAGGTTGTGGGAATGGTTGGAGTTTCCTCAACCAAAGCTGTAGGAATAGCCAGAG
T
Found at i:2019537 original size:99 final size:99
Alignment explanation
Indices: 2019335--2019551 Score: 272
Period size: 99 Copynumber: 2.2 Consensus size: 99
2019325 GACTGGTTGG
* *
2019335 AGTTTCCTCACCCAAGGTTTTAGGATTGGCTAGAGTTTCCTCATCTAATGTTGAGGTAATAGTTG
1 AGTTTCCTCACCCAAGATTTTAGGATTGGCTAGAGTTTCCTCATCCAATGTTGAGGTAATAGTTG
* * **
2019400 GAGTTACCTCAACCAAAGCTGTGGGAATAGCCGG
66 GAGTTACCTCAACCAAAGCTGTGAGAACAGCCAC
* * * * *
2019434 AGTTTCCTCACCCAAGATTTTAGGATTGGTTGGAGTTTCCTCGTCCGATGTTGTGGTAATAGTTG
1 AGTTTCCTCACCCAAGATTTTAGGATTGGCTAGAGTTTCCTCATCCAATGTTGAGGTAATAGTTG
* ** * *
2019499 GAGTTTCCTCGGCCGAAGTTGTGAGAACAGCCAC
66 GAGTTACCTCAACCAAAGCTGTGAGAACAGCCAC
**
2019533 AGTTTCCTCATGCAAGATT
1 AGTTTCCTCACCCAAGATT
2019552 GTGGGGGCAG
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (99 bp):
AGTTTCCTCACCCAAGATTTTAGGATTGGCTAGAGTTTCCTCATCCAATGTTGAGGTAATAGTTG
GAGTTACCTCAACCAAAGCTGTGAGAACAGCCAC
Found at i:2019691 original size:33 final size:33
Alignment explanation
Indices: 2019654--2019803 Score: 148
Period size: 33 Copynumber: 4.5 Consensus size: 33
2019644 TAACATTACT
* * *
2019654 GGAATGGTAGGAGTTTCTTCGCTGAA-GTTGTGA
1 GGAATGGCAGGAGTTTCTTCACTGAAGGTCG-GA
* * *
2019687 GGAATGGCCGGCGTTTCTTCGCTGAAGGTCGGA
1 GGAATGGCAGGAGTTTCTTCACTGAAGGTCGGA
2019720 GGAATGGCCA-GAGTTTCTTCACTGAAGGTCGGA
1 GGAATGG-CAGGAGTTTCTTCACTGAAGGTCGGA
* *
2019753 GGAATGGCCA-GAGTTTCTTCACTGTAGG-CTGTA
1 GGAATGG-CAGGAGTTTCTTCACTGAAGGTC-GGA
2019786 GGAATGG-ATGGAGTTTCT
1 GGAATGGCA-GGAGTTTCT
2019804 CCGCCCAAGT
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
31 1 0.01
32 1 0.01
33 97 0.94
34 4 0.04
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (33 bp):
GGAATGGCAGGAGTTTCTTCACTGAAGGTCGGA
Found at i:2019887 original size:33 final size:32
Alignment explanation
Indices: 2019826--2019936 Score: 96
Period size: 33 Copynumber: 3.4 Consensus size: 32
2019816 CCGGGAATAC
* * **
2019826 TAGGGGTTTCCTCAACCAAGGTCACGGGATGGG
1 TAGGAGTTTCTTCAACCAAGGTTGCGGGAT-GG
*
2019859 TAGGAGTTTCTTCATCCAAGGTTGCGGGAATGG
1 TAGGAGTTTCTTCAACCAAGGTTGCGGG-ATGG
* * * *
2019892 TATGAGTTTCTTCACCCGAGGTTGTGGGAATGG
1 TAGGAGTTTCTTCAACCAAGGTTGCGGG-ATGG
* *
2019925 TTGAAGTTTCTT
1 TAGGAGTTTCTT
2019937 GACCTAAGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 63 0.97
34 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (32 bp):
TAGGAGTTTCTTCAACCAAGGTTGCGGGATGG
Found at i:2025957 original size:16 final size:17
Alignment explanation
Indices: 2025918--2025958 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2025908 AATAAATGAT
2025918 TAAAAAATTAAGTAAAA
1 TAAAAAATTAAGTAAAA
*
2025935 -AATAAATTAA-TAAAA
1 TAAAAAATTAAGTAAAA
2025950 TAAAAAATT
1 TAAAAAATT
2025959 CGTTTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAAAAATTAAGTAAAA
Found at i:2028966 original size:2 final size:2
Alignment explanation
Indices: 2028959--2028984 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2028949 TCATCTCTGC
2028959 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
2028985 CTGAAAATGT
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:2030713 original size:16 final size:16
Alignment explanation
Indices: 2030692--2030728 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2030682 TTTTCTTTTG
2030692 ATCTCCAACCCCCGTC
1 ATCTCCAACCCCCGTC
*
2030708 ATCTCCAACCCTCGTC
1 ATCTCCAACCCCCGTC
*
2030724 TTCTC
1 ATCTC
2030729 TGCTCTCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.51, G:0.05, T:0.27
Consensus pattern (16 bp):
ATCTCCAACCCCCGTC
Found at i:2033284 original size:2 final size:2
Alignment explanation
Indices: 2033277--2033301 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2033267 AGGGTTTTAA
2033277 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 A
2033302 ACCTCAAGGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2033745 original size:18 final size:17
Alignment explanation
Indices: 2033720--2033773 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
2033710 TATTAAATGT
2033720 AATTAATTTAAATAATAA
1 AATTAATTTAAAT-ATAA
*
2033738 ATTTAATTTTAAAT-TAA
1 AATTAA-TTTAAATATAA
2033755 AATT-ATTTAAATATAA
1 AATTAATTTAAATATAA
2033771 AAT
1 AAT
2033774 AATATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 6 0.19
18 5 0.16
19 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATTTAAATATAA
Found at i:2034170 original size:27 final size:26
Alignment explanation
Indices: 2034137--2034209 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
2034127 AAAAAATTAA
2034137 AATATAATATAATATAAAAATAATATT
1 AATATAATATAATATAAAAAT-ATATT
* * *
2034164 AATATAAAATAAATATATAAATTTATT
1 AATATAATAT-AATATAAAAATATATT
*
2034191 AAAATTAATATAATATAAA
1 AATA-TAATATAATATAAA
2034210 TTTTTAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATATAATATAATATAAAAATATATT
Found at i:2034178 original size:38 final size:37
Alignment explanation
Indices: 2034119--2034209 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
2034109 AATACAGTTA
* * *
2034119 AATATGATAAAAAATTAAA-ATATAATATAATATAAAAAT
1 AATATAATATAAAA-TAAATATATAA-ATTAT-TAAAAAT
*
2034158 AATATTAATATAAAATAAATATATAAATTTATTAAAATT
1 AATA-TAATATAAAATAAATATATAAA-TTATTAAAAAT
2034197 AATATAATATAAA
1 AATATAATATAAA
2034210 TTTTTAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 9 0.20
39 19 0.42
40 17 0.38
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (37 bp):
AATATAATATAAAATAAATATATAAATTATTAAAAAT
Found at i:2034215 original size:27 final size:26
Alignment explanation
Indices: 2034132--2034213 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 26
2034122 ATGATAAAAA
**
2034132 ATTAAAATATAATATAATATAAAAATAAT
1 ATTAAAAT-TAATATAATAT--AAATTTT
* * *
2034161 ATTAATA-TAAAATAAATATATAAATTT
1 ATTAAAATTAATAT-AATATA-AATTTT
2034188 ATTAAAATTAATATAATATAAATTTT
1 ATTAAAATTAATATAATATAAATTTT
2034214 TAATATATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
26 6 0.14
27 20 0.48
28 10 0.24
29 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTAAAATTAATATAATATAAATTTT
Found at i:2034235 original size:18 final size:18
Alignment explanation
Indices: 2034195--2034231 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2034185 TTTATTAAAA
2034195 TTAATATAATATAAATTT
1 TTAATATAATATAAATTT
2034213 TTAATAT-ATATAAATTT
1 TTAATATAATATAAATTT
2034230 TT
1 TT
2034232 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATATAATATAAATTT
Found at i:2034978 original size:18 final size:18
Alignment explanation
Indices: 2034955--2034997 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2034945 ATTTAAACTT
2034955 TTATATTTTA-TAAATTG
1 TTATATTTTAGTAAATTG
*
2034972 ATTATATTTTAGTATATTG
1 -TTATATTTTAGTAAATTG
2034991 TTATATT
1 TTATATT
2034998 AAAACCTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TTATATTTTAGTAAATTG
Found at i:2037820 original size:22 final size:22
Alignment explanation
Indices: 2037795--2037839 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2037785 AAATTAGCCC
2037795 AGCATTTGTAAACAGGCACAAG
1 AGCATTTGTAAACAGGCACAAG
2037817 AGCATTTGTAAACAGGCACAAG
1 AGCATTTGTAAACAGGCACAAG
2037839 A
1 A
2037840 CACTTACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (22 bp):
AGCATTTGTAAACAGGCACAAG
Found at i:2039383 original size:18 final size:19
Alignment explanation
Indices: 2039355--2039393 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2039345 AGACTTCACC
2039355 AAGTCTAATAG-CATAGAAA
1 AAGTCTAATAGCCAT-GAAA
2039374 AAGT-TAATAGCCATGAAA
1 AAGTCTAATAGCCATGAAA
2039392 AA
1 AA
2039394 TGTAAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (19 bp):
AAGTCTAATAGCCATGAAA
Found at i:2042683 original size:17 final size:18
Alignment explanation
Indices: 2042651--2042685 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2042641 TAATATTTAA
2042651 ATTTTTATTTTATTAAAT
1 ATTTTTATTTTATTAAAT
2042669 ATTTTTATTTT-TTAAAT
1 ATTTTTATTTTATTAAAT
2042686 TAATATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTTATTAAAT
Found at i:2042817 original size:23 final size:23
Alignment explanation
Indices: 2042791--2042834 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2042781 AATTTTAAAA
2042791 TTTT-TAAAATTTTAGATTTTTAT
1 TTTTATAAAATTTTA-ATTTTTAT
*
2042814 TTTTATAAATTTTTAATTTTT
1 TTTTATAAAATTTTAATTTTT
2042835 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTATAAAATTTTAATTTTTAT
Found at i:2042825 original size:16 final size:15
Alignment explanation
Indices: 2042800--2042845 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2042790 ATTTTTAAAA
*
2042800 TTTTAGATTTTTATT
1 TTTTAAATTTTTATT
2042815 TTTATAAATTTTTAATT
1 TTT-TAAATTTTT-ATT
*
2042832 TTTTAAAATTTTAT
1 TTTTAAATTTTTAT
2042846 AATGATGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.59
17 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTAAATTTTTATT
Found at i:2042836 original size:18 final size:18
Alignment explanation
Indices: 2042813--2042848 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2042803 TAGATTTTTA
2042813 TTTTTATAAATTTT-TAAT
1 TTTTTA-AAATTTTATAAT
2042831 TTTTTAAAATTTTATAAT
1 TTTTTAAAATTTTATAAT
2042849 GATGTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTAAAATTTTATAAT
Found at i:2043530 original size:22 final size:23
Alignment explanation
Indices: 2043505--2043557 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
2043495 AAAATAGTAA
2043505 AATATTAAAAATATTTT-TAATT
1 AATATTAAAAATATTTTATAATT
*
2043527 AATATT-TAAATATTTTATAATT
1 AATATTAAAAATATTTTATAATT
*
2043549 AAAATTAAA
1 AATATTAAA
2043558 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 16 0.62
23 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTAAAAATATTTTATAATT
Found at i:2043539 original size:21 final size:21
Alignment explanation
Indices: 2043513--2043559 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2043503 AAAATATTAA
*
2043513 AAATATTTT-TAATTAATATTT
1 AAATATTTTATAATTAA-AATT
2043534 AAATATTTTATAATTAAAATT
1 AAATATTTTATAATTAAAATT
2043555 AAATA
1 AAATA
2043560 AAAATAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTTTATAATTAAAATT
Found at i:2045662 original size:13 final size:13
Alignment explanation
Indices: 2045644--2045685 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2045634 GAACTCATAA
2045644 AATTTACAAATAT
1 AATTTACAAATAT
**
2045657 AATTTACGTATAT
1 AATTTACAAATAT
2045670 AATTTACAAATAT
1 AATTTACAAATAT
2045683 AAT
1 AAT
2045686 AGCATACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (13 bp):
AATTTACAAATAT
Found at i:2046347 original size:19 final size:19
Alignment explanation
Indices: 2046325--2046373 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2046315 ATTTTTAAAT
*
2046325 TAAATAAAAATATCAAAAA
1 TAAATAAAAAAATCAAAAA
*
2046344 TAAA-AGAAAAAATGAAAAA
1 TAAATA-AAAAAATCAAAAA
2046363 TAAATAAAAAA
1 TAAATAAAAAA
2046374 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (19 bp):
TAAATAAAAAAATCAAAAA
Found at i:2046356 original size:12 final size:11
Alignment explanation
Indices: 2046339--2046381 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2046329 TAAAAATATC
2046339 AAAAATAAAAGA
1 AAAAATAAAA-A
*
2046351 AAAAATGAAAA
1 AAAAATAAAAA
*
2046362 ATAAATAAAAA
1 AAAAATAAAAA
2046373 AGAAAATAA
1 A-AAAATAA
2046382 TTAAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:2046391 original size:19 final size:18
Alignment explanation
Indices: 2046325--2046378 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2046315 ATTTTTAAAT
* *
2046325 TAAATAAAAATATCAAAAA
1 TAAAGAAAAA-ATGAAAAA
2046344 TAAAAGAAAAAATGAAAAA
1 T-AAAGAAAAAATGAAAAA
*
2046363 TAAATAAAAAA-GAAAA
1 TAAAGAAAAAATGAAAA
2046379 TAATTAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 5 0.16
18 9 0.29
19 9 0.29
20 8 0.26
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.15
Consensus pattern (18 bp):
TAAAGAAAAAATGAAAAA
Found at i:2047836 original size:16 final size:17
Alignment explanation
Indices: 2047817--2047858 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
2047807 TTATTCGAGA
*
2047817 TAAAAATTATAA-ATAT
1 TAAATATTATAATATAT
2047833 TAAATATTA-AATATAT
1 TAAATATTATAATATAT
2047849 TAAATATTAT
1 TAAATATTAT
2047859 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTATAATATAT
Found at i:2048968 original size:3 final size:3
Alignment explanation
Indices: 2048960--2049001 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2048950 CATGTCAAGT
2048960 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2049002 AGAAGGATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:2053656 original size:26 final size:26
Alignment explanation
Indices: 2053627--2053676 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2053617 ATTTTAAAAT
*
2053627 TTAT-TTAATATAAATTATTAATATAA
1 TTATATTAATAT-AATTATAAATATAA
*
2053653 TTATATTTATATAATTATAAATAT
1 TTATATTAATATAATTATAAATAT
2053677 TTTAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATATTAATATAATTATAAATATAA
Found at i:2053659 original size:14 final size:14
Alignment explanation
Indices: 2053627--2053671 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
2053617 ATTTTAAAAT
2053627 TTAT-TTAATATAA
1 TTATATTAATATAA
*
2053640 AT-TATTAATATAA
1 TTATATTAATATAA
*
2053653 TTATATTTATATAA
1 TTATATTAATATAA
2053667 TTATA
1 TTATA
2053672 AATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 1 0.04
13 11 0.41
14 15 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:2053687 original size:35 final size:32
Alignment explanation
Indices: 2053625--2053692 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 32
2053615 ATATTTTAAA
*
2053625 ATTTATTTAATATAAATTATTAATATAATTAT
1 ATTTATATAATATAAATTATTAATATAATTAT
*
2053657 ATTTATATAATTATAAATATTTTAAATATAATTAT
1 ATTTATATAA-TATAAAT-TATT-AATATAATTAT
2053692 A
1 A
2053693 ATGTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 9 0.29
33 7 0.23
34 3 0.10
35 12 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTATATAATATAAATTATTAATATAATTAT
Found at i:2053814 original size:18 final size:18
Alignment explanation
Indices: 2053791--2053826 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2053781 TTAGTTAAAT
2053791 TTAAAAAA-AAAATTATTA
1 TTAAAAAATAAAA-TATTA
2053809 TTAAAAAATAAAATATTA
1 TTAAAAAATAAAATATTA
2053827 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAATAAAATATTA
Found at i:2053846 original size:24 final size:24
Alignment explanation
Indices: 2053819--2053898 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
2053809 TTAAAAAATA
2053819 AAATATTAAA-AAAA-ATTTTATATT
1 AAAT-TTAAATAAAATATTTT-TATT
2053843 AAATTTAAATAAAATATTTTTATT
1 AAATTTAAATAAAATATTTTTATT
* **
2053867 -AA-TTAAATAATA-ATTTAAATT
1 AAATTTAAATAAAATATTTTTATT
*
2053888 AAATTAAAATA
1 AAATTTAAATA
2053899 TTTTACTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
21 7 0.15
22 11 0.23
23 13 0.27
24 12 0.25
25 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAAATAAAATATTTTTATT
Found at i:2053853 original size:35 final size:31
Alignment explanation
Indices: 2053795--2053860 Score: 87
Period size: 35 Copynumber: 2.0 Consensus size: 31
2053785 TTAAATTTAA
2053795 AAAAAAAATTATTATTAAAAAATAAAATATT
1 AAAAAAAATTATTATTAAAAAATAAAATATT
*
2053826 AAAAAAAATTTTATATTAAATTTAAATAAAATATT
1 AAAAAAAATTAT-TATTAAA---AAATAAAATATT
2053861 TTTATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 11 0.37
32 7 0.23
35 12 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAAAAAATTATTATTAAAAAATAAAATATT
Found at i:2053875 original size:22 final size:23
Alignment explanation
Indices: 2053823--2053944 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 23
2053813 AAAATAAAAT
2053823 ATTAAA-AAAAATTTTATATTAA
1 ATTAAATAAAAATTTTATATTAA
2053845 ATTTAAATAAAATATTTT-TATT-A
1 A-TTAAATAAAA-ATTTTATATTAA
* *
2053868 ATTAAATAATAA-TTTAAATTAA
1 ATTAAATAAAAATTTTATATTAA
*
2053890 ATT--A-AAATATTTTACT-TTAA
1 ATTAAATAAAAATTTTA-TATTAA
* * *
2053910 ATTTAAT-TAAATTTAAT-TTAA
1 ATTAAATAAAAATTTTATATTAA
2053931 ATTAAATTAAAAAT
1 ATTAAA-TAAAAAT
2053945 AATCTTATAC
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
19 3 0.04
20 15 0.19
21 14 0.18
22 22 0.28
23 11 0.14
24 8 0.10
25 5 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTAAATAAAAATTTTATATTAA
Found at i:2053888 original size:21 final size:22
Alignment explanation
Indices: 2053835--2053947 Score: 88
Period size: 21 Copynumber: 5.0 Consensus size: 22
2053825 TAAAAAAAAT
* *
2053835 TTTATATTAAATTTAAATAAAATA
1 TTTAAATTAAA-TTAAATAATA-A
**
2053859 TTTTTATT-AATTAAATAATAA
1 TTTAAATTAAATTAAATAATAA
* *
2053880 TTTAAATTAAATTAAAATATTTTAC
1 TTTAAATTAAATT-AAATA--ATAA
* *
2053905 TTTAAATTTAATTAAAT-TTAA
1 TTTAAATTAAATTAAATAATAA
2053926 TTTAAATTAAATTAAA-AATAA
1 TTTAAATTAAATTAAATAATAA
2053947 T
1 T
2053948 CTTATACTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
21 29 0.39
22 13 0.18
23 7 0.09
24 11 0.15
25 14 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATTAAATTAAATAATAA
Found at i:2053897 original size:6 final size:5
Alignment explanation
Indices: 2053867--2053941 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
2053857 TATTTTTATT
* * ** ** *
2053867 AATTA AATAATA ATTTA AATTA AATTA AAATA TTTTA CTTTA AATTT AATTA
1 AATTA AAT--TA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA
*
2053919 AATTTA ATTTA AATTA AATTA AA
1 AA-TTA AATTA AATTA AATTA AA
2053942 AATAATCTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
5 46 0.85
6 4 0.07
7 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (5 bp):
AATTA
Found at i:2054169 original size:27 final size:26
Alignment explanation
Indices: 2054107--2054262 Score: 244
Period size: 26 Copynumber: 6.0 Consensus size: 26
2054097 TTTATTATTT
2054107 AATAATATTTTAATAATA-TAATAAA
1 AATAATATTTTAATAATATTAATAAA
*
2054132 AATAATATTTTAATAATCTTAATAATA
1 AATAATATTTTAATAATATTAATAA-A
*
2054159 AATAATATTTTAATAATATAAATAAA
1 AATAATATTTTAATAATATTAATAAA
*
2054185 AATAATATTTTAATAATCTTAATAATA
1 AATAATATTTTAATAATATTAATAA-A
*
2054212 AATAATATTTTAATAATATAAATAAA
1 AATAATATTTTAATAATATTAATAAA
2054238 AATAATATTTTAATAATA-TAATAAA
1 AATAATATTTTAATAATATTAATAAA
2054263 TTTATAAATA
Statistics
Matches: 120, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
25 23 0.19
26 49 0.41
27 48 0.40
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (26 bp):
AATAATATTTTAATAATATTAATAAA
Found at i:2054199 original size:53 final size:53
Alignment explanation
Indices: 2054107--2054254 Score: 289
Period size: 53 Copynumber: 2.8 Consensus size: 53
2054097 TTTATTATTT
2054107 AATAATATTTTAATAATAT-AATAAAAATAATATTTTAATAATCTTAATAATA
1 AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAATCTTAATAATA
2054159 AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAATCTTAATAATA
1 AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAATCTTAATAATA
2054212 AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAAT
1 AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAAT
2054255 ATAATAAATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 19 0.20
53 76 0.80
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (53 bp):
AATAATATTTTAATAATATAAATAAAAATAATATTTTAATAATCTTAATAATA
Found at i:2060074 original size:2 final size:2
Alignment explanation
Indices: 2060067--2060101 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2060057 AGTTATTTGT
2060067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2060102 GATTGTGATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2060253 original size:1 final size:1
Alignment explanation
Indices: 2060247--2060276 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2060237 ATCAACTTTC
*
2060247 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2060277 AGGCTGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:2060574 original size:30 final size:30
Alignment explanation
Indices: 2060486--2060584 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
2060476 TATATTAGGA
** *
2060486 GTTTATTTAAGTATAAATTAAAGATTAGAG
1 GTTTATTTAAGTGCAAATTAAAGATTAAAG
* * *
2060516 TTTTATTTAGGTGCAAGTTAAAGATTAAAG
1 GTTTATTTAAGTGCAAATTAAAGATTAAAG
2060546 GTTTATTTAAGTGCAAATTAAA-AGTTAAAAG
1 GTTTATTTAAGTGCAAATTAAAGA-TT-AAAG
*
2060577 ATTTATTT
1 GTTTATTT
2060585 TAATATAGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.79
31 11 0.19
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.41
Consensus pattern (30 bp):
GTTTATTTAAGTGCAAATTAAAGATTAAAG
Found at i:2060652 original size:3 final size:3
Alignment explanation
Indices: 2060646--2060671 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2060636 CGTTGTTATT
2060646 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2060672 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2063995 original size:14 final size:14
Alignment explanation
Indices: 2063976--2064007 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2063966 AAATGTTGGG
2063976 TAGGCTTTTGAATT
1 TAGGCTTTTGAATT
2063990 TAGGCTTTTGAATT
1 TAGGCTTTTGAATT
2064004 TAGG
1 TAGG
2064008 TAGGTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (14 bp):
TAGGCTTTTGAATT
Found at i:2065453 original size:15 final size:15
Alignment explanation
Indices: 2065433--2065474 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2065423 TTATCTATAA
2065433 AAATAATATATATTT
1 AAATAATATATATTT
*
2065448 AAATAATAAATATTT
1 AAATAATATATATTT
*
2065463 AAA-AATTTATAT
1 AAATAATATATAT
2065475 CTACATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAATATATATTT
Found at i:2066166 original size:17 final size:17
Alignment explanation
Indices: 2066146--2066186 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2066136 AAATAACGAT
*
2066146 ATTTTAATAATAAATAA
1 ATTTAAATAATAAATAA
*
2066163 ATTTAAATATTAAATAA
1 ATTTAAATAATAAATAA
2066180 ATTTAAA
1 ATTTAAA
2066187 AGTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAATAATAAATAA
Found at i:2067228 original size:2 final size:2
Alignment explanation
Indices: 2067221--2067260 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2067211 CTATGTGCTT
* * *
2067221 TA TA TA TA TA TA TA TA TA TT TA TA TG TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2067261 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2068833 original size:23 final size:22
Alignment explanation
Indices: 2068807--2068866 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
2068797 TTATGTGGAT
* *
2068807 ATAAATAAAACATTAAGGATTTA
1 ATAAGTAAAA-ATTAAGGACTTA
*
2068830 ATAAGTAAAAGTTAAGGACTTA
1 ATAAGTAAAAATTAAGGACTTA
*
2068852 ATAAGTAAAAGTTAA
1 ATAAGTAAAAATTAA
2068867 AATGTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.28
Consensus pattern (22 bp):
ATAAGTAAAAATTAAGGACTTA
Found at i:2068847 original size:22 final size:22
Alignment explanation
Indices: 2068819--2068866 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
2068809 AAATAAAACA
*
2068819 TTAAGGATTTAATAAGTAAAAG
1 TTAAGGACTTAATAAGTAAAAG
2068841 TTAAGGACTTAATAAGTAAAAG
1 TTAAGGACTTAATAAGTAAAAG
2068863 TTAA
1 TTAA
2068867 AATGTTTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (22 bp):
TTAAGGACTTAATAAGTAAAAG
Found at i:2069453 original size:2 final size:2
Alignment explanation
Indices: 2069446--2069486 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2069436 TTTATGCGTT
2069446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2069487 TATTAAACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2070347 original size:12 final size:11
Alignment explanation
Indices: 2070324--2070358 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2070314 TACATGATAT
2070324 AAAAATAATAA
1 AAAAATAATAA
*
2070335 AAAAATAATTA
1 AAAAATAATAA
*
2070346 AAATATAATAA
1 AAAAATAATAA
2070357 AA
1 AA
2070359 TATAATTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:2070348 original size:10 final size:11
Alignment explanation
Indices: 2070323--2070365 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
2070313 TTACATGATA
2070323 TAAAA-ATAAT
1 TAAAATATAAT
* *
2070333 AAAAAAATAAT
1 TAAAATATAAT
2070344 TAAAATATAA-
1 TAAAATATAAT
2070354 TAAAATATAAT
1 TAAAATATAAT
2070365 T
1 T
2070366 TGATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:2070419 original size:17 final size:16
Alignment explanation
Indices: 2070394--2070451 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
2070384 AACATGATGT
*
2070394 AAATATATAAAGTATTA
1 AAATTTATAAA-TATTA
2070411 AAATTTATATAATA-T-
1 AAATTTATA-AATATTA
2070426 AAA-TTATTAATATATTA
1 AAATTTA-TAA-ATATTA
2070443 AAATTTATA
1 AAATTTATA
2070452 TTAAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 4 0.12
15 8 0.24
16 2 0.06
17 15 0.44
18 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAATTTATAAATATTA
Found at i:2071812 original size:2 final size:2
Alignment explanation
Indices: 2071805--2071832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2071795 TAAATATGCC
2071805 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
2071833 ACTTTTTGTT
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:2073716 original size:2 final size:2
Alignment explanation
Indices: 2073709--2073733 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2073699 AAATTTGTTT
2073709 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 T
2073734 TATTTTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2076543 original size:18 final size:18
Alignment explanation
Indices: 2076506--2076541 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2076496 GGGAGGTGCA
2076506 TTCTTTTTTTATTTTCTT
1 TTCTTTTTTTATTTTCTT
2076524 TTCTTTTTTT-TTTT-TT
1 TTCTTTTTTTATTTTCTT
2076540 TT
1 TT
2076542 TTGATGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (18 bp):
TTCTTTTTTTATTTTCTT
Found at i:2079145 original size:31 final size:29
Alignment explanation
Indices: 2079108--2079180 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
2079098 AATATACTGT
**
2079108 TTTTAAAATTTTTTATATT-TATTTATTTGA
1 TTTTAAAATTTTGAATATTATATTTA-TT-A
2079138 TGTTTAAAAGTTTTGAATATTAATATTTATTA
1 T-TTTAAAA-TTTTGAATATT-ATATTTATTA
2079170 TTTTAAAATTT
1 TTTTAAAATTT
2079181 ATATTTGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 4 0.11
31 14 0.38
32 11 0.30
33 2 0.05
34 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (29 bp):
TTTTAAAATTTTGAATATTATATTTATTA
Found at i:2079933 original size:2 final size:2
Alignment explanation
Indices: 2079926--2079966 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2079916 ATGATTGCTT
2079926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2079967 CTTGTTACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2088962 original size:2 final size:2
Alignment explanation
Indices: 2088957--2088982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2088947 ATATATTTTC
2088957 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
2088983 TAATACAATA
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:2089097 original size:24 final size:23
Alignment explanation
Indices: 2089055--2089101 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
2089045 TTTATAAATT
2089055 TTCAAAATTATAAATATTTAATA
1 TTCAAAATTATAAATATTTAATA
*
2089078 TTCAAAATTTTTAAATATTTAATA
1 TTCAAAA-TTATAAATATTTAATA
2089102 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTCAAAATTATAAATATTTAATA
Found at i:2096409 original size:24 final size:24
Alignment explanation
Indices: 2096381--2096428 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2096371 CGGTTATACA
2096381 TATAAACTCTATTAACAAGATTCT
1 TATAAACTCTATTAACAAGATTCT
2096405 TATAAACTCTATTAACAAGATTCT
1 TATAAACTCTATTAACAAGATTCT
2096429 AAAATAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (24 bp):
TATAAACTCTATTAACAAGATTCT
Found at i:2102959 original size:19 final size:18
Alignment explanation
Indices: 2102918--2102959 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2102908 TATTTTAAAT
2102918 TTAAT-TATAATATAATA
1 TTAATATATAATATAATA
**
2102935 AAAATATATAAATATAATA
1 TTAATATAT-AATATAATA
2102954 TTAATA
1 TTAATA
2102960 AAAAGGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.16
18 3 0.16
19 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATATATAATATAATA
Found at i:2104426 original size:19 final size:19
Alignment explanation
Indices: 2104404--2104515 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 19
2104394 ATTTTAGGTA
2104404 AAATATAATTATAAAATTT
1 AAATATAATTATAAAATTT
* *
2104423 AAATATTATATAAAAAATTT
1 AAATATAAT-TATAAAATTT
**
2104443 AAAATATAA-TATAAAAAAT
1 -AAATATAATTATAAAATTT
* *
2104462 AATATAAAATTATTTAAATTT
1 AA-ATATAATTA-TAAAATTT
* * *
2104483 ATATAATATTTTTAAAA-TT
1 AAAT-ATAATTATAAAATTT
2104502 -AATATAA-TATAAAA
1 AAATATAATTATAAAA
2104516 ATAATATATT
Statistics
Matches: 69, Mismatches: 18, Indels: 15
0.68 0.18 0.15
Matches are distributed among these distances:
16 6 0.09
17 3 0.04
18 4 0.06
19 22 0.32
20 17 0.25
21 17 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATAATTATAAAATTT
Found at i:2104449 original size:21 final size:21
Alignment explanation
Indices: 2104402--2104461 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
2104392 TAATTTTAGG
*
2104402 TAAAATATAAT-TATAAAATT
1 TAAAATATAATATAAAAAATT
*
2104422 T-AAATATTATATAAAAAATT
1 TAAAATATAATATAAAAAATT
2104442 TAAAATATAATATAAAAAAT
1 TAAAATATAATATAAAAAAT
2104462 AATATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.23
20 10 0.29
21 17 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATATAATATAAAAAATT
Found at i:2104463 original size:12 final size:12
Alignment explanation
Indices: 2104423--2104470 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
2104413 TATAAAATTT
* *
2104423 AAATATTATATA
1 AAATAATATAAA
*
2104435 AAA-AATTTAAA
1 AAATAATATAAA
*
2104446 ATATAATATAAA
1 AAATAATATAAA
2104458 AAATAATATAAA
1 AAATAATATAAA
2104470 A
1 A
2104471 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAATATAAA
Found at i:2104509 original size:20 final size:21
Alignment explanation
Indices: 2104456--2104511 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
2104446 ATATAATATA
* *
2104456 AAAAATAATATAAAATTATTT
1 AAAATTAATATAATATTATTT
*
2104477 -AAATTTATATAATATT-TTT
1 AAAATTAATATAATATTATTT
2104496 AAAATTAATATAATAT
1 AAAATTAATATAATAT
2104512 AAAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTAATATAATATTATTT
Found at i:2104772 original size:10 final size:10
Alignment explanation
Indices: 2104757--2104816 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
2104747 ATTTAAATAA
2104757 AAATTAATTT
1 AAATTAATTT
2104767 AAATTAATTT
1 AAATTAATTT
**
2104777 AAATT-ATAA
1 AAATTAATTT
2104786 AAATTTATATTT
1 AAA-TTA-ATTT
*
2104798 AAATCAATTT
1 AAATTAATTT
2104808 AATATTAAT
1 AA-ATTAAT
2104817 CGACTTTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 5 0.12
10 23 0.57
11 7 0.17
12 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATTAATTT
Found at i:2104778 original size:15 final size:14
Alignment explanation
Indices: 2104760--2104815 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 14
2104750 TAAATAAAAA
2104760 TTAATTTAAATTAAT
1 TTAATTTAAA-TAAT
2104775 TTAAATTATAAA-AAT
1 TT-AATT-TAAATAAT
2104790 TTATATTTAAATCAAT
1 TTA-ATTTAAAT-AAT
2104806 TTAATATTAA
1 TTAAT-TTAA
2104816 TCGACTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.14
15 12 0.34
16 14 0.40
17 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTTAAATAAT
Done.