Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 157 of 198
Found at i:49634866 original size:50 final size:50
Alignment explanation
Indices: 49634744--49635085 Score: 400
Period size: 50 Copynumber: 6.7 Consensus size: 50
49634734 CATTTGGGTA
* * * *
49634744 AAGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGACATCCTTGAGATC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C
*
49634798 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * *
49634850 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* *
49634900 GAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * * * * *
49634950 AAGAGGTCCTATGTAAAACCATGTCTAGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * *
49635000 AAGAGGTCCCCTATAAGACCATGTCTGGGACGTGGCATGGGCACC-A-AC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
**
49635048 ATGAGAACATCCCATGTAAGACCATGTCTGGGACATGG
1 A--AG-AGGTCCCATGTAAGACCATGTCTGGGACATGG
49635086 ATTTGGCATG
Statistics
Matches: 249, Mismatches: 34, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
48 2 0.01
49 1 0.00
50 171 0.69
51 27 0.11
52 2 0.01
53 4 0.02
54 1 0.00
55 2 0.01
56 39 0.16
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
Found at i:49634936 original size:100 final size:100
Alignment explanation
Indices: 49634744--49635085 Score: 463
Period size: 100 Copynumber: 3.4 Consensus size: 100
49634734 CATTTGGGTA
* * * *
49634744 AAGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGACATCCTTGAGATCATGAGAGATCC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATGAGAGGTCC
*
49634809 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
60 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
*
49634850 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTGTA
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTGTA
49634915 AGACCATGTCTGGGACATGGCATGGGCACCGAGAC
66 AGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * * * * *
49634950 AAGAGGTCCTATGTAAAACCATGTCTAGGACATGGCGTTGGCACCGAGATAAGAGGTCCCCTATA
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTGTA
*
49635015 AGACCATGTCTGGGACGTGGCATGGGCACC-A-AC
66 AGACCATGTCTGGGACATGGCATGGGCACCGAGAC
*
49635048 ATGAGAACATCCCATGTAAGACCATGTCTGGGACATGG
1 A--AG-AGATCCCATGTAAGACCATGTCTGGGACATGG
49635086 ATTTGGCATG
Statistics
Matches: 216, Mismatches: 17, Indels: 11
0.89 0.07 0.05
Matches are distributed among these distances:
98 3 0.01
99 1 0.00
100 141 0.65
101 27 0.12
103 3 0.01
105 2 0.01
106 39 0.18
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (100 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTGTA
AGACCATGTCTGGGACATGGCATGGGCACCGAGAC
Found at i:49634997 original size:150 final size:154
Alignment explanation
Indices: 49634745--49635085 Score: 447
Period size: 150 Copynumber: 2.2 Consensus size: 154
49634735 ATTTGGGTAA
* *
49634745 AGAGATCCCATGTAAGACCATGTCTGGGACATGTCATTGACATCCTTGAGATCATGAGAGATCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGACATCC-TGAGATCA-GAGAGATCCC
* * *
49634810 ATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACAAGAGGTCCCATGTAAGACCATGTC
64 ATGTAAAACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGTC
* * * *
49634875 TGGGACATGGCGTTGGCACCGAGATG
129 TGGGACATGGCATGGGCACCAACATG
* * * * *
49634901 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCA-CC-GAGA-CA-AGAGGTCCTAT
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGACATCCTGAGATCAGAGAGATCCCAT
* * * *
49634962 GTAAAACCATGTCTAGGACATGGCGTTGGCACCGAGATAAGAGGTCCCCTATAAGACCATGTCTG
66 GTAAAACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGTCTG
*
49635027 GGACGTGGCATGGGCACCAACATG
131 GGACATGGCATGGGCACCAACATG
*
49635051 AGAACATCCCATGTAAGACCATGTCTGGGACATGG
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGG
49635086 ATTTGGCATG
Statistics
Matches: 162, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
150 88 0.54
151 29 0.18
152 2 0.01
153 4 0.02
155 2 0.01
156 37 0.23
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (154 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGACATCCTGAGATCAGAGAGATCCCAT
GTAAAACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGTCTG
GGACATGGCATGGGCACCAACATG
Found at i:49637852 original size:23 final size:23
Alignment explanation
Indices: 49637826--49637869 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
49637816 ATCTATATTT
49637826 TAATTATTATAAATTT-AAATATA
1 TAATT-TTATAAATTTGAAATATA
*
49637849 TAATTTTATATATTTGAAATA
1 TAATTTTATAAATTTGAAATA
49637870 AATTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATTTTATAAATTTGAAATATA
Found at i:49637875 original size:20 final size:22
Alignment explanation
Indices: 49637826--49637876 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
49637816 ATCTATATTT
49637826 TAATTATTATAAATTTAAATATA
1 TAATT-TTATAAATTTAAATATA
* *
49637849 TAATTTTATATATTTGAA-ATA
1 TAATTTTATAAATTTAAATATA
49637870 -AATTTTA
1 TAATTTTA
49637877 ATTGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 11 0.42
23 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTTTATAAATTTAAATATA
Found at i:49641918 original size:36 final size:37
Alignment explanation
Indices: 49641871--49641943 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 37
49641861 TCTTAAGTTT
*
49641871 AACTTGACT-AGACAATCAATTTTATAGGAAAAATTC
1 AACTTGACTAAGACAATCAATTCTATAGGAAAAATTC
49641907 AACTTGACTAGAGACAATCAATTCTATAGGAAAAATT
1 AACTTGACTA-AGACAATCAATTCTATAGGAAAAATT
49641944 TAAGGTAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 9 0.26
38 25 0.74
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (37 bp):
AACTTGACTAAGACAATCAATTCTATAGGAAAAATTC
Found at i:49646840 original size:44 final size:44
Alignment explanation
Indices: 49646792--49646877 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 44
49646782 TTCACCGATG
* * * * * *
49646792 TGGCTTTAATCTGTTCCACCGCAATCTCAGTGAGATGAGATTTC
1 TGGCTTCAATATGCTCCACCGCAACCTCAGGGAGATAAGATTTC
* *
49646836 TGGCTTCAATATGCTCCACTGTAACCTCAGGGAGATAAGATT
1 TGGCTTCAATATGCTCCACCGCAACCTCAGGGAGATAAGATT
49646878 CACCATTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
TGGCTTCAATATGCTCCACCGCAACCTCAGGGAGATAAGATTTC
Found at i:49666146 original size:7 final size:7
Alignment explanation
Indices: 49666134--49666163 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49666124 AACATATACT
49666134 TTTTATA
1 TTTTATA
49666141 TTTTATA
1 TTTTATA
*
49666148 TTTCATA
1 TTTTATA
49666155 TTTTATA
1 TTTTATA
49666162 TT
1 TT
49666164 CTTTATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:49666814 original size:107 final size:107
Alignment explanation
Indices: 49666619--49666935 Score: 519
Period size: 107 Copynumber: 3.0 Consensus size: 107
49666609 GTTTTTTTCT
* *
49666619 AAATAAGGC-ATATTTCGCGTTTGGAAAATCAAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
49666683 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* *
49666725 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTTCGACT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
* * *
49666790 TCTCGTTTGCCCAAATAGCCAAATATTCTTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
*
49666832 AAATAAGGCAATACTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
* * * *
49666897 TTTCGTTCGACTAAATAGCCAAATATCCTCTTAAAACTT
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTT
49666936 CAAAGTATGG
Statistics
Matches: 193, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
106 9 0.05
107 184 0.95
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (107 bp):
AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
Found at i:49669569 original size:20 final size:20
Alignment explanation
Indices: 49669546--49669604 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
49669536 AACTCGTTAA
49669546 AAAACAATTTAACTTGATTG
1 AAAACAATTTAACTTGATTG
*
49669566 AAAA-AATTCTAACATGATTG
1 AAAACAATT-TAACTTGATTG
* *
49669586 AAATCATTTTAACTTGATT
1 AAAACAATTTAACTTGATT
49669605 TGGAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (20 bp):
AAAACAATTTAACTTGATTG
Found at i:49669942 original size:14 final size:14
Alignment explanation
Indices: 49669925--49669971 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
49669915 TCCTTTTGAT
*
49669925 TTCTTTCTTTCTTC
1 TTCTTTTTTTCTTC
49669939 TTCTTTTTTTCTTCC
1 TTCTTTTTTTCTT-C
* *
49669954 TTATTTTTTTCATC
1 TTCTTTTTTTCTTC
49669968 TTCT
1 TTCT
49669972 CCTTAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTTTTTTCTTC
Found at i:49670608 original size:6 final size:6
Alignment explanation
Indices: 49670599--49670623 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49670589 TAGATTTAGA
49670599 TGATGG TGATGG TGATGG TGATGG T
1 TGATGG TGATGG TGATGG TGATGG T
49670624 AAGTGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TGATGG
Found at i:49672931 original size:14 final size:15
Alignment explanation
Indices: 49672912--49672940 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49672902 TAAACTTAAA
49672912 TAAAGTAAA-ATCTT
1 TAAAGTAAATATCTT
49672926 TAAAGTAAATATCTT
1 TAAAGTAAATATCTT
49672941 GTCTCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAAGTAAATATCTT
Found at i:49674945 original size:5 final size:5
Alignment explanation
Indices: 49674935--49674988 Score: 58
Period size: 5 Copynumber: 11.0 Consensus size: 5
49674925 TGATACTTTC
* * *
49674935 ATTTT ATTTT ATTTC ATTTTT GTTTT ATTTT ATTTT A--TC ATTTT ATTTT
1 ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
49674984 ATTTT
1 ATTTT
49674989 TCATCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
3 2 0.05
5 35 0.88
6 3 0.08
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:49674980 original size:18 final size:17
Alignment explanation
Indices: 49674936--49674992 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
49674926 GATACTTTCA
*
49674936 TTTT-ATTTTATTTCAT
1 TTTTCATTTTATTTTAT
*
49674952 TTTT-GTTTTATTTTAT
1 TTTTCATTTTATTTTAT
49674968 TTTATCATTTTATTTTAT
1 TTT-TCATTTTATTTTAT
49674986 TTTTCAT
1 TTTTCAT
49674993 CTCGAAACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.47
17 5 0.14
18 14 0.39
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTCATTTTATTTTAT
Found at i:49679525 original size:44 final size:44
Alignment explanation
Indices: 49679474--49679960 Score: 194
Period size: 44 Copynumber: 11.1 Consensus size: 44
49679464 GTAGTAGAGA
* * * *
49679474 AGCAGATTTAAGCCACTAGATCCTATCTCCCTGAGCAGTAGTGG
1 AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* ** * *
49679518 AGTAGATTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGG
1 AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* * * * *
49679562 AGCAGATCGAAGACGGT-GAATCTTATCTTTCC-AAGGTAGTAG-GG
1 AGCAGATTGAAGACAGTAG-ATCCTATC-TCCCTAA-GCAGTAGTGG
* * * * * *
49679606 AAACAGATTTAAGCCACTA-ATCATATCTCCCTAAGCAGCAGTGG
1 -AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* * **
49679650 AGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* ** * *
49679694 AGCAGATCGAAGATGGT-GAATCTTATCTTCCC-AAGGTAGTAG-GG
1 AGCAGATTGAAGACAGTAG-ATCCTATC-TCCCTAA-GCAGTAGTGG
* * ** *
49679738 AAGCAGATTTAAAACACCAG--CCTTATCTCCCTGAGCAGTAGTGG
1 -AGCAGATTGAAGACAGTAGATCC-TATCTCCCTAAGCAGTAGTGG
* * * * * * *
49679782 AGTAGGTTGAAGATTA-CAGATCCTGTCTCCCAAAGTAGTAGTGG
1 AGCAGATTGAAGA-CAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* ** * * * *
49679826 AGTAGATCAAAGAC-GACAAATCTTATCTTCCC-AATGTAGTAG-GG
1 AGCAGATTGAAGACAG-TAGATCCTATC-TCCCTAA-GCAGTAGTGG
* * ** * * *
49679870 AAGCAGATTTAAGTCACCAG-TCCAATATCCCTTAGCAGTAGTGG
1 -AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
* ** * *
49679914 AGTAGGATT-AAGATTGTAGATCCTGTCTCCCTGAGCAGTAGTGG
1 AGCA-GATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
49679958 AGC
1 AGC
49679961 GGATCAAAGA
Statistics
Matches: 324, Mismatches: 90, Indels: 58
0.69 0.19 0.12
Matches are distributed among these distances:
43 61 0.19
44 196 0.60
45 66 0.20
46 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
AGCAGATTGAAGACAGTAGATCCTATCTCCCTAAGCAGTAGTGG
Found at i:49679679 original size:132 final size:132
Alignment explanation
Indices: 49679441--49679988 Score: 715
Period size: 132 Copynumber: 4.2 Consensus size: 132
49679431 TGAAGTCATC
* * * *
49679441 ACGGTGAATCTTATCTTTCCAAGGTAGTAGAGAAGCAGATTTAAGCCACTAGATCCTATCTCCCT
1 ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCA-ATCATATCTCCCT
* * *
49679506 GAGCAGTAGTGGAGTAGATTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCG
65 GAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCA
49679571 AAG
130 AAG
* * * *
49679574 ACGGTGAATCTTATCTTTCCAAGGTAGTAGGGAAACAGATTTAAGCCACTAATCATATCTCCCTA
1 ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCATATCTCCCTG
* * *
49679639 AGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
66 AGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAA
49679704 AG
131 AG
* ** ** *
49679706 ATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAAACACCAGCCTTATCTCCCTG
1 ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCATATCTCCCTG
** * * *
49679771 AGCAGTAGTGGAGTAGGTTGAAGATTACAGATCCTGTCTCCCAAAGTAGTAGTGGAGTAGATCAA
66 AGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAA
49679836 AG
131 AG
*** * * * *
49679838 ACGACAAATCTTATCTTCCCAATGTAGTAGGGAAGCAGATTTAAGTCACCAGTCCA-ATATCCCT
1 ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT-CATATCTCCCT
* * *
49679902 TAGCAGTAGTGGAGTAGGATT-AAGATTGTAGATCCTGTCTCCCTGAGCAGTAGTGGAGCGGATC
65 GAGCAGTAGTGGAGTAGG-TTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATC
49679966 AAAG
129 AAAG
* *
49679970 ACAGCGAATCTTAT-TTCCC
1 ACGGTGAATCTTATCTTCCC
49679989 TAGCTTTGTA
Statistics
Matches: 366, Mismatches: 47, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
131 5 0.01
132 309 0.84
133 52 0.14
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAATCATATCTCCCTG
AGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAA
AG
Found at i:49680166 original size:181 final size:179
Alignment explanation
Indices: 49679972--49680456 Score: 713
Period size: 181 Copynumber: 2.7 Consensus size: 179
49679962 GATCAAAGAC
*
49679972 AGCGAATCTTATTTCCCT-AGCTTTGTAGTGGAACAGATTGAAGCTATAAATTACAGATCTTAT-
1 AGCGAATCTTATTTCCCTAAG--TTGTAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATC
* * *
49680035 TTTTTAGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGTGGCAG
64 TCTCT-GAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTG-GGCAA
* *
49680100 GTTGAAATTACGAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGGAGAT
127 GCTGAAATTACAAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGGAGAT
*
49680153 AGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCT
1 AGCGAATCTTATTTCCCT-AAGTTGTAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCT
* *
49680218 CTCTGAAGTTGCAGTAGAGCAGATCATATCAAACATCATCTCCCTGAAGTTACAGTAGGGCAAGC
65 CTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGT-GGGCAAGC
* * *
49680283 TGAAATTACAAGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGACTGGAGAT
129 TGAAATTACAAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGGAGAT
* * *
49680334 AACGAATCTTATTTCCTTGAAGTTGTAGTGGAACAGATCGAAGCTATAAATAACAGATCTTATCT
1 AGCGAATCTTATTTCCCT-AAGTTGTAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCT
* ** * *
49680399 CTCTGAAGTTGCAGTAGAGCAGATCAGATCAAGTCTTATCTCCCTAAAGTTGCAGTGG
65 CTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGG
49680457 AGCAGTTGCA
Statistics
Matches: 277, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
180 2 0.01
181 269 0.97
182 4 0.01
183 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (179 bp):
AGCGAATCTTATTTCCCTAAGTTGTAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCTC
TCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGGGCAAGCTG
AAATTACAAGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTGGAGAT
Found at i:49680241 original size:51 final size:50
Alignment explanation
Indices: 49680158--49680423 Score: 166
Period size: 51 Copynumber: 5.7 Consensus size: 50
49680148 GAGATAGCGA
* * *
49680158 ATCTTATTTCCCTGAAGTTGCAGTGGAACAGATCGAAGCTATAAATTACAG
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGCTATAAA-TACAG
* *
49680209 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC--A--TATCAA-AC--
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGCTATAAATACAG
* *
49680252 ATC--ATCTCCCTGAAGTTACAGTAG-G--G--C-AAGCTGA-AATTACA-
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGCT-ATAAATACAG
* * *
49680293 AGTCTTATTTCCCTGAAGTTGCAGTGGAGCAGA-CTGGAG--AT--A-AC-G
1 A-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-GAAGCTATAAATACAG
* * * * *
49680338 AATCTTATTTCCTTGAAGTTGTAGTGGAACAGATCGAAGCTATAAATAACAG
1 -ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGCTATAAAT-ACAG
*
49680390 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC
49680424 AGATCAAGTC
Statistics
Matches: 165, Mismatches: 24, Indels: 52
0.68 0.10 0.22
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.01
40 4 0.02
41 20 0.12
42 2 0.01
43 3 0.02
44 18 0.11
45 36 0.22
46 2 0.01
47 9 0.05
48 1 0.01
49 2 0.01
50 2 0.01
51 60 0.36
52 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (50 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGCTATAAATACAG
Found at i:49680465 original size:14 final size:14
Alignment explanation
Indices: 49680446--49680475 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49680436 ATCTCCCTAA
49680446 AGTTGCAGTGGAGC
1 AGTTGCAGTGGAGC
49680460 AGTTGCAGTGGAGC
1 AGTTGCAGTGGAGC
49680474 AG
1 AG
49680476 ATTGAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.43, T:0.20
Consensus pattern (14 bp):
AGTTGCAGTGGAGC
Found at i:49681139 original size:21 final size:21
Alignment explanation
Indices: 49681113--49681160 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
49681103 TGATACTTTC
49681113 ATTTTATTTCAT-TTTTGTTTT
1 ATTTTATTTCATATTTT-TTTT
*
49681134 ATTTTATTTTATCATTTTTTTT
1 ATTTTATTTCAT-ATTTTTTTT
49681156 ATTTT
1 ATTTT
49681161 TCATTTCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 9 0.38
23 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (21 bp):
ATTTTATTTCATATTTTTTTT
Found at i:49681157 original size:17 final size:17
Alignment explanation
Indices: 49681109--49681166 Score: 75
Period size: 16 Copynumber: 3.5 Consensus size: 17
49681099 AAGGTGATAC
*
49681109 TTTCATTTTATTTCATT
1 TTTCATTTTATTTTATT
*
49681126 TTT-GTTTTATTTTATT
1 TTTCATTTTATTTTATT
49681142 TTATCATTTT-TTTTATT
1 TT-TCATTTTATTTTATT
49681159 TTTCATTT
1 TTTCATTT
49681167 CGAAACAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 19 0.53
17 13 0.36
18 4 0.11
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTCATTTTATTTTATT
Found at i:49684787 original size:36 final size:36
Alignment explanation
Indices: 49684577--49684780 Score: 144
Period size: 36 Copynumber: 5.6 Consensus size: 36
49684567 CTGTGCCAAA
* * * *
49684577 GTTTTGCGCCCAGCGCTAGTTGAATAAACCGACGAT
1 GTTTTGTGCCCAGCACTAGTCGGATAAACCGACGAT
* * * * *
49684613 AG--GTGTGCCTC-GCACTAGCCAGATAATCCGATGAT
1 -GTTTTGTGCC-CAGCACTAGTCGGATAAACCGACGAT
* * * *
49684648 GTTTTGCGCCTAGCACTAGTCGGATAAATCGATGAT
1 GTTTTGTGCCCAGCACTAGTCGGATAAACCGACGAT
* *
49684684 ATCAATTGTGTGCCCAGCACTAGTTGGATAAACCGACGAT
1 GT---TT-TGTGCCCAGCACTAGTCGGATAAACCGACGAT
** * * *
49684724 GTTTTGCACCCATCATTAGTCGGATAAATCGACGAT
1 GTTTTGTGCCCAGCACTAGTCGGATAAACCGACGAT
*
49684760 GTTTTGTGCCCAGCGCTAGTC
1 GTTTTGTGCCCAGCACTAGTC
49684781 AAATAAAACC
Statistics
Matches: 125, Mismatches: 34, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
34 1 0.01
35 22 0.18
36 69 0.55
37 3 0.02
39 2 0.02
40 28 0.22
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (36 bp):
GTTTTGTGCCCAGCACTAGTCGGATAAACCGACGAT
Found at i:49690090 original size:18 final size:17
Alignment explanation
Indices: 49690067--49690101 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49690057 GAATCGATTT
49690067 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
49690085 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
49690102 ACCCTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:49690942 original size:18 final size:17
Alignment explanation
Indices: 49690911--49690945 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49690901 GATCTAGGGT
49690911 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
49690928 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
49690946 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:49697679 original size:24 final size:24
Alignment explanation
Indices: 49697652--49697709 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
49697642 TTTTACTATG
*
49697652 AGAAACAAAAGAGATAAAAAGGAT
1 AGAAACAAAAGAGAGAAAAAGGAT
49697676 AGAAACAAAAGAGAGAAAAAGGAT
1 AGAAACAAAAGAGAGAAAAAGGAT
*
49697700 AAAAACAAAA
1 AGAAACAAAA
49697710 AGCATCTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.71, C:0.05, G:0.19, T:0.05
Consensus pattern (24 bp):
AGAAACAAAAGAGAGAAAAAGGAT
Found at i:49708437 original size:30 final size:30
Alignment explanation
Indices: 49708403--49708465 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
49708393 ACTTATTTTA
*
49708403 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
49708433 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
49708463 TTG
1 TTG
49708466 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:49708583 original size:17 final size:17
Alignment explanation
Indices: 49708546--49708584 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
49708536 GGGAAATATT
*
49708546 TATTTTGATGTTTTTAG
1 TATTTTGATGTTTGTAG
49708563 TATTTTGATGTATTGTA-
1 TATTTTGATGT-TTGTAG
49708580 TATTT
1 TATTT
49708585 AAAAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (17 bp):
TATTTTGATGTTTGTAG
Found at i:49710735 original size:20 final size:21
Alignment explanation
Indices: 49710712--49710758 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
49710702 CTCATATTAG
* *
49710712 ATATTAACATAGCATAT-AAA
1 ATATTAACATAACAAATAAAA
* *
49710732 ATATAAACCTAACAAATAAAA
1 ATATTAACATAACAAATAAAA
49710753 ATATTA
1 ATATTA
49710759 CAAGTATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (21 bp):
ATATTAACATAACAAATAAAA
Found at i:49711490 original size:19 final size:19
Alignment explanation
Indices: 49711463--49711501 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
49711453 AAAATCATTC
*
49711463 TAGTCTTTTATTTGATTTT
1 TAGTCTTTTATTTAATTTT
* *
49711482 TAGTTTTTTTTTTAATTTT
1 TAGTCTTTTATTTAATTTT
49711501 T
1 T
49711502 TAATTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (19 bp):
TAGTCTTTTATTTAATTTT
Found at i:49716066 original size:27 final size:25
Alignment explanation
Indices: 49716024--49716089 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 25
49716014 TTTATTTCCC
*
49716024 TTTTCTTTTTTTATTTATTTGTCATT
1 TTTTCTTTTTCTATTTATTTGTC-TT
* *
49716050 TTTTCGTTTTTCTATTTGTTTTTCTT
1 TTTTC-TTTTTCTATTTATTTGTCTT
49716076 TATTTCCTTTTTCT
1 T-TTT-CTTTTTCT
49716090 GTTTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 8 0.24
27 25 0.74
28 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.05, T:0.76
Consensus pattern (25 bp):
TTTTCTTTTTCTATTTATTTGTCTT
Found at i:49716113 original size:34 final size:34
Alignment explanation
Indices: 49716049--49716113 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
49716039 TATTTGTCAT
*
49716049 TTTTTCGTTTTTCTATTTGTTTTTCTTTATTTCC
1 TTTTTCGTTTTTCTATTTGTTTTTCATTATTTCC
49716083 TTTTTCTGTTTTT-TATTTGTTTATT-ATTATT
1 TTTTTC-GTTTTTCTATTTGTTT-TTCATTATT
49716114 ATTTACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (34 bp):
TTTTTCGTTTTTCTATTTGTTTTTCATTATTTCC
Found at i:49716973 original size:135 final size:136
Alignment explanation
Indices: 49716731--49716997 Score: 437
Period size: 135 Copynumber: 2.0 Consensus size: 136
49716721 CAAGCAGGAT
* *
49716731 GCTTTATCAGAAGAATTTCTGAAATTGCTCCCACGTGAACGCGCTTTTGCTACAGTAGGTCCTGA
1 GCTTTATCAGAAGAATTTATGAAATCGCTCCCACGTGAACGCGCTTTTGCTACAGTAGGTCCTGA
*
49716796 AAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGCAT-AAAAACGCTTCAAGCAGGATGCTTT
66 AAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGCATAAAAAACGCTTCAAGCAGCATGCTTT
49716860 ATGAGA
131 ATGAGA
* ** * *
49716866 GCTTTATCAGAAGAATTTATTAAATCGCTCCCACGTGGGCGCGTTTTTGCTACAGTAGGTCTTGA
1 GCTTTATCAGAAGAATTTATGAAATCGCTCCCACGTGAACGCGCTTTTGCTACAGTAGGTCCTGA
* *
49716931 AAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGCATGCTTT
66 AAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGCATAAAAAACGCTTCAAGCAGCATGCTTT
49716996 AT
131 AT
49716998 TAGAAGAATT
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
135 95 0.79
136 26 0.21
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (136 bp):
GCTTTATCAGAAGAATTTATGAAATCGCTCCCACGTGAACGCGCTTTTGCTACAGTAGGTCCTGA
AAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGCATAAAAAACGCTTCAAGCAGCATGCTTT
ATGAGA
Found at i:49718338 original size:51 final size:51
Alignment explanation
Indices: 49718277--49718376 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
49718267 AAATAATTAA
49718277 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* *
49718328 AAATATGGATTTCAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
49718377 GGAAATTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:49718373 original size:11 final size:11
Alignment explanation
Indices: 49718357--49718387 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
49718347 ATTTAGAAGG
49718357 AAATTGAGAGC
1 AAATTGAGAGC
*
49718368 AAATTGAGAGG
1 AAATTGAGAGC
49718379 AAATTGAGA
1 AAATTGAGA
49718388 AAATAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:49718379 original size:22 final size:22
Alignment explanation
Indices: 49718341--49718391 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
49718331 TATGGATTTC
*
49718341 AGAGAAATTTAGAAGGAAATTG
1 AGAGAAATTGAGAAGGAAATTG
49718363 AGAGCAAATTGAG-AGGAAATTG
1 AGAG-AAATTGAGAAGGAAATTG
49718385 AGA-AAAT
1 AGAGAAAT
49718392 AATTGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.27, T:0.20
Consensus pattern (22 bp):
AGAGAAATTGAGAAGGAAATTG
Found at i:49725986 original size:2 final size:2
Alignment explanation
Indices: 49725979--49726018 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
49725969 CATTTATAAG
49725979 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
49726019 ATCATATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49726845 original size:40 final size:40
Alignment explanation
Indices: 49726729--49726829 Score: 193
Period size: 40 Copynumber: 2.5 Consensus size: 40
49726719 AATTTCAGAA
49726729 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
49726769 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
*
49726809 CACCAGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
49726830 GTACAGAACC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
Found at i:49734309 original size:47 final size:47
Alignment explanation
Indices: 49734257--49734367 Score: 213
Period size: 47 Copynumber: 2.4 Consensus size: 47
49734247 ACTGTTATAA
*
49734257 TTGTGTATAGTGTAGTCATCTTGCATGTAGTAAATGCTTTGTTCTAC
1 TTGTGTACAGTGTAGTCATCTTGCATGTAGTAAATGCTTTGTTCTAC
49734304 TTGTGTACAGTGTAGTCATCTTGCATGTAGTAAATGCTTTGTTCTAC
1 TTGTGTACAGTGTAGTCATCTTGCATGTAGTAAATGCTTTGTTCTAC
49734351 TTGTGTACAGTGTAGTC
1 TTGTGTACAGTGTAGTC
49734368 GTCTAATTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.43
Consensus pattern (47 bp):
TTGTGTACAGTGTAGTCATCTTGCATGTAGTAAATGCTTTGTTCTAC
Found at i:49747759 original size:22 final size:22
Alignment explanation
Indices: 49747722--49747804 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
49747712 ACTAATAGAG
* *
49747722 CAATAAGCATCGAAGTGCAAAT
1 CAATAAGCACCGAAGTGCAAAA
* *
49747744 CACTAAGCACCAAAGTGCAAAA
1 CAATAAGCACCGAAGTGCAAAA
* *
49747766 CAATAGGCACCGAAGTGCAGAA
1 CAATAAGCACCGAAGTGCAAAA
*
49747788 CGATAAGCACCGAAGTG
1 CAATAAGCACCGAAGTG
49747805 TGAGACAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (22 bp):
CAATAAGCACCGAAGTGCAAAA
Found at i:49748356 original size:19 final size:19
Alignment explanation
Indices: 49748320--49748358 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
49748310 GACTACAATA
49748320 TTCATATATTCTTATATTT
1 TTCATATATTCTTATATTT
49748339 TTCACTATATTCTT-TATTT
1 TTCA-TATATTCTTATATTT
49748358 T
1 T
49748359 CCAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCATATATTCTTATATTT
Found at i:49751077 original size:15 final size:16
Alignment explanation
Indices: 49751057--49751098 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
49751047 TTATGTACTC
49751057 TTATTATTATTATT-T
1 TTATTATTATTATTGT
*
49751072 TTATTATTATTGTTGT
1 TTATTATTATTATTGT
49751088 TT-TTATTATTA
1 TTATTATTATTA
49751099 ATATTGCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (16 bp):
TTATTATTATTATTGT
Found at i:49751080 original size:18 final size:18
Alignment explanation
Indices: 49751057--49751103 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
49751047 TTATGTACTC
49751057 TTATTATTATTATTTTTA
1 TTATTATTATTATTTTTA
* *
49751075 TTATTATTGTTGTTTTTA
1 TTATTATTATTATTTTTA
*
49751093 TTATTAATATT
1 TTATTATTATT
49751104 GCCACGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTATTATTATTTTTA
Found at i:49756653 original size:30 final size:30
Alignment explanation
Indices: 49756591--49756667 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
49756581 TAAAATTTTA
* ** **
49756591 AAAAGTACATGGACTGAAATTGACCAGTTT
1 AAAAGTACATGGACTAAAACAGACCAAATT
*
49756621 AAAAGTACATGGACTAAAACAGATCAAATT
1 AAAAGTACATGGACTAAAACAGACCAAATT
* *
49756651 AAAA-TATAAGGACTAAA
1 AAAAGTACATGGACTAAA
49756668 CCCACAAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.22
Consensus pattern (30 bp):
AAAAGTACATGGACTAAAACAGACCAAATT
Found at i:49757101 original size:8 final size:8
Alignment explanation
Indices: 49757090--49757116 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
49757080 TAATAAAAAA
49757090 TTATAATT
1 TTATAATT
49757098 TTATAATT
1 TTATAATT
49757106 TTATAATT
1 TTATAATT
49757114 TTA
1 TTA
49757117 ATTGATTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATAATT
Found at i:49757156 original size:19 final size:18
Alignment explanation
Indices: 49757101--49757182 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 18
49757091 TATAATTTTA
49757101 TAATTTTATAATTTT-AAT
1 TAATTTTA-AATTTTAAAT
*
49757119 TGATTTCCTATATATTTTATAAT
1 TAATTT--TA-A-ATTTTA-AAT
*
49757142 TAATTTTAAATTTTAAAAA
1 TAATTTTAAATTTT-AAAT
*
49757161 TAATTTTAATTATTTAAAT
1 TAATTTTAAAT-TTTAAAT
49757180 TAA
1 TAA
49757183 ATCTAAGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 5 0.10
19 23 0.44
20 9 0.17
21 7 0.13
23 8 0.15
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (18 bp):
TAATTTTAAATTTTAAAT
Found at i:49764154 original size:18 final size:19
Alignment explanation
Indices: 49764133--49764170 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
49764123 TTTAAAAAAA
49764133 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
49764151 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
49764170 T
1 T
49764171 TTGAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:49764180 original size:19 final size:19
Alignment explanation
Indices: 49764136--49764180 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
49764126 AAAAAAATAT
49764136 AAATTTTGGAATTTTTATA
1 AAATTTTGGAATTTTTATA
*
49764155 AATATTTT-GAATTTTTTTGA
1 AA-ATTTTGGAATTTTTAT-A
49764175 AAATTT
1 AAATTT
49764181 GAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (19 bp):
AAATTTTGGAATTTTTATA
Found at i:49766141 original size:2 final size:2
Alignment explanation
Indices: 49766091--49766133 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
49766081 ATCTACTAAT
49766091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
49766133 T
1 T
49766134 TCATATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49775040 original size:15 final size:15
Alignment explanation
Indices: 49775020--49775049 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49775010 TGATAGTATT
49775020 TACAGTCTTAAACTC
1 TACAGTCTTAAACTC
49775035 TACAGTCTTAAACTC
1 TACAGTCTTAAACTC
49775050 ACATACTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
TACAGTCTTAAACTC
Found at i:49776458 original size:5 final size:5
Alignment explanation
Indices: 49776450--49776475 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49776440 GAGATGGAAT
49776450 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
49776476 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:49776475 original size:26 final size:26
Alignment explanation
Indices: 49776424--49776475 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
49776414 TGAAGTTTTC
* * *
49776424 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
49776450 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
49776476 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:49780728 original size:29 final size:29
Alignment explanation
Indices: 49780696--49780761 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
49780686 TGATTGTTTT
49780696 TTTTTGTACGTATTATATCTGACTTTCAA
1 TTTTTGTACGTATTATATCTGACTTTCAA
* * * *
49780725 TTTTTAATTCGTATTATATCTGACTTTTAT
1 TTTTT-GTACGTATTATATCTGACTTTCAA
49780755 TTTTTGT
1 TTTTTGT
49780762 TATTGTTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (29 bp):
TTTTTGTACGTATTATATCTGACTTTCAA
Found at i:49780861 original size:11 final size:10
Alignment explanation
Indices: 49780834--49781018 Score: 54
Period size: 10 Copynumber: 18.0 Consensus size: 10
49780824 GGTATGTTTA
49780834 TTATGTATGT
1 TTATGTATGT
*
49780844 TTCTGTACTGT
1 TTATGTA-TGT
49780855 TTATGTATG-
1 TTATGTATGT
49780864 -TATGTATG-
1 TTATGTATGT
49780872 TTATGT-T-T
1 TTATGTATGT
*
49780880 TTAAACAGTTATGT
1 TT--A-TG-TATGT
*
49780894 ATAT-TATG-
1 TTATGTATGT
49780902 -TATGTTATGT
1 TTATG-TATGT
*
49780912 TTAATGTTAAGT
1 TT-ATG-TATGT
*
49780924 TT-TGTATATT
1 TTATGTAT-GT
49780934 TGTATGTATG-
1 T-TATGTATGT
49780944 TTATGTACTG-
1 TTATGTA-TGT
49780954 TTATGTATGT
1 TTATGTATGT
49780964 ATGTATGTTATGT
1 -T-TATG-TATGT
49780977 TTACTGTTATGT
1 TTA-TG-TATGT
* *
49780989 TTGTATAT-T
1 TTATGTATGT
49780998 TGTATGTATG-
1 T-TATGTATGT
49781008 TTATGTTATGT
1 TTATG-TATGT
49781019 ACTGTCATGT
Statistics
Matches: 135, Mismatches: 13, Indels: 53
0.67 0.06 0.26
Matches are distributed among these distances:
7 3 0.02
8 11 0.08
9 29 0.21
10 36 0.27
11 16 0.12
12 32 0.24
13 6 0.04
14 2 0.01
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (10 bp):
TTATGTATGT
Found at i:49780869 original size:8 final size:9
Alignment explanation
Indices: 49780834--49781030 Score: 96
Period size: 8 Copynumber: 21.9 Consensus size: 9
49780824 GGTATGTTTA
49780834 TTATGTATG
1 TTATGTATG
*
49780843 TTTCTGTACTG
1 -TTATGTA-TG
49780854 TTTATGTATG
1 -TTATGTATG
49780864 -TATGTATG
1 TTATGTATG
*
49780872 TTATGT-TT
1 TTATGTATG
***
49780880 TTAAACA-G
1 TTATGTATG
*
49780888 TTATGTATA
1 TTATGTATG
49780897 TTATGTATG
1 TTATGTATG
49780906 TTATGTTTAATG
1 TTATG--T-ATG
* *
49780918 TTAAGTTTTG
1 TTATG-TATG
49780928 TATAT-T-TG
1 T-TATGTATG
49780936 -TATGTATG
1 TTATGTATG
49780944 TTATGTACTG
1 TTATGTA-TG
49780954 TTATGTATG
1 TTATGTATG
49780963 -TATGTATG
1 TTATGTATG
49780971 TTATG--T-
1 TTATGTATG
49780977 TTACTGTTATG
1 TTA-TG-TATG
*
49780988 TT-TGTATA
1 TTATGTATG
49780996 TT-TGTATG
1 TTATGTATG
49781004 -TATGTTATG
1 TTATG-TATG
49781013 TTATGTACTG
1 TTATGTA-TG
*
49781023 TCATGTAT
1 TTATGTAT
49781031 ATCCAGATGG
Statistics
Matches: 147, Mismatches: 18, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
6 6 0.04
7 5 0.03
8 40 0.27
9 40 0.27
10 33 0.22
11 16 0.11
12 7 0.05
ACGTcount: A:0.22, C:0.04, G:0.19, T:0.55
Consensus pattern (9 bp):
TTATGTATG
Found at i:49780902 original size:38 final size:35
Alignment explanation
Indices: 49780860--49781014 Score: 112
Period size: 33 Copynumber: 4.5 Consensus size: 35
49780850 ACTGTTTATG
*
49780860 TATGTATGTATGTTATGTTTTTAAACAGTTATGTATAT
1 TATGTATGTATGTTATGTTGTT--A-AGTTATGTATAT
** *
49780898 TATGTATGTTATGTT-TAATGTTAAGTTTTGTATAT
1 TATGTATG-TATGTTATGTTGTTAAGTTATGTATAT
** *
49780933 T-TGTATGTATGTTATG-TACT--GTTATGTAT-G
1 TATGTATGTATGTTATGTTGTTAAGTTATGTATAT
** *
49780963 TATGTATGTTATGTT-TACTGTTATGTT-TGTATAT
1 TATGTATG-TATGTTATGTTGTTAAGTTATGTATAT
49780997 T-TGTATGTATGTTATGTT
1 TATGTATGTATGTTATGTT
49781015 ATGTACTGTC
Statistics
Matches: 93, Mismatches: 15, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
30 1 0.01
31 15 0.16
32 14 0.15
33 21 0.23
34 11 0.12
35 12 0.13
36 1 0.01
38 12 0.13
39 6 0.06
ACGTcount: A:0.23, C:0.02, G:0.19, T:0.56
Consensus pattern (35 bp):
TATGTATGTATGTTATGTTGTTAAGTTATGTATAT
Found at i:49780912 original size:5 final size:5
Alignment explanation
Indices: 49780887--49781018 Score: 75
Period size: 5 Copynumber: 26.4 Consensus size: 5
49780877 TTTTTAAACA
* * *
49780887 GTTAT G-TAT ATTAT G-TAT GTTAT GTTTAAT GTTAA GTTTT GTATAT
1 GTTAT GTTAT GTTAT GTTAT GTTAT G-TT-AT GTTAT GTTAT GT-TAT
*
49780933 TTGTAT G-TAT GTTAT G-TACT GTTAT G-TAT G-TAT G-TAT GTTAT GTTTACT
1 GT-TAT GTTAT GTTAT GTTA-T GTTAT GTTAT GTTAT GTTAT GTTAT G-TTA-T
*
49780982 GTTAT GTT-T GTATAT TTGTAT G-TAT GTTAT GTTAT GT
1 GTTAT GTTAT GT-TAT GT-TAT GTTAT GTTAT GTTAT GT
49781019 ACTGTCATGT
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
4 32 0.32
5 41 0.41
6 23 0.23
7 5 0.05
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.57
Consensus pattern (5 bp):
GTTAT
Found at i:49780941 original size:12 final size:13
Alignment explanation
Indices: 49780926--49781019 Score: 72
Period size: 12 Copynumber: 7.3 Consensus size: 13
49780916 TGTTAAGTTT
49780926 TGTATATT-TGTA
1 TGTATATTATGTA
*
49780938 TGTATGTTATGTA
1 TGTATATTATGTA
49780951 CTGT-TATGTATGTA
1 -TGTATAT-TATGTA
*
49780965 TGTATGTTATGT-
1 TGTATATTATGTA
* *
49780977 T-TACTGTTATGTT
1 TGTA-TATTATGTA
49780990 TGTATATT-TGTA
1 TGTATATTATGTA
*
49781002 TGTATGTTATGTTA
1 TGTATATTATG-TA
49781016 TGTA
1 TGTA
49781020 CTGTCATGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
11 2 0.03
12 26 0.39
13 20 0.30
14 19 0.28
ACGTcount: A:0.21, C:0.02, G:0.20, T:0.56
Consensus pattern (13 bp):
TGTATATTATGTA
Found at i:49780943 original size:4 final size:4
Alignment explanation
Indices: 49780934--49781030 Score: 63
Period size: 4 Copynumber: 22.2 Consensus size: 4
49780924 TTTGTATATT
49780934 TGTA TGTA TGTTA TGTA CTGTTA TGTA TGTA TGTA TGTTA TGT- T-TA
1 TGTA TGTA TG-TA TGTA -TG-TA TGTA TGTA TGTA TG-TA TGTA TGTA
* * *
49780980 CTGTTA TGTT TGTA TATT TGTA TGTA TGTTA TGTTA TGTA CTGTCA TGTA
1 -TG-TA TGTA TGTA TGTA TGTA TGTA TG-TA TG-TA TGTA -TGT-A TGTA
49781030 T
1 T
49781031 ATCCAGATGG
Statistics
Matches: 76, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
2 1 0.01
3 1 0.01
4 40 0.53
5 29 0.38
6 5 0.07
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.55
Consensus pattern (4 bp):
TGTA
Found at i:49780993 original size:29 final size:27
Alignment explanation
Indices: 49780932--49781028 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 27
49780922 GTTTTGTATA
49780932 TTTGTATGTATGTTATGTACTGTTATG
1 TTTGTATGTATGTTATGTACTGTTATG
*
49780959 TATGTATGTATGTTATGTTTACTGTTATG
1 TTTGTATGTATGTTATG--TACTGTTATG
* *
49780988 TTTGTATATTTG-TATGTA-TGTTATG
1 TTTGTATGTATGTTATGTACTGTTATG
49781013 TTATGTACTGTCATGT
1 TT-TGTA-TGT-ATGT
49781029 ATATCCAGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
25 9 0.16
26 6 0.10
27 18 0.31
28 6 0.10
29 19 0.33
ACGTcount: A:0.20, C:0.04, G:0.21, T:0.56
Consensus pattern (27 bp):
TTTGTATGTATGTTATGTACTGTTATG
Found at i:49781009 original size:64 final size:66
Alignment explanation
Indices: 49780887--49781013 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 66
49780877 TTTTTAAACA
*
49780887 GTTATGTATATTATGTATGTTATGTTTAATGTTAAGTTTTGTATATTTGTATGTATGTTATGTAC
1 GTTATGTATAGTATGTATGTTATGTTTAATGTTAAGTTTTGTATATTTGTATGTATGTTATGTAC
49780952 T
66 T
* *
49780953 GTTATGTAT-GTATGTATGTTATGTTTACTGTTATG-TTTGTATATTTGTATGTATGTTATGT
1 GTTATGTATAGTATGTATGTTATGTTTAATGTTAAGTTTTGTATATTTGTATGTATGTTATGT
49781014 TATGTACTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 26 0.45
65 23 0.40
66 9 0.16
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.57
Consensus pattern (66 bp):
GTTATGTATAGTATGTATGTTATGTTTAATGTTAAGTTTTGTATATTTGTATGTATGTTATGTAC
T
Found at i:49784748 original size:29 final size:32
Alignment explanation
Indices: 49784695--49784766 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
49784685 CTGTTTTCTA
*
49784695 CCTTTTCCTTTTACATATTTAAAATT-T-AGT
1 CCTTTTACTTTTACATATTTAAAATTGTAAGT
*
49784725 CCTTTTACTTTT-CATATTTCAAATTGTAAGT
1 CCTTTTACTTTTACATATTTAAAATTGTAAGT
*
49784756 -CTTTTAATTTT
1 CCTTTTACTTTT
49784767 TTTATTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 12 0.32
30 22 0.59
31 3 0.08
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (32 bp):
CCTTTTACTTTTACATATTTAAAATTGTAAGT
Found at i:49785673 original size:23 final size:21
Alignment explanation
Indices: 49785631--49785689 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
49785621 TAAATCTTTG
*
49785631 TTATATAGATTATTATT--TA
1 TTATATAGAGTATTATTAATA
49785650 TCTATATAGAGTATTATT-A-A
1 T-TATATAGAGTATTATTAATA
49785670 TTATATAGAGTATTATTAAT
1 TTATATAGAGTATTATTAAT
49785690 CCATAGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (21 bp):
TTATATAGAGTATTATTAATA
Found at i:49785676 original size:19 final size:19
Alignment explanation
Indices: 49785631--49785689 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
49785621 TAAATCTTTG
* *
49785631 TTATATAGATTATTATTTA
1 TTATATAGAGTATTATTAA
49785650 TCTATATAGAGTATTATTAA
1 T-TATATAGAGTATTATTAA
49785670 TTATATAGAGTATTATTAA
1 TTATATAGAGTATTATTAA
49785689 T
1 T
49785690 CCATAGATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (19 bp):
TTATATAGAGTATTATTAA
Found at i:49793636 original size:14 final size:15
Alignment explanation
Indices: 49793619--49793651 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49793609 CAAAAAAACT
49793619 AGAAAGAAAAGA-AA
1 AGAAAGAAAAGAGAA
49793633 AGAAAGAAAAGAGAA
1 AGAAAGAAAAGAGAA
49793648 AGAA
1 AGAA
49793652 GAACGCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAAGAGAA
Found at i:49793963 original size:2 final size:2
Alignment explanation
Indices: 49793956--49793992 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49793946 TGTTTAAATG
49793956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49793993 GAGAATTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49796110 original size:2 final size:2
Alignment explanation
Indices: 49796103--49796140 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49796093 TTGAAATTGA
49796103 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
49796141 GTATTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49801702 original size:43 final size:41
Alignment explanation
Indices: 49801593--49801745 Score: 200
Period size: 43 Copynumber: 3.7 Consensus size: 41
49801583 CGCTAACGAC
* *
49801593 AACGTCGCTAAAGGTCATGTTCTTTAGCGGCGCTT-AGAAA
1 AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAA
* *
49801633 AACGCCGCTAAAGATCATGTTCTTTAGCGGTGCTTAAAAAAA
1 AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AAGAAA
* * *
49801675 AGACGACGCTAAAGATCATGTTTTTTAGCGGCACTTGAAGAAA
1 A-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-AAGAAA
*
49801718 AATGCCGCTAAAGATCATGTTCTTTAGC
1 AACGCCGCTAAAGATCATGTTCTTTAGC
49801746 AACAAATAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 32 0.33
42 29 0.30
43 36 0.37
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (41 bp):
AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAA
Found at i:49801756 original size:85 final size:83
Alignment explanation
Indices: 49801598--49801756 Score: 210
Period size: 85 Copynumber: 1.9 Consensus size: 83
49801588 ACGACAACGT
* * **
49801598 CGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAACGCCGCTAAAGATCATGTTCTTTAGCGG
1 CGCTAAAGATCATGTTCTTTAGCGGCACTTAGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAA
****
49801663 TGCTTAAAAAAAAGACGA
66 CAAATAAAAAAAAGACGA
* *
49801681 CGCTAAAGATCATGTTTTTTAGCGGCACTTGAAGAAAAATGCCGCTAAAGATCATGTTCTTTAGC
1 CGCTAAAGATCATGTTCTTTAGCGGCACTT--AGAAAAACGCCGCTAAAGATCATGTTCTTTAGC
49801746 AACAAATAAAA
64 AACAAATAAAA
49801757 TTTTTGCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 27 0.42
85 37 0.58
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (83 bp):
CGCTAAAGATCATGTTCTTTAGCGGCACTTAGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAA
CAAATAAAAAAAAGACGA
Found at i:49802148 original size:21 final size:21
Alignment explanation
Indices: 49802122--49802186 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
49802112 GAACATCTAT
49802122 TTCTCTCGCTGCAGCCTCTGC
1 TTCTCTCGCTGCAGCCTCTGC
*
49802143 TTCTCTCGCTGCAGCCTCTAC
1 TTCTCTCGCTGCAGCCTCTGC
* *
49802164 TTCCCTCGCTGCCGCCTCTGC
1 TTCTCTCGCTGCAGCCTCTGC
49802185 TT
1 TT
49802187 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.05, C:0.45, G:0.17, T:0.34
Consensus pattern (21 bp):
TTCTCTCGCTGCAGCCTCTGC
Found at i:49803813 original size:9 final size:9
Alignment explanation
Indices: 49803802--49804163 Score: 225
Period size: 9 Copynumber: 40.3 Consensus size: 9
49803792 ACAGCACATA
*
49803802 TAAGTTATA
1 TAAGTTATG
49803811 TAAGTTATG
1 TAAGTTATG
*
49803820 TAAGTTATA
1 TAAGTTATG
*
49803829 TAAGCTATG
1 TAAGTTATG
49803838 TAAGTTATTATG
1 TAAG---TTATG
*
49803850 TAAGTTAAG
1 TAAGTTATG
*
49803859 ATATAATATATG
1 -TA-AGT-TATG
49803871 TAAGTTATG
1 TAAGTTATG
*
49803880 T-A-TTAAG
1 TAAGTTATG
*
49803887 TAAATTATG
1 TAAGTTATG
49803896 TAAGTTATG
1 TAAGTTATG
*
49803905 T-A-TTAAG
1 TAAGTTATG
**
49803912 TAAAATATG
1 TAAGTTATG
49803921 TAAGTTATG
1 TAAGTTATG
* *
49803930 TATATATTATA
1 TA-A-GTTATG
* *
49803941 AAAGATATG
1 TAAGTTATG
49803950 TAAGTTATG
1 TAAGTTATG
49803959 T-A-TTATG
1 TAAGTTATG
*
49803966 TAAGTTATA
1 TAAGTTATG
49803975 TAAGTTATG
1 TAAGTTATG
*
49803984 TAAGTTATA
1 TAAGTTATG
*
49803993 TAAGCTATG
1 TAAGTTATG
49804002 TAAGTTATTATG
1 TAAG---TTATG
*
49804014 TAAGTTAAG
1 TAAGTTATG
*
49804023 ATATAATATATG
1 -TA-AGT-TATG
* *
49804035 T-TGATTATA
1 TAAG-TTATG
*
49804044 T-A-TTAAG
1 TAAGTTATG
*
49804051 TAAATTATG
1 TAAGTTATG
49804060 TAAGTTATG
1 TAAGTTATG
49804069 T-A-TTATG
1 TAAGTTATG
49804076 TAAGTTATG
1 TAAGTTATG
* *
49804085 T-ATTTATT
1 TAAGTTATG
49804093 TAAGTTATG
1 TAAGTTATG
49804102 T-A-TTATG
1 TAAGTTATG
*
49804109 TAAGTTATA
1 TAAGTTATG
49804118 TAAGTTATG
1 TAAGTTATG
*
49804127 TAGGTTATG
1 TAAGTTATG
49804136 T-A-TTATG
1 TAAGTTATG
*
49804143 TAGGTTATG
1 TAAGTTATG
49804152 TAAGTTATG
1 TAAGTTATG
49804161 TAA
1 TAA
49804164 TGTGTCAATA
Statistics
Matches: 271, Mismatches: 52, Indels: 60
0.71 0.14 0.16
Matches are distributed among these distances:
7 38 0.14
8 17 0.06
9 173 0.64
10 9 0.03
11 12 0.04
12 22 0.08
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:49803909 original size:16 final size:16
Alignment explanation
Indices: 49803867--49804163 Score: 158
Period size: 16 Copynumber: 18.4 Consensus size: 16
49803857 AGATATAATA
49803867 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
* *
49803883 TAAGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
49803901 TATGT-A-TTAAGTAAAA
1 TATGTAAGTTATGT--AT
49803917 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
* *
49803933 ATAT-T-A-TAAAAG-A-
1 -TATGTAAGT-TATGTAT
49803946 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
49803962 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
* *
49803980 TATGTAAGTTATATAAGC
1 TATGTAAGTTATGT-A-T
49803998 TATGTAAG---T-TAT
1 TATGTAAGTTATGTAT
*
49804010 TATGTAAGTTAAGATAT
1 TATGTAAGTTATG-TAT
* * *
49804027 AATATATGTTGAT-TAT
1 TATGTAAGTT-ATGTAT
*
49804043 ATAT-TAAG-TA--AAT
1 -TATGTAAGTTATGTAT
49804056 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
49804072 TATGTAAGTTATGTATT
1 TATGTAAGTTATGTA-T
*
49804089 TATTTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
49804105 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
*
49804123 TATGTAGGTTATGTAT
1 TATGTAAGTTATGTAT
*
49804139 TATGTAGGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
49804157 TATGTAA
1 TATGTAA
49804164 TGTGTCAATA
Statistics
Matches: 222, Mismatches: 29, Indels: 58
0.72 0.09 0.19
Matches are distributed among these distances:
12 14 0.06
13 8 0.04
14 9 0.04
15 7 0.03
16 88 0.40
17 39 0.18
18 57 0.26
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:49804121 original size:25 final size:27
Alignment explanation
Indices: 49803802--49804163 Score: 225
Period size: 25 Copynumber: 13.4 Consensus size: 27
49803792 ACAGCACATA
* *
49803802 TAAGTTATATAAGTTATGTAAGTTATA
1 TAAGTTATGTAAGTTATGTAAGTTATG
* *
49803829 TAAGCTATGTAAGTTATTATGTAAGTTAAG
1 TAAGTTATGTAAG---TTATGTAAGTTATG
* *
49803859 ATATAATATATGTAAGTTATGT-A-TTAAG
1 -TA-AGT-TATGTAAGTTATGTAAGTTATG
* *
49803887 TAAATTATGTAAGTTATGT-A-TTAAG
1 TAAGTTATGTAAGTTATGTAAGTTATG
** * *
49803912 TAAAATATGTAAGTTATGTATATATTATA
1 TAAGTTATGTAAGTTATGTA-A-GTTATG
* *
49803941 AAAGATATGTAAGTTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGTAAGTTATG
* *
49803966 TAAGTTATATAAGTTATGTAAGTTATA
1 TAAGTTATGTAAGTTATGTAAGTTATG
* *
49803993 TAAGCTATGTAAGTTATTATGTAAGTTAAG
1 TAAGTTATGTAAG---TTATGTAAGTTATG
* * * *
49804023 ATATAATATATGT-TGATTATAT-A-TTAAG
1 -TA-AGT-TATGTAAG-TTATGTAAGTTATG
*
49804051 TAAATTATGTAAGTTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGTAAGTTATG
* *
49804076 TAAGTTATGT-ATTTATTTAAGTTATG
1 TAAGTTATGTAAGTTATGTAAGTTATG
*
49804102 T-A-TTATGTAAGTTATATAAGTTATG
1 TAAGTTATGTAAGTTATGTAAGTTATG
* *
49804127 TAGGTTATGT-A-TTATGTAGGTTATG
1 TAAGTTATGTAAGTTATGTAAGTTATG
49804152 TAAGTTATGTAA
1 TAAGTTATGTAA
49804164 TGTGTCAATA
Statistics
Matches: 274, Mismatches: 36, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
24 12 0.04
25 120 0.44
26 16 0.06
27 38 0.14
28 10 0.04
29 22 0.08
30 36 0.13
31 4 0.01
32 3 0.01
33 13 0.05
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.45
Consensus pattern (27 bp):
TAAGTTATGTAAGTTATGTAAGTTATG
Found at i:49804208 original size:19 final size:19
Alignment explanation
Indices: 49804186--49804236 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
49804176 AAAAAAATTA
*
49804186 ATATATAAAT-TTTAAA-T
1 ATATATAAATATTAAAACT
*
49804203 ATATATATATATTAAAACT
1 ATATATAAATATTAAAACT
49804222 ATATATAAATATTAA
1 ATATATAAATATTAA
49804237 TAAGTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.31
18 5 0.17
19 15 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATATAAATATTAAAACT
Found at i:49806086 original size:15 final size:16
Alignment explanation
Indices: 49806057--49806089 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49806047 ATTTAACCCA
*
49806057 TTTTGATATATATATT
1 TTTTGAAATATATATT
49806073 TTTTGAAATA-ATATT
1 TTTTGAAATATATATT
49806088 TT
1 TT
49806090 ATATTTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTGAAATATATATT
Found at i:49806149 original size:15 final size:15
Alignment explanation
Indices: 49806131--49806173 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
49806121 AAATCTAACT
*
49806131 CTAAACCCTAAAATC
1 CTAAACCCTAAAACC
* *
49806146 CTAAACCATTAAACC
1 CTAAACCCTAAAACC
49806161 CTTAAACCCTAAA
1 C-TAAACCCTAAA
49806174 CTTTAACCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
CTAAACCCTAAAACC
Found at i:49806280 original size:28 final size:28
Alignment explanation
Indices: 49806236--49806316 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
49806226 AATATACCAT
*
49806236 AAACCTTAAA-TCATAAATCCTAAACCCC
1 AAACCTAAAACTC-TAAATCCTAAACCCC
**
49806264 AAACCTAAAACTCTAAA-CTCTAAACCGT
1 AAACCTAAAACTCTAAATC-CTAAACCCC
** *
49806292 AAACCCCAAACTGT-AATCCTAAACC
1 AAACCTAAAACTCTAAATCCTAAACC
49806317 ATATTTTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 10 0.23
28 32 0.73
29 2 0.05
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (28 bp):
AAACCTAAAACTCTAAATCCTAAACCCC
Found at i:49806302 original size:21 final size:20
Alignment explanation
Indices: 49806264--49806316 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
49806254 CCTAAACCCC
* *
49806264 AAACCTAAAACTCTAAACTCT
1 AAACCT-AAACCCCAAACTCT
*
49806285 AAACCGTAAACCCCAAACTGT
1 AAACC-TAAACCCCAAACTCT
*
49806306 AATCCTAAACC
1 AAACCTAAACC
49806317 ATATTTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.22
21 20 0.74
22 1 0.04
ACGTcount: A:0.45, C:0.32, G:0.04, T:0.19
Consensus pattern (20 bp):
AAACCTAAACCCCAAACTCT
Found at i:49806487 original size:20 final size:20
Alignment explanation
Indices: 49806449--49806505 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
49806439 TCTTCAATTT
49806449 CCAAACT-AAACCCTAAAACC
1 CCAAACTCAAA-CCTAAAACC
* *
49806469 CTAAACTCAAACCTTAAACC
1 CCAAACTCAAACCTAAAACC
49806489 CCAAACTCAAACTCTAA
1 CCAAACTCAAAC-CTAA
49806506 CACATAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (20 bp):
CCAAACTCAAACCTAAAACC
Found at i:49806664 original size:7 final size:7
Alignment explanation
Indices: 49806640--49806724 Score: 55
Period size: 7 Copynumber: 11.7 Consensus size: 7
49806630 GCGTTGAAAT
49806640 CCTAA-C
1 CCTAACC
49806646 CCTAACCC
1 CCTAA-CC
49806654 CCTAACC
1 CCTAACC
**
49806661 CCTAAAG
1 CCTAACC
*
49806668 CATAACC
1 CCTAACC
49806675 CCTAACC
1 CCTAACC
*
49806682 CATAAATCC
1 CCT-AA-CC
49806691 CCATAACC
1 CC-TAACC
**
49806699 CCTAAAG
1 CCTAACC
* *
49806706 CATAACA
1 CCTAACC
49806713 CCTAACC
1 CCTAACC
49806720 CCTAA
1 CCTAA
49806725 ATCTTAAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
6 5 0.08
7 36 0.61
8 12 0.20
9 5 0.08
10 1 0.02
ACGTcount: A:0.38, C:0.45, G:0.02, T:0.15
Consensus pattern (7 bp):
CCTAACC
Found at i:49806701 original size:38 final size:37
Alignment explanation
Indices: 49806640--49806727 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 37
49806630 GCGTTGAAAT
* *
49806640 CCTAACCCT-AA-CCCCCTAACCCCTAAAGCATAACC
1 CCTAACCCTAAATCCCCATAACCCCTAAAGCATAACA
49806675 CCTAACCCATAAATCCCCATAACCCCTAAAGCATAACA
1 CCTAACCC-TAAATCCCCATAACCCCTAAAGCATAACA
49806713 CCTAACCCCTAAATC
1 CCTAA-CCCTAAATC
49806728 TTAAATCCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 8 0.17
36 1 0.02
37 2 0.04
38 33 0.70
39 3 0.06
ACGTcount: A:0.38, C:0.44, G:0.02, T:0.16
Consensus pattern (37 bp):
CCTAACCCTAAATCCCCATAACCCCTAAAGCATAACA
Found at i:49807217 original size:114 final size:114
Alignment explanation
Indices: 49806962--49807424 Score: 566
Period size: 114 Copynumber: 4.0 Consensus size: 114
49806952 TAAATTATTT
* * * * * *
49806962 TAAATCCCTGACCATTAGCGACGCTTTATTAAAAACGCCGCTAAATCCCCTGAAAGCTCCGAAAA
1 TAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCC-AAAAGCTCAGAAAA
* * *
49807027 CGGCGCCGTTGGGTTTAGGTTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
65 CGGCACCGTTGGGCTTAGG--TTTTTTAGCGGCGCTTTCCCAAAAACGCCGC
* * * *
49807079 TAAAGCCCTGAACATTAGCAGCGCTTTCTTCAAAACACCGCTAAATCCCCAAAATCTCAGAAAAC
1 TAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC
* * * * * **
49807144 GGCACCGTTGTGCTTAGGTTCTTTAGCAGCGCTTTCCCAAAAATGGCAA
66 GGCACCGTTGGGCTTAGGTTTTTTAGCGGCGCTTTCCCAAAAACGCCGC
* * * * * * *
49807193 TAAATCTCTGAGCATTAGTGGCGCTTTCCTAAAAACGCCGCTCAATCCCCAAAATCTCAGAAAAC
1 TAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC
* * * *
49807258 GGCGCCGTTGTGCTTAGGTTTTTTCGCGGCGCTTTCTCAAAAACGCCGC
66 GGCACCGTTGGGCTTAGGTTTTTTAGCGGCGCTTTCCCAAAAACGCCGC
* * *
49807307 TAAAGCCCTGAACATTAGCGGCGCTTTCTTCAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAC
1 TAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC
* * *
49807372 GACATCGTTGGGCTTAGGTTTTTTAGCGGCGCTTTCCCAAAAACGCTGC
66 GGCACCGTTGGGCTTAGGTTTTTTAGCGGCGCTTTCCCAAAAACGCCGC
49807421 TAAA
1 TAAA
49807425 TCCCCGAAAT
Statistics
Matches: 291, Mismatches: 55, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
114 221 0.76
116 27 0.09
117 43 0.15
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (114 bp):
TAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC
GGCACCGTTGGGCTTAGGTTTTTTAGCGGCGCTTTCCCAAAAACGCCGC
Found at i:49807415 original size:73 final size:73
Alignment explanation
Indices: 49807321--49807567 Score: 302
Period size: 73 Copynumber: 3.4 Consensus size: 73
49807311 GCCCTGAACA
* *
49807321 TTAGCGGCGCTTTCTTC-AAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACATCGTTGGGC
1 TTAGCGGCGCTTTC-TCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGC
49807385 TTAGGTTTT
65 TTAGGTTTT
* * * * *
49807394 TTAGCGGCGCTTTCCCAAAAACGCTGCTAAATCCCCGAAATCTCAGAAAACGATGCCGTTGGGCT
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCT
49807459 TAGGTTTT
66 TAGGTTTT
* * * * * * *
49807467 TTAGCGGCGCTTTCTCAAAAATGCCGCTAAATCCCCAAAAGCTCGGTAAATGGCGTCGTTGAGCT
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCT
*
49807532 TAGGTTCT
66 TAGGTTTT
***
49807540 TT-GCGGCGC-TTCTGGGAAACGCCGCTAA
1 TTAGCGGCGCTTTCTCAAAAACGCCGCTAA
49807568 TGATCGATCT
Statistics
Matches: 149, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
71 15 0.10
72 8 0.05
73 126 0.85
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (73 bp):
TTAGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCT
TAGGTTTT
Found at i:49815090 original size:17 final size:17
Alignment explanation
Indices: 49815055--49815101 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
49815045 AAACAAAAAT
**
49815055 AAAAAAATTT-ATTTTA
1 AAAAAAATTTAAAATTA
* *
49815071 AAAATATTTTAAAATTA
1 AAAAAAATTTAAAATTA
49815088 AAAAAAATTTAAAA
1 AAAAAAATTTAAAA
49815102 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAAAATTTAAAATTA
Found at i:49815657 original size:9 final size:9
Alignment explanation
Indices: 49815643--49815670 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49815633 TATAGTTTGA
49815643 TATTCGAAT
1 TATTCGAAT
49815652 TATTCGAAT
1 TATTCGAAT
49815661 TATTCGAAT
1 TATTCGAAT
49815670 T
1 T
49815671 CGAAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:49817999 original size:15 final size:15
Alignment explanation
Indices: 49817981--49818014 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49817971 ATGAATGTCG
*
49817981 CAATAACGAATACAA
1 CAATAACAAATACAA
*
49817996 CAATAATAAATACAA
1 CAATAACAAATACAA
49818011 CAAT
1 CAAT
49818015 GACATAGAAA
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:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:49818040 original size:13 final size:14
Alignment explanation
Indices: 49818021--49818058 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
49818011 CAATGACATA
49818021 GAAATAATATAAAC
1 GAAATAATATAAAC
49818035 -AAATAA-ATAAAC
1 GAAATAATATAAAC
49818047 GAAACTAATATA
1 GAAA-TAATATA
49818059 CATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 3 0.14
15 3 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:49818069 original size:27 final size:26
Alignment explanation
Indices: 49818021--49818073 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
49818011 CAATGACATA
*
49818021 GAAATAATATAAACAAATAAATAAAC
1 GAAATAATATAAACAAAAAAATAAAC
* *
49818047 GAAACTAATATACATAAAAAAATAAAC
1 GAAA-TAATATAAACAAAAAAATAAAC
49818074 AATGACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.19
Consensus pattern (26 bp):
GAAATAATATAAACAAAAAAATAAAC
Found at i:49818309 original size:25 final size:27
Alignment explanation
Indices: 49818281--49818335 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
49818271 ATTTATGAAA
49818281 ATAAA-GAAAA-ATATATAAAAAATAT
1 ATAAATGAAAATATATATAAAAAATAT
* * *
49818306 ATAAATTAAAATATGTATTAAAAATAT
1 ATAAATGAAAATATATATAAAAAATAT
49818333 ATA
1 ATA
49818336 TGTATTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
ATAAATGAAAATATATATAAAAAATAT
Found at i:49818489 original size:28 final size:28
Alignment explanation
Indices: 49818456--49818587 Score: 90
Period size: 28 Copynumber: 5.0 Consensus size: 28
49818446 AATAAATCTA
49818456 TACATATATATAAATTATAAAAAATAAT
1 TACATATATATAAATTATAAAAAATAAT
* *
49818484 TACATATATATAAA-AAT-AATAATAAT
1 TACATATATATAAATTATAAAAAATAAT
**
49818510 TACAT-TAT-TGAAA-T-TAATTAATAA-
1 TACATATATAT-AAATTATAAAAAATAAT
* *
49818534 -A-A-ATACATAAATTATGAAAACATTAAT
1 TACATATATATAAATTAT-AAAA-AATAAT
49818561 TACATATA-A-AAATTATTAAAAAATAAT
1 TACATATATATAAATTA-TAAAAAATAAT
49818588 AAAAATTATA
Statistics
Matches: 82, Mismatches: 9, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
22 6 0.07
23 3 0.04
24 3 0.04
25 15 0.18
26 17 0.21
27 7 0.09
28 25 0.30
29 3 0.04
30 3 0.04
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (28 bp):
TACATATATATAAATTATAAAAAATAAT
Found at i:49818495 original size:30 final size:32
Alignment explanation
Indices: 49818439--49818505 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
49818429 TGTACATATA
* *
49818439 TATAAAAAATAAATCTATACATATATATAAAT
1 TATAAAAAATAAATCTACACATATATAAAAAT
*
49818471 TATAAAAAAT-AAT-TACATATATATAAAAAT
1 TATAAAAAATAAATCTACACATATATAAAAAT
*
49818501 AATAA
1 TATAA
49818506 TAATTACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 18 0.58
31 3 0.10
32 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (32 bp):
TATAAAAAATAAATCTACACATATATAAAAAT
Found at i:49820360 original size:44 final size:43
Alignment explanation
Indices: 49820236--49820393 Score: 133
Period size: 44 Copynumber: 3.7 Consensus size: 43
49820226 TTTTGGGTAT
** * * * *
49820236 GCTCCACTGCAACTTCAGGGAGATAAGA-CCT-GATATGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGTGGCTTTAATCC
* * * * *
49820277 GCT-CTCTACAGCTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGTGGCTTTAATCC
* * *
49820320 GCTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-GTGGCTTTAATCC
* *
49820364 GCTCTACTGCAACTTCAGGGAAATAAGATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT
49820394 TGTCATCTTC
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
40 20 0.22
41 3 0.03
42 1 0.01
43 10 0.11
44 57 0.63
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGTGGCTTTAATCC
Found at i:49820892 original size:45 final size:44
Alignment explanation
Indices: 49820837--49820981 Score: 130
Period size: 45 Copynumber: 3.3 Consensus size: 44
49820827 TGTCTTCGAT
* * *
49820837 CTACTTCACTGTCAGCACAAGAAGGCAAGATCTGCTATTTTCAAC
1 CTACTCCACTG-CAGCACAGGAAGACAAGATCTGCTATTTTCAAC
* * * * * * * *
49820882 CTACTCCACTGCTGCTCAGGGAGACAAG-GCTGATATCTTCCAT
1 CTACTCCACTGCAGCACAGGAAGACAAGATCTGCTATTTTCAAC
** **
49820925 CTACTTTACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAAC
1 CTACTCCACTG-CAGCACAGGAAGACAAGATCTGCTATTTTCAAC
49820970 CTACTCCACTGC
1 CTACTCCACTGC
49820982 TGCTTAGGGA
Statistics
Matches: 73, Mismatches: 25, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
43 19 0.26
44 25 0.34
45 29 0.40
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (44 bp):
CTACTCCACTGCAGCACAGGAAGACAAGATCTGCTATTTTCAAC
Found at i:49820978 original size:88 final size:88
Alignment explanation
Indices: 49820829--49821002 Score: 267
Period size: 88 Copynumber: 2.0 Consensus size: 88
49820819 AAGACTAATG
* * * *
49820829 TCTTCGATCTACTTCACTGTCAGCACAAGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCCATCTACTTCACTGCCAACACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
49820894 TGCTCAGGGAGACAAGGCTGATA
66 TGCTCAGGGAGACAAGGCTGATA
* * *
49820917 TCTTCCATCTACTTTACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCCATCTACTTCACTGCCAACACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
49820982 TGCTTAGGGAGATAAGGCTGA
66 TGCTCAGGGAGACAAGGCTGA
49821003 AATATCACCG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (88 bp):
TCTTCCATCTACTTCACTGCCAACACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTGATA
Found at i:49833192 original size:16 final size:14
Alignment explanation
Indices: 49833164--49833211 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
49833154 ATAAAGAAAA
*
49833164 ATATATAAAAATAT
1 ATATAAAAAAATAT
49833178 ATATAAATTAAAATAT
1 ATATAAA--AAAATAT
* *
49833194 GTATTAAAAAATAT
1 ATATAAAAAAATAT
49833208 ATAT
1 ATAT
49833212 GTATTTGAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATAAAAAAATAT
Found at i:49833379 original size:28 final size:26
Alignment explanation
Indices: 49833306--49833379 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 26
49833296 TATTTACATG
**
49833306 TACATATATATATAAAAAT-AAATCTA
1 TACATATATATA-AAAAATAAAAAATA
**
49833332 TACATATATATAAATTATAAAAAATAA
1 TACATATATATAAAAAATAAAAAAT-A
49833359 TTACATATATATAAAAAATAA
1 -TACATATATATAAAAAATAA
49833380 TAATTACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.10
26 16 0.41
27 1 0.03
28 18 0.46
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (26 bp):
TACATATATATAAAAAATAAAAAATA
Found at i:49847607 original size:19 final size:20
Alignment explanation
Indices: 49847580--49847620 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49847570 TATTTATACA
*
49847580 AAATGTAATA-ATTAAGAAT
1 AAATGTAATATATTAAAAAT
*
49847599 AAATTTAATATATTAAAAAT
1 AAATGTAATATATTAAAAAT
49847619 AA
1 AA
49847621 TAGCTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATGTAATATATTAAAAAT
Found at i:49848810 original size:19 final size:17
Alignment explanation
Indices: 49848757--49848811 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 17
49848747 AATCTATTTG
*
49848757 TTTAG-AAA-TTTAGGT
1 TTTAGAAAATTTTAGAT
49848772 TTTAGAAAATTTTAGAAT
1 TTTAGAAAATTTTAG-AT
49848790 TTTATGAAAAATTTTAGAT
1 TTTA-G-AAAATTTTAGAT
49848809 TTT
1 TTT
49848812 TTGCACTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 5 0.15
18 5 0.15
19 6 0.18
20 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
TTTAGAAAATTTTAGAT
Found at i:49848899 original size:21 final size:20
Alignment explanation
Indices: 49848875--49848921 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
49848865 TAAGAAATAC
*
49848875 CATAAAATTCTTAAAATTTTT
1 CATAAAATTC-TAAAAGTTTT
**
49848896 CATAATTTTCTAAAAGTTTT
1 CATAAAATTCTAAAAGTTTT
49848916 C-TAAAA
1 CATAAAA
49848922 ACAATACAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.45
Consensus pattern (20 bp):
CATAAAATTCTAAAAGTTTT
Found at i:49860040 original size:45 final size:46
Alignment explanation
Indices: 49859986--49860086 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
49859976 TATTTCTAAT
49859986 AATTATTTGAAATATT-TCACATATAAA-AATAATGATATTTGAAAC
1 AATTATTTGAAATATTAT-ACATATAAATAATAATGATATTTGAAAC
* * * *
49860031 AATTTTTTGAAATATTATATATATAAATAATAGTGATATTTGAAAT
1 AATTATTTGAAATATTATACATATAAATAATAATGATATTTGAAAC
49860077 AATTATTTGA
1 AATTATTTGA
49860087 TATTTTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 23 0.47
46 26 0.53
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (46 bp):
AATTATTTGAAATATTATACATATAAATAATAATGATATTTGAAAC
Found at i:49860086 original size:46 final size:46
Alignment explanation
Indices: 49859965--49860086 Score: 151
Period size: 45 Copynumber: 2.7 Consensus size: 46
49859955 ATGTAGGTGA
* **
49859965 AAAT-ATATTGATATTTCTAATAATTATTTGAAATATTTCACATAT
1 AAATAATAATGATATTTGAAATAATTATTTGAAATATTTCACATAT
* * *
49860010 AAA-AATAATGATATTTGAAACAATTTTTTGAAATATTAT-ATATAT
1 AAATAATAATGATATTTGAAATAATTATTTGAAATATT-TCACATAT
*
49860055 AAATAATAGTGATATTTGAAATAATTATTTGA
1 AAATAATAATGATATTTGAAATAATTATTTGA
49860087 TATTTTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
45 39 0.60
46 26 0.40
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (46 bp):
AAATAATAATGATATTTGAAATAATTATTTGAAATATTTCACATAT
Found at i:49869761 original size:25 final size:28
Alignment explanation
Indices: 49869713--49869780 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 28
49869703 AAAATAAAAG
49869713 TTTACCAAAATATTATAACTTTTTTTTTA
1 TTTACCAAAATA-TATAACTTTTTTTTTA
49869742 TTTACCAAAATAT-T-AC-TTTTTTTTA
1 TTTACCAAAATATATAACTTTTTTTTTA
*
49869767 TTTACGAAAATATA
1 TTTACCAAAATATA
49869781 CCAAAAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 21 0.57
26 2 0.05
27 1 0.03
28 1 0.03
29 12 0.32
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTACCAAAATATATAACTTTTTTTTTA
Found at i:49870103 original size:3 final size:3
Alignment explanation
Indices: 49870095--49870131 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
49870085 TTTTAGTTAG
*
49870095 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
49870132 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:49870136 original size:3 final size:3
Alignment explanation
Indices: 49870130--49870179 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
49870120 ATTATTATTA
49870130 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
49870178 TT
1 TT
49870180 AGTATTAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:49870311 original size:44 final size:45
Alignment explanation
Indices: 49870258--49870365 Score: 184
Period size: 44 Copynumber: 2.4 Consensus size: 45
49870248 TTATTATGGT
49870258 TAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAAC
1 TAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAAC
49870303 T-GTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAAC
1 TAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAAC
49870347 TAG-TATTATTATTCTATTT
1 TAGTTATTATT-TT-TATTT
49870366 TTAGTAAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
44 51 0.85
45 4 0.07
46 5 0.08
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (45 bp):
TAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAAC
Found at i:49873373 original size:11 final size:11
Alignment explanation
Indices: 49873357--49873383 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
49873347 GCTTATGCTT
49873357 AAATTGTATCC
1 AAATTGTATCC
49873368 AAATTGTATCC
1 AAATTGTATCC
49873379 AAATT
1 AAATT
49873384 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:49877030 original size:12 final size:12
Alignment explanation
Indices: 49877015--49877069 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
49877005 ATATGTATTA
49877015 AAATATATATAT
1 AAATATATATAT
*
49877027 AAATATATATGT
1 AAATATATATAT
*
49877039 AAATATATAAAT
1 AAATATATATAT
*
49877051 ACACATATAAATAT
1 A-A-ATATATATAT
49877065 AAATA
1 AAATA
49877070 AGTTACAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.69
13 2 0.06
14 9 0.25
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (12 bp):
AAATATATATAT
Found at i:49877046 original size:20 final size:20
Alignment explanation
Indices: 49877021--49877065 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
49877011 ATTAAAATAT
* * *
49877021 ATATATAAATATATATGTAA
1 ATATATAAATACACATATAA
49877041 ATATATAAATACACATATAA
1 ATATATAAATACACATATAA
49877061 ATATA
1 ATATA
49877066 AATAAGTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATATAAATACACATATAA
Found at i:49878720 original size:13 final size:13
Alignment explanation
Indices: 49878694--49878726 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49878684 CCTGGGGTAG
*
49878694 TGGGT-TTAGGTT
1 TGGGTATTAGATT
49878706 TGGGTATTAGATT
1 TGGGTATTAGATT
49878719 TGGGTATT
1 TGGGTATT
49878727 TGGTTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.48
Consensus pattern (13 bp):
TGGGTATTAGATT
Found at i:49878733 original size:13 final size:13
Alignment explanation
Indices: 49878702--49878742 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
49878692 AGTGGGTTTA
*
49878702 GGTTTGGGTATTA
1 GGTTTGGGTATTT
*
49878715 GATTTGGGTATTT
1 GGTTTGGGTATTT
*
49878728 GGTTTGGGAATTT
1 GGTTTGGGTATTT
49878741 GG
1 GG
49878743 GTTGCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.46
Consensus pattern (13 bp):
GGTTTGGGTATTT
Found at i:49878909 original size:27 final size:26
Alignment explanation
Indices: 49878871--49879005 Score: 109
Period size: 27 Copynumber: 5.0 Consensus size: 26
49878861 TTTTTTTCCC
*
49878871 TTTTTTTCCTTCC-TTCCATCTTCTTT
1 TTTTTTTCTTTCCTTTCC-TCTTCTTT
*
49878897 TTTTTTTCTCTTCTCTTTTCCTTTTCTTT
1 TTTTTTTCT-TTC-C-TTTCCTCTTCTTT
*
49878926 CTTTTTTCTTCTCCTTTCCTCTTCTTCT
1 TTTTTTTCTT-TCCTTTCCTCTTCTT-T
*
49878954 TCTTTTTT-TTTCCTTTCCTTTTCTTT
1 T-TTTTTTCTTTCCTTTCCTCTTCTTT
49878980 CCTTCTTTTTCTTT-CTTT-CT-TTCTTT
1 --TT-TTTTTCTTTCCTTTCCTCTTCTTT
49879006 CCCTCTCCTT
Statistics
Matches: 92, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
26 15 0.16
27 31 0.34
28 16 0.17
29 26 0.28
30 4 0.04
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTTTTCTTTCCTTTCCTCTTCTTT
Found at i:49878910 original size:16 final size:16
Alignment explanation
Indices: 49878889--49878932 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
49878879 CTTCCTTCCA
49878889 TCTTCTTTTTTTTTTC
1 TCTTCTTTTTTTTTTC
*
49878905 TCTTCTCTTTTCCTTTTC
1 TCTTCT-TTTT-TTTTTC
49878923 T-TTCTTTTTT
1 TCTTCTTTTTT
49878933 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTCTTTTTTTTTTC
Found at i:49878915 original size:18 final size:17
Alignment explanation
Indices: 49878892--49878999 Score: 69
Period size: 18 Copynumber: 6.1 Consensus size: 17
49878882 CCTTCCATCT
*
49878892 TCTTTTTTTTTTCTCTTC
1 TCTTTTTCTTTTCT-TTC
*
49878910 TCTTTTCCTTTTCTTTC
1 TCTTTTTCTTTTCTTTC
*
49878927 T-TTTTTCTTCTCCTTTCC
1 TCTTTTTCTT-TTCTTT-C
*
49878945 TCTTCTTCTTCTTTT-TTTT
1 TC-T-TT-TTCTTTTCTTTC
* *
49878964 TCCTTTCCTTTTCTTTCC
1 TCTTTTTCTTTTCTTT-C
49878982 TTCTTTTTC-TTTCTTTC
1 -TCTTTTTCTTTTCTTTC
49878999 T
1 T
49879000 TTCTTTCCCT
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 14 0.20
17 15 0.21
18 21 0.30
19 8 0.11
20 4 0.06
21 3 0.04
22 5 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTC
Found at i:49878925 original size:5 final size:5
Alignment explanation
Indices: 49878891--49879005 Score: 53
Period size: 5 Copynumber: 23.2 Consensus size: 5
49878881 TCCTTCCATC
* * * *
49878891 TTCTT TT-TT TT-TT CTCTT CTCTT TTCCTT TTCTT TCTTTT TTCTT CTCCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT-CTT TTCTT T-TCTT TTCTT -TTCTT
* * * * * *
49878942 TCCTC TTCTT CTTCTT TTTTT TTCCTT TCCTT TTCTT TCCTT CT-TT TTC-T
1 TTCTT TTCTT -TTCTT TTCTT TT-CTT TTCTT TTCTT TTCTT TTCTT TTCTT
49878992 TTC-T TTC-T TTCTT T
1 TTCTT TTCTT TTCTT T
49879006 CCCTCTCCTT
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
4 22 0.26
5 43 0.50
6 21 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (5 bp):
TTCTT
Found at i:49878928 original size:4 final size:4
Alignment explanation
Indices: 49878919--49879006 Score: 55
Period size: 4 Copynumber: 22.0 Consensus size: 4
49878909 CTCTTTTCCT
49878919 TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC -TTC -TTC TTT- TTT-
1 TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC TTTC TTTC TTTC TTTC
*
49878962 TTTCC TTTCC TTTTC TTTC CTTC -TT- TTTC TTTC TTTC TTTC TTTC
1 TTT-C TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
49879007 CCTCTCCTTC
Statistics
Matches: 73, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
3 19 0.26
4 34 0.47
5 12 0.16
6 8 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:49878931 original size:10 final size:10
Alignment explanation
Indices: 49878913--49879005 Score: 53
Period size: 11 Copynumber: 8.7 Consensus size: 10
49878903 TCTCTTCTCT
*
49878913 TTTCCTTTTC
1 TTTCTTTTTC
49878923 TTTCTTTTTTC
1 TTTC-TTTTTC
* *
49878934 TTCTCCTTTCC
1 TT-TCTTTTTC
*
49878945 TCTTCTTCTTC
1 T-TTCTTTTTC
*
49878956 TTTTTTTTTCC
1 TTTCTTTTT-C
*
49878967 TTTCCTTTTC
1 TTTCTTTTTC
*
49878977 TTTCCTTCTT-
1 TTT-CTTTTTC
49878987 TTTCTTTCTTTC
1 TTTC-TT-TTTC
49878999 TTTCTTT
1 TTTCTTT
49879006 CCCTCTCCTT
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
9 1 0.02
10 20 0.32
11 34 0.55
12 7 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:49878938 original size:32 final size:32
Alignment explanation
Indices: 49878861--49879006 Score: 110
Period size: 33 Copynumber: 4.5 Consensus size: 32
49878851 AAAAATTACC
*
49878861 TTTTT-TTCCCTTT-TTTTCCTTCCTTCCATCTTCT
1 TTTTTCTTTCCTTTCTTTTCCTT-CTT-C-T-TTCT
*
49878895 TTTTTTTTTCTCTTCTCTTTTCCTT-TTCTTTCT
1 TTTTTCTTTC-CTT-TCTTTTCCTTCTTCTTTCT
*
49878928 TTTTTCTTCTCCTTTCCTCTT-CTTCTTCTTT-T
1 TTTTTCTT-TCCTTT-CTTTTCCTTCTTCTTTCT
49878960 TTTTTCCTTTCCTTT-TCTTTCCTTCTT-TTTCT
1 TTTTT-CTTTCCTTTCT-TTTCCTTCTTCTTTCT
49878992 TTCTTTCTTT-CTTTC
1 TT-TTTCTTTCCTTTC
49879007 CCTCTCCTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 28
0.75 0.03 0.22
Matches are distributed among these distances:
30 1 0.01
31 9 0.09
32 29 0.31
33 30 0.32
34 8 0.08
35 4 0.04
36 5 0.05
37 1 0.01
38 8 0.08
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.71
Consensus pattern (32 bp):
TTTTTCTTTCCTTTCTTTTCCTTCTTCTTTCT
Found at i:49879015 original size:32 final size:32
Alignment explanation
Indices: 49878875--49879017 Score: 118
Period size: 32 Copynumber: 4.4 Consensus size: 32
49878865 TTTCCCTTTT
* *
49878875 TTTCCT-TCCTTCCATC-TTCTTTTTTTTTTCTC
1 TTTCCTCTCCTT-CTTCTTTCTTTTTTCTTTC-C
* *
49878907 TTCTCTTTTCCTT-TTCTTTCTTTTTTCTTCTCC
1 TT-TCCTCTCCTTCTTCTTTCTTTTTTCTT-TCC
*
49878940 TTTCCTCTTCTTCTTCTTT-TTTTTTCCTTTCC
1 TTTCCTCTCCTTCTTCTTTCTTTTTT-CTTTCC
* *
49878972 TTTTCTTTCCTTCTT-TTTCTTTCTTTCTTT-C
1 TTTCCTCTCCTTCTTCTTTCTTT-TTTCTTTCC
49879003 TTTCCCTCTCCTTCT
1 TTT-CCTCTCCTTCT
49879018 CCCCCCCAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
31 7 0.08
32 48 0.53
33 29 0.32
34 7 0.08
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (32 bp):
TTTCCTCTCCTTCTTCTTTCTTTTTTCTTTCC
Found at i:49879183 original size:28 final size:27
Alignment explanation
Indices: 49879142--49879207 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
49879132 TTTTGGTATT
* *
49879142 TTTTGGTAATTAAAAAATAATAATAATA
1 TTTTGGTAAATAAAAAA-AAGAATAATA
* *
49879170 TTTTGGTAAATAAAAAAAGGGATAATA
1 TTTTGGTAAATAAAAAAAAGAATAATA
49879197 TTTTGGTAAAT
1 TTTTGGTAAAT
49879208 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (27 bp):
TTTTGGTAAATAAAAAAAAGAATAATA
Found at i:49881184 original size:21 final size:21
Alignment explanation
Indices: 49881137--49881185 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
49881127 AAAACTAAGT
*
49881137 TAATATATATTATAATAAAACA
1 TAATA-ATAATATAATAAAACA
* * *
49881159 AAATAATAATATAATAACATA
1 TAATAATAATATAATAAAACA
49881180 TAATAA
1 TAATAA
49881186 AACAAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATAATATAATAAAACA
Done.