Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 73 of 129
Found at i:11537854 original size:18 final size:17
Alignment explanation
Indices: 11537820--11537878 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
11537810 TTATATCATA
11537820 AATAATTTTATTATTATTTT
1 AATAA-TTTA-TATTA-TTT
11537840 AATAATTTATATTATTT
1 AATAATTTATATTATTT
* *
11537857 AATATAATAATATTATTT
1 AATA-ATTTATATTATTT
11537875 AATA
1 AATA
11537879 GTATGACCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.19
18 20 0.56
19 4 0.11
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATAATTTATATTATTT
Found at i:11537873 original size:21 final size:21
Alignment explanation
Indices: 11537779--11537873 Score: 59
Period size: 21 Copynumber: 4.4 Consensus size: 21
11537769 AAATAGTTTT
11537779 ATATTATTATTTTAATAATAAATA
1 ATATTATTA-TTTAAT-AT-AATA
* * * *
11537803 AAAATACTTATATCATA-AATA
1 ATATTA-TTATTTAATATAATA
* * *
11537824 ATTTTATTA-TTATTTTAATA
1 ATATTATTATTTAATATAATA
*
11537844 ATTTATATTATTTAATATAATA
1 ATAT-TATTATTTAATATAATA
11537866 ATATTATT
1 ATATTATT
11537874 TAATAGTATG
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 2 0.04
20 11 0.21
21 16 0.30
22 12 0.23
23 1 0.02
24 8 0.15
25 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTATTATTTAATATAATA
Found at i:11537950 original size:28 final size:28
Alignment explanation
Indices: 11537910--11537970 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
11537900 TTTTAATATT
* *
11537910 TTTTATTTAAAATATATTAATTTTA-TA
1 TTTTATTGAAAATATATTAATATTACTA
* *
11537937 TTTTATTGACAAATTTATTCATATTACTA
1 TTTTATTGA-AAATATATTAATATTACTA
11537966 TTTTA
1 TTTTA
11537971 ATAATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.29
28 13 0.46
29 7 0.25
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTATTGAAAATATATTAATATTACTA
Found at i:11538053 original size:22 final size:23
Alignment explanation
Indices: 11538009--11538054 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
11537999 TTCATAATTT
11538009 AATAATAAATATTTTCAATATAA
1 AATAATAAATATTTTCAATATAA
*
11538032 AATAA-AACTATTTT-AATAATAA
1 AATAATAAATATTTTCAAT-ATAA
11538054 A
1 A
11538055 TATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.62
23 5 0.24
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAATAAATATTTTCAATATAA
Found at i:11538055 original size:21 final size:20
Alignment explanation
Indices: 11537983--11538056 Score: 51
Period size: 22 Copynumber: 3.4 Consensus size: 20
11537973 AATAAATATA
* *
11537983 AATAAATAATATATTTTTCAT
1 AATAAATAAAATA-TTTTAAT
*
11538004 AATTTAATAATAAATATTTTCAAT
1 AA-TAAAT-A-AAATATTTT-AAT
11538028 -ATAAAATAAAACTATTTTAAT
1 AAT-AAATAAAA-TATTTTAAT
11538049 AATAAATA
1 AATAAATA
11538057 TATTTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 13 0.31
22 14 0.33
23 9 0.21
24 6 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAATAAAATATTTTAAT
Found at i:11538516 original size:3 final size:3
Alignment explanation
Indices: 11538508--11538541 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11538498 GTATTTTTTA
11538508 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11538542 CAAATAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11546592 original size:9 final size:9
Alignment explanation
Indices: 11546578--11546640 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
11546568 AAAATCAAAA
11546578 CATTTTTTT
1 CATTTTTTT
11546587 CA-TTTTTT
1 CATTTTTTT
*
11546595 C-TAATTTTT
1 CAT-TTTTTT
11546604 CATTTTTTT
1 CATTTTTTT
11546613 CATTTTTTTTT
1 CA--TTTTTTT
*
11546624 CAATTTTTT
1 CATTTTTTT
11546633 CACTTTTT
1 CA-TTTTT
11546641 AAGAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
8 7 0.16
9 23 0.52
10 5 0.11
11 9 0.20
ACGTcount: A:0.14, C:0.13, G:0.00, T:0.73
Consensus pattern (9 bp):
CATTTTTTT
Found at i:11546622 original size:20 final size:21
Alignment explanation
Indices: 11546599--11546640 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11546589 TTTTTTCTAA
*
11546599 TTTTTCATTTTTTTCA-TTTT
1 TTTTTCAATTTTTTCACTTTT
11546619 TTTTTCAATTTTTTCACTTTT
1 TTTTTCAATTTTTTCACTTTT
11546640 T
1 T
11546641 AAGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCAATTTTTTCACTTTT
Found at i:11550994 original size:24 final size:24
Alignment explanation
Indices: 11550962--11551007 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
11550952 TGATGTTGGT
11550962 AGCAATGCAACCTAACATGCCTAG
1 AGCAATGCAACCTAACATGCCTAG
11550986 AGCAATGCAACCTAACATGCCT
1 AGCAATGCAACCTAACATGCCT
11551008 TAAGAGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.17
Consensus pattern (24 bp):
AGCAATGCAACCTAACATGCCTAG
Found at i:11551732 original size:20 final size:20
Alignment explanation
Indices: 11551707--11551744 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11551697 ATGACATTTA
11551707 ATATCATGCCTAATATTTGT
1 ATATCATGCCTAATATTTGT
*
11551727 ATATCATGCCTATTATTT
1 ATATCATGCCTAATATTT
11551745 TGTAGGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (20 bp):
ATATCATGCCTAATATTTGT
Found at i:11557524 original size:23 final size:23
Alignment explanation
Indices: 11557498--11557548 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
11557488 GATTGATCTT
* *
11557498 TGTTTTAAGTTGAAATTATTTTG
1 TGTTTTAAGTTCAAATTACTTTG
**
11557521 TGTTCGAAGTTCAAATTACTTTG
1 TGTTTTAAGTTCAAATTACTTTG
11557544 T-TTTT
1 TGTTTT
11557549 GAATCCTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.55
Consensus pattern (23 bp):
TGTTTTAAGTTCAAATTACTTTG
Found at i:11558196 original size:21 final size:21
Alignment explanation
Indices: 11558139--11558197 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
11558129 ACCATGTACC
11558139 CTCCCTTTCTCCTCTTCCTTTCT
1 CTCCCTTTC-CCTC-TCCTTTCT
*
11558162 -TCCCTTTTCCTCTCCTTTCT
1 CTCCCTTTCCCTCTCCTTTCT
11558182 CTCCCTTTCCCTCTCC
1 CTCCCTTTCCCTCTCC
11558198 CAACAACCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.24
21 18 0.55
22 7 0.21
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (21 bp):
CTCCCTTTCCCTCTCCTTTCT
Found at i:11567865 original size:25 final size:25
Alignment explanation
Indices: 11567819--11567866 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
11567809 TAATAGTTAT
* **
11567819 TTTTTTATTATAATTTTTTAATTTA
1 TTTTTTATTATAATGTCATAATTTA
*
11567844 TTTTTTATTTTAATGTCATAATT
1 TTTTTTATTATAATGTCATAATT
11567867 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTTTATTATAATGTCATAATTTA
Found at i:11568058 original size:15 final size:15
Alignment explanation
Indices: 11568040--11568070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11568030 AATTAAGTAT
*
11568040 TAAAAATATATTTTA
1 TAAAAAAATATTTTA
11568055 TAAAAAAATATTTTA
1 TAAAAAAATATTTTA
11568070 T
1 T
11568071 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAAAAATATTTTA
Found at i:11568806 original size:16 final size:16
Alignment explanation
Indices: 11568785--11568818 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11568775 ATTTTTTTAA
* *
11568785 TTGTATGTTATAGATG
1 TTGTATATTAGAGATG
11568801 TTGTATATTAGAGATG
1 TTGTATATTAGAGATG
11568817 TT
1 TT
11568819 ATGGATGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (16 bp):
TTGTATATTAGAGATG
Found at i:11569569 original size:33 final size:32
Alignment explanation
Indices: 11569523--11569586 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
11569513 ACTTGATAGT
*
11569523 AAATTTAATAATTTATGTATTTATATCATATA
1 AAATTTAATAATTTATATATTTATATCATATA
*
11569555 AAATATTAATAATTTATATATTTATATTATAT
1 AAAT-TTAATAATTTATATATTTATATCATAT
11569587 TTTATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATTTAATAATTTATATATTTATATCATATA
Found at i:11569659 original size:31 final size:33
Alignment explanation
Indices: 11569626--11569685 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 33
11569616 AATCGATATA
11569626 AAAATATAAAAT-ATATT-TTTTA-ATTTTATT
1 AAAATATAAAATAATATTATTTTATATTTTATT
* *
11569656 AAAATTTTAAATAATATTATTTTATATTTT
1 AAAATATAAAATAATATTATTTTATATTTT
11569686 TTATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 5 0.20
32 5 0.20
33 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AAAATATAAAATAATATTATTTTATATTTTATT
Found at i:11569708 original size:21 final size:22
Alignment explanation
Indices: 11569678--11569732 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
11569668 AATATTATTT
*
11569678 TATATTTTT-TAT-TTATATATA
1 TATATTTTTATATATTAT-CATA
11569699 TATATGTTTTATATATTATCATA
1 TATAT-TTTTATATATTATCATA
11569722 TCATATTTTTA
1 T-ATATTTTTA
11569733 AGTATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 5 0.17
22 4 0.14
23 12 0.41
24 8 0.28
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATTTTTATATATTATCATA
Found at i:11574674 original size:49 final size:49
Alignment explanation
Indices: 11574570--11574735 Score: 178
Period size: 49 Copynumber: 3.4 Consensus size: 49
11574560 TATTTAATTG
* * *
11574570 CAAATTTTTAAAGTTTCAATGCCTTTATTAGGAAAGAA-TATTTTGGTTG
1 CAAATTTTAAAAGTTTCAATGCCTTT-TTAGGAAAGAAGTTTTTTGGTTA
** *
11574619 TGAATTTTTAAAGTTTCAATGCCTTTGTTAGGAAA-AAGTTTTTTGGTTA
1 CAAATTTTAAAAGTTTCAATGCCTTT-TTAGGAAAGAAGTTTTTTGGTTA
* * *
11574668 CAAATTTTAAAAATTTCAACGCCTTCTTT-GGAAATG-AGTTTTTGGGTTA
1 CAAATTTTAAAAGTTTCAATGCCTT-TTTAGGAAA-GAAGTTTTTTGGTTA
*
11574717 CAAATTTTAAAATTTTCAA
1 CAAATTTTAAAAGTTTCAA
11574736 AACCTCTATT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
48 7 0.07
49 93 0.92
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (49 bp):
CAAATTTTAAAAGTTTCAATGCCTTTTTAGGAAAGAAGTTTTTTGGTTA
Found at i:11575299 original size:23 final size:24
Alignment explanation
Indices: 11575272--11575317 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11575262 TTGCTATGAA
*
11575272 TTTTTG-GAAATTTCTAGGTTTTT
1 TTTTTGTGAAATTTCTAGATTTTT
*
11575295 TTTTTGTTAAATTTCTAGATTTT
1 TTTTTGTGAAATTTCTAGATTTT
11575318 GGTTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.20, C:0.04, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTTTGTGAAATTTCTAGATTTTT
Found at i:11575725 original size:12 final size:11
Alignment explanation
Indices: 11575710--11575769 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 11
11575700 TCTCTTTATC
11575710 TTTATCTTTTTT
1 TTTAT-TTTTTT
11575722 TTTATATATTTTT
1 TTTAT-T-TTTTT
11575735 TATTATTTTTATT
1 T-TTATTTTT-TT
11575748 TTT-TTTTATTT
1 TTTATTTT-TTT
*
11575759 TTAATTTTTTT
1 TTTATTTTTTT
11575770 AATTTACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.27
12 16 0.39
13 10 0.24
14 4 0.10
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:11575749 original size:26 final size:26
Alignment explanation
Indices: 11575711--11575770 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
11575701 CTCTTTATCT
*
11575711 TTATCTTTT-TTTTTATATATTTTTTA
1 TTAT-TTTTATTTTTATATATTTTTAA
* *
11575737 TTATTTTTATTTTTTTTTATTTTTAA
1 TTATTTTTATTTTTATATATTTTTAA
11575763 TT-TTTTTA
1 TTATTTTTA
11575771 ATTTACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (26 bp):
TTATTTTTATTTTTATATATTTTTAA
Found at i:11575758 original size:10 final size:10
Alignment explanation
Indices: 11575716--11575760 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
11575706 TATCTTTATC
11575716 TTTTTTTTTA
1 TTTTTTTTTA
*
11575726 TATATTTTTTA
1 T-TTTTTTTTA
*
11575737 -TTATTTTTA
1 TTTTTTTTTA
11575746 TTTTTTTTTA
1 TTTTTTTTTA
11575756 TTTTT
1 TTTTT
11575761 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 7 0.24
10 14 0.48
11 8 0.28
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:11575769 original size:10 final size:9
Alignment explanation
Indices: 11575717--11575774 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
11575707 ATCTTTATCT
11575717 TTTTTTTTA
1 TTTTTTTTA
11575726 TATATTTTTTA
1 T-T-TTTTTTA
*
11575737 TTATTTTTA
1 TTTTTTTTA
11575746 TTTTTTTT-
1 TTTTTTTTA
* *
11575754 TATTTTTAA
1 TTTTTTTTA
*
11575763 TTTTTTTAA
1 TTTTTTTTA
11575772 TTT
1 TTT
11575775 ACATTTCCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 6 0.15
9 25 0.61
10 2 0.05
11 8 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:11575769 original size:16 final size:16
Alignment explanation
Indices: 11575716--11575774 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
11575706 TATCTTTATC
*
11575716 TTTTTT-TTTATATATT
1 TTTTTTATTTTTA-ATT
*
11575732 TTTTATTATTTTTATTT
1 TTTT-TTATTTTTAATT
11575749 TTTTTTATTTTTAATT
1 TTTTTTATTTTTAATT
*
11575765 TTTTTAATTT
1 TTTTTTATTT
11575775 ACATTTCCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 24 0.65
17 8 0.22
18 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTATTTTTAATT
Found at i:11575912 original size:11 final size:11
Alignment explanation
Indices: 11575857--11575895 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
11575847 CTTTGGTTGA
11575857 ATTTTTATGAT
1 ATTTTTATGAT
*
11575868 ATTTTTA-AAT
1 ATTTTTATGAT
11575878 AATTTTTATGAT
1 -ATTTTTATGAT
11575890 ATTTTT
1 ATTTTT
11575896 TATTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
ATTTTTATGAT
Found at i:11575919 original size:13 final size:13
Alignment explanation
Indices: 11575901--11575942 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
11575891 TTTTTTATTT
11575901 TATAATATTTTTG
1 TATAATATTTTTG
*
11575914 TATAATACTTTTG
1 TATAATATTTTTG
**
11575927 CCTAATATTTTTG
1 TATAATATTTTTG
11575940 TAT
1 TAT
11575943 GCTTAGTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TATAATATTTTTG
Found at i:11584213 original size:20 final size:21
Alignment explanation
Indices: 11584177--11584228 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11584167 CCTGAAATTA
11584177 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
11584199 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
11584220 AT-AAATATT
1 ATAAAATATT
11584229 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:11584219 original size:21 final size:22
Alignment explanation
Indices: 11584177--11584228 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
11584167 CCTGAAATTA
11584177 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
11584199 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
11584220 AT-AAATATT
1 ATAAAATATT
11584229 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:11584263 original size:30 final size:30
Alignment explanation
Indices: 11584195--11584264 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
11584185 TTATTTTTTA
* * *
11584195 AAATATAAAATATTATTTTTTAAATATAAAT
1 AAATA-AAAATATCATTATATAAATATAAAT
** *
11584226 ATTTAAAAATATCATTATATAAATATATAT
1 AAATAAAAATATCATTATATAAATATAAAT
11584256 AAATAAAAA
1 AAATAAAAA
11584265 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
AAATAAAAATATCATTATATAAATATAAAT
Found at i:11586093 original size:2 final size:2
Alignment explanation
Indices: 11586086--11586142 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
11586076 TAAAAATGTG
* *
11586086 AT AT AT AT AT AT AT AC AT AT AT AT -T AT AT -T GT GAT 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
*
11586127 AC AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
11586143 GTTATCTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
1 3 0.07
2 42 0.91
3 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11586119 original size:33 final size:35
Alignment explanation
Indices: 11586082--11586147 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
11586072 TTATTAAAAA
*
11586082 TGTGATATATATATATATACA-TATATA-TTATAT
1 TGTGATATATATACATATACATTATATAGTTATAT
*
11586115 TGTGATATATATACATATATATTATATAGTTAT
1 TGTGATATATATACATATACATTATATAGTTAT
11586148 CTTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.66
34 6 0.21
35 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (35 bp):
TGTGATATATATACATATACATTATATAGTTATAT
Found at i:11586854 original size:3 final size:3
Alignment explanation
Indices: 11586846--11586897 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
11586836 TAAAACATCA
11586846 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11586894 AAT A
1 AAT A
11586898 TGATTGAACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11587954 original size:13 final size:14
Alignment explanation
Indices: 11587929--11587962 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
11587919 AAAGAAAGGT
11587929 AATTTATAATTTAA
1 AATTTATAATTTAA
*
11587943 TATTTA-AATTTAA
1 AATTTATAATTTAA
11587956 AATTTAT
1 AATTTAT
11587963 GTAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTATAATTTAA
Found at i:11589000 original size:26 final size:27
Alignment explanation
Indices: 11588971--11589036 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
11588961 ATTTTATTTG
*
11588971 AATTTAAATAATTATCCAGAC-TATTA
1 AATTTAAATAATTATCCAAACATATTA
*
11588997 AATTTACATAATTATCCAAACATATTA
1 AATTTAAATAATTATCCAAACATATTA
* *
11589024 GACTTAAATAATT
1 AATTTAAATAATT
11589037 TATTAAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (27 bp):
AATTTAAATAATTATCCAAACATATTA
Found at i:11589164 original size:2 final size:2
Alignment explanation
Indices: 11589157--11589186 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11589147 TATATTTTGT
11589157 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
11589187 ACCGTTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11591177 original size:16 final size:16
Alignment explanation
Indices: 11591156--11591187 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11591146 AAAATTTTAG
11591156 AAAAAACAAAATAAAT
1 AAAAAACAAAATAAAT
*
11591172 AAAAAATAAAATAAAT
1 AAAAAACAAAATAAAT
11591188 CTAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAACAAAATAAAT
Found at i:11592615 original size:17 final size:19
Alignment explanation
Indices: 11592582--11592616 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
11592572 AATGGTGGAA
11592582 ATTAAAAGGCAAATTTATG
1 ATTAAAAGGCAAATTTATG
11592601 ATTAAAA-GC-AATTTAT
1 ATTAAAAGGCAAATTTAT
11592617 AAGTTTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (19 bp):
ATTAAAAGGCAAATTTATG
Found at i:11595931 original size:21 final size:20
Alignment explanation
Indices: 11595907--11595949 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
11595897 CAATTTGTAG
11595907 ATTAAATAAATAAATTAACAT
1 ATTAAATAAATAAATTAA-AT
*
11595928 ATTAAATAAATAATTTAAAT
1 ATTAAATAAATAAATTAAAT
11595948 AT
1 AT
11595950 AATTGTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTAAATAAATAAATTAAAT
Found at i:11597654 original size:53 final size:52
Alignment explanation
Indices: 11597597--11597697 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
11597587 TGTACAATAA
11597597 GACTTGTAAAAAGAAAAATTTTAAGA-GAAAGATGATTCTTAATAGGTAAATTT
1 GACTTG-AAAAAGAAAAATTTTAAGAGGAAAGA-GATTCTTAATAGGTAAATTT
* * * * * *
11597650 GACTTGCAGAATAAGATTTTTAAGAGGAAAGAGATTTTTAATAGGTAA
1 GACTTGAAAAAGAAAAATTTTAAGAGGAAAGAGATTCTTAATAGGTAA
11597698 GTTTATATAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 29 0.71
53 12 0.29
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (52 bp):
GACTTGAAAAAGAAAAATTTTAAGAGGAAAGAGATTCTTAATAGGTAAATTT
Found at i:11599061 original size:31 final size:30
Alignment explanation
Indices: 11599026--11599098 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
11599016 ATGAATAATT
11599026 TTTAAATTATAATAAAATATT-TAATGTGATA
1 TTTAAATTATAA-AAAAT-TTATAATGTGATA
*
11599057 TTTAAATT-TTAAAAATTTATAATGTGATA
1 TTTAAATTATAAAAAATTTATAATGTGATA
* *
11599086 TCTGAATTATAAA
1 TTTAAATTATAAA
11599099 TTTATTAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 5 0.14
31 8 0.22
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (30 bp):
TTTAAATTATAAAAAATTTATAATGTGATA
Found at i:11605472 original size:19 final size:19
Alignment explanation
Indices: 11605442--11605536 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
11605432 GTTATTTAAC
11605442 ATTTATAAAATTAATAAATA
1 ATTTA-AAAATTAATAAATA
* *
11605462 ATTTAAAAATTATTAAATT
1 ATTTAAAAATTAATAAATA
* **
11605481 ATTTTAATGTTAA-ATAATA
1 ATTTAAAAATTAATA-AATA
*
11605500 ATTT---TATTAATAAATA
1 ATTTAAAAATTAATAAATA
11605516 A-TTAAAAATTAATAAAATA
1 ATTTAAAAATTAAT-AAATA
11605535 AT
1 AT
11605537 AATACATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
15 2 0.03
16 10 0.17
17 1 0.02
18 7 0.12
19 34 0.58
20 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
ATTTAAAAATTAATAAATA
Found at i:11605528 original size:27 final size:27
Alignment explanation
Indices: 11605449--11605538 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
11605439 AACATTTATA
11605449 AAATTAATAAATAATTTAAAAATT-ATT
1 AAATTAATAAATAA-TTAAAAATTAATT
* * *
11605476 AAATTATTTTAAT-GTTAAATAA-TAATT
1 AAATTA-ATAAATAATTAAA-AATTAATT
**
11605503 TTATTAATAAATAATTAAAAATTAA-T
1 AAATTAATAAATAATTAAAAATTAATT
*
11605529 AAAATAATAA
1 AAATTAATAA
11605539 TACATAAAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
26 20 0.43
27 23 0.49
28 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATTAATAAATAATTAAAAATTAATT
Found at i:11607206 original size:20 final size:19
Alignment explanation
Indices: 11607169--11607221 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
11607159 TATTAGTTTT
11607169 AATTAATTTA--AAAT-AA
1 AATTAATTTATTAAATAAA
*
11607185 AATTTATATTATTAAATAAA
1 AATTAAT-TTATTAAATAAA
*
11607205 AATTAATTTGTTAAATA
1 AATTAATTTATTAAATA
11607222 TATAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.20
17 3 0.10
19 13 0.43
20 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTAATTTATTAAATAAA
Found at i:11608508 original size:2 final size:2
Alignment explanation
Indices: 11608501--11608530 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11608491 GTTTTGTGGT
11608501 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11608531 ATTTTCGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11609879 original size:17 final size:16
Alignment explanation
Indices: 11609857--11609888 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11609847 AATTCATAAA
11609857 TTAAATATTATAAATAT
1 TTAAATATT-TAAATAT
11609874 TTAAATATTTAAATA
1 TTAAATATTTAAATA
11609889 CAAATCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATATTTAAATAT
Found at i:11609880 original size:8 final size:8
Alignment explanation
Indices: 11609857--11609888 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
11609847 AATTCATAAA
11609857 TTAAATAT
1 TTAAATAT
11609865 TATAAATAT
1 T-TAAATAT
11609874 TTAAATAT
1 TTAAATAT
11609882 TTAAATA
1 TTAAATA
11609889 CAAATCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTAAATAT
Found at i:11615940 original size:152 final size:154
Alignment explanation
Indices: 11615633--11615947 Score: 510
Period size: 152 Copynumber: 2.1 Consensus size: 154
11615623 GCTAAAACAA
*
11615633 AATTTCACATTTGAAAGCTTGACTCTAGCAAAAATTATTTTCAAACCAAAAACTTGATATTTAAA
1 AATTTCACATTTGAAAGCTTGACTCTAGCAAAAATTATTTTCAAACCAAAAACTTGAGATTTAAA
11615698 AATCATTAAGTTATGTGTGCTTCCCTTAAGTTTGTGCATAACGATAAAAACAATTAAGCACATAA
66 AATCATTAAGTTATGTGTGCTTCCCTTAAGTTTGTGCATAACGATAAAAACAATTAAGCACATAA
* *
11615763 TTAATCGCACCAAGTACGAATAAT
131 GTAATCGCACCAAGTACCAATAAT
*
11615787 AATTTCACATTTGAAAGCTTGACTCTAGCAAAAATTATTTTCAAAGC-AAAACTTGAGATTTAAA
1 AATTTCACATTTGAAAGCTTGACTCTAGCAAAAATTATTTTCAAACCAAAAACTTGAGATTTAAA
* * * * *
11615851 AATCATTAAGTTTTGTGTGC-T-CCTCTAAGTTTGTGTATAGCTATAAAAATAATTAAGCACATA
66 AATCATTAAGTTATGTGTGCTTCCCT-TAAGTTTGTGCATAACGATAAAAACAATTAAGCACATA
*
11615914 AGTAATTGCACCAAGTACCAATAAT
130 AGTAATCGCACCAAGTACCAATAAT
11615939 AATTTCACA
1 AATTTCACA
11615948 AAGCACGATA
Statistics
Matches: 150, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
151 3 0.02
152 66 0.44
153 35 0.23
154 46 0.31
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (154 bp):
AATTTCACATTTGAAAGCTTGACTCTAGCAAAAATTATTTTCAAACCAAAAACTTGAGATTTAAA
AATCATTAAGTTATGTGTGCTTCCCTTAAGTTTGTGCATAACGATAAAAACAATTAAGCACATAA
GTAATCGCACCAAGTACCAATAAT
Found at i:11617202 original size:137 final size:137
Alignment explanation
Indices: 11617061--11617332 Score: 447
Period size: 137 Copynumber: 2.0 Consensus size: 137
11617051 AATTTTCTTT
* *
11617061 TTTTCTCTATTCGACT-TTTCTCTTTTAGTATCTATTTTCTTTCTTTAACTGTAGCTTTCTTTTC
1 TTTTCTCTATTCAACTCCTT-TCTTTTAGTATCTATTTTCTTTCTTTAACTGTAGCTTTCTTTTC
* * *
11617125 CTTCTAACAACTTTATTCACAATACAAAATTTGTGTGCTTTAGTTGTGTGTTTTTGGATATGGCA
65 CTTCTAACAACATTATTCACAATACAAAATTTGTGTACTTTAGCTGTGTGTTTTTGGATATGGCA
11617190 TTTATTTC
130 TTTATTTC
* *
11617198 TTTTCTCTATTCAACTCCTTTCTTTTAGTATCTATTTTCTTTCTTTAACTTTGGCTTTCTTTTCC
1 TTTTCTCTATTCAACTCCTTTCTTTTAGTATCTATTTTCTTTCTTTAACTGTAGCTTTCTTTTCC
* *
11617263 TTTTAACAACATTATTCATAATACAAAATTTGTGTACTTTAGCTGTGTGTTTTTGGATATGGCAT
66 TTCTAACAACATTATTCACAATACAAAATTTGTGTACTTTAGCTGTGTGTTTTTGGATATGGCAT
11617328 TTATT
131 TTATT
11617333 AAAGTCTAGG
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
137 123 0.98
138 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (137 bp):
TTTTCTCTATTCAACTCCTTTCTTTTAGTATCTATTTTCTTTCTTTAACTGTAGCTTTCTTTTCC
TTCTAACAACATTATTCACAATACAAAATTTGTGTACTTTAGCTGTGTGTTTTTGGATATGGCAT
TTATTTC
Found at i:11621583 original size:21 final size:21
Alignment explanation
Indices: 11621559--11621603 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11621549 TAACATGCCT
* *
11621559 AAATAATAATAATAATAATTA
1 AAATAACAAAAATAATAATTA
*
11621580 AAATAACAAAAATAATATTTA
1 AAATAACAAAAATAATAATTA
11621601 AAA
1 AAA
11621604 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAACAAAAATAATAATTA
Found at i:11622090 original size:28 final size:26
Alignment explanation
Indices: 11622036--11622087 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
11622026 GTTTTGGTCA
* *
11622036 TTTTTTTTTTTTTGTGTGTTGTTGGT
1 TTTTTTTTTTTTTATGTGGTGTTGGT
11622062 TTTTTTTTTTTTTATGTCGGTGTTGG
1 TTTTTTTTTTTTTATGT-GGTGTTGG
11622088 GTTCCCCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.02, C:0.02, G:0.23, T:0.73
Consensus pattern (26 bp):
TTTTTTTTTTTTTATGTGGTGTTGGT
Found at i:11631127 original size:14 final size:14
Alignment explanation
Indices: 11631110--11631136 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11631100 ATATACATGT
11631110 ATATTGATTTATTA
1 ATATTGATTTATTA
11631124 ATATTGATTTATT
1 ATATTGATTTATT
11631137 TATTAATATG
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:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
ATATTGATTTATTA
Found at i:11631596 original size:12 final size:13
Alignment explanation
Indices: 11631564--11631601 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
11631554 TTTTGAATTT
11631564 TACTTAAAAAACTA
1 TACTTAAAAAA-TA
11631578 TACTTAAAAAATA
1 TACTTAAAAAATA
*
11631591 T-GTTAAAAAAT
1 TACTTAAAAAAT
11631602 TTACCAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 11 0.48
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (13 bp):
TACTTAAAAAATA
Found at i:11636130 original size:29 final size:30
Alignment explanation
Indices: 11636079--11636227 Score: 158
Period size: 30 Copynumber: 5.0 Consensus size: 30
11636069 TTAAGGCTTC
* * *
11636079 GTTTTTAGAGTTTAGAGGATTTAGGGTTTC
1 GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
* * * *
11636109 G-TTTCATGGTTTTGAGGGTTTA-GATTTT
1 GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
* *
11636137 GTTTTTAGGGTTTTGAGAGTTTAGGGTTTT
1 GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
* *
11636167 GTTTTTAGGGTTTAGAAGGTTTAGGGTTTA
1 GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
* * *
11636197 GTTTTTAGGCTTTAAAGGGTTTAGGATTTT
1 GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
11636227 G
1 G
11636228 AAATTTAGGT
Statistics
Matches: 97, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 5 0.05
29 34 0.35
30 58 0.60
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (30 bp):
GTTTTTAGGGTTTAGAGGGTTTAGGGTTTT
Found at i:11636175 original size:14 final size:14
Alignment explanation
Indices: 11636133--11636179 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
11636123 AGGGTTTAGA
11636133 TTTTGTTTTTAGGG
1 TTTTGTTTTTAGGG
**
11636147 TTTTGAGAGTTTAGGG
1 TTTT--GTTTTTAGGG
11636163 TTTTGTTTTTAGGG
1 TTTTGTTTTTAGGG
11636177 TTT
1 TTT
11636180 AGAAGGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.11, C:0.00, G:0.30, T:0.60
Consensus pattern (14 bp):
TTTTGTTTTTAGGG
Found at i:11636611 original size:3 final size:3
Alignment explanation
Indices: 11636605--11636631 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11636595 CATTTTTTAG
11636605 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11636632 TAAGCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11638114 original size:15 final size:13
Alignment explanation
Indices: 11638086--11638125 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 13
11638076 TTTCCTTTAT
11638086 TTTTTCTTTTTTTG
1 TTTTT-TTTTTTTG
11638100 TTTGTTTTGTTTTTG
1 TTT-TTTT-TTTTTG
11638115 TTTTTTTTTTT
1 TTTTTTTTTTT
11638126 ATCAACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
15 11 0.46
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:11638124 original size:11 final size:11
Alignment explanation
Indices: 11638067--11638124 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
11638057 CTTTCTGCTA
11638067 TCTTTTTTTTT
1 TCTTTTTTTTT
*
11638078 TCCTTTATTTTT
1 T-CTTTTTTTTT
11638090 TCTTTTTTTGTT
1 TCTTTTTTT-TT
* *
11638102 TGTTTTGTTTT
1 TCTTTTTTTTT
*
11638113 TGTTTTTTTTT
1 TCTTTTTTTTT
11638124 T
1 T
11638125 TATCAACTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 21 0.52
12 19 0.47
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:11643648 original size:15 final size:15
Alignment explanation
Indices: 11643628--11643665 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11643618 ATTTTAAATA
*
11643628 TAAAAAAAAAATTTC
1 TAAAAAAAAAATTAC
*
11643643 TAAAAAAACAATTAC
1 TAAAAAAAAAATTAC
11643658 -AAAAAAAA
1 TAAAAAAAA
11643666 TTTTGATGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAAAAAAAAATTAC
Found at i:11643781 original size:30 final size:31
Alignment explanation
Indices: 11643745--11643805 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
11643735 TATAATAAAT
11643745 ACCCATTTATGGAAATTA-CTGATTAGCAAA
1 ACCCATTTATGGAAATTACCTGATTAGCAAA
11643775 ACCCATTTATGGAAATTACCTGATTAGCAAA
1 ACCCATTTATGGAAATTACCTGATTAGCAAA
11643806 GCCGACTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (31 bp):
ACCCATTTATGGAAATTACCTGATTAGCAAA
Found at i:11644533 original size:36 final size:37
Alignment explanation
Indices: 11644466--11644543 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 37
11644456 GATGAAAAGA
*
11644466 AACTTTTAAATCAACAAAAGATATTAAAAAAAAAGTGT
1 AACTTTTAAATAAACAAAAGATATT-AAAAAAAAGTGT
*
11644504 AACTTTTAAATAAACAAAAGATATT-AAAAAAAGTTT
1 AACTTTTAAATAAACAAAAGATATTAAAAAAAAGTGT
11644540 AACT
1 AACT
11644544 CCTTTCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 14 0.37
38 24 0.63
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (37 bp):
AACTTTTAAATAAACAAAAGATATTAAAAAAAAGTGT
Found at i:11648670 original size:20 final size:20
Alignment explanation
Indices: 11648633--11648670 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11648623 TAAAATAAAA
*
11648633 ATAAATTAAATAAGAAATGG
1 ATAAATTAAATAAAAAATGG
*
11648653 ATAAATTAATTAAAAAAT
1 ATAAATTAAATAAAAAAT
11648671 AACAAACATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
ATAAATTAAATAAAAAATGG
Found at i:11648725 original size:12 final size:12
Alignment explanation
Indices: 11648710--11648744 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11648700 AAAAACTCTA
*
11648710 AAAATAAAAAAT
1 AAAATAAAAAAG
11648722 AAAATAAAAAAG
1 AAAATAAAAAAG
*
11648734 AAAAGAAAAAA
1 AAAATAAAAAA
11648745 AATTTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAATAAAAAAG
Found at i:11653382 original size:144 final size:143
Alignment explanation
Indices: 11653165--11653575 Score: 423
Period size: 144 Copynumber: 2.9 Consensus size: 143
11653155 AAAAGTACAA
* * * * * ** **
11653165 AATTACTAAAATACCC-TTTAGGGGTTTTTTCGTATTTTAGCCTTCTTGAGCTTGGATTTTCATG
1 AATTACCAAAATACCCATATAAGGGTATTTTCATAACTTAGCCTTCCCGAGCTTGGATTTTCATG
* * *
11653229 AAACCTTTCAGATCTTAATTTCATCATATTTCATAATTTTTGGTGCATTAAAATCACAATAGCAC
66 AAACTTTTCAGATATTAATTTCATAATATTTCATAATTTTTGGTGCATTAAAATCACAATAGCAC
** *
11653294 CTTAAAAAGTGTG
131 CCCAAAAAATGTG
* * * * *
11653307 AAATTACCAAAATGCTCC-TATAAGGGTATTTTTATAATTTATCCTTCCCGAGTTTGGATTTTCA
1 -AATTACCAAAATAC-CCATATAAGGGTATTTTCATAACTTAGCCTTCCCGAGCTTGGATTTTCA
* ** * *
11653371 TGAAACTTTTCAGATTTTAATTTCATAATATTTCATAATTTTTGAAGCATTTGAAATCACAGTAG
64 TGAAACTTTTCAGATATTAATTTCATAATATTTCATAATTTTTGGTGCA-TTAAAATCACAATAG
*
11653436 TACCCCAAAAAATGTG
128 CACCCCAAAAAATGTG
* * * * * *
11653452 AATTACCAAAATACCCATATAAGGGTGTTTTCGTAACTTGGCCTTCTCGAGCTCGGATTGTCATG
1 AATTACCAAAATACCCATATAAGGGTATTTTCATAACTTAGCCTTCCCGAGCTTGGATTTTCATG
* * * ***
11653517 AAAATTTTTAGATATCT-ATTTCATAATATTTCATGATTTTTGGTATTTTAAAATCACAA
66 AAACTTTTCAGATAT-TAATTTCATAATATTTCATAATTTTTGGTGCATTAAAATCACAA
11653576 AAATGAGGAT
Statistics
Matches: 219, Mismatches: 45, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
143 24 0.11
144 169 0.77
145 26 0.12
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (143 bp):
AATTACCAAAATACCCATATAAGGGTATTTTCATAACTTAGCCTTCCCGAGCTTGGATTTTCATG
AAACTTTTCAGATATTAATTTCATAATATTTCATAATTTTTGGTGCATTAAAATCACAATAGCAC
CCCAAAAAATGTG
Found at i:11668071 original size:36 final size:38
Alignment explanation
Indices: 11667994--11668075 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
11667984 AAACAAGATT
* * * *
11667994 TTTTAAAAATTTCAAAGCCTTTGTTTAGGGGGGAGCCA
1 TTTTCAAAATTTCAAAGCCTTTATTTAGAGGGGAGCAA
*
11668032 TTTTCAAAGTTTCAAAGCC-TTATTTA-AGGGGAGCAA
1 TTTTCAAAATTTCAAAGCCTTTATTTAGAGGGGAGCAA
11668068 TTTTCAAA
1 TTTTCAAA
11668076 CAAGATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 16 0.41
37 6 0.15
38 17 0.44
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (38 bp):
TTTTCAAAATTTCAAAGCCTTTATTTAGAGGGGAGCAA
Found at i:11668122 original size:90 final size:89
Alignment explanation
Indices: 11667905--11668129 Score: 296
Period size: 89 Copynumber: 2.5 Consensus size: 89
11667895 AAAAATAAGA
* * *
11667905 TTTT-AAAAGTTTCAAAGCCTCTATTTAGAGGGAGCCATTTCCAAAATTTCAAAACCTCTCTTTA
1 TTTTAAAAAGTTTCAAAGCCTTTATTTAG-GGGAGCCATTTTCAAAATTTCAAAACCTCTATTTA
*
11667969 GATAGAGCAATTTTCAAACAAGATT
65 GAGAGAGCAATTTTCAAACAAGATT
* * *
11667994 TTTTAAAAA-TTTCAAAGCCTTTGTTTAGGGGGGAGCCATTTTCAAAGTTTCAAAGCCT-TATTT
1 TTTTAAAAAGTTTCAAAGCCTTTATTTA--GGGGAGCCATTTTCAAAATTTCAAAACCTCTATTT
*
11668057 A-AGGGGAGCAATTTTCAAACAAGATT
64 AGA-GAGAGCAATTTTCAAACAAGATT
11668083 TTTTAAAAAAGTTTCAAAGCCTTTATTTAGGGGAAGCCATTTTCAAA
1 TTTT-AAAAAGTTTCAAAGCCTTTATTTAGGGG-AGCCATTTTCAAA
11668130 CAATATTTAA
Statistics
Matches: 120, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
88 1 0.01
89 54 0.45
90 47 0.39
91 18 0.15
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (89 bp):
TTTTAAAAAGTTTCAAAGCCTTTATTTAGGGGAGCCATTTTCAAAATTTCAAAACCTCTATTTAG
AGAGAGCAATTTTCAAACAAGATT
Found at i:11668198 original size:50 final size:50
Alignment explanation
Indices: 11668031--11668279 Score: 272
Period size: 50 Copynumber: 5.0 Consensus size: 50
11668021 GGGGGGAGCC
* *
11668031 ATTTTCAAAGTTTCAAAGCCT-TATTTAAGGGGAGCAATTTTCAAACAAG
1 ATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAG
*
11668080 ATTTTTTAAAAAAGTTTCAAAGCCTTTATTT-AGGGGAAGCCATTTTCAAAC-A-
1 A-TTTTT---AAAGTTTCAAAGCCTCTATTTAAGGGG-AGCCATTTTCAAACAAG
* * * * * * *
11668132 ATATTTAAAGTGTCAAAGGCTCTGTTTAAGGAGAGCTATTTTCAAATAAG
1 ATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAG
* *
11668182 ATTTTTAAAGTTTCAAAGCCTCTATTTAGGGGGAGCCATTCTCAAACAAG
1 ATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAG
* * * **
11668232 ATTTTCAAAATTTCAAAGCCCCTATTTAAGGAAAGCCATTTTCAAACA
1 ATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACA
11668280 TTTTAAAATT
Statistics
Matches: 165, Mismatches: 26, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
48 29 0.18
49 6 0.04
50 86 0.52
51 4 0.02
52 1 0.01
53 21 0.13
54 18 0.11
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (50 bp):
ATTTTTAAAGTTTCAAAGCCTCTATTTAAGGGGAGCCATTTTCAAACAAG
Found at i:11668213 original size:98 final size:102
Alignment explanation
Indices: 11668031--11668279 Score: 319
Period size: 98 Copynumber: 2.5 Consensus size: 102
11668021 GGGGGGAGCC
*
11668031 ATTTTCAAAGTTTCAAAGCCT-TATTTAAGGGGAGCAATTTTCAAACAAGATTTTTTAAAAAAGT
1 ATTTTCAAAGTTTCAAAGCCTCTATTTAAGGAGAGCAATTTTCAAACAAGATTTTTT--AAAAGT
* * *
11668095 TTCAAAGCCTTTATTTAGGGGAAGCCATTTTCAAACAAT
64 TTCAAAGCCTCTATTTAGGGGAAGCCATTCTCAAACAAG
* * * * *
11668134 A-TTT-AAAGTGTCAAAGGCTCTGTTTAAGGAGAGCTATTTTCAAATAAGA-TTTTT-AAAGTTT
1 ATTTTCAAAGTTTCAAAGCCTCTATTTAAGGAGAGCAATTTTCAAACAAGATTTTTTAAAAGTTT
*
11668195 CAAAGCCTCTATTTAGGGGGAGCCATTCTCAAACAAG
66 CAAAGCCTCTATTTAGGGGAAGCCATTCTCAAACAAG
* * * *
11668232 ATTTTCAAAATTTCAAAGCCCCTATTTAAGGAAAGCCATTTTCAAACA
1 ATTTTCAAAGTTTCAAAGCCTCTATTTAAGGAGAGCAATTTTCAAACA
11668280 TTTTAAAATT
Statistics
Matches: 125, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
98 41 0.33
99 3 0.02
100 34 0.27
101 18 0.14
102 28 0.22
103 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (102 bp):
ATTTTCAAAGTTTCAAAGCCTCTATTTAAGGAGAGCAATTTTCAAACAAGATTTTTTAAAAGTTT
CAAAGCCTCTATTTAGGGGAAGCCATTCTCAAACAAG
Found at i:11668546 original size:22 final size:21
Alignment explanation
Indices: 11668521--11668564 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
11668511 TTAAGACCTC
11668521 TGGGCATA-ATCTGTAAGTCTTT
1 TGGGCA-AGATCTGTAAGT-TTT
*
11668543 TGGGCAAGATTTGTAAGTTTT
1 TGGGCAAGATCTGTAAGTTTT
11668564 T
1 T
11668565 CAAGCCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (21 bp):
TGGGCAAGATCTGTAAGTTTT
Found at i:11668642 original size:146 final size:147
Alignment explanation
Indices: 11668379--11668678 Score: 388
Period size: 146 Copynumber: 2.0 Consensus size: 147
11668369 ACCTTATGGT
* * * *
11668379 ATAATCTATAAGTCATTTGGGCAAGATTCATAACTCTTTCACGCTAAATCTATTTTTAATTTTGA
1 ATAATCTATAAGTCATTTGGGCAAGATTCATAACTCTTTCAAGCCAAATCTATTGTTAATTTTAA
* * * *
11668444 GATTTGTAAGTACTCCAAGCAAGATTTGTAAATCTTTCAAGCTGAATCTATTTTAATTTTGAGAT
66 AATTTGTAAGTACTCCAAGCAAGATTCGTAAATCTTCCAAGCTAAATCTATTTTAATTTTGAGAT
* * *
11668509 TTTTAAGACCTCTGGGC
131 CTATAAGACATCTGGGC
* * ** * * *
11668526 ATAATCTGTAAGTCTTTTGGGCAAGATTTGTAAGTTTTTCAAGCCGAATCTA-TGTTAATTTTAA
1 ATAATCTATAAGTCATTTGGGCAAGATTCATAACTCTTTCAAGCCAAATCTATTGTTAATTTTAA
*
11668590 AATTTGTAAGT-CTTCCAAGCAAGATTCGTAAGTCTTCCAAGCTAAATCTATTTTAATTTTGAGA
66 AATTTGTAAGTAC-TCCAAGCAAGATTCGTAAATCTTCCAAGCTAAATCTATTTTAATTTTGAGA
*
11668654 TCTATAAGACATCTGGTC
130 TCTATAAGACATCTGGGC
*
11668672 ATGATCT
1 ATAATCT
11668679 CTTATTTTAT
Statistics
Matches: 131, Mismatches: 21, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
145 1 0.01
146 87 0.66
147 43 0.33
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (147 bp):
ATAATCTATAAGTCATTTGGGCAAGATTCATAACTCTTTCAAGCCAAATCTATTGTTAATTTTAA
AATTTGTAAGTACTCCAAGCAAGATTCGTAAATCTTCCAAGCTAAATCTATTTTAATTTTGAGAT
CTATAAGACATCTGGGC
Found at i:11668967 original size:51 final size:54
Alignment explanation
Indices: 11668891--11669019 Score: 147
Period size: 56 Copynumber: 2.4 Consensus size: 54
11668881 AATACCTTTG
**
11668891 TTTAAAGGAAGAAATTTTCAAACAAG-TTT-TTCTT-AAATTTCAAAACCTCTA
1 TTTAAAGGAAGCCATTTTCAAACAAGATTTATTCTTAAAATTTCAAAACCTCTA
* * *
11668942 TTTAAAGGAAGCCATTTTCAAACAAGATTTTATTTTTAAAAATTTTAAAGCCTCTA
1 TTTAAAGGAAGCCATTTTCAAACAAGA-TTTATTCTT-AAAATTTCAAAACCTCTA
** *
11668998 TTTCGAGGGAGCCATTTTCAAA
1 TTTAAAGGAAGCCATTTTCAAA
11669020 GTTTCAAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
51 24 0.37
53 3 0.05
54 4 0.06
56 34 0.52
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (54 bp):
TTTAAAGGAAGCCATTTTCAAACAAGATTTATTCTTAAAATTTCAAAACCTCTA
Found at i:11669114 original size:68 final size:68
Alignment explanation
Indices: 11669040--11669173 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
11669030 CTCTGTTTAA
* *
11669040 AGGGAGCAATTTTCAAACAAGATTTTATTTTTAAAAGCTTCAAAGCTTCTGTTTAGGGGGAACCA
1 AGGGAGCAATTTTCAAACAAAATTTTATTTTTAAAAGCTTCAAAGCTTCTGTTTAAGGGGAACCA
11669105 TAG
66 TAG
*
11669108 AGGGAGCAATTTTCAAACAAAATTTTATTTTTAAAAGTTTCAAAGCTTCTGTTTAAGGGGAACCA
1 AGGGAGCAATTTTCAAACAAAATTTTATTTTTAAAAGCTTCAAAGCTTCTGTTTAAGGGGAACCA
11669173 T
66 T
11669174 TTTCAAAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (68 bp):
AGGGAGCAATTTTCAAACAAAATTTTATTTTTAAAAGCTTCAAAGCTTCTGTTTAAGGGGAACCA
TAG
Found at i:11669278 original size:14 final size:14
Alignment explanation
Indices: 11669251--11669294 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
11669241 AGAGACCATT
11669251 AACAAAAGGAAAAAA
1 AACAAAA-GAAAAAA
*
11669266 AACAAAAGAAAAAG
1 AACAAAAGAAAAAA
*
11669280 AGCAAAA-AAAAAA
1 AACAAAAGAAAAAA
11669293 AA
1 AA
11669295 AACTCTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 6 0.24
14 12 0.48
15 7 0.28
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (14 bp):
AACAAAAGAAAAAA
Found at i:11670127 original size:145 final size:145
Alignment explanation
Indices: 11669801--11670317 Score: 505
Period size: 145 Copynumber: 3.6 Consensus size: 145
11669791 CTTTTAGGGG
* *** * * *
11669801 GTATTTTCATAATTTAACCTTCCCGAGCTT-GTATTTTCATG-AAACTTTCAGATCTTAATTTCA
1 GTATTTTCATAATTTATCCTTTTTGAGCTTAG-ATTTTCATGAAAATTTTTAAATCTTAATTTCA
* * * * ** * * * *
11669864 TAATATTTCATAATTTTTGGTACATTTGAAATCACAACAATATAAC-A-AAAATGTGAAATTACC
65 TAATATTTCATGATTTTTGGTGCATTTGAAATCATAACAGTA-CCCTAGAAAGTATAAAATTATC
* * * * **
11669927 AATATGCCTCTACAAGG
129 AAAATACCCCTATAAAA
* * *
11669944 GTATTTTTATAATTTTTCCTTCTTGAGCTTAGATTTTCATGAAAATTTTTAAATCTTAATTTCAT
1 GTATTTTCATAATTTATCCTTTTTGAGCTTAGATTTTCATGAAAATTTTTAAATCTTAATTTCAT
* * * * * *
11670009 AATATTTTATGATTTTTGGTGCATTTGAAATCATAGCAGTGCCTTA-AATTGTTTAAAATTA-CT
66 AATATTTCATGATTTTTGGTGCATTTGAAATCATAACAGTACCCTAGAA-AGTATAAAATTATC-
*
11670072 AAAATGCACCC-ATAAAA
129 AAAATAC-CCCTATAAAA
** * *
11670089 GTATTTTGGTAATTTATCCTTTTTGAGCTCAGATTTTCATGAAACA-TTTTAGATCTTAATTTCA
1 GTATTTTCATAATTTATCCTTTTTGAGCTTAGATTTTCATGAAA-ATTTTTAAATCTTAATTTCA
*
11670153 TAATATTTCATGATTTTTGGTGCATTTGAAATCATAACAGTACCCTAGAAAGTATGAAATTATCA
65 TAATATTTCATGATTTTTGGTGCATTTGAAATCATAACAGTACCCTAGAAAGTATAAAATTATCA
*
11670218 AAATACCCCTATAAAG
130 AAATACCCCTATAAAA
* * ** *
11670234 GTATTTTCTTAATTTGA-CCTTTTTGAGCTTGGATTTTCATGAAGCTTTTTAAATCTCAATTT-A
1 GTATTTTCATAATTT-ATCCTTTTTGAGCTTAGATTTTCATGAAAATTTTTAAATCTTAATTTCA
11670297 TAATATTTCATGATTTTTGGT
65 TAATATTTCATGATTTTTGGT
11670318 TGTTTAAAAT
Statistics
Matches: 312, Mismatches: 50, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
143 34 0.11
144 84 0.27
145 187 0.60
146 7 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (145 bp):
GTATTTTCATAATTTATCCTTTTTGAGCTTAGATTTTCATGAAAATTTTTAAATCTTAATTTCAT
AATATTTCATGATTTTTGGTGCATTTGAAATCATAACAGTACCCTAGAAAGTATAAAATTATCAA
AATACCCCTATAAAA
Found at i:11674573 original size:45 final size:45
Alignment explanation
Indices: 11674509--11674596 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
11674499 GAAAAAGATA
11674509 GTTGTATTTTCAATTTAAGAATAGTGGATTGAAGCCTTAATGTAG
1 GTTGTATTTTCAATTTAAGAATAGTGGATTGAAGCCTTAATGTAG
*
11674554 GTTGTATTTTTAATTTAAGAATAGTGGATTGAAGCCTTAATGT
1 GTTGTATTTTCAATTTAAGAATAGTGGATTGAAGCCTTAATGT
11674597 GGACAACCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (45 bp):
GTTGTATTTTCAATTTAAGAATAGTGGATTGAAGCCTTAATGTAG
Found at i:11682494 original size:23 final size:22
Alignment explanation
Indices: 11682468--11682513 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
11682458 AAATGTGTAA
* *
11682468 AATAATAATTAAAAATAAATAAT
1 AATAATAAGT-AAAATAAAAAAT
11682491 AATAATAAGTAAAATAAAAAAT
1 AATAATAAGTAAAATAAAAAAT
11682513 A
1 A
11682514 GACAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAATAAGTAAAATAAAAAAT
Found at i:11684032 original size:17 final size:18
Alignment explanation
Indices: 11684012--11684049 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11684002 TAAGATTCTC
*
11684012 AAAGGTTCT-AAATTCGT
1 AAAGATTCTCAAATTCGT
*
11684029 AAAGATTTTCAAATTCGT
1 AAAGATTCTCAAATTCGT
11684047 AAA
1 AAA
11684050 AATATTCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (18 bp):
AAAGATTCTCAAATTCGT
Found at i:11684057 original size:18 final size:18
Alignment explanation
Indices: 11684021--11684057 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11684011 CAAAGGTTCT
* *
11684021 AAATTCGTAAAGATTTTC
1 AAATTCGTAAAAATATTC
11684039 AAATTCGTAAAAATATTC
1 AAATTCGTAAAAATATTC
11684057 A
1 A
11684058 GGCTCGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (18 bp):
AAATTCGTAAAAATATTC
Found at i:11684284 original size:18 final size:18
Alignment explanation
Indices: 11684219--11684292 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 18
11684209 CAAGATGCAT
*
11684219 AAGAATTCAAAGATTCAC
1 AAGAATTCAAAGATTCTC
*** *
11684237 AAG-ATTTTTAGATT-TGT
1 AAGAATTCAAAGATTCT-C
11684254 AAGAATTCAAAGATTCTC
1 AAGAATTCAAAGATTCTC
*
11684272 AAGAATTGC-AAGATTTTC
1 AAGAATT-CAAAGATTCTC
11684290 AAG
1 AAG
11684293 TTTTTCAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
17 11 0.26
18 29 0.69
19 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGAATTCAAAGATTCTC
Found at i:11684541 original size:47 final size:46
Alignment explanation
Indices: 11684490--11684586 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 46
11684480 GGATTCACAT
* *
11684490 AAAAAGCTTCAAG-GTTCACAGCCAAAATTTAAAGATTCTCATTCGA
1 AAAAAACTTCAAGAGTTCACAGCCAAAAGTTAAAGATTCTCATTC-A
* * * * *
11684536 AAAAAATTTTAAGATTTCACATCCAAAAGTTAAAGATTTTCATTCA
1 AAAAAACTTCAAGAGTTCACAGCCAAAAGTTAAAGATTCTCATTCA
11684582 AAAAA
1 AAAAA
11684587 CTTAGAGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 16 0.37
47 27 0.63
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (46 bp):
AAAAAACTTCAAGAGTTCACAGCCAAAAGTTAAAGATTCTCATTCA
Found at i:11684563 original size:25 final size:25
Alignment explanation
Indices: 11684513--11684563 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
11684503 GTTCACAGCC
* *
11684513 AAAATTTAAAGATTCTCATTCGAAA
1 AAAATTTAAAGATTCTCAATCCAAA
*
11684538 AAAATTTTAAGATT-TCACATCCAAA
1 AAAATTTAAAGATTCTCA-ATCCAAA
11684563 A
1 A
11684564 GTTAAAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (25 bp):
AAAATTTAAAGATTCTCAATCCAAA
Found at i:11684616 original size:21 final size:21
Alignment explanation
Indices: 11684536--11684621 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 21
11684526 TCTCATTCGA
11684536 AAAAAATTTTAAGATTTCACAT
1 AAAAAATTTTAAGA-TTCACAT
** * * **
11684558 CCAAAAGTTAAAGATTTTCATT
1 AAAAAATTTTAAGATTCACA-T
*
11684580 CAAAAAA-CTTAGAGATTCACAT
1 -AAAAAATTTTA-AGATTCACAT
11684602 AAAAAATTTTAAGATT-ACAT
1 AAAAAATTTTAAGATTCACAT
11684622 TCAAATACTT
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
20 4 0.09
21 15 0.32
22 17 0.36
23 11 0.23
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAAAATTTTAAGATTCACAT
Found at i:11686146 original size:7 final size:7
Alignment explanation
Indices: 11686102--11686174 Score: 76
Period size: 7 Copynumber: 9.7 Consensus size: 7
11686092 ACCTTATCAA
11686102 TTTTTTC
1 TTTTTTC
*
11686109 TTCATTT-
1 TT-TTTTC
11686116 TTTTTTC
1 TTTTTTC
11686123 TTTCTTTC
1 TTT-TTTC
11686131 TCTTATTTC
1 T-TT-TTTC
11686140 TTTTTTC
1 TTTTTTC
11686147 TTCTTTTTC
1 -T-TTTTTC
11686156 TTTTTTC
1 TTTTTTC
11686163 TTTTTTC
1 TTTTTTC
11686170 TTTTT
1 TTTTT
11686175 CATCATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
6 3 0.05
7 29 0.51
8 12 0.21
9 13 0.23
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:11686183 original size:23 final size:23
Alignment explanation
Indices: 11686103--11686185 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
11686093 CCTTATCAAT
*
11686103 TTTTTCTTCATTTTTTTTTCTTTC
1 TTTTTCTTCATTTTTCTTT-TTTC
*
11686127 TTTCTCTT-A--TTTCTTTTTTC
1 TTTTTCTTCATTTTTCTTTTTTC
*
11686147 TTCTTT-TTCTTTTTTCTTTTTTC
1 TT-TTTCTTCATTTTTCTTTTTTC
*
11686170 TTTTTCATCATTTTTC
1 TTTTTCTTCATTTTTC
11686186 AAGAAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.17
21 8 0.17
22 3 0.06
23 22 0.46
24 7 0.15
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTCTTCATTTTTCTTTTTTC
Found at i:11686185 original size:16 final size:14
Alignment explanation
Indices: 11686117--11686185 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 14
11686107 TCTTCATTTT
11686117 TTTTTCTTTCTTTCTC
1 TTTTTC-TT-TTTCTC
11686133 TTATTTCTTTTTTCTTC
1 TT-TTTC-TTTTTC-TC
11686150 TTTTTCTTTTT-TC
1 TTTTTCTTTTTCTC
11686163 TTTTTTCTTTTTCATC
1 -TTTTTCTTTTTC-TC
11686179 ATTTTTC
1 -TTTTTC
11686186 AAGAAAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
13 2 0.04
14 11 0.23
15 5 0.11
16 18 0.38
17 11 0.23
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:11690885 original size:28 final size:28
Alignment explanation
Indices: 11690845--11690902 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
11690835 ACTGCGTAAG
11690845 TTAGTTTTTCTATCCTGGTGTAGTTTAT
1 TTAGTTTTTCTATCCTGGTGTAGTTTAT
11690873 TTAGTTTTTCTATCCTGGTGTAGTTTAT
1 TTAGTTTTTCTATCCTGGTGTAGTTTAT
11690901 TT
1 TT
11690903 TAGACCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.59
Consensus pattern (28 bp):
TTAGTTTTTCTATCCTGGTGTAGTTTAT
Found at i:11696337 original size:46 final size:48
Alignment explanation
Indices: 11696232--11696353 Score: 128
Period size: 46 Copynumber: 2.6 Consensus size: 48
11696222 ACAAAATAAT
* *
11696232 ACAATGCACATGCAATGCAACAAATTAAAAAATGTAAATGCCAACTACTA
1 ACAATGCACATG-AATACAATAAATTAAAAAATGTAAATGCCAACTA-TA
* **
11696282 A-AA-AC-CATGAATACAATAAATTAAGCAATGTAAATGCCAA-T-TA
1 ACAATGCACATGAATACAATAAATTAAAAAATGTAAATGCCAACTATA
*
11696325 ACAATGCACATGAATACAATCAAAATAAA
1 ACAATGCACATGAATACAAT-AAATTAAA
11696354 TTGGGTGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
43 3 0.05
44 2 0.03
45 2 0.03
46 39 0.65
47 10 0.17
48 1 0.02
49 2 0.03
50 1 0.02
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.20
Consensus pattern (48 bp):
ACAATGCACATGAATACAATAAATTAAAAAATGTAAATGCCAACTATA
Found at i:11696492 original size:26 final size:24
Alignment explanation
Indices: 11696430--11696509 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
11696420 TAGGTTTTGA
* *
11696430 GGTTTAGACAAAGGTT-TAATTTGG
1 GGTTTAGA-AAAGGTTCAAATTTAG
*
11696454 GGTTTGGGAAAAGGGTTCAAATTTAG
1 GGTTT-AGAAAA-GGTTCAAATTTAG
*
11696480 GGTTTAGATAAAGG-TCAAACATTAG
1 GGTTTAGA-AAAGGTTCAAA-TTTAG
11696505 GGTTT
1 GGTTT
11696510 GACTTTTAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 13 0.28
25 19 0.41
26 14 0.30
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (24 bp):
GGTTTAGAAAAGGTTCAAATTTAG
Found at i:11696766 original size:26 final size:26
Alignment explanation
Indices: 11696735--11696784 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11696725 GAGCTTACGA
11696735 TTTGGTTCAAG-GTTTAGGCTAAGGGG
1 TTTGGTT-AAGAGTTTAGGCTAAGGGG
*
11696761 TTTGGTTTAGAGTTTAGGCTAAGG
1 TTTGGTTAAGAGTTTAGGCTAAGG
11696785 CTAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.20, C:0.06, G:0.36, T:0.38
Consensus pattern (26 bp):
TTTGGTTAAGAGTTTAGGCTAAGGGG
Found at i:11697377 original size:19 final size:19
Alignment explanation
Indices: 11697353--11697392 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11697343 TAATGTAACA
*
11697353 AAATGACCAAACAACACAT
1 AAATGAACAAACAACACAT
*
11697372 AAATGAACAAAGAACACAT
1 AAATGAACAAACAACACAT
11697391 AA
1 AA
11697393 TTAAGCACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.20, G:0.07, T:0.10
Consensus pattern (19 bp):
AAATGAACAAACAACACAT
Found at i:11699255 original size:24 final size:24
Alignment explanation
Indices: 11699228--11699316 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
11699218 TCTTATTTGA
11699228 AAAAAATTTTAAAGATTCACATTC
1 AAAAAATTTTAAAGATTCACATTC
* **
11699252 AAAATACGTTAAAGATTCACA-TC
1 AAAAAATTTTAAAGATTCACATTC
* ** *
11699275 -TAAAATTCCAAAGATTCACATTT
1 AAAAAATTTTAAAGATTCACATTC
* *
11699298 GAAAAATTTTAGAGATTCA
1 AAAAAATTTTAAAGATTCA
11699317 TATCCAAAGT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
22 14 0.29
23 3 0.06
24 32 0.65
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.31
Consensus pattern (24 bp):
AAAAAATTTTAAAGATTCACATTC
Found at i:11699369 original size:89 final size:91
Alignment explanation
Indices: 11699270--11699437 Score: 207
Period size: 90 Copynumber: 1.9 Consensus size: 91
11699260 TTAAAGATTC
* * * *
11699270 ACATCTAAAATTCCAAAGATTCACATTTG-AAAAATTTTAGAGA-TTCATATCCAAAGTTTCAAA
1 ACATCCAAAATTCCAAAGATTCACATTCGAAAAAATTTTAG-GATTTCACATCCAAAATTTCAAA
**
11699333 G-TTCTTTTTCAAAACTTTATGGCTTT
65 GATTCTCATTCAAAACTTTATGGCTTT
** ** *
11699359 ACATCCAAAATTTTAAAGATTCTTATTCGAAAAAATTTTTGGATTTCACATCCAAAATTTCAAAG
1 ACATCCAAAATTCCAAAGATTCACATTCGAAAAAATTTTAGGATTTCACATCCAAAATTTCAAAG
11699424 ATTCTCATTCAAAA
66 ATTCTCATTCAAAA
11699438 AACTCTTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 25 0.38
90 29 0.45
91 11 0.17
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (91 bp):
ACATCCAAAATTCCAAAGATTCACATTCGAAAAAATTTTAGGATTTCACATCCAAAATTTCAAAG
ATTCTCATTCAAAACTTTATGGCTTT
Found at i:11699439 original size:47 final size:46
Alignment explanation
Indices: 11699267--11699439 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 46
11699257 ACGTTAAAGA
* * * ** *
11699267 TTCACATCTAAAATTCCAAAGATTCACATTTGAAAAATTTTAGAGA-
1 TTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAATTTTTG-GAT
* * ** * * *
11699313 TTCATATCCAAAGTTTCAAAG-TTCTTTTTC-AAAACTTTATGGCT
1 TTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAATTTTTGGAT
* *
11699357 TT-ACATCCAAAATTTTAAAGATTCTTATTCGAAAAAATTTTTGGAT
1 TTCACATCCAAAATTTCAAAGATTCTCATTC-AAAAAATTTTTGGAT
11699403 TTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAA
1 TTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAA
11699440 CTCTTTTAAA
Statistics
Matches: 101, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
43 16 0.16
44 18 0.18
45 5 0.05
46 36 0.36
47 26 0.26
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (46 bp):
TTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAATTTTTGGAT
Found at i:11700771 original size:17 final size:16
Alignment explanation
Indices: 11700749--11700809 Score: 70
Period size: 16 Copynumber: 3.6 Consensus size: 16
11700739 CATCAATTTC
11700749 TTTTTCATTTTCTTTTT
1 TTTTTC-TTTTCTTTTT
11700766 TTTTTCTTTCTCTTATTT
1 TTTTTCTTT-TCTT-TTT
*
11700784 TTTTTCTTCTT-TTTCT
1 TTTTTCTT-TTCTTTTT
11700800 TTTTTCTTTT
1 TTTTTCTTTT
11700810 TTCCTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 2 0.05
16 13 0.32
17 12 0.30
18 12 0.30
19 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:11700785 original size:21 final size:20
Alignment explanation
Indices: 11700761--11700812 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
11700751 TTTCATTTTC
11700761 TTTTTTTTTTCTTTCTCTTAT
1 TTTTTTTTTTCTTTCTCTT-T
* *
11700782 TTTTTTTCTTCTTTTTCTTT
1 TTTTTTTTTTCTTTCTCTTT
*
11700802 TTTCTTTTTTC
1 TTTTTTTTTTC
11700813 CTTTTCATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTTCTTTCTCTTT
Found at i:11700798 original size:9 final size:8
Alignment explanation
Indices: 11700749--11700817 Score: 54
Period size: 8 Copynumber: 8.2 Consensus size: 8
11700739 CATCAATTTC
11700749 TTTTTCATT
1 TTTTTC-TT
11700758 TTCTTT-TT
1 TT-TTTCTT
11700766 TTTTTCTT
1 TTTTTCTT
11700774 TCTCTTAT-TT
1 T-T-TT-TCTT
11700784 TTTTTCTT
1 TTTTTCTT
11700792 CTTTTTC-T
1 -TTTTTCTT
11700800 TTTTTCTT
1 TTTTTCTT
*
11700808 TTTTCCTT
1 TTTTTCTT
11700816 TT
1 TT
11700818 CATCATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
7 10 0.20
8 22 0.43
9 10 0.20
10 8 0.16
11 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:11700803 original size:6 final size:6
Alignment explanation
Indices: 11700745--11700810 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
11700735 ACCTCATCAA
* * *
11700745 TTTCTT TTTCAT TTTCTT TTT-TT TTTCTT TCTCTTAT TTTTTT TCTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-T-T TTTCTT T-TTCTT
11700795 TTTCTTT TTTCTT TTT
1 TTTC-TT TTTCTT TTT
11700811 TCCTTTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
5 5 0.10
6 28 0.57
7 13 0.27
8 3 0.06
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:11700816 original size:21 final size:19
Alignment explanation
Indices: 11700749--11700818 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
11700739 CATCAATTTC
*
11700749 TTTTTCATTTTC--TTTTT
1 TTTTTCTTTTTCTTTTTTT
*
11700766 TTTTTCTTTCTCTTATTTTT
1 TTTTTCTTTTTCTT-TTTTT
11700786 TTTCTTCTTTTTCTTTTTTCT
1 TTT-TTCTTTTTCTTTTTT-T
*
11700807 TTTTTCCTTTTC
1 TTTTTCTTTTTC
11700819 ATCATTTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 10 0.23
20 20 0.45
21 14 0.32
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTTTT
Found at i:11710936 original size:46 final size:48
Alignment explanation
Indices: 11710832--11710952 Score: 126
Period size: 46 Copynumber: 2.6 Consensus size: 48
11710822 ACAAAATAAT
* * *
11710832 ACAATGCACATGCATGCAACAAATTAAAAAATGTAAATGCCAACTACTA
1 ACAATGCACATGAATACAATAAATTAAAAAATGTAAATGCCAACTA-TA
* **
11710881 A-AA-AC-CATGAATACAATAAATTAAGCAATGTAAATGCCAA-T-TA
1 ACAATGCACATGAATACAATAAATTAAAAAATGTAAATGCCAACTATA
*
11710924 ACAATGCACATGAATACAATCAAAATAAA
1 ACAATGCACATGAATACAAT-AAATTAAA
11710953 TTGGGTGTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
43 3 0.05
44 2 0.03
45 2 0.03
46 42 0.71
47 7 0.12
48 2 0.03
49 1 0.02
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.21
Consensus pattern (48 bp):
ACAATGCACATGAATACAATAAATTAAAAAATGTAAATGCCAACTATA
Found at i:11711239 original size:19 final size:18
Alignment explanation
Indices: 11711196--11711241 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11711186 TTGACTTTTT
* *
11711196 GTTTAGTGTAGGTTTAGG
1 GTTTAGGGTAGGTTTAGA
11711214 GTTTAGGGTAGGTTTAAGA
1 GTTTAGGGTAGGTTT-AGA
*
11711233 TTTTAGGGT
1 GTTTAGGGT
11711242 TTCAATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (18 bp):
GTTTAGGGTAGGTTTAGA
Found at i:11711365 original size:26 final size:26
Alignment explanation
Indices: 11711334--11711383 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11711324 GAGCTTACGA
11711334 TTTGGTTCAAG-GTTTAGGCTAAGGGG
1 TTTGGTT-AAGAGTTTAGGCTAAGGGG
*
11711360 TTTGGTTTAGAGTTTAGGCTAAGG
1 TTTGGTTAAGAGTTTAGGCTAAGG
11711384 CTAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.20, C:0.06, G:0.36, T:0.38
Consensus pattern (26 bp):
TTTGGTTAAGAGTTTAGGCTAAGGGG
Found at i:11714990 original size:6 final size:7
Alignment explanation
Indices: 11714962--11714989 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
11714952 AATTATATTG
11714962 TATTTTT
1 TATTTTT
11714969 TATTTTT
1 TATTTTT
11714976 TATTTTT
1 TATTTTT
11714983 TATTTTT
1 TATTTTT
11714990 AATATACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:11719476 original size:16 final size:17
Alignment explanation
Indices: 11719434--11719476 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
11719424 TTGAGTGTTA
11719434 TTAATAT-TTTTAAAAT
1 TTAATATATTTTAAAAT
* *
11719450 TTAAAAAATTTT-AAAT
1 TTAATATATTTTAAAAT
11719466 TTAATATATTT
1 TTAATATATTT
11719477 AATACTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATATTTTAAAAT
Found at i:11719989 original size:31 final size:32
Alignment explanation
Indices: 11719940--11720002 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
11719930 TTAAAACAAT
* *
11719940 AATTTATATAATACAAATATTTCTAAAATTTAA
1 AATTTATATAATACAAATAATT-GAAAATTTAA
*
11719973 AATTTA-A-AATATAAATAATTGAAAATTTAA
1 AATTTATATAATACAAATAATTGAAAATTTAA
11720003 TATTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.33
31 11 0.41
32 1 0.04
33 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
AATTTATATAATACAAATAATTGAAAATTTAA
Found at i:11721736 original size:29 final size:29
Alignment explanation
Indices: 11721699--11721755 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
11721689 TTCGCTCTAG
* * *
11721699 CGATTAAAGTTTCCTACTCATATATATAA
1 CGATAAAAGTTTCCCACCCATATATATAA
11721728 CGATAAAAGTTTCCCACCCATATATATA
1 CGATAAAAGTTTCCCACCCATATATATA
11721756 GGAATTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (29 bp):
CGATAAAAGTTTCCCACCCATATATATAA
Found at i:11724958 original size:24 final size:24
Alignment explanation
Indices: 11724931--11724980 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
11724921 TTGTTCCAAA
11724931 CTTTCTTCACATTACTTTAGCAAG
1 CTTTCTTCACATTACTTTAGCAAG
* *
11724955 CTTTCTTCACATTGCTTTATCAAG
1 CTTTCTTCACATTACTTTAGCAAG
11724979 CT
1 CT
11724981 CTTCACCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.44
Consensus pattern (24 bp):
CTTTCTTCACATTACTTTAGCAAG
Found at i:11729268 original size:7 final size:6
Alignment explanation
Indices: 11729258--11729694 Score: 87
Period size: 7 Copynumber: 66.0 Consensus size: 6
11729248 TTTGGGGTAA
*
11729258 TTTATGG TTTAGG -TTAGG ATTTTGG TTTTAAGG TTTAAGG -TTAGGG
1 TTTA-GG TTTAGG TTTAGG -TTTAGG -TTT-AGG TTT-AGG TTTA-GG
* * * * * * **
11729304 CTT-GG CTTAGAG TTTGGG GTTAGGG TTTAGG ATAAGG TTTGAGG TTTATCA
1 TTTAGG TTTAG-G TTTAGG TTTAG-G TTTAGG TTTAGG TTT-AGG TTTA-GG
* * **
11729355 TTTAGGG TTT-GG TTGAAGG TTTAGGG TTTATG TTTAGGG TTTAAA TTTAGGG
1 TTTA-GG TTTAGG TTTA-GG TTTA-GG TTTAGG TTTA-GG TTTAGG TTTA-GG
* *
11729407 TTAAAG TTTAAGG TTTAGG TTTTAGG TTTAGG ATTTAGG TTTTAGGG TTTAGG
1 TTTAGG TTT-AGG TTTAGG -TTTAGG TTTAGG -TTTAGG -TTTA-GG TTTAGG
** * * * *
11729460 TTTTAGG TTTATAA TTCAGGG TTT-GG TTGAAAG TTTAGGG TTTATG TTTAGGG
1 -TTTAGG TTTA-GG TTTA-GG TTTAGG TT-TAGG TTTA-GG TTTAGG TTTA-GG
** * * * **
11729513 TTTAAA TTTAAGG TTAAAG TTTAAAG TTTAGGG TTTAGG TTTACAA TTTAGGG
1 TTTAGG TTT-AGG TTTAGG TTT-AGG TTTA-GG TTTAGG TTTA-GG TTTA-GG
** *
11729566 TTTACAA TTTAGGG TTTAGG TTTAAGG TTT-GAG TTTACAG TTTAAGG
1 TTTA-GG TTTA-GG TTTAGG TTT-AGG TTTAG-G TTTA-GG TTT-AGG
* * *
11729613 TTT-GAG TTTACAG TTTAAGG TTTAGGG CTTAGG TTTTAGGG TTTAAGT
1 TTTAG-G TTTA-GG TTT-AGG TTTA-GG TTTAGG -TTTA-GG TTT-AGG
11729661 TTTAGG TTTATGG TTTATGG TTTTAAGG TTTAGG
1 TTTAGG TTTA-GG TTTA-GG -TTT-AGG TTTAGG
11729695 GTTTGTGGAA
Statistics
Matches: 315, Mismatches: 71, Indels: 89
0.66 0.15 0.19
Matches are distributed among these distances:
5 21 0.07
6 90 0.29
7 189 0.60
8 14 0.04
9 1 0.00
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46
Consensus pattern (6 bp):
TTTAGG
Found at i:11729360 original size:33 final size:33
Alignment explanation
Indices: 11729323--11729397 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
11729313 GAGTTTGGGG
11729323 TTAGGGTTTAGGAT-AAGGTTT-GAGGTTTATCAT
1 TTAGGGTTTAGGATGAAGGTTTAG-GGTTTAT-AT
* *
11729356 TTAGGGTTT-GGTTGAAGGTTTAGGGTTTATGT
1 TTAGGGTTTAGGATGAAGGTTTAGGGTTTATAT
11729388 TTAGGGTTTA
1 TTAGGGTTTA
11729398 AATTTAGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
32 13 0.35
33 23 0.62
34 1 0.03
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.45
Consensus pattern (33 bp):
TTAGGGTTTAGGATGAAGGTTTAGGGTTTATAT
Found at i:11729391 original size:13 final size:13
Alignment explanation
Indices: 11729258--11729694 Score: 133
Period size: 13 Copynumber: 33.0 Consensus size: 13
11729248 TTTGGGGTAA
*
11729258 TTTATGGTTTAGG
1 TTTAGGGTTTAGG
* *
11729271 -TTAGGATTTTGG
1 TTTAGGGTTTAGG
*
11729283 TTTTAAGGTTTAAGG
1 -TTTAGGGTTT-AGG
*
11729298 -TTAGGGCTT-GG
1 TTTAGGGTTTAGG
* * *
11729309 CTTAGAGTTTGGG
1 TTTAGGGTTTAGG
*
11729322 GTTAGGGTTTAGG
1 TTTAGGGTTTAGG
* *
11729335 -ATAAGGTTTGAGG
1 TTTAGGGTTT-AGG
***
11729348 TTTATCATTTAGGG
1 TTTAGGGTTTA-GG
*
11729362 TTT--GGTTGAAGG
1 TTTAGGGTT-TAGG
*
11729374 TTTAGGGTTTATG
1 TTTAGGGTTTAGG
**
11729387 TTTAGGGTTTAAA
1 TTTAGGGTTTAGG
* *
11729400 TTTAGGGTTAAAG
1 TTTAGGGTTTAGG
*
11729413 TTTAAGGTTTAGG
1 TTTAGGGTTTAGG
11729426 TTTTA-GGTTTAGG
1 -TTTAGGGTTTAGG
*
11729439 ATTTAGGTTTTAGGG
1 -TTTAGGGTTTA-GG
*
11729454 TTTAGGTTTTAGG
1 TTTAGGGTTTAGG
*** *
11729467 TTTATAATTCAGGG
1 TTTAGGGTTTA-GG
* *
11729481 TTT--GGTTGAAAG
1 TTTAGGGTT-TAGG
*
11729493 TTTAGGGTTTATG
1 TTTAGGGTTTAGG
**
11729506 TTTAGGGTTTAAA
1 TTTAGGGTTTAGG
* * *
11729519 TTTAAGGTTAAAG
1 TTTAGGGTTTAGG
**
11729532 TTTAAAGTTTAGGG
1 TTTAGGGTTTA-GG
**
11729546 TTTA-GGTTTACAA
1 TTTAGGGTTTA-GG
**
11729559 TTTAGGGTTTACAA
1 TTTAGGGTTTA-GG
11729573 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
*
11729586 TTTAAGGTTT-GAG
1 TTTAGGGTTTAG-G
**
11729599 TTTACAGTTTAAGG
1 TTTAGGGTTT-AGG
* *
11729613 TTT-GAGTTTACAG
1 TTTAGGGTTTA-GG
*
11729626 TTTAAGGTTTAGGG
1 TTTAGGGTTTA-GG
* *
11729640 CTTAGGTTTTAGGG
1 TTTAGGGTTTA-GG
* *
11729654 TTTAAGTTTTAGG
1 TTTAGGGTTTAGG
*
11729667 TTTATGGTTTATGG
1 TTTAGGGTTTA-GG
*
11729681 TTTTAAGGTTTAGG
1 -TTTAGGGTTTAGG
11729695 GTTTGTGGAA
Statistics
Matches: 323, Mismatches: 74, Indels: 53
0.72 0.16 0.12
Matches are distributed among these distances:
11 2 0.01
12 38 0.12
13 159 0.49
14 109 0.34
15 15 0.05
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46
Consensus pattern (13 bp):
TTTAGGGTTTAGG
Found at i:11729397 original size:20 final size:20
Alignment explanation
Indices: 11729355--11729698 Score: 148
Period size: 20 Copynumber: 17.1 Consensus size: 20
11729345 AGGTTTATCA
* *
11729355 TTTAGGGTTT-GGTTGAAGG
1 TTTAGGGTTTAGGTTTAGGG
*
11729374 TTTAGGGTTTATGTTTAGGG
1 TTTAGGGTTTAGGTTTAGGG
** * **
11729394 TTTA-AATTTAGGGTTAAAG
1 TTTAGGGTTTAGGTTTAGGG
*
11729413 TTTAAGGTTTAGGTTTTA-GG
1 TTTAGGGTTTAGG-TTTAGGG
*
11729433 TTTAGGATTTAGGTTTTAGGG
1 TTTAGGGTTTAGG-TTTAGGG
* ***
11729454 TTTAGGTTTTAGGTTTATAA
1 TTTAGGGTTTAGGTTTAGGG
* * **
11729474 TTCAGGGTTT-GGTTGAAAG
1 TTTAGGGTTTAGGTTTAGGG
*
11729493 TTTAGGGTTTATGTTTAGGG
1 TTTAGGGTTTAGGTTTAGGG
** **
11729513 TTTA-AATTTAAGG-TTAAAG
1 TTTAGGGTTT-AGGTTTAGGG
**
11729532 TTTAAAGTTTAGGGTTTA-GG
1 TTTAGGGTTTA-GGTTTAGGG
*** ***
11729552 TTTACAATTTAGGGTTTACAA
1 TTTAGGGTTTA-GGTTTAGGG
*
11729573 TTTAGGGTTTAGGTTTAAGG
1 TTTAGGGTTTAGGTTTAGGG
* * *
11729593 TTT-GAGTTTACAGTTTAAGG
1 TTTAGGGTTTA-GGTTTAGGG
* * *
11729613 TTT-GAGTTTACAGTTTAAGG
1 TTTAGGGTTTA-GGTTTAGGG
*
11729633 TTTAGGGCTTAGGTTTTAGGG
1 TTTAGGGTTTAGG-TTTAGGG
* * *
11729654 TTTAAGTTTTAGGTTTATGG
1 TTTAGGGTTTAGGTTTAGGG
*
11729674 TTTATGGTTTTAAGGTTTAGGG
1 TTTA-GGGTTT-AGGTTTAGGG
11729696 TTT
1 TTT
11729699 GTGGAATGCA
Statistics
Matches: 252, Mismatches: 58, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
19 56 0.22
20 130 0.52
21 54 0.21
22 12 0.05
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTTAGGG
Found at i:11729481 original size:119 final size:119
Alignment explanation
Indices: 11729338--11729589 Score: 378
Period size: 119 Copynumber: 2.1 Consensus size: 119
11729328 GTTTAGGATA
* * * *
11729338 AGGTTTGAGGTTTATCATTTAGGGTTTGGTTGAAGGTTTAGGGTTTATGTTTAGGGTTTAAATTT
1 AGGTTTTAGGTTTATAATTCAGGGTTTGGTTGAAAGTTTAGGGTTTATGTTTAGGGTTTAAATTT
* * * ** * ***
11729403 AGGGTTAAAGTTTAAGGTTTAGGTTTTAGGTTTAGGATTTAGGTTTTAGGGTTT
66 AAGGTTAAAGTTTAAAGTTTAGGGTTTAGGTTTACAATTTAGGGTTTACAATTT
11729457 AGGTTTTAGGTTTATAATTCAGGGTTTGGTTGAAAGTTTAGGGTTTATGTTTAGGGTTTAAATTT
1 AGGTTTTAGGTTTATAATTCAGGGTTTGGTTGAAAGTTTAGGGTTTATGTTTAGGGTTTAAATTT
11729522 AAGGTTAAAGTTTAAAGTTTAGGGTTTAGGTTTACAATTTAGGGTTTACAATTT
66 AAGGTTAAAGTTTAAAGTTTAGGGTTTAGGTTTACAATTTAGGGTTTACAATTT
*
11729576 AGGGTTTAGGTTTA
1 AGGTTTTAGGTTTA
11729590 AGGTTTGAGT
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.46
Consensus pattern (119 bp):
AGGTTTTAGGTTTATAATTCAGGGTTTGGTTGAAAGTTTAGGGTTTATGTTTAGGGTTTAAATTT
AAGGTTAAAGTTTAAAGTTTAGGGTTTAGGTTTACAATTTAGGGTTTACAATTT
Found at i:11729496 original size:73 final size:73
Alignment explanation
Indices: 11729374--11729516 Score: 173
Period size: 73 Copynumber: 2.0 Consensus size: 73
11729364 TGGTTGAAGG
* * * * *
11729374 TTTAGGGTTTATGTTTAGGGTTTAAATTTAGGGTTAAAGTTTAAGGTTTAGGTTTTAGGTTTAGG
1 TTTAGGGTTTAGGTTTAGGGTTTAAATTCAGGGTTAAAGTTGAAAGTTTAGGGTTTAGGTTTAGG
11729439 ATTTAGGT
66 ATTTAGGT
** *
11729447 TTTAGGGTTTAGGTTTTA-GGTTTATAATTCAGGGTT-TGGTTGAAAGTTTAGGGTTTATGTTTA
1 TTTAGGGTTTAGG-TTTAGGGTTTA-AATTCAGGGTTAAAGTTGAAAGTTTAGGGTTTAGGTTTA
*
11729510 GGGTTTA
64 GGATTTA
11729517 AATTTAAGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 45 0.76
74 14 0.24
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (73 bp):
TTTAGGGTTTAGGTTTAGGGTTTAAATTCAGGGTTAAAGTTGAAAGTTTAGGGTTTAGGTTTAGG
ATTTAGGT
Found at i:11729502 original size:46 final size:47
Alignment explanation
Indices: 11729447--11729554 Score: 132
Period size: 46 Copynumber: 2.3 Consensus size: 47
11729437 GGATTTAGGT
* **
11729447 TTTAGGGTTTAGGTTTTA-GGTTTATAATTCAGGGTT-TGGTTGAAAG
1 TTTAGGGTTTAGGTTTTAGGGTTTA-AATTCAAGGTTAAAGTTGAAAG
* * *
11729493 TTTAGGGTTTATG-TTTAGGGTTTAAATTTAAGGTTAAAGTTTAAAG
1 TTTAGGGTTTAGGTTTTAGGGTTTAAATTCAAGGTTAAAGTTGAAAG
11729539 TTTAGGGTTTAGGTTT
1 TTTAGGGTTTAGGTTT
11729555 ACAATTTAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
45 13 0.25
46 37 0.71
47 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (47 bp):
TTTAGGGTTTAGGTTTTAGGGTTTAAATTCAAGGTTAAAGTTGAAAG
Found at i:11729697 original size:7 final size:7
Alignment explanation
Indices: 11729355--11729698 Score: 119
Period size: 7 Copynumber: 51.4 Consensus size: 7
11729345 AGGTTTATCA
11729355 TTTAGGG
1 TTTAGGG
11729362 TTT--GG
1 TTTAGGG
* *
11729367 TTGAAGG
1 TTTAGGG
11729374 TTTAGGG
1 TTTAGGG
*
11729381 TTTA-TG
1 TTTAGGG
11729387 TTTAGGG
1 TTTAGGG
**
11729394 TTTA-AA
1 TTTAGGG
11729400 TTTAGGG
1 TTTAGGG
**
11729407 -TTAAAG
1 TTTAGGG
*
11729413 TTTAAGG
1 TTTAGGG
*
11729420 TTTAGGT
1 TTTAGGG
11729427 TTTA-GG
1 TTTAGGG
*
11729433 TTTAGGA
1 TTTAGGG
*
11729440 TTTAGGT
1 TTTAGGG
11729447 TTTAGGG
1 TTTAGGG
*
11729454 TTTAGGT
1 TTTAGGG
11729461 TTTA-GG
1 TTTAGGG
***
11729467 TTTATAA
1 TTTAGGG
*
11729474 TTCAGGG
1 TTTAGGG
11729481 TTT--GG
1 TTTAGGG
* **
11729486 TTGAAAG
1 TTTAGGG
11729493 TTTAGGG
1 TTTAGGG
*
11729500 TTTA-TG
1 TTTAGGG
11729506 TTTAGGG
1 TTTAGGG
**
11729513 TTTA-AA
1 TTTAGGG
*
11729519 TTTAAGG
1 TTTAGGG
**
11729526 -TTAAAG
1 TTTAGGG
**
11729532 TTTAAAG
1 TTTAGGG
11729539 TTTAGGG
1 TTTAGGG
11729546 TTTA-GG
1 TTTAGGG
***
11729552 TTTACAA
1 TTTAGGG
11729559 TTTAGGG
1 TTTAGGG
***
11729566 TTTACAA
1 TTTAGGG
11729573 TTTAGGG
1 TTTAGGG
11729580 TTTA-GG
1 TTTAGGG
*
11729586 TTTAAGG
1 TTTAGGG
*
11729593 TTT-GAG
1 TTTAGGG
**
11729599 TTTACAG
1 TTTAGGG
*
11729606 TTTAAGG
1 TTTAGGG
*
11729613 TTT-GAG
1 TTTAGGG
**
11729619 TTTACAG
1 TTTAGGG
*
11729626 TTTAAGG
1 TTTAGGG
11729633 TTTAGGG
1 TTTAGGG
* *
11729640 CTTAGGT
1 TTTAGGG
11729647 TTTAGGG
1 TTTAGGG
* *
11729654 TTTAAGT
1 TTTAGGG
11729661 TTTA-GG
1 TTTAGGG
*
11729667 TTTATGG
1 TTTAGGG
*
11729674 TTTATGGT
1 TTTA-GGG
*
11729682 TTTAAGG
1 TTTAGGG
11729689 TTTAGGG
1 TTTAGGG
11729696 TTT
1 TTT
11729699 GTGGAATGCA
Statistics
Matches: 244, Mismatches: 75, Indels: 36
0.69 0.21 0.10
Matches are distributed among these distances:
5 8 0.03
6 62 0.25
7 169 0.69
8 5 0.02
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:11731280 original size:143 final size:143
Alignment explanation
Indices: 11731003--11731309 Score: 307
Period size: 143 Copynumber: 2.1 Consensus size: 143
11730993 TTTTAATGGT
* *
11731003 CCAAAAATCATGAAATAATATAAAACCATGATTTGATGCATTTCGTGAAAAACCAACCTTGGAAA
1 CCAAAAATCATGAAATAATATAAAACCATGATTAGATGCATTTCATGAAAAACCAACCTTGGAAA
* * * * * * * * *
11731068 AGTTAAATTATGAAAATACTCCTAAGGGTACTTTGATAATTTTACACCTTCTAAGGTGCAATTAT
66 AGTCAAATTATCAAAATACCCCTAAAGGTACTTTGATAATCTCACACCTTCTAAGATGCAATCAA
11731133 GGTTTTT-AGTAAA
131 GGTTTTTGA-TAAA
* ***
11731146 CCAAAAATCATGAAATAATATAAAATCATGATCTAGA-GCATTTCATGAAAAATTGACCTTGGAA
1 CCAAAAATCATGAAATAATATAAAACCATGAT-TAGATGCATTTCATGAAAAACCAACCTTGGAA
* * * * * * * *
11731210 AGGTCAATTTA-CAAAAGTGCCCCTAAAGGTATTTTGGTAATCTCACATC-TCTCAGAATGCGAT
65 AAGTCAAATTATCAAAA-TACCCCTAAAGGTACTTTGATAATCTCACACCTTCTAAG-ATGCAAT
*
11731273 CAAGGTTTTTGATATA
128 CAAGGTTTTTGATAAA
* * *
11731289 TCAAAAATTATAAAATAATAT
1 CCAAAAATCATGAAATAATAT
11731310 TTAAATACGA
Statistics
Matches: 133, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
142 9 0.07
143 120 0.90
144 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (143 bp):
CCAAAAATCATGAAATAATATAAAACCATGATTAGATGCATTTCATGAAAAACCAACCTTGGAAA
AGTCAAATTATCAAAATACCCCTAAAGGTACTTTGATAATCTCACACCTTCTAAGATGCAATCAA
GGTTTTTGATAAA
Found at i:11736401 original size:18 final size:18
Alignment explanation
Indices: 11736370--11736405 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11736360 AAGACATTTA
*
11736370 GTATTGATTCCATGCATT
1 GTATTCATTCCATGCATT
*
11736388 GTATTCATTGCATGCATT
1 GTATTCATTCCATGCATT
11736406 TCATGCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
GTATTCATTCCATGCATT
Found at i:11736879 original size:22 final size:22
Alignment explanation
Indices: 11736814--11736889 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
11736804 CTTAATTCTT
* *
11736814 CAAGCACGATCTATAAGATCTC
1 CAAGCATGATCTATAAGACCTC
* * * *
11736836 AAAACATAATCT-TCAAGTCCTC
1 CAAGCATGATCTAT-AAGACCTC
11736858 CAAGCATGATCTATAAGACCTC
1 CAAGCATGATCTATAAGACCTC
**
11736880 CTGGCATGAT
1 CAAGCATGAT
11736890 ATTTTTAAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAGCATGATCTATAAGACCTC
Found at i:11737392 original size:30 final size:28
Alignment explanation
Indices: 11737322--11737393 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
11737312 ATTATCGAAC
* *
11737322 TTTATTT-TTTTCTTTATTTGTATATAT
1 TTTATTTATTTTATTTATTTCTATATAT
* *
11737349 GTT-TTTATCTTATTTATCTTCTATATAT
1 TTTATTTATTTTATTTAT-TTCTATATAT
11737377 TTTATTTGATTTTATTT
1 TTTATTT-ATTTTATTT
11737394 TTTAACTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.09
27 10 0.29
28 11 0.31
29 3 0.09
30 8 0.23
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (28 bp):
TTTATTTATTTTATTTATTTCTATATAT
Found at i:11738203 original size:20 final size:21
Alignment explanation
Indices: 11738173--11738211 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11738163 AAAAGAGAAA
11738173 AAGGAAGAAGAAAAATTTGAG
1 AAGGAAGAAGAAAAATTTGAG
*
11738194 AAGGAA-AAGAAAGATTTG
1 AAGGAAGAAGAAAAATTTG
11738212 GGGTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (21 bp):
AAGGAAGAAGAAAAATTTGAG
Found at i:11738800 original size:94 final size:95
Alignment explanation
Indices: 11738702--11738910 Score: 239
Period size: 94 Copynumber: 2.2 Consensus size: 95
11738692 AGTCTCTAAA
* *
11738702 TTAAGTCTTACTAAACTATTA-AGAGACTGAA-AGAATTTTTATAAAAAA-TA-ATTTTTAAATC
1 TTAAGTCTTACCAAACTATTAGAGA-ACTGAATA-AATCTTTATAAAAAATTATATTTTTAAATC
* * *
11738763 CTACCGAACTATT-AAAAGATTTAAACTTTTAAG
64 CTACCAAACTATTGAAAA-ATTTAAA-TCTCAAG
* * * *
11738796 TTAAGTCTTACCAAACTATTGGAGAACTTAATAAATCTTTATAAAAAATTATTTTTTTCAATCCT
1 TTAAGTCTTACCAAACTATTAGAGAACTGAATAAATCTTTATAAAAAATTATATTTTTAAATCCT
* *
11738861 ACTAAACTATTGAAAAATTTAAATCTCGAG
66 ACCAAACTATTGAAAAATTTAAATCTCAAG
*
11738891 TTAAATCTTACCAAACTATT
1 TTAAGTCTTACCAAACTATT
11738911 GAAAGATTTA
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
94 38 0.39
95 29 0.30
96 27 0.28
97 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (95 bp):
TTAAGTCTTACCAAACTATTAGAGAACTGAATAAATCTTTATAAAAAATTATATTTTTAAATCCT
ACCAAACTATTGAAAAATTTAAATCTCAAG
Done.