Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 52 of 226
Found at i:21231147 original size:25 final size:25
Alignment explanation
Indices: 21231115--21231202 Score: 106
Period size: 25 Copynumber: 3.6 Consensus size: 25
21231105 GCTATTAACG
*
21231115 GGAAGCTCATGAGAGCCATATATCA
1 GGAAGCTCATGAGAGTCATATATCA
*
21231140 GGAAGCTCGTGAGAGTCATATATCA
1 GGAAGCTCATGAGAGTCATATATCA
* * * *
21231165 TGAAACTCAAGAGATTCA-ATATCA
1 GGAAGCTCATGAGAGTCATATATCA
*
21231189 GGATGCTCATGAGA
1 GGAAGCTCATGAGA
21231203 ACTAATAACG
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 16 0.31
25 36 0.69
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (25 bp):
GGAAGCTCATGAGAGTCATATATCA
Found at i:21232572 original size:137 final size:137
Alignment explanation
Indices: 21232423--21232701 Score: 549
Period size: 137 Copynumber: 2.0 Consensus size: 137
21232413 TCGAAACTAA
21232423 TATTTCGATTTCACTGAAAACGGGCTATTACACACTCGTATTTTTGAGTTACTTCATATTGATTT
1 TATTTCGATTTCACTGAAAACGGGCTATTACACACTCGTATTTTTGAGTTACTTCATATTGATTT
21232488 ATAAGGGTTTCATGATACTCTATTTTGTAGATCTCATTATTTTTTGGCATTGGTTGATGATTTCT
66 ATAAGGGTTTCATGATACTCTATTTTGTAGATCTCATTATTTTTTGGCATTGGTTGATGATTTCT
21232553 CTCGTGC
131 CTCGTGC
*
21232560 TATTTCGATTTCACTGAAAACGGGCTATTACACACTCGTATTTTTGAGTTACTTCATTTTGATTT
1 TATTTCGATTTCACTGAAAACGGGCTATTACACACTCGTATTTTTGAGTTACTTCATATTGATTT
21232625 ATAAGGGTTTCATGATACTCTATTTTGTAGATCTCATTATTTTTTGGCATTGGTTGATGATTTCT
66 ATAAGGGTTTCATGATACTCTATTTTGTAGATCTCATTATTTTTTGGCATTGGTTGATGATTTCT
21232690 CTCGTGC
131 CTCGTGC
21232697 TATTT
1 TATTT
21232702 GGGTATATCT
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 141 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (137 bp):
TATTTCGATTTCACTGAAAACGGGCTATTACACACTCGTATTTTTGAGTTACTTCATATTGATTT
ATAAGGGTTTCATGATACTCTATTTTGTAGATCTCATTATTTTTTGGCATTGGTTGATGATTTCT
CTCGTGC
Found at i:21244757 original size:36 final size:36
Alignment explanation
Indices: 21244709--21244777 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
21244699 ACTTGATTAA
* *
21244709 TACAATACTAATATTTTTATAATTCAATTAGAACAT
1 TACAATACTAATATTTTAAAAATTCAATTAGAACAT
*
21244745 TACAATATTAATATTTTAAAAATTCAATTAGAA
1 TACAATACTAATATTTTAAAAATTCAATTAGAA
21244778 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.41
Consensus pattern (36 bp):
TACAATACTAATATTTTAAAAATTCAATTAGAACAT
Found at i:21248970 original size:12 final size:11
Alignment explanation
Indices: 21248930--21248962 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
21248920 GTTGTAAAGT
21248930 TTTA-TTTTTA
1 TTTATTTTTTA
21248940 TTTATTTATTTA
1 TTTATTT-TTTA
21248952 TTTATTTTTTA
1 TTTATTTTTTA
21248963 CTTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:21252680 original size:12 final size:11
Alignment explanation
Indices: 21252640--21252672 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
21252630 GTTGTAAAGT
21252640 TTTA-TTTTTA
1 TTTATTTTTTA
21252650 TTTATTTATTTA
1 TTTATTT-TTTA
21252662 TTTATTTTTTA
1 TTTATTTTTTA
21252673 CTTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:21258778 original size:16 final size:16
Alignment explanation
Indices: 21258739--21258780 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
21258729 AAAAATATAA
*
21258739 AAATATATTTTAAAAT
1 AAATATATTTAAAAAT
*
21258755 -ATTAATATTTAAAAAT
1 AAAT-ATATTTAAAAAT
21258771 AAATATATTT
1 AAATATATTT
21258781 GCAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.10
16 17 0.81
17 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATATTTAAAAAT
Found at i:21264879 original size:17 final size:17
Alignment explanation
Indices: 21264850--21264882 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21264840 TTATATTATG
21264850 TTATTAGTTTTGTATTA
1 TTATTAGTTTTGTATTA
21264867 TTATT-GTTATTGTATT
1 TTATTAGTT-TTGTATT
21264883 TCTATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (17 bp):
TTATTAGTTTTGTATTA
Found at i:21264946 original size:13 final size:13
Alignment explanation
Indices: 21264928--21264952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21264918 TTAATCTTGT
21264928 ATTATTATTATTG
1 ATTATTATTATTG
21264941 ATTATTATTATT
1 ATTATTATTATT
21264953 TACTCATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATTATTATTATTG
Found at i:21265013 original size:18 final size:18
Alignment explanation
Indices: 21264990--21265024 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21264980 ATTTTGTTAT
21264990 ATACATA-TATATATATAC
1 ATACATACT-TATATATAC
21265008 ATACATACTTATATATA
1 ATACATACTTATATATA
21265025 TTTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
ATACATACTTATATATAC
Found at i:21265144 original size:18 final size:18
Alignment explanation
Indices: 21265106--21265145 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21265096 TACCTATATA
* *
21265106 TTTATATATATATATTAT
1 TTTATATATATACATCAT
*
21265124 TTTATATATATACATCCT
1 TTTATATATATACATCAT
21265142 TTTA
1 TTTA
21265146 CATTTTTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATATATATACATCAT
Found at i:21266372 original size:14 final size:14
Alignment explanation
Indices: 21266350--21266385 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21266340 TTTCATCATG
*
21266350 TTTTATATTTTAAA
1 TTTTTTATTTTAAA
21266364 TTTTTTATTTTAAA
1 TTTTTTATTTTAAA
21266378 TTTTTTAT
1 TTTTTTAT
21266386 GCCTTTCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTATTTTAAA
Found at i:21267312 original size:19 final size:18
Alignment explanation
Indices: 21267271--21267313 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
21267261 GTCTCTTTTT
21267271 TGCATTCATTTCATGCATC
1 TGCATTCATTTCATGCA-C
21267290 TGCATTGCATTTCATTGCA-
1 TGCATT-CATTTCA-TGCAC
21267309 TGCAT
1 TGCAT
21267314 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCATTCATTTCATGCAC
Found at i:21268600 original size:17 final size:18
Alignment explanation
Indices: 21268578--21268614 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
21268568 TTATTCTTTT
21268578 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
21268595 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
21268613 AT
1 AT
21268615 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:21269352 original size:16 final size:17
Alignment explanation
Indices: 21269330--21269382 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
21269320 AGTTCAGACT
21269330 CAAAAAAAACAAAAATA
1 CAAAAAAAACAAAAATA
*
21269347 -AAAAAACACAAAAA-A
1 CAAAAAAAACAAAAATA
*
21269362 CAAAAATAAAAAAAAAT-
1 CAAAAA-AAACAAAAATA
21269379 CAAA
1 CAAA
21269383 GTCAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.03
16 18 0.60
17 11 0.37
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (17 bp):
CAAAAAAAACAAAAATA
Found at i:21270729 original size:50 final size:50
Alignment explanation
Indices: 21270616--21270857 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
21270606 ATTTGGGTAA
* * *
21270616 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
21270672 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
21270722 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * * *
21270772 AGATGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCATC-AGCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG-ACG
**
21270822 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
21270858 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 2 0.01
50 90 0.54
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:21270806 original size:100 final size:103
Alignment explanation
Indices: 21270616--21270865 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
21270606 ATTTGGGTAA
21270616 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
*
21270681 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG-ACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-AGCACG
* * * *
21270722 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGATGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
* *
21270784 TAAGACCATGTCTGGGACATGGCATGGGCATCAGCATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAGCACG
* *
21270822 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
21270866 GTTATTATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 2 0.02
100 48 0.37
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAGCACG
Found at i:21272996 original size:14 final size:15
Alignment explanation
Indices: 21272967--21273004 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
21272957 ATATATATAA
21272967 AAAAAATGAATGAAAG
1 AAAAAATGAA-GAAAG
21272983 AAAAAATGAA-AAAG
1 AAAAAATGAAGAAAG
*
21272997 TAAAAATG
1 AAAAAATG
21273005 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
16 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAAAATGAAGAAAG
Found at i:21274487 original size:44 final size:44
Alignment explanation
Indices: 21274367--21274665 Score: 134
Period size: 44 Copynumber: 6.8 Consensus size: 44
21274357 NNNNNNNNNN
* *
21274367 TTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTTCTGTA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTCTCTGTA
** * * *
21274411 TTGACA-GCGAAGCAGGTCGAAGACACAA-ATCTTGCCTCTCTCG-A
1 TTGTGATG-G-AGCTGGTTGAAGACAAAAGATCTTGCCTCTCT-GTA
* * * *
21274455 TTGTGATGGAGCTGGTTGAGGACAAAAGATCTTACCTTTCTATA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTCTCTGTA
** * * * * * *
21274499 TTGACA-GCGAAGCAGGTCGAAGACACAA-ACCTTGCCTCCCTCG-G
1 TTGTGATG-G-AGCTGGTTGAAGACAAAAGATCTTGCCTCTCT-GTA
* * * *
21274543 TTGTGATGGAGTTGGTTGAACACAACAGATCTTGCCT-TCCTGCA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTCT-CTGTA
** ** ** * * *
21274587 TTGACA-GCGAAGCAAGTCAAAGACATAA-ACCTTGCCT-T-TTTCA
1 TTGTGATG-G-AGCTGGTTGAAGACAAAAGATCTTGCCTCTCTGT-A
21274630 GTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGC
1 -TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGC
21274666 ATTCCTACAT
Statistics
Matches: 176, Mismatches: 60, Indels: 38
0.64 0.22 0.14
Matches are distributed among these distances:
42 1 0.01
43 44 0.25
44 89 0.51
45 42 0.24
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTCTCTGTA
Found at i:21274516 original size:88 final size:88
Alignment explanation
Indices: 21274367--21274705 Score: 473
Period size: 88 Copynumber: 3.9 Consensus size: 88
21274357 NNNNNNNNNN
* * **
21274367 TTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAA
*
21274432 GACACAAATCTTGCCTCTCTCGA
66 GACACAAACCTTGCCTCTCTCGA
* * * *
21274455 TTGTGATGGAGCTGGTTGAGGACAAAAGATCTTACCTTTCTATATTGACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAA
* *
21274520 GACACAAACCTTGCCTCCCTCGG
66 GACACAAACCTTGCCTCTCTCGA
* * * * * *
21274543 TTGTGATGGAGTTGGTTGAACACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAAGTCAAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAA
* * *
21274608 GACATAAACCTTGCCTTTTTC-A
66 GACACAAACCTTGCCTCTCTCGA
*
21274630 GTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCATTCCTACATTGACAGCGAAGCAGGTCGA
1 -TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGA
21274695 AGACACAAACC
65 AGACACAAACC
21274706 AGATATTTTA
Statistics
Matches: 220, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
88 220 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (88 bp):
TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAA
GACACAAACCTTGCCTCTCTCGA
Found at i:21280707 original size:11 final size:11
Alignment explanation
Indices: 21280693--21280792 Score: 60
Period size: 11 Copynumber: 8.7 Consensus size: 11
21280683 AAATATCTCT
*
21280693 AAAATAATAGC
1 AAAATAATAAC
*
21280704 AAAATTAATAAT
1 AAAA-TAATAAC
21280716 AAAATAATAA-
1 AAAATAATAAC
* *
21280726 ATATATAATATTC
1 A-AAATAATA-AC
21280739 -AAATAATAAC
1 AAAATAATAAC
*
21280749 AACAATATAATAGC
1 -A-AA-ATAATAAC
*
21280763 AATATAATAAC
1 AAAATAATAAC
* *
21280774 AAAATGATAGC
1 AAAATAATAAC
21280785 AAAATAAT
1 AAAATAAT
21280793 GAAAAAAAAG
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
10 2 0.03
11 46 0.68
12 10 0.15
13 3 0.04
14 7 0.10
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:21280756 original size:25 final size:25
Alignment explanation
Indices: 21280728--21280775 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
21280718 AATAATAAAT
*
21280728 ATATAATATTCAA-ATAATAACAACA
1 ATATAATA-GCAATATAATAACAACA
21280753 ATATAATAGCAATATAATAACAA
1 ATATAATAGCAATATAATAACAA
21280776 AATGATAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (25 bp):
ATATAATAGCAATATAATAACAACA
Found at i:21280774 original size:22 final size:22
Alignment explanation
Indices: 21280693--21280792 Score: 69
Period size: 22 Copynumber: 4.4 Consensus size: 22
21280683 AAATATCTCT
* **
21280693 AAAATAATAGCAAAATTAATAAT
1 AAAATAATAACAAAA-TAATAGC
* *
21280716 AAAATAATAA-ATATATAATATTC
1 AAAATAATAACA-AAATAATA-GC
21280739 -AAATAATAACAACAATATAATAGC
1 AAAATAATAAC-A-AA-ATAATAGC
* *
21280763 AATATAATAACAAAATGATAGC
1 AAAATAATAACAAAATAATAGC
21280785 AAAATAAT
1 AAAATAAT
21280793 GAAAAAAAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
22 29 0.48
23 13 0.21
24 4 0.07
25 15 0.25
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAATAATAACAAAATAATAGC
Found at i:21280801 original size:24 final size:22
Alignment explanation
Indices: 21280739--21280800 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
21280729 TATAATATTC
*
21280739 AAATAATAACAACAATATAATAGCA
1 AAATAATAA-AA-AA-ATGATAGCA
* *
21280764 ATATAATAACAAAATGATAGCA
1 AAATAATAAAAAAATGATAGCA
21280786 AAATAATGAAAAAAA
1 AAATAAT-AAAAAAA
21280801 AGTAATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 14 0.45
23 8 0.26
24 1 0.03
25 8 0.26
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.19
Consensus pattern (22 bp):
AAATAATAAAAAAATGATAGCA
Found at i:21283412 original size:134 final size:134
Alignment explanation
Indices: 21283168--21283415 Score: 444
Period size: 134 Copynumber: 1.9 Consensus size: 134
21283158 TTGTTGTTGC
*
21283168 TAGTCCCTCAAGCTTCACTACATTGGGATGATCCAACTTCTGTAATATCATTATTTTTTTGTGCC
1 TAGTCCCTCAAGCTTCACTACATTGGGATGATCCAACTTCTGTAATATCATTATTTATTTGTGCC
*
21283233 ATAAATTTCACACTCCCAGGATCTGATATGTCAAACCGAAACTTCTTCACTTTTATGCTCCATTA
66 ATAAATTTCACACTCCCAAGATCTGATATGTCAAACCGAAACTTCTTCACTTTTATGCTCCATTA
21283298 CCTG
131 CCTG
21283302 TAGTCCCTCAAGCTTCACTACATTGGGATGATCCAACTTCTGTAATATCATTATTTATTT-TGCC
1 TAGTCCCTCAAGCTTCACTACATTGGGATGATCCAACTTCTGTAATATCATTATTTATTTGTGCC
* *
21283366 ATAAATTTCACACTCCCAAGATCTGATATTTCAAACCGGAACCTTCTTCA
66 ATAAATTTCACACTCCCAAGATCTGATATGTCAAACC-GAAACTTCTTCA
21283416 AGTCAACTAT
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
133 39 0.36
134 70 0.64
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (134 bp):
TAGTCCCTCAAGCTTCACTACATTGGGATGATCCAACTTCTGTAATATCATTATTTATTTGTGCC
ATAAATTTCACACTCCCAAGATCTGATATGTCAAACCGAAACTTCTTCACTTTTATGCTCCATTA
CCTG
Found at i:21288942 original size:16 final size:17
Alignment explanation
Indices: 21288911--21288944 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21288901 CATGTATATA
21288911 TTTTTTAAAATATTTAT
1 TTTTTTAAAATATTTAT
*
21288928 TTTTTTAATAT-TTTAT
1 TTTTTTAAAATATTTAT
21288944 T
1 T
21288945 GAACTCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAAAATATTTAT
Found at i:21292995 original size:36 final size:36
Alignment explanation
Indices: 21292954--21293093 Score: 271
Period size: 36 Copynumber: 3.9 Consensus size: 36
21292944 CTTTAGCTAC
*
21292954 ACTTATCTGATCAAGTGAAAAAGTGATAAGTATTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
21292990 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
21293026 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
21293062 ACTTATCTGATCAAGTGAAAAAGTGATAAGTG
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTG
21293094 GTAGCCTAGC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (36 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
Found at i:21293041 original size:21 final size:20
Alignment explanation
Indices: 21293013--21293078 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
21293003 AGTGAAAAAG
21293013 TGATAAGTGTTATACTTATC
1 TGATAAGTGTTATACTTATC
* **
21293033 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGTTATACTTATC
21293049 TGATAAGTGTTATACTTATC
1 TGATAAGTGTTATACTTATC
21293069 TGATCAAGTG
1 TGAT-AAGTG
21293079 AAAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (20 bp):
TGATAAGTGTTATACTTATC
Found at i:21293901 original size:2 final size:2
Alignment explanation
Indices: 21293894--21293943 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
21293884 AATTCATCGA
21293894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21293936 AT A- AT AT A
1 AT AT AT AT A
21293944 AGTAAAGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21295066 original size:2 final size:2
Alignment explanation
Indices: 21295059--21295102 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21295049 ATACTAGTAC
21295059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21295101 TA
1 TA
21295103 AATGATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21301058 original size:21 final size:21
Alignment explanation
Indices: 21301032--21301075 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
21301022 TATAATTATG
21301032 TAATCAG-TTACCATCCATACC
1 TAATCAGATT-CCATCCATACC
21301053 TAATCAGATTCCATCCATACC
1 TAATCAGATTCCATCCATACC
21301074 TA
1 TA
21301076 TTATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TAATCAGATTCCATCCATACC
Found at i:21305491 original size:6 final size:6
Alignment explanation
Indices: 21305480--21305529 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
21305470 ATATGTGTAA
21305480 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
21305528 AT
1 AT
21305530 CTGGAGATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:21305830 original size:11 final size:10
Alignment explanation
Indices: 21305813--21305845 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
21305803 TTGTTTAAAC
21305813 TTTTTTTCTT
1 TTTTTTTCTT
21305823 TCTTTTTTCTT
1 T-TTTTTTCTT
21305834 TTTTTTT-TT
1 TTTTTTTCTT
21305843 TTT
1 TTT
21305846 GTACTTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:21307703 original size:88 final size:85
Alignment explanation
Indices: 21307564--21307835 Score: 323
Period size: 88 Copynumber: 3.1 Consensus size: 85
21307554 TTAAGGGTGT
* * * *
21307564 AAAAA-GCCCTCAAAC-TTTTCAAAAAAAGCAATTAAGTTCCTACCTTTTTTTGCACACAATTAG
1 AAAAATGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCT--TTTTTTTTGCACTCAATTGG
*
21307627 GTACTTGAACTTTCAAGATGCATA
63 GTACTTGAACTTTCAA-ATGCATC
* * *
21307651 AAAAATGCCGTCAAACTTTTTCAAAAATAGTAATTAAGCCCCTTTTTATTTTGCACTCAATTGGG
1 AAAAATGCCCTCAAACTTTTTCAAAAAAAGCAATTAAG-CCCTTTTT-TTTTGCACTCAATTGGG
21307716 TACTTGAACTTTCAAAATGCATC
64 TACTTGAACTTTC-AAATGCATC
* * * *
21307739 AAAAAGGCCCTAAAACTTTTTCAAAAAAAAGCAATTAAGCTCTTTTTTTTGGCACTCAATTGGGT
1 AAAAATGCCCTCAAACTTTTTC-AAAAAAAGCAATTAAGCCCTTTTTTTTTGCACTCAATTGGGT
* **
21307804 ATTTGAACGGTCAAATGCATC
65 ACTTGAACTTTCAAATGCATC
21307825 AAAAATGCCCT
1 AAAAATGCCCT
21307836 TTGACCATTA
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
86 19 0.12
87 34 0.21
88 69 0.43
89 38 0.24
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (85 bp):
AAAAATGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCTTTTTTTTTGCACTCAATTGGGTA
CTTGAACTTTCAAATGCATC
Found at i:21308003 original size:21 final size:19
Alignment explanation
Indices: 21307956--21308071 Score: 58
Period size: 19 Copynumber: 5.9 Consensus size: 19
21307946 ACAAAAATCA
* *
21307956 ATAAAAGTT-ATAAAAAAT
1 ATAAAATTTAATAAAAATT
*
21307974 -TAAATTTTAATAGAAAATAT
1 ATAAAATTTAATA-AAAAT-T
*
21307994 ATAAAATTTATTAAAAATT
1 ATAAAATTTAATAAAAATT
* * *
21308013 AGAAAATAAATTTATAAAAATC
1 ATAAAAT---TTAATAAAAATT
*
21308035 ATAAAAAATT-ATAAAAAATT
1 AT-AAAATTTAAT-AAAAATT
* *
21308055 GTAAAATTTTATAAAAA
1 ATAAAATTTAATAAAAA
21308072 AATCATTAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
17 6 0.08
18 3 0.04
19 24 0.32
20 17 0.23
21 10 0.14
22 10 0.14
23 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (19 bp):
ATAAAATTTAATAAAAATT
Found at i:21308042 original size:32 final size:32
Alignment explanation
Indices: 21307988--21308050 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
21307978 TTTTAATAGA
* * *
21307988 AAATATATAAAATTTATTAAAAATTAGAAAAT
1 AAATATATAAAAATCATAAAAAATTAGAAAAT
* *
21308020 AAATTTATAAAAATCATAAAAAATTATAAAA
1 AAATATATAAAAATCATAAAAAATTAGAAAA
21308051 AATTGTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (32 bp):
AAATATATAAAAATCATAAAAAATTAGAAAAT
Found at i:21308050 original size:41 final size:41
Alignment explanation
Indices: 21307969--21308092 Score: 105
Period size: 42 Copynumber: 2.9 Consensus size: 41
21307959 AAAGTTATAA
21307969 AAAATTAAATTTTAATAGAAAAT-ATATAAAATTTATTAAAAATTAG-
1 AAAA-TAAA-TTT-ATA-AAAATCATA-AAAATTTA-TAAAAATT-GT
*
21308015 AAAATAAATTTATAAAAATCATAAAAAATTATAAAAAATTGT
1 AAAATAAATTTATAAAAATCATAAAAATTTAT-AAAAATTGT
21308057 AAAAT---TTTATAAAAAAATCATTAAAAATTTATAAAA
1 AAAATAAATTTAT--AAAAATCA-TAAAAATTTATAAAA
21308093 TGCATGAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
39 5 0.07
41 14 0.20
42 34 0.49
43 6 0.09
44 3 0.04
45 4 0.06
46 4 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (41 bp):
AAAATAAATTTATAAAAATCATAAAAATTTATAAAAATTGT
Found at i:21308051 original size:20 final size:20
Alignment explanation
Indices: 21307948--21308092 Score: 86
Period size: 21 Copynumber: 7.2 Consensus size: 20
21307938 TATAAAAAAC
*
21307948 AAAAATCA-ATAAAAGTTATA
1 AAAAATCATA-AAAATTTATA
*
21307968 AAAAAT--T-AAATTTTAATA
1 AAAAATCATAAAAATTT-ATA
*
21307986 GAAAAT-ATATAAAATTTATTA
1 AAAAATCATA-AAAATTTA-TA
* * *
21308007 AAAATTAGAAAATAAATTTAT-
1 AAAAAT-CATAA-AAATTTATA
*
21308028 AAAAATCATAAAAAATTATA
1 AAAAATCATAAAAATTTATA
** *
21308048 AAAAATTGTAAAATTTTATAA
1 AAAAATCATAAAAATTTAT-A
21308069 AAAAATCATTAAAAATTTATA
1 AAAAATCA-TAAAAATTTATA
21308090 AAA
1 AAA
21308093 TGCATGAAAA
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.05
18 8 0.08
19 8 0.08
20 25 0.26
21 28 0.29
22 12 0.13
23 9 0.09
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATCATAAAAATTTATA
Found at i:21308060 original size:9 final size:10
Alignment explanation
Indices: 21307987--21308092 Score: 63
Period size: 10 Copynumber: 10.2 Consensus size: 10
21307977 ATTTTAATAG
21307987 AAAA-TATATA
1 AAAATTATA-A
* *
21307997 AAATTTATTA
1 AAAATTATAA
*
21308007 AAAATTAGAAA
1 AAAATTA-TAA
21308018 ATAAATT-TATA
1 A-AAATTATA-A
*
21308029 AAAATCATAA
1 AAAATTATAA
21308039 AAAATTATAA
1 AAAATTATAA
*
21308049 AAAATTGTAA
1 AAAATTATAA
**
21308059 AATTTTATAAA
1 AAAATTAT-AA
*
21308070 AAAATCATTAA
1 AAAATTA-TAA
*
21308081 AAATTTATAA
1 AAAATTATAA
21308091 AA
1 AA
21308093 TGCATGAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
10 44 0.61
11 22 0.31
12 6 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:21308318 original size:17 final size:16
Alignment explanation
Indices: 21308298--21308330 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
21308288 TTTTCTATGA
21308298 TTTTTATATTTCTTTAC
1 TTTTTATATTT-TTTAC
21308315 TTTTTATATTTTTTAC
1 TTTTTATATTTTTTAC
21308331 GACTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATATTTTTTAC
Found at i:21308356 original size:54 final size:57
Alignment explanation
Indices: 21308298--21308428 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
21308288 TTTTCTATGA
* * * *
21308298 TTTTTATATTTCTTTACTTTTTAT-A-TTTTTTACGA-CTTTATAAAAT-TTATAATT
1 TTTTTATATTTCTATA-TATTTATAATTTTTTTACGATCTTTATAAAATAATACAATT
* *
21308352 TTTTTATATTTCTATATATTTATAATTTTTTTATGATTTTTATAAAATAATACAATT
1 TTTTTATATTTCTATATATTTATAATTTTTTTACGATCTTTATAAAATAATACAATT
21308409 TTTTTATGATTT-TATA-ATTT
1 TTTTTAT-ATTTCTATATATTT
21308429 TTTTATAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
53 6 0.09
54 16 0.24
55 9 0.14
56 14 0.21
57 17 0.26
58 4 0.06
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (57 bp):
TTTTTATATTTCTATATATTTATAATTTTTTTACGATCTTTATAAAATAATACAATT
Found at i:21308411 original size:30 final size:29
Alignment explanation
Indices: 21308334--21308425 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 29
21308324 TTTTTACGAC
21308334 TTTATAAAATTTATAATTTTTTTAT-ATT
1 TTTATAAAATTTATAATTTTTTTATGATT
* *
21308362 TCTAT-ATATTTATAATTTTTTTATGATT
1 TTTATAAAATTTATAATTTTTTTATGATT
* *
21308390 TTTATAAAATAATACAATTTTTTTATGA-T
1 TTTATAAAAT-TTATAATTTTTTTATGATT
21308419 TTTATAA
1 TTTATAA
21308426 TTTTTTTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 18 0.33
28 11 0.20
29 11 0.20
30 15 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTATAAAATTTATAATTTTTTTATGATT
Found at i:21308429 original size:18 final size:18
Alignment explanation
Indices: 21308405--21308459 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
21308395 AAAATAATAC
*
21308405 AATTTTTTTATGATTTTAT
1 AATTTTTTTATAATTTT-T
21308424 AATTTTTTTATAATTTTT
1 AATTTTTTTATAATTTTT
* *
21308442 AATATTTTTATAGTTTTT
1 AATTTTTTTATAATTTTT
21308460 TATTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
AATTTTTTTATAATTTTT
Found at i:21308460 original size:11 final size:10
Alignment explanation
Indices: 21308343--21308462 Score: 51
Period size: 10 Copynumber: 12.5 Consensus size: 10
21308333 CTTTATAAAA
21308343 TTTATA-ATT
1 TTTATATATT
*
21308352 TTTTTATATT
1 TTTATATATT
*
21308362 TCTATATA--
1 TTTATATATT
21308370 TTTATA-ATT
1 TTTATATATT
*
21308379 TTTTTATGATT
1 TTTATAT-ATT
* *
21308390 TTTATAAAAT
1 TTTATATATT
** *
21308400 AATACA-ATT
1 TTTATATATT
*
21308409 TTTTTATGA-T
1 TTTATAT-ATT
21308419 TTTATA-ATT
1 TTTATATATT
*
21308428 TTTTTATAATT
1 TTTATAT-ATT
21308439 TTTA-ATATT
1 TTTATATATT
21308448 TTTATAGT-TT
1 TTTATA-TATT
21308458 TTTAT
1 TTTAT
21308463 TAAAATTCAA
Statistics
Matches: 80, Mismatches: 19, Indels: 23
0.66 0.16 0.19
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 27 0.34
10 30 0.38
11 16 0.20
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTATATATT
Found at i:21313071 original size:11 final size:11
Alignment explanation
Indices: 21313057--21313100 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
21313047 CATTTTAGTC
21313057 TTGTTTTTTTA
1 TTGTTTTTTTA
*
21313068 TTGTCTTTTTA
1 TTGTTTTTTTA
*
21313079 TTTTTATTTTTA
1 TTGTT-TTTTTA
21313091 TT-TTTTTTTA
1 TTGTTTTTTTA
21313101 AATTTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 6 0.21
11 15 0.52
12 8 0.28
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (11 bp):
TTGTTTTTTTA
Found at i:21318231 original size:44 final size:43
Alignment explanation
Indices: 21318049--21318751 Score: 198
Period size: 44 Copynumber: 16.4 Consensus size: 43
21318039 TGAAGCTAGT
* * *
21318049 AATCCTATCTCCCTGAGATTATAGTGGAGCGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
* * ** * * *** *
21318092 GGATTTTATCTCTTTGA-AGTGACAGTAGAGTGGA-TCGTAT-CA
1 -AATCTTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAATAAA
** * ** ** **
21318134 GGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAA
* *
21318178 AATCCTATCTCCCTGAGATTACAGTAGAGTGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
* * *** *
21318221 ATATCTTATCT--CTGA-AGTGACAGTAGAGTGGA-TCGTAT-CA
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAATAAA
** * * ** ** **
21318261 GGTTTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAA
* * *
21318305 AATCCTATCTCTCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
* * * * * *** *
21318348 GGATCTCATCTCTCTGA-AGTGACAGTAGAGTGGA-TCGTAT-TA
1 -AATCTTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAATAAA
** *** * ** ** **
21318390 GGTCTTATCTTTTTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAA
* *
21318434 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
* * * * *** *
21318477 AGATATTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTAT-CA
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAATAAA
** * * * ** ** **
21318519 TGTCTTATCTCCTTAAGATTACAGCGGAGTAAATTGAAGCTATT
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAA
* *
21318563 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
* * * * *** *
21318606 GGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTAT-CA
1 -AATCTTATCTCCCTGAGA-TTACAGTGGAGTGGATTAAAATAAA
* * * ** **
21318648 AGTCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAA
* *
21318692 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
*
21318735 AGATCTTATCTCTCTGA
1 A-ATCTTATCTCCCTGA
21318752 AGTTATAGTA
Statistics
Matches: 450, Mismatches: 177, Indels: 64
0.65 0.26 0.09
Matches are distributed among these distances:
39 7 0.02
40 1 0.00
41 110 0.24
42 32 0.07
43 44 0.10
44 256 0.57
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAA
Found at i:21318786 original size:85 final size:85
Alignment explanation
Indices: 21318439--21318815 Score: 230
Period size: 85 Copynumber: 4.4 Consensus size: 85
21318429 CTAGTAATCC
* * *
21318439 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATATTATCTCTCTGA-AGTTACAGT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAGA-TTACAGT
* *
21318503 AGAGTAGATCGTATCATGTCT
65 AGAGTAGATCGAATCAAGTCT
* * * * * ** ** *
21318524 TATCTCCTTAAGATTACAGCGGAGTAAATTGAAGCTATTA-ATCCTATCTCCCTGAGATTACAGT
1 TATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAAGATCTTATCTCCCTGAGATTACAGT
* ** ** *
21318588 GGAGCGGATTAAAATAAAGGATCT
65 AGAGTAGA-TCGAATCAA-G-TCT
* * * *** * *
21318612 TATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGTAT-CAAG-TCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAGATTACAGT
* * * * *
21318673 GGAGTAGATTGAAGCTAGTAATCC
65 AGAGTAGATCGAATC-A--AGTCT
* * *
21318697 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGA-AGTTATAGT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAGA-TTACAGT
*
21318761 AGAGTAGATCGTATCAAGTCT
65 AGAGTAGATCGAATCAAGTCT
* * *
21318782 TATCTCCCTGACG-TTGCAGTGGAGTAGACTAAAA
1 TATCTCCCTGA-GATTACAGTGGAGCAGATTAAAA
21318816 CCACGAATCT
Statistics
Matches: 212, Mismatches: 64, Indels: 32
0.69 0.21 0.10
Matches are distributed among these distances:
84 3 0.01
85 132 0.62
86 16 0.08
87 9 0.04
88 52 0.25
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (85 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCCCTGAGATTACAGTA
GAGTAGATCGAATCAAGTCT
Found at i:21318809 original size:129 final size:129
Alignment explanation
Indices: 21318002--21318792 Score: 1244
Period size: 129 Copynumber: 6.1 Consensus size: 129
21317992 TCAAAGAATC
* * *
21318002 TCAGATCTTATCTCCTTGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * * * *
21318067 TTATAGTGGAGCGGATTAAAATAAAGGATTTTATCTCTTTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
21318131 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * * *
21318196 TTACAGTAGAGTGGATTAAAATAAAATATCTTA--TCTCTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
* *
21318258 TCAGGTTTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCTCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
21318323 TTACAGTGGAGCGGATTAAAATAAAGGATCTCATCTCTCTGAAGTGACAGTAGAGTGGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
* ***
21318387 TTAGGTCTTATCTTTTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
21318452 TTACAGTGGAGCGGATTAAAATAAAAGATATTATCTCTCTGAAGTTACAGTAGAGTAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
* * * * * *
21318516 TCATGTCTTATCTCCTTAAGATTACAGCGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
21318581 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
* *
21318645 TCAAGTCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
21318710 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
*
21318774 TCAAGTCTTATCTCCCTGA
1 TCAGGTCTTATCTCCCTGA
21318793 CGTTGCAGTG
Statistics
Matches: 615, Mismatches: 45, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
127 119 0.19
129 496 0.81
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGTA
Found at i:21320380 original size:2 final size:2
Alignment explanation
Indices: 21320375--21320405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21320365 GCTGCACATC
21320375 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 T
21320406 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21322516 original size:30 final size:29
Alignment explanation
Indices: 21322450--21322519 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
21322440 TTTAATCGCG
* * *
21322450 TATATTTTTATAATTTTAAAAGATTAAAT
1 TATAATTTTATAATTTTAAAAGATCAAAA
* * *
21322479 TAAAATTTTATCAATTTTAAAGGGTCAAAA
1 TATAATTTTAT-AATTTTAAAAGATCAAAA
21322509 TATAATTTTAT
1 TATAATTTTAT
21322520 TTTTATTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (29 bp):
TATAATTTTATAATTTTAAAAGATCAAAA
Found at i:21323157 original size:29 final size:30
Alignment explanation
Indices: 21323093--21323160 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
21323083 AATATTAAAA
21323093 TTATACATGAATTTTGATTCAATGTGTAATG
1 TTATACATGAATTTTGATT-AATGTGTAATG
* * *
21323124 TTATACATGAATTTTGATT-TTGTGTGATT
1 TTATACATGAATTTTGATTAATGTGTAATG
21323153 TTATACAT
1 TTATACAT
21323161 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.44
31 19 0.56
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (30 bp):
TTATACATGAATTTTGATTAATGTGTAATG
Found at i:21328133 original size:62 final size:62
Alignment explanation
Indices: 21328067--21328184 Score: 236
Period size: 62 Copynumber: 1.9 Consensus size: 62
21328057 TAAATAAAGA
21328067 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
1 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
21328129 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAA
1 TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAA
21328185 TTAGTTCAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (62 bp):
TGGAGCCATTTAATAAGCATCCCTTTATTAATGGCTCCACATCATTTTAATAATAAATGAGG
Found at i:21347615 original size:24 final size:24
Alignment explanation
Indices: 21347581--21347652 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
21347571 TCGTTTTGTG
*
21347581 GCAAAGAATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
21347605 GCAAAGGATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
21347629 GCAAAGGATGAATTGACGGCAAAT
1 GCAAAGGATGAATTGACGGTAAAT
21347653 TACCCAAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGTAAAT
Found at i:21347754 original size:21 final size:21
Alignment explanation
Indices: 21347729--21347792 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
21347719 TGAGCTTCTA
21347729 TTAACTCATATGAGTTTCCGT
1 TTAACTCATATGAGTTTCCGT
* * *
21347750 TTAAC-CCTAATGGGTTCCCGT
1 TTAACTCAT-ATGAGTTTCCGT
* * *
21347771 TTAGCTCTTATGAGCTTCCGT
1 TTAACTCATATGAGTTTCCGT
21347792 T
1 T
21347793 CAACCTTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (21 bp):
TTAACTCATATGAGTTTCCGT
Found at i:21347850 original size:19 final size:21
Alignment explanation
Indices: 21347807--21347851 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21347797 CTTTATAAGT
* *
21347807 TTCTGTTTAGCACTTATGTGC
1 TTCTGTTTAGCACTTACGGGC
21347828 TTCTGTTTAGC-CTT-CGGGC
1 TTCTGTTTAGCACTTACGGGC
21347847 TTCTG
1 TTCTG
21347852 AAAACGATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAGCACTTACGGGC
Found at i:21351079 original size:18 final size:18
Alignment explanation
Indices: 21351058--21351102 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
21351048 TTTGAAAAGT
*
21351058 TATTAAATATTTAAA-AAA
1 TATTAAA-ATTAAAATAAA
21351076 TATTAAAATTAAAATAAA
1 TATTAAAATTAAAATAAA
*
21351094 TATAAAAAT
1 TATTAAAAT
21351103 AATATCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAAATTAAAATAAA
Found at i:21351610 original size:29 final size:30
Alignment explanation
Indices: 21351543--21351611 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
21351533 TTAATTTAAT
* *
21351543 TTAATTTAATTGTTTTGAATAATATAATGA
1 TTAATTTAATTGTTTTGAATAATAAAAAGA
* * *
21351573 TAAAATTAATT-TATTT-AATAATAAAAAGG
1 TTAATTTAATTGT-TTTGAATAATAAAAAGA
21351602 TTAATTTAAT
1 TTAATTTAAT
21351612 CATGTCCCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TTAATTTAATTGTTTTGAATAATAAAAAGA
Found at i:21361927 original size:15 final size:15
Alignment explanation
Indices: 21361909--21361942 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21361899 TATTAAATTA
21361909 TTTAAAATTAATTTT
1 TTTAAAATTAATTTT
* *
21361924 TTTAATATTGATTTT
1 TTTAAAATTAATTTT
21361939 TTTA
1 TTTA
21361943 TTGATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTAAAATTAATTTT
Found at i:21365685 original size:44 final size:44
Alignment explanation
Indices: 21365636--21365721 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
21365626 TCAATCGGAC
21365636 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
21365680 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAG
1 TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAG
21365722 ATTAAGAGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (44 bp):
TCTGTTTAAAAGGTTGATGGTTGAATTTAACTCTTTTAAAAGGT
Found at i:21366573 original size:14 final size:14
Alignment explanation
Indices: 21366554--21366580 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21366544 TTGATAATTG
21366554 AAAAATAATTATTA
1 AAAAATAATTATTA
21366568 AAAAATAATTATT
1 AAAAATAATTATT
21366581 GAATTTAGTG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATAATTATTA
Found at i:21367262 original size:89 final size:90
Alignment explanation
Indices: 21367129--21367302 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 90
21367119 GTTCCTTTTT
* ** *
21367129 TTTTTTTACACTCAATTTGGGTACTTGAGTTTTTAAAATATATCAAAAAGACCCTCAAA-TCTTT
1 TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACT-TTT
21367193 TCA-AAAAAAGCAATCAAGCCCCTTAC
65 TCATAAAAAA-CAATCAAGCCCCTTAC
* *
21367219 TTTTTTTGCACTCAA-TTGGGTACTTAAACTTTCAAAA-AGTATCAAAAAGATCCTCAAACTTTT
1 TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATA-TATCAAAAAGACCCTCAAACTTTT
*
21367282 TCATAAAAAACAATTAAGCCC
65 TCATAAAAAACAATCAAGCCC
21367303 ATGCATTTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
88 1 0.01
89 52 0.70
90 21 0.28
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (90 bp):
TTTTTTTACACTCAATTTGGGTACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTTTTT
CATAAAAAACAATCAAGCCCCTTAC
Found at i:21367337 original size:7 final size:7
Alignment explanation
Indices: 21367311--21367353 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
21367301 CCATGCATTT
21367311 ATTAAAA
1 ATTAAAA
21367318 ATTATAAA
1 ATTA-AAA
21367326 A--AAAA
1 ATTAAAA
21367331 ATTAAAA
1 ATTAAAA
21367338 TATTAAAA
1 -ATTAAAA
21367346 ATTAAAA
1 ATTAAAA
21367353 A
1 A
21367354 ATATATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 1 0.03
7 16 0.50
8 11 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATTAAAA
Found at i:21367362 original size:18 final size:19
Alignment explanation
Indices: 21367334--21367384 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
21367324 AAAAAAAATT
21367334 AAAATAT-TAAAAAT-TAA
1 AAAATATATAAAAATATAA
21367351 AAAATATATAAAAATCATAA
1 AAAATATATAAAAAT-ATAA
* *
21367371 TAATTATATAAAAA
1 AAAATATATAAAAA
21367385 ATTGTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
20 15 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATATAAAAATATAA
Found at i:21367461 original size:20 final size:20
Alignment explanation
Indices: 21367311--21367461 Score: 63
Period size: 19 Copynumber: 8.0 Consensus size: 20
21367301 CCATGCATTT
*
21367311 ATTA-AAAATTATAAAAAAA
1 ATTATAAAATTATATAAAAA
*
21367330 AAT-TAAAA-TAT-T-AAAA
1 ATTATAAAATTATATAAAAA
*
21367346 ATTA-AAAAATATAT-AAAA
1 ATTATAAAATTATATAAAAA
*
21367364 ATCATAATAATTATATAAAAA
1 ATTATAA-AATTATATAAAAA
* * * *
21367385 ATTGTACATTTTTAT-AAAA
1 ATTATAAAATTATATAAAAA
* * * **
21367404 ATCATAAAA-AATTATGAAGC
1 ATTATAAAATTA-TATAAAAA
*
21367424 A-TATATAAATAATA-AAAAA
1 ATTATA-AAATTATATAAAAA
*
21367443 ATTATAAAATTTTATAAAA
1 ATTATAAAATTATATAAAA
21367462 TCGTAAGAAA
Statistics
Matches: 95, Mismatches: 24, Indels: 25
0.66 0.17 0.17
Matches are distributed among these distances:
16 10 0.11
17 3 0.03
18 11 0.12
19 32 0.34
20 29 0.31
21 10 0.11
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTATAAAATTATATAAAAA
Found at i:21367472 original size:21 final size:21
Alignment explanation
Indices: 21367448--21367492 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21367438 AAAAAATTAT
* *
21367448 AAAATTTTATAAAATCGT-AAG
1 AAAATTATACAAAAT-GTAAAG
21367469 AAAATTATACAAAATGTAAAG
1 AAAATTATACAAAATGTAAAG
21367490 AAA
1 AAA
21367493 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATTATACAAAATGTAAAG
Found at i:21367738 original size:19 final size:18
Alignment explanation
Indices: 21367710--21367756 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
21367700 ATTTATGTTT
21367710 TTTATAATTTTAT-TAAAA
1 TTTATAATTTT-TCTAAAA
21367728 TTTAGTAATTTTTCTAAAA
1 TTTA-TAATTTTTCTAAAA
*
21367747 TTTATTATTT
1 TTTATAATTT
21367757 ATGATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATAATTTTTCTAAAA
Found at i:21367739 original size:27 final size:29
Alignment explanation
Indices: 21367679--21367739 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
21367669 TTTTTATAAA
*
21367679 AATTTTCTAATTTTTAATAAAATTTATGT
1 AATTTTATAATTTTTAATAAAATTTATGT
* *
21367708 -TTTTTATAA-TTTTATTAAAATTTA-GT
1 AATTTTATAATTTTTAATAAAATTTATGT
21367734 AATTTT
1 AATTTT
21367740 TCTAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 18 0.67
28 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTTATAATTTTTAATAAAATTTATGT
Found at i:21367764 original size:47 final size:48
Alignment explanation
Indices: 21367661--21367767 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
21367651 TTGTTAATTT
*
21367661 TTTTATGAT--TTTTATAAAAATTTTCTAATTTTTAATAAAATTTATG
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
* * * *
21367707 TTTT-TTATAATTTTATTAAAATTTAGTAATTTTT-CTAAAATTTAT-
1 TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
21367752 TATTTATGATAATTTT
1 T-TTTATGATAATTTT
21367768 TTTCTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.08
46 17 0.33
47 30 0.59
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (48 bp):
TTTTATGATAATTTTATAAAAATTTACTAATTTTTAATAAAATTTATG
Found at i:21368311 original size:121 final size:121
Alignment explanation
Indices: 21368156--21368410 Score: 343
Period size: 129 Copynumber: 2.1 Consensus size: 121
21368146 AGAATTTGTG
* * *
21368156 TTTTT-TTTTGTTTAAGTTAGACTTTAAATTTGACAATTGTTCTCACATTAGGGTTTATA-ATTT
1 TTTTTGTTTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATATATTT
*
21368219 TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGGGCTTGTACTT
66 TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
*
21368275 TTTTTGTTGTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTGTCACATTACGGTTTATACTCT
1 TTTTTGTT-TTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATA----
* * * *
21368340 TTTTTTTTTTTTTCTATATTAGGCCTTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
61 ---TATTTTTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
21368404 TTTTTGT
1 TTTTTGT
21368411 CAAAGTTAGG
Statistics
Matches: 117, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
119 5 0.04
120 2 0.02
121 48 0.41
129 62 0.53
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (121 bp):
TTTTTGTTTTGTCTAAGTTAGACTTTAAATGTGACAATTGTTCTCACATTACGGTTTATATATTT
TTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGAGCTTGTACTT
Found at i:21368314 original size:64 final size:64
Alignment explanation
Indices: 21368242--21368410 Score: 162
Period size: 65 Copynumber: 2.6 Consensus size: 64
21368232 GGCCCTAGGC
*
21368242 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTA-AGTTAGACTTTA-AA
1 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTATA-TTAGACCTTAGAA
* * * ** * * * * * * *
21368305 TGTGACAATTGTTGTCACATTACGGTTTATACTCTTTTTTTTTTTTTTCTATATTAGGCCTTAGG
1 T-TGACAATTATTCTAACATTGGGGCTTGTACT-TTTTTTGTTGTTGTCTATATTAGACCTTAGA
*
21368370 C
64 A
*
21368371 TTGACAATTATTCTAACATTGGAGCTTGTACTTTTTTTGT
1 TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGT
21368411 CAAAGTTAGG
Statistics
Matches: 79, Mismatches: 23, Indels: 7
0.72 0.21 0.06
Matches are distributed among these distances:
63 1 0.01
64 31 0.39
65 45 0.57
66 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (64 bp):
TTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTTGTTGTTGTCTATATTAGACCTTAGAA
Found at i:21368390 original size:65 final size:63
Alignment explanation
Indices: 21368216--21368408 Score: 165
Period size: 64 Copynumber: 3.0 Consensus size: 63
21368206 GGGTTTATAA
* ** *
21368216 TTTTTTGTCTAAATTAGGCCCTAGGCTTGACAATTATTCTAACATTGGGGCTTGTACTTTTTTT
1 TTTTTTGTCT-AATTAGGCCTTAGGCTTGACAATTATTCTAACATTACGGCTTATACTTTTTTT
* * * * ** * * * *
21368280 GTTGTTGTCTAAGTTAGACTTTA-AATGTGACAATTGTTGTCACATTACGGTTTATACTCTTTTT
1 TTTTTTGTCTAA-TTAGGCCTTAGGCT-TGACAATTATTCTAACATTACGGCTTATACT-TTTTT
21368344 T
63 T
* * *
21368345 TTTTTTTTCTATATTAGGCCTTAGGCTTGACAATTATTCTAACATT-GGAGCTTGTACTTTTTTT
1 TTTTTTGTCTA-ATTAGGCCTTAGGCTTGACAATTATTCTAACATTACG-GCTTATACTTTTTTT
21368409 GTCAAAGTTA
Statistics
Matches: 96, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
63 3 0.03
64 46 0.48
65 45 0.47
66 2 0.02
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (63 bp):
TTTTTTGTCTAATTAGGCCTTAGGCTTGACAATTATTCTAACATTACGGCTTATACTTTTTTT
Found at i:21393247 original size:60 final size:59
Alignment explanation
Indices: 21393121--21393252 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
21393111 AGATCTTACT
** * * * *
21393121 AGCCTCCACCATAGGTTTTCACTCAATACAATTCTCCAAGCTAGCTTCCCAATCTTTTCC
1 AGCCTCCA-CATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTTGTCA
* *
21393181 AGCCTCCAGCATAGACTTCCACTCAATATAATTCTCCAAGCTATCTTCCCAACCTTAGT-A
1 AGCCTCCA-CATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTT-GTCA
*
21393241 ATCCTCCACATA
1 AGCCTCCACATA
21393253 CATATTTCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.07
60 56 0.92
61 1 0.02
ACGTcount: A:0.28, C:0.35, G:0.08, T:0.30
Consensus pattern (59 bp):
AGCCTCCACATAGACTTCCACTCAATACAATTCTCCAAGCTAGCTTCCCAACCTTGTCA
Found at i:21400057 original size:92 final size:92
Alignment explanation
Indices: 21399898--21400079 Score: 337
Period size: 92 Copynumber: 2.0 Consensus size: 92
21399888 CCAACAAAAA
*
21399898 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTATAA
1 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
*
21399963 GGAGAAGCGTATCTCTGGTGGGAATAT
66 GGAGAAACGTATCTCTGGTGGGAATAT
*
21399990 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTATTACAA
1 GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
21400055 GGAGAAACGTATCTCTGGTGGGAAT
66 GGAGAAACGTATCTCTGGTGGGAAT
21400080 CTGTGGTTAG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (92 bp):
GAGTTTTGCAACAATTAGATTGCACTCCCCGAGAGAATCTAATATGTGTTGTATCACTACTACAA
GGAGAAACGTATCTCTGGTGGGAATAT
Found at i:21404634 original size:17 final size:16
Alignment explanation
Indices: 21404612--21404645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21404602 ATTATATAAT
21404612 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
21404629 TAATGATATTATATTA
1 TAATGATATTAAATTA
21404645 T
1 T
21404646 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:21407336 original size:7 final size:7
Alignment explanation
Indices: 21407317--21407349 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
21407307 TTAAAATAAA
21407317 TAAATTT
1 TAAATTT
21407324 TAAAATTT
1 T-AAATTT
21407332 TAAATTT
1 TAAATTT
21407339 TAAATTT
1 TAAATTT
21407346 TAAA
1 TAAA
21407350 CATTAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:21413318 original size:12 final size:12
Alignment explanation
Indices: 21413301--21413330 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21413291 TAGGTAGTAA
21413301 AAGAAAAAGAAG
1 AAGAAAAAGAAG
21413313 AAGAAAAAGAAG
1 AAGAAAAAGAAG
21413325 -AGAAAA
1 AAGAAAA
21413331 TCTTTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:21418493 original size:31 final size:29
Alignment explanation
Indices: 21418455--21418530 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
21418445 TTAATGGCTC
* *
21418455 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
21418486 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
21418515 AGTGACTAAAATGTAA
1 AGTGACTAAAATGTAA
21418531 TTTGAGCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.54
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:21428508 original size:19 final size:19
Alignment explanation
Indices: 21428466--21428523 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
21428456 TCTCTCTAAG
*
21428466 AAAAATACAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
21428485 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
21428504 AAAAAATTCCAAA-ATTTAT
1 -AAAAATTCAAAATATTTAT
21428523 A
1 A
21428524 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 5 0.15
19 18 0.55
20 10 0.30
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:21428511 original size:20 final size:19
Alignment explanation
Indices: 21428486--21428523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
21428476 AATAATTTTT
21428486 AAAATTCAAAATATTTATAA
1 AAAATTCAAAA-ATTTATAA
*
21428506 AAAATTCCAAAATTTATA
1 AAAATTCAAAAATTTATA
21428524 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAAATTTATAA
Found at i:21428537 original size:18 final size:19
Alignment explanation
Indices: 21428514--21428561 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
21428504 AAAAAATTCC
*
21428514 AAAATT-TATATTTTTAAA
1 AAAATTATAAATTTTTAAA
21428532 AAAATTATAAATTTTTAAA
1 AAAATTATAAATTTTTAAA
*
21428551 AAAATTCTAAA
1 AAAATTATAAA
21428562 GAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTATAAATTTTTAAA
Found at i:21438959 original size:3 final size:3
Alignment explanation
Indices: 21438951--21438983 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21438941 TGCACGGTTT
21438951 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
21438984 TTTACTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:21440076 original size:24 final size:24
Alignment explanation
Indices: 21440048--21440093 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21440038 AAATATTATT
21440048 TTATTTTATTGAATACTAATATGA
1 TTATTTTATTGAATACTAATATGA
* *
21440072 TTATTTTATTTAATATTAATAT
1 TTATTTTATTGAATACTAATAT
21440094 TAATATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTTTATTGAATACTAATATGA
Found at i:21440195 original size:53 final size:51
Alignment explanation
Indices: 21440123--21440252 Score: 131
Period size: 53 Copynumber: 2.5 Consensus size: 51
21440113 ATTATTATCT
* * *
21440123 TTTTTATATATTTTAAAATTTTGTA-TATTATTTTTGT-AAACAGTGTTT-TTTA
1 TTTTTATATATTTTTAAATTTT-TATTA-TATTTTTGTGAAA-A-TATTTATGTA
*
21440175 TTTTTATATACTTTTTAAATTTATTATTATATTTTTTTGAAAATATTTATGTA
1 TTTTTATATA-TTTTTAAATTT-TTATTATATTTTTGTGAAAATATTTATGTA
21440228 TTTTTATATATTTCTTTAAATTTTT
1 TTTTTATATA-TT-TTTAAATTTTT
21440253 TAAATTAGGA
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
52 14 0.21
53 38 0.57
54 15 0.22
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (51 bp):
TTTTTATATATTTTTAAATTTTTATTATATTTTTGTGAAAATATTTATGTA
Found at i:21450436 original size:68 final size:70
Alignment explanation
Indices: 21450327--21450542 Score: 287
Period size: 68 Copynumber: 3.0 Consensus size: 70
21450317 TTACAAAAAA
* *
21450327 AAAACATCAAGTTTGTTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAA-AATAA
1 AAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATAACAA
21450391 -TAAT
66 CTAAT
*
21450395 AAAACATCAAGTTTATTTTACTAATCAAATGTTATATTTTGTTACAACAATTAATACAATTAACA
1 AAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAA-TAACA
21450460 ACTAAT
65 ACTAAT
*
21450466 ACAATTA-AT-AATTTGATAATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAA
1 A-AA--ACATCAAGTT--T-ATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAA
*
21450529 TTAACAAGTAAT
60 -TAACAACTAAT
21450541 AA
1 AA
21450543 TTTGATAATT
Statistics
Matches: 133, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
68 57 0.43
70 4 0.03
71 5 0.04
72 6 0.05
73 2 0.02
74 3 0.02
75 56 0.42
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.38
Consensus pattern (70 bp):
AAAACATCAAGTTTATTTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATAACAA
CTAAT
Found at i:21450465 original size:16 final size:16
Alignment explanation
Indices: 21450440--21450473 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21450430 ATTTTGTTAC
*
21450440 AACAATTAATACAATT
1 AACAACTAATACAATT
21450456 AACAACTAATACAATT
1 AACAACTAATACAATT
21450472 AA
1 AA
21450474 TAATTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACAACTAATACAATT
Found at i:21450569 original size:16 final size:16
Alignment explanation
Indices: 21450548--21450589 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
21450538 AATAATTTGA
*
21450548 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
21450564 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
21450580 TAGTTTTAAT
1 TAATTTTAAT
21450590 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:21451534 original size:19 final size:19
Alignment explanation
Indices: 21451507--21451546 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21451497 ATTTTAAAAA
21451507 AATTCTTTAT-ATATTCTTT
1 AATTCTTTATAATATT-TTT
*
21451526 AATTTTTTATAATATTTTT
1 AATTCTTTATAATATTTTT
21451545 AA
1 AA
21451547 AAATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTCTTTATAATATTTTT
Found at i:21451573 original size:26 final size:26
Alignment explanation
Indices: 21451530--21451586 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
21451520 TTCTTTAATT
*
21451530 TTTTATAATATTTTTAAAAATATAAA
1 TTTTAGAATATTTTTAAAAATATAAA
* *
21451556 TTTTAGAAT-TTTTATAAAAATTTGAA
1 TTTTAGAATATTTT-TAAAAATATAAA
21451582 TTTTA
1 TTTTA
21451587 AAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTAGAATATTTTTAAAAATATAAA
Found at i:21453680 original size:22 final size:22
Alignment explanation
Indices: 21453655--21453698 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21453645 TAATTTCACT
*
21453655 GCTACAGTATCCAATCTCACCG
1 GCTACAGTAACCAATCTCACCG
*
21453677 GCTACAGTAACTAATCTCACCG
1 GCTACAGTAACCAATCTCACCG
21453699 CCACCGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (22 bp):
GCTACAGTAACCAATCTCACCG
Found at i:21467284 original size:22 final size:22
Alignment explanation
Indices: 21467253--21467302 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
21467243 AATTTAAAAT
*
21467253 TTAATTATAAAAGTATATAATTA
1 TTAA-TATAAAAATATATAATTA
*
21467276 TTAATATAAAAATATATATTTA
1 TTAATATAAAAATATATAATTA
*
21467298 ATAAT
1 TTAAT
21467303 TTGTTGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAATATAAAAATATATAATTA
Found at i:21467888 original size:23 final size:22
Alignment explanation
Indices: 21467844--21467904 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
21467834 ATAATGATAT
* *
21467844 TATAATATATATTTTTGTATTAA
1 TATAA-ATATAATTTTATATTAA
21467867 TATAAATATAATTTTATAATTAA
1 TATAAATATAATTTTAT-ATTAA
* *
21467890 AATTAAATAAAATTT
1 TA-TAAATATAATTT
21467905 AAAAAAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.31
23 11 0.34
24 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAAATATAATTTTATATTAA
Found at i:21468313 original size:11 final size:11
Alignment explanation
Indices: 21468297--21468335 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
21468287 TTTATAAATA
21468297 TATAAATTAAT
1 TATAAATTAAT
*
21468308 TATAAAGTATAT
1 TATAAATTA-AT
21468320 TATTAAATTAAT
1 TA-TAAATTAAT
21468332 TATA
1 TATA
21468336 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:21468347 original size:14 final size:17
Alignment explanation
Indices: 21468315--21468352 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
21468305 AATTATAAAG
21468315 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
21468332 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
21468346 TATATTA
1 TATATTA
21468353 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:21468488 original size:3 final size:3
Alignment explanation
Indices: 21468482--21468546 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
21468472 TATTGTTGTA
*
21468482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
21468530 ATC ATT ATT AAT ATT AT
1 ATT ATT ATT ATT ATT AT
21468547 CAAATAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:21489260 original size:16 final size:17
Alignment explanation
Indices: 21489223--21489260 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21489213 TAAATAAATC
*
21489223 ATTAAAAAGATAAAATA
1 ATTAAAAAGATAAAAAA
*
21489240 TTTAAAAA-ATAAAAAA
1 ATTAAAAAGATAAAAAA
21489256 ATTAA
1 ATTAA
21489261 TTCAATCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATTAAAAAGATAAAAAA
Found at i:21494962 original size:13 final size:14
Alignment explanation
Indices: 21494944--21494976 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21494934 ATCAATTTAA
21494944 TTTTAAATA-AATT
1 TTTTAAATACAATT
*
21494957 TTTTAACTACAATT
1 TTTTAAATACAATT
21494971 TTTTAA
1 TTTTAA
21494977 TTACTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAATACAATT
Found at i:21508762 original size:67 final size:67
Alignment explanation
Indices: 21508631--21508762 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 67
21508621 GGTTATGGCA
* * * *
21508631 ACATAGAGGGTCCGCGAGGACATTAAGCATTTGGGTAAAATGTGTGAGACCATAGCTCGACTATG
1 ACATAGAGGGTCCACGAGGACATTAAACA-TTGGGTAAAATGTGTAAGACCATAGCTAGACTATG
21508696 ATG
65 ATG
* * * *
21508699 ACATAGAGGGTCCACTAGGACCTTAAACA-TGGTGTAAAATGTGTAAGACCATGGCTAGGCTATG
1 ACATAGAGGGTCCACGAGGACATTAAACATTGG-GTAAAATGTGTAAGACCATAGCTAGACTATG
21508763 GCAGCATATG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 3 0.05
67 27 0.49
68 25 0.45
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (67 bp):
ACATAGAGGGTCCACGAGGACATTAAACATTGGGTAAAATGTGTAAGACCATAGCTAGACTATGA
TG
Found at i:21509913 original size:3 final size:3
Alignment explanation
Indices: 21509905--21509967 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
21509895 ATCTTTATAT
21509905 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
21509953 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
21509968 AAGTTACATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21511352 original size:22 final size:22
Alignment explanation
Indices: 21511320--21511383 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
21511310 TAAAAAATAA
21511320 TTTTTCCCTATAAAAACTCAAG
1 TTTTTCCCTATAAAAACTCAAG
*
21511342 TTTTTCTCTATAAAAA-TCAAG
1 TTTTTCCCTATAAAAACTCAAG
** *
21511363 TAATTCCCTATAAAATCTCAA
1 TTTTTCCCTATAAAAACTCAA
21511384 ATTTATCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTTTCCCTATAAAAACTCAAG
Found at i:21511361 original size:21 final size:21
Alignment explanation
Indices: 21511312--21511377 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
21511302 ATTAATTCTA
21511312 AAAAAT-AA-TTTTTCCCTAT
1 AAAAATCAAGTTTTTCCCTAT
*
21511331 AAAAACTCAAGTTTTTCTCTAT
1 AAAAA-TCAAGTTTTTCCCTAT
**
21511353 AAAAATCAAGTAATTCCCTAT
1 AAAAATCAAGTTTTTCCCTAT
21511374 AAAA
1 AAAA
21511378 TCTCAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.12
20 1 0.03
21 19 0.47
22 15 0.38
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAATCAAGTTTTTCCCTAT
Found at i:21516783 original size:20 final size:20
Alignment explanation
Indices: 21516749--21516790 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21516739 AACTATTTAA
** *
21516749 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
21516769 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
21516789 AT
1 AT
21516791 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:21518870 original size:15 final size:15
Alignment explanation
Indices: 21518850--21518878 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21518840 GAAGCGCTTG
21518850 ATAAATCTAAAGTTT
1 ATAAATCTAAAGTTT
21518865 ATAAATCTAAAGTT
1 ATAAATCTAAAGTT
21518879 GAACTTTAGT
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:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
ATAAATCTAAAGTTT
Found at i:21522663 original size:371 final size:371
Alignment explanation
Indices: 21521980--21522724 Score: 1260
Period size: 371 Copynumber: 2.0 Consensus size: 371
21521970 GGAATGAGAT
*
21521980 TTCATTTGGAAAACACACCAACAAATTCTAATATTTTTTCTTTCCTTCCTTCATTTTCTAATATT
1 TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
21522045 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
66 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
* * *
21522110 TTACTCAGTGTATTGTGGACTATTCTCGTTAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
131 TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
* *
21522175 TCCTCGAGGTTAATTTGCTTGGAACTCATTTGCACATCGAAGATAGGTGGAGGCGAATATAACCT
196 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
*
21522240 TAAAGATAGTGACTTGATACACGCCTTGGAGTCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
261 TAAAGATAGTGACTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
21522305 CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTCG-ACTAACAA
326 CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTT-GAACTAACAA
* * *
21522351 TTCATTTGGAAGACACACCAACAAATTCTTATATTCTTTCTTTCCTTCCTTCATTTTCTAATGTT
1 TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
* * *
21522416 ATTAGATTATTCTATAAAGTATTACTGTAGAAATCCTTTGTAGAAATTGAGTTTCTTGTTATACA
66 ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
* *
21522481 TTGCTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTTCATTGTA
131 TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
*
21522546 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGGGGCGAATATAACCT
196 TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
* *
21522611 TAAAGATAGT-AGCTTGATACACGCCTTGGAGCCTTGTCCTATTTCTTCTTTTTCTGTTTGAGTT
261 TAAAGATAGTGA-CTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTT
* * * *
21522675 CCGTTCGTGTGTTCGAGATTTTTCTTACCGGAGATTTGAACTAACAA
325 CCGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTGAACTAACAA
21522722 TTC
1 TTC
21522725 CAACTATTAT
Statistics
Matches: 350, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
370 2 0.01
371 348 0.99
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (371 bp):
TTCATTTGGAAAACACACCAACAAATTCTAATATTCTTTCTTTCCTTCCTTCATTTTCTAATATT
ATTAGATTATTCTATAAAGTATTACTGCAGAAATCATTTGTAAAAATTGAGTTTCTTGTTATACA
TTACTCAGTGCATAGTGGACTATTCTCGTCAGTGCAAAACGCAAATAGTCATTGGCTCCATTGTA
TCCTCAAGGTTAATTTGCTTGGAACTCATTTGCACACCGAAGATAGGTGGAGGCGAATATAACCT
TAAAGATAGTGACTTGATACACGCCTTGGAGCCTTGTCATATTTCTTCTTTTTCTGTTCGAGTTC
CGTTCATGTGTTCGAGATTTTCCTCACCCGAGATTTGAACTAACAA
Found at i:21527473 original size:29 final size:30
Alignment explanation
Indices: 21527422--21527478 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
21527412 AAATTGAATT
*
21527422 AAATTAATATTTTATATATAAAATTACACA
1 AAATTAATAATTTATATATAAAATTACACA
21527452 AAATTAA-AATTTATATATAAAATTACA
1 AAATTAATAATTTATATATAAAATTACA
21527479 TTGAAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATTAATAATTTATATATAAAATTACACA
Found at i:21527498 original size:31 final size:29
Alignment explanation
Indices: 21527434--21527498 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
21527424 ATTAATATTT
* *
21527434 TATATATAAAATTACACAAAATTAAAATT
1 TATATATAAAATTACACAAAATCAAAATC
* *
21527463 TATATATAAAATTACATTGAAAGTCAAAATC
1 TATATATAAAATTACA--CAAAATCAAAATC
21527494 TATAT
1 TATAT
21527499 CTAACTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
TATATATAAAATTACACAAAATCAAAATC
Found at i:21536306 original size:32 final size:30
Alignment explanation
Indices: 21536250--21536308 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
21536240 TAACAATTAG
*
21536250 AAATTAATTAAATACGAATGTTTTAATAAT
1 AAATTAATTAAATACGAATATTTTAATAAT
*
21536280 AAATGTAATATAAATATGAATATTTTAAT
1 AAAT-TAAT-TAAATACGAATATTTTAAT
21536309 TATCTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 4 0.16
32 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (30 bp):
AAATTAATTAAATACGAATATTTTAATAAT
Found at i:21539056 original size:25 final size:26
Alignment explanation
Indices: 21538968--21539049 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
21538958 TAAGAGCTAC
* * * * *
21538968 AATCAGGAAGTTCACAAAGAACTTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
21538994 AATCAAGAAGCTCA-GAAGAGCCTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
*
21539019 AAACAAGAAGCTCACGAAGAGCCTTT
1 AATCAAGAAGCTCACGAAGAGCCTTT
21539045 AATCA
1 AATCA
21539050 GGAGCTCCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 21 0.44
26 27 0.56
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (26 bp):
AATCAAGAAGCTCACGAAGAGCCTTT
Found at i:21539634 original size:11 final size:11
Alignment explanation
Indices: 21539620--21539645 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21539610 TTAACATCAA
21539620 TTCATGTTCAT
1 TTCATGTTCAT
21539631 TTCATGTTCAT
1 TTCATGTTCAT
21539642 TTCA
1 TTCA
21539646 ATTCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (11 bp):
TTCATGTTCAT
Found at i:21540781 original size:8 final size:8
Alignment explanation
Indices: 21540768--21540796 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
21540758 TTTAAAATGA
21540768 TATTTTAT
1 TATTTTAT
21540776 TATTTTAT
1 TATTTTAT
21540784 TATTTTAT
1 TATTTTAT
21540792 TATTT
1 TATTT
21540797 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:21544298 original size:13 final size:13
Alignment explanation
Indices: 21544280--21544318 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
21544270 GAAAGGTTAT
21544280 TTTAAAAATCATG
1 TTTAAAAATCATG
21544293 TTTAAAAAT-A--
1 TTTAAAAATCATG
21544303 TTTAAAAATCATG
1 TTTAAAAATCATG
21544316 TTT
1 TTT
21544319 TCCTTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTAAAAATCATG
Found at i:21544380 original size:2 final size:2
Alignment explanation
Indices: 21544373--21544399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21544363 TGCTGATACA
21544373 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21544400 GTGTCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21545557 original size:31 final size:29
Alignment explanation
Indices: 21545487--21545543 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
21545477 AAATTGAATT
*
21545487 AAATCAATATTTTATATATAAAATTACACA
1 AAATCAA-AATTTATATATAAAATTACACA
*
21545517 AAATTAAAATTTATATATAAAATTACA
1 AAATCAAAATTTATATATAAAATTACA
21545544 TTGAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTACACA
Found at i:21545563 original size:31 final size:29
Alignment explanation
Indices: 21545499--21545563 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
21545489 ATCAATATTT
* *
21545499 TATATATAAAATTACACAAAATTAAAATT
1 TATATATAAAATTACACAAAATCAAAATC
* *
21545528 TATATATAAAATTACATTGAAAGTCAAAATC
1 TATATATAAAATTACA--CAAAATCAAAATC
21545559 TATAT
1 TATAT
21545564 CTAACTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
TATATATAAAATTACACAAAATCAAAATC
Found at i:21549575 original size:15 final size:16
Alignment explanation
Indices: 21549555--21549584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21549545 CAGAAAGCCA
21549555 ATATTA-AAATTTTAT
1 ATATTATAAATTTTAT
21549570 ATATTATAAATTTTA
1 ATATTATAAATTTTA
21549585 ATAAAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTATAAATTTTAT
Found at i:21554814 original size:25 final size:25
Alignment explanation
Indices: 21554785--21554832 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21554775 GTTAATACTA
*
21554785 TTAAAAGTGTTTTGTTAAATTCAAG
1 TTAAAAGTATTTTGTTAAATTCAAG
21554810 TTAAAAGTATTTTGTTAAATTCA
1 TTAAAAGTATTTTGTTAAATTCA
21554833 GGTTGACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (25 bp):
TTAAAAGTATTTTGTTAAATTCAAG
Found at i:21555632 original size:20 final size:20
Alignment explanation
Indices: 21555607--21555645 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21555597 CCCTTTTAAT
* *
21555607 TTTCCATCATTCTATTTTTC
1 TTTCCACCATTCCATTTTTC
21555627 TTTCCACCATTCCATTTTT
1 TTTCCACCATTCCATTTTT
21555646 TGAACAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTCCACCATTCCATTTTTC
Found at i:21556536 original size:7 final size:7
Alignment explanation
Indices: 21556524--21556550 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
21556514 TGTAATGGGT
21556524 TTAGGGC
1 TTAGGGC
21556531 TTAGGGC
1 TTAGGGC
21556538 TTAGGGC
1 TTAGGGC
21556545 TTAGGG
1 TTAGGG
21556551 TTTCTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.44, T:0.30
Consensus pattern (7 bp):
TTAGGGC
Found at i:21556930 original size:43 final size:43
Alignment explanation
Indices: 21556882--21557010 Score: 231
Period size: 43 Copynumber: 3.0 Consensus size: 43
21556872 CAAAATAAAA
* * *
21556882 ATGAAAATGGAAAAATGGAATCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
21556925 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
21556968 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
1 ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
21557011 TCTCCAAAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (43 bp):
ATGAAAATGAAAAAATAGAACCATTTGGAAATGAATGTGGTTT
Found at i:21559339 original size:10 final size:10
Alignment explanation
Indices: 21559327--21559364 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
21559317 TTATTGCTTA
21559327 AAAATAT-TT
1 AAAATATATT
21559336 AAAATTTATATT
1 AAAA--TATATT
21559348 AAAATATATT
1 AAAATATATT
21559358 AAAATAT
1 AAAATAT
21559365 TAACAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 13 0.50
11 3 0.12
12 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATATATT
Found at i:21578953 original size:16 final size:17
Alignment explanation
Indices: 21578932--21578967 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
21578922 CATTAATTTA
*
21578932 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
21578948 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
21578965 AAT
1 AAT
21578968 CCAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:21585377 original size:3 final size:3
Alignment explanation
Indices: 21585369--21585458 Score: 69
Period size: 3 Copynumber: 30.0 Consensus size: 3
21585359 ATATTGCATC
* *
21585369 ATT ATT ATT -GT ATT ATT ATTT ATT ATT ATT A-T AGT AGTT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT
* * ** *
21585414 ATT ATT ACT ATT CTT ATT GCT ATT AATG A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
21585459 TATATATATT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 4 0.06
3 57 0.84
4 7 0.10
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Done.