Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167857.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_127, 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: 75388
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:814 original size:13 final size:13
Alignment explanation
Indices: 798--1017 Score: 130
Period size: 13 Copynumber: 17.0 Consensus size: 13
788 ACCCTACATA
798 CAAACCCTAAACC
1 CAAACCCTAAACC
*
811 CAAACCCCAAA-C
1 CAAACCCTAAACC
* * *
823 TAAACTCTAAATC
1 CAAACCCTAAACC
*
836 AAAACCCTAAACC
1 CAAACCCTAAACC
*
849 CTAAACCCTAAATC
1 C-AAACCCTAAACC
*
863 CAAACCCTATATCC
1 CAAACCCTA-AACC
877 C-AACCCTAAACC
1 CAAACCCTAAACC
* *
889 CTAA-CCTTAACC
1 CAAACCCTAAACC
*
901 CTAAA-CCTAAAGC
1 C-AAACCCTAAACC
*
914 CAAATCCTAAATCC
1 CAAACCCTAAA-CC
*
928 TAAACCC-AAATCC
1 CAAACCCTAAA-CC
* * *
941 TAAAACAT-AACC
1 CAAACCCTAAACC
*
953 CTAAACCCTTAACC
1 C-AAACCCTAAACC
* * *
967 C-AATCTTAAAAC
1 CAAACCCTAAACC
*
979 CTAACCCTAAACC
1 CAAACCCTAAACC
**
992 CAAACCCTAAAAT
1 CAAACCCTAAACC
*
1005 CTAACCCTAAACC
1 CAAACCCTAAACC
1018 TTAATTTAAA
Statistics
Matches: 159, Mismatches: 37, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
12 34 0.21
13 99 0.62
14 26 0.16
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (13 bp):
CAAACCCTAAACC
Found at i:821 original size:20 final size:19
Alignment explanation
Indices: 798--1002 Score: 107
Period size: 20 Copynumber: 10.6 Consensus size: 19
788 ACCCTACATA
798 CAAACCCTAAACCCAAACCC
1 CAAACCCTAAACCCAAA-CC
* *
818 CAAA--CTAAACTCTAAATC
1 CAAACCCTAAAC-CCAAACC
*
836 AAAACCCTAAACCCTAAACC
1 CAAACCCTAAACCC-AAACC
* *
856 CTAAATCC-AAACCCTATATCC
1 C-AAACCCTAAACCC-A-AACC
*
877 C-AACCCTAAACCCTAACC
1 CAAACCCTAAACCCAAACC
** * *
895 TTAACCCTAAACCTAAAGC
1 CAAACCCTAAACCCAAACC
* *
914 CAAATCCTAAATCCTAAACC
1 CAAACCCTAAA-CCCAAACC
* *
934 CAAATCCTAAA-ACATAACC
1 CAAACCCTAAACCCA-AACC
* * *
953 CTAAACCCTTAACCCAATCT
1 C-AAACCCTAAACCCAAACC
* *
973 TAAAACCT-AACCCTAAACC
1 CAAACCCTAAACCC-AAACC
992 CAAACCCTAAA
1 CAAACCCTAAA
1003 ATCTAACCCT
Statistics
Matches: 139, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
18 19 0.14
19 51 0.37
20 58 0.42
21 11 0.08
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (19 bp):
CAAACCCTAAACCCAAACC
Found at i:960 original size:78 final size:77
Alignment explanation
Indices: 798--1015 Score: 194
Period size: 78 Copynumber: 2.8 Consensus size: 77
788 ACCCTACATA
** * * *
798 CAAACCCTAAACCCAAACCCCAAACTAAACTCTAAATCAAAACCCTAAACCCTAAACCCTAAATC
1 CAAACCCTAAACCC-AACCTTAACCTAAAC-CTAAACCCAAACCCTAAACCCTAAACCCTAAATC
* *
863 CAAACCCTATATCC
64 CAAACACTATAACC
* * *
877 C-AACCCTAAACCCTAACCTTAACCCTAAACCTAAAGCCAAATCCTAAATCCTAAACCC-AAATC
1 CAAACCCTAAACCC-AACCTTAA-CCTAAACCTAAACCCAAACCCTAAACCCTAAACCCTAAATC
940 CTAAA-AC-ATAACC
64 C-AAACACTATAACC
* * * **
953 CTAAACCCTTAACCCAATCTTAAAACCTAACCCTAAACCCAAACCCTAAAATCT-AACCCTAAA
1 C-AAACCCTAAACCCAACCTT--AACCTAAACCTAAACCCAAACCCTAAACCCTAAACCCTAAA
1016 CCTTAATTTA
Statistics
Matches: 115, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
76 6 0.05
77 17 0.15
78 83 0.72
79 9 0.08
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (77 bp):
CAAACCCTAAACCCAACCTTAACCTAAACCTAAACCCAAACCCTAAACCCTAAACCCTAAATCCA
AACACTATAACC
Found at i:984 original size:32 final size:33
Alignment explanation
Indices: 885--992 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 33
875 CCCAACCCTA
* *
885 AACCCT-AA-CCTTAACCCTAAA-CCTAAAGCCA
1 AACCCTAAACCCTTAACCC-AAATCCTAAAACCT
* * * *
916 AATCCTAAATCCTAAACCCAAATCCTAAAACAT
1 AACCCTAAACCCTTAACCCAAATCCTAAAACCT
*
949 AACCCTAAACCCTTAACCC-AATCTTAAAACCT
1 AACCCTAAACCCTTAACCCAAATCCTAAAACCT
981 AACCCTAAACCC
1 AACCCTAAACCC
993 AAACCCTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
31 5 0.08
32 28 0.44
33 31 0.48
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.19
Consensus pattern (33 bp):
AACCCTAAACCCTTAACCCAAATCCTAAAACCT
Found at i:1011 original size:51 final size:51
Alignment explanation
Indices: 956--1056 Score: 116
Period size: 51 Copynumber: 2.0 Consensus size: 51
946 CATAACCCTA
* *
956 AACCCTTAACC-CAATCTTAAAACCTAACCCTAA-ACCCAAACCCTAAAATCT
1 AACCCTAAACCTCAAT-TTAAAACCTAAACC-AATACCCAAACCCTAAAATCT
* * * *
1007 AACCCTAAACCTTAATTTAAACCCTAAACCAATCCCCGAACCCTAAAATC
1 AACCCTAAACCTCAATTTAAAACCTAAACCAATACCCAAACCCTAAAATC
1057 ATTAATGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
50 2 0.05
51 37 0.88
52 3 0.07
ACGTcount: A:0.43, C:0.37, G:0.01, T:0.20
Consensus pattern (51 bp):
AACCCTAAACCTCAATTTAAAACCTAAACCAATACCCAAACCCTAAAATCT
Found at i:1036 original size:7 final size:7
Alignment explanation
Indices: 799--1017 Score: 132
Period size: 7 Copynumber: 33.7 Consensus size: 7
789 CCCTACATAC
799 AAACCCT
1 AAACCCT
806 AAACCC-
1 AAACCCT
*
812 AAACCCC
1 AAACCCT
819 AAA--CT
1 AAACCCT
*
824 AAACTCT
1 AAACCCT
* *
831 AAA-TCA
1 AAACCCT
837 AAACCCT
1 AAACCCT
844 AAACCCT
1 AAACCCT
851 AAACCCT
1 AAACCCT
*
858 AAATCC-
1 AAACCCT
864 AAACCCT
1 AAACCCT
*
871 ATATCCC-
1 A-AACCCT
878 -AACCCT
1 AAACCCT
884 AAACCCT
1 AAACCCT
891 -AA-CCT
1 AAACCCT
*
896 TAACCCT
1 AAACCCT
903 AAA-CCT
1 AAACCCT
*
909 AAAGCC-
1 AAACCCT
*
915 AAATCCT
1 AAACCCT
*
922 AAATCCT
1 AAACCCT
929 AAACCC-
1 AAACCCT
*
935 AAATCCT
1 AAACCCT
* *
942 AAAACAT
1 AAACCCT
949 -AACCCT
1 AAACCCT
955 AAACCCT
1 AAACCCT
*
962 TAACCC-
1 AAACCCT
* *
968 -AATCTT
1 AAACCCT
*
974 AAAACCT
1 AAACCCT
981 -AACCCT
1 AAACCCT
987 AAACCC-
1 AAACCCT
993 AAACCCT
1 AAACCCT
**
1000 AAAATCT
1 AAACCCT
1007 -AACCCT
1 AAACCCT
1013 AAACC
1 AAACC
1018 TTAATTTAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 38
0.72 0.11 0.16
Matches are distributed among these distances:
5 14 0.08
6 55 0.33
7 94 0.56
8 4 0.02
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:1126 original size:21 final size:21
Alignment explanation
Indices: 1101--1141 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091 ATGTGGATTT
1101 TTATATTACCATGCATTCATA
1 TTATATTACCATGCATTCATA
**
1122 TTATATTGTCATGCATTCAT
1 TTATATTACCATGCATTCAT
1142 CACATGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (21 bp):
TTATATTACCATGCATTCATA
Found at i:1525 original size:45 final size:45
Alignment explanation
Indices: 1431--1527 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
1421 AAAAATTTTA
* * * * *
1431 AAAAAAAGTTTTGTTTTGAATTTGATTTGGTTTTGTTTTTAAAAG
1 AAAAAAAGTTTTGTTTTAAATTTGATCTAGTTTTGTTTTCAAAAC
*
1476 AAAAAAAGTTTTGTTTTAAATTTGATCTATTTCTTG-TTTCAAAAC
1 AAAAAAAGTTTTGTTTTAAATTTGATCTAGTT-TTGTTTTCAAAAC
1521 AAAAAAA
1 AAAAAAA
1528 AAAAGAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 42 0.93
46 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.45
Consensus pattern (45 bp):
AAAAAAAGTTTTGTTTTAAATTTGATCTAGTTTTGTTTTCAAAAC
Found at i:2071 original size:18 final size:17
Alignment explanation
Indices: 2011--2071 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
2001 AAAAAAATCT
2011 AAAAAAATGGAAAAATGAA
1 AAAAAAATGG-AAAATG-A
2030 AATACAAAAT--AAAATGA
1 AA-A-AAAATGGAAAATGA
*
2047 AACAAAATGGAAAAGTGA
1 AAAAAAATGGAAAA-TGA
2065 AAAAAAA
1 AAAAAAA
2072 ATAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.14
17 7 0.20
18 15 0.43
19 2 0.06
20 1 0.03
21 5 0.14
ACGTcount: A:0.72, C:0.03, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAAAATGGAAAATGA
Found at i:2101 original size:29 final size:28
Alignment explanation
Indices: 2020--2093 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
2010 TAAAAAAATG
*
2020 GAAAAATGAAAATACAAAATAAAATGAAA
1 GAAAAATGAAAAT-GAAAATAAAATGAAA
* *
2049 -CAAAATGGAAAAGTGAAAAAAAAAT-AAA
1 GAAAAAT-GAAAA-TGAAAATAAAATGAAA
2077 GAAAAATGAAAATGAAA
1 GAAAAATGAAAATGAAA
2094 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 5 0.13
28 13 0.34
29 19 0.50
30 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.14, T:0.12
Consensus pattern (28 bp):
GAAAAATGAAAATGAAAATAAAATGAAA
Found at i:2154 original size:25 final size:25
Alignment explanation
Indices: 2119--2297 Score: 209
Period size: 25 Copynumber: 7.2 Consensus size: 25
2109 GTGTGTTTTA
2119 CATTTCATGCATATTTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
2144 TATTTCATGCATATTTTAATTATAT
1 CATTTCATGCATATTTTAATTATGT
* * *
2169 CATTTCATGGC-TATTGTAAATATAT
1 CATTTCAT-GCATATTTTAATTATGT
* *
2194 CATTGCATGCATATTTTAA-TATTT
1 CATTTCATGCATATTTTAATTATGT
* *
2218 CATTTCATGTATATTTTACTTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
2243 CATTTCATGAATATTTTAATTATTT
1 CATTTCATGCATATTTTAATTATGT
* * *
2268 CATTTCATGTATATTTAAATTGTGT
1 CATTTCATGCATATTTTAATTATGT
2293 CATTT
1 CATTT
2298 ATTTTATATT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
24 22 0.17
25 108 0.82
26 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (25 bp):
CATTTCATGCATATTTTAATTATGT
Found at i:2277 original size:50 final size:50
Alignment explanation
Indices: 2119--2297 Score: 234
Period size: 50 Copynumber: 3.6 Consensus size: 50
2109 GTGTGTTTTA
* * *
2119 CATTTCATGCATATTTTAATTATGTTATTTCATGCATATTTTAATTATAT
1 CATTTCATGTATATTTTAATTATGTCATTTCATGCATATTTTAATTATTT
** * * * *
2169 CATTTCATGGCTATTGTAAATATATCATTGCATGCATATTTTAA-TATTT
1 CATTTCATGTATATTTTAATTATGTCATTTCATGCATATTTTAATTATTT
* *
2218 CATTTCATGTATATTTTACTTATGTCATTTCATGAATATTTTAATTATTT
1 CATTTCATGTATATTTTAATTATGTCATTTCATGCATATTTTAATTATTT
* *
2268 CATTTCATGTATATTTAAATTGTGTCATTT
1 CATTTCATGTATATTTTAATTATGTCATTT
2298 ATTTTATATT
Statistics
Matches: 109, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
49 40 0.37
50 69 0.63
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (50 bp):
CATTTCATGTATATTTTAATTATGTCATTTCATGCATATTTTAATTATTT
Found at i:11517 original size:19 final size:20
Alignment explanation
Indices: 11470--11506 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11460 ATACTATGCT
11470 TGAAA-AAAAAG-AAAAGAA
1 TGAAAGAAAAAGAAAAAGAA
11488 TGAAAGAAAAAGAAAAAGA
1 TGAAAGAAAAAGAAAAAGA
11507 TAAAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (20 bp):
TGAAAGAAAAAGAAAAAGAA
Found at i:11522 original size:26 final size:27
Alignment explanation
Indices: 11471--11536 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 27
11461 TACTATGCTT
*
11471 GAAAAAAAAGA-AAAGAATGAAAGAAA
1 GAAAAAAAAGATAAAGAATAAAAGAAA
*
11497 -AAGAAAAAGATAAAG-ATAAAATGAAA
1 GAAAAAAAAGATAAAGAATAAAA-GAAA
11523 GAAAAAAAAG-TAAA
1 GAAAAAAAAGATAAA
11537 TGGAAAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 14 0.41
26 12 0.35
27 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.08
Consensus pattern (27 bp):
GAAAAAAAAGATAAAGAATAAAAGAAA
Found at i:11536 original size:20 final size:21
Alignment explanation
Indices: 11508--11579 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
11498 AGAAAAAGAT
11508 AAAGATAAAAT-GAAAGAAAAA
1 AAAG-TAAAATGGAAAGAAAAA
11529 AAAGT-AAATGGAAAGGAAAAA
1 AAAGTAAAATGGAAA-GAAAAA
* * *
11550 AAGGAAAAAAGGAAA-AAATAA
1 AAAGTAAAATGGAAAGAAA-AA
*
11571 AAAATAAAA
1 AAAGTAAAA
11580 AGAAAAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 4 0.10
20 8 0.20
21 21 0.51
22 8 0.20
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (21 bp):
AAAGTAAAATGGAAAGAAAAA
Found at i:13479 original size:50 final size:49
Alignment explanation
Indices: 13223--13580 Score: 296
Period size: 49 Copynumber: 7.3 Consensus size: 49
13213 ATTTATAGTC
* * *
13223 TGATGCTTATTTTATAGAAG-CCTTTTTTAAACAATTTTTTTAAAAAGTT
1 TGATGCCTATTTTATAGAAGCCCTTTTCTAGACAATTTTTTT-AAAAGTT
* * *
13272 TGATGCCTATTTTATAGGAGCCC-TTTCTAGAGAAATTTTTT-AAAGTT
1 TGATGCCTATTTTATAGAAGCCCTTTTCTAGACAATTTTTTTAAAAGTT
** * *
13319 TGAAACCTATTTTATA-ATAG-CCTTTTCCAGAC-TTTTGTTTTAAAAGTT
1 TGATGCCTATTTTATAGA-AGCCCTTTTCTAGACAATTT-TTTTAAAAGTT
*
13367 TGATGCCTATTTTATA-AGAGCCCTTTTCTAGATAGA-TTTTTTATAAA-TT
1 TGATGCCTATTTTATAGA-AGCCCTTTTCTAGACA-ATTTTTTTA-AAAGTT
*
13416 TGATGCCTTTTTTATAGAAGCCCTTTTCTAGACAGATTTTTTTAAAAGTT
1 TGATGCCTATTTTATAGAAGCCCTTTTCTAGACA-ATTTTTTTAAAAGTT
** * * * *
13466 CAATGCCTATTTTATAGGAGCCCTTTTC-AAACATTTTTTTTTTTTTAAAGTT
1 TGATGCCTATTTTATAGAAGCCCTTTTCTAGACA----ATTTTTTTAAAAGTT
* * **
13518 TGATGCCTATTTTATTA-TAGCCTTTTTC-A-A-ATAGATTTTT-AAAGTT
1 TGATGCCTATTTTA-TAGAAGCCCTTTTCTAGACA-ATTTTTTTAAAAGTT
13564 TGATGCCTATTTTATAG
1 TGATGCCTATTTTATAG
13581 GATCCATTTT
Statistics
Matches: 256, Mismatches: 36, Indels: 37
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 24 0.09
47 39 0.15
48 23 0.09
49 88 0.34
50 42 0.16
51 1 0.00
52 35 0.14
53 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (49 bp):
TGATGCCTATTTTATAGAAGCCCTTTTCTAGACAATTTTTTTAAAAGTT
Found at i:15611 original size:10 final size:10
Alignment explanation
Indices: 15596--15622 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
15586 AATAATAGAA
15596 ACTTTGATTG
1 ACTTTGATTG
15606 ACTTTGATTG
1 ACTTTGATTG
15616 ACTTTGA
1 ACTTTGA
15623 ATATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (10 bp):
ACTTTGATTG
Found at i:16292 original size:78 final size:78
Alignment explanation
Indices: 16194--16345 Score: 205
Period size: 78 Copynumber: 1.9 Consensus size: 78
16184 AATAATAAAG
* * * * *
16194 AAAATTGGTGAAAATGTGAAAATAGCTAGACATATATGCAAATCACTAAGAAGTTTCTATTTGAG
1 AAAAATGGTGAAAATATGAAAATAACAAGACATATATGCAAATCACTAAGAAGTTGCTATTTGAG
16259 AAAAAAAGAGAGA
66 AAAAAAAGAGAGA
** * * *
16272 AAAAATGGTGAAAATATGAAAATAACAAGGTATATATGCAAATCATTAAGAAGTTGCTGTTTGAT
1 AAAAATGGTGAAAATATGAAAATAACAAGACATATATGCAAATCACTAAGAAGTTGCTATTTGAG
*
16337 AAGAAAAGA
66 AAAAAAAGA
16346 AAGGAGAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (78 bp):
AAAAATGGTGAAAATATGAAAATAACAAGACATATATGCAAATCACTAAGAAGTTGCTATTTGAG
AAAAAAAGAGAGA
Found at i:23823 original size:15 final size:15
Alignment explanation
Indices: 23811--23840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23801 CAAAAAAAGA
23811 AGAAAAGAAAAAAAT
1 AGAAAAGAAAAAAAT
*
23826 AGAAAATAAAAAAAT
1 AGAAAAGAAAAAAAT
23841 GAATGTGGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (15 bp):
AGAAAAGAAAAAAAT
Found at i:24465 original size:22 final size:22
Alignment explanation
Indices: 24434--24493 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
24424 AGCTTAGTAA
*
24434 AACTGGCACATAAGCCCAAATT
1 AACTGACACATAAGCCCAAATT
*
24456 AGCTGACACATAAGCCCAAATT
1 AACTGACACATAAGCCCAAATT
*
24478 AACTGGCACATAAGCC
1 AACTGACACATAAGCC
24494 TAGTCTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (22 bp):
AACTGACACATAAGCCCAAATT
Found at i:24802 original size:34 final size:34
Alignment explanation
Indices: 24725--25072 Score: 154
Period size: 34 Copynumber: 10.5 Consensus size: 34
24715 CTTAGTGAAA
* * *
24725 ATTTAAGCTCAACTTAGTTGGCA-TCCATAAAAA-
1 ATTTAAGCCCAATTTAGCTGGCACT-CATAAAAAG
* * *
24758 TTTTAAGCCTAATTTAGCTGGCACTCTTAAAAAG
1 ATTTAAGCCCAATTTAGCTGGCACTCATAAAAAG
* * * *
24792 ATTTAAGCCTAGTTTAGCTAGCA-TCGAT---AGG
1 ATTTAAGCCCAATTTAGCTGGCACTC-ATAAAAAG
* * ** * *
24823 AATTAAGCCCATTTTAGCTAACACTCATCAAAGG
1 ATTTAAGCCCAATTTAGCTGGCACTCATAAAAAG
* * *
24857 ATTTAAGCCCAAATTATCTGGCACTCA-ATGAAA-
1 ATTTAAGCCCAATTTAGCTGGCACTCATA-AAAAG
* *
24890 ATTTAAG-CCAAGCTTAGCTGGTA-TCCATAAAAA-
1 ATTTAAGCCCAA-TTTAGCTGGCACT-CATAAAAAG
* *
24923 ATTTTAAGCCCAATTTAGCTTGCACTCATGAAAAG
1 A-TTTAAGCCCAATTTAGCTGGCACTCATAAAAAG
* * * * *
24958 ATTTAAGCCTAGTATAGCT-G-ACACA-AATGAAG
1 ATTTAAGCCCAATTTAGCTGGCACTCATAA-AAAG
* * * * * * **
24990 ATTTAAGCCTAGTCTAGTTGGTA-ACA-ATGAAG
1 ATTTAAGCCCAATTTAGCTGGCACTCATAAAAAG
* *
25022 TTTTAAGCCCAATTTAGCTAGCACTCATGAAAAA-
1 ATTTAAGCCCAATTTAGCTGGCACTCAT-AAAAAG
*
25056 ATTTAAGCCCAACTTAG
1 ATTTAAGCCCAATTTAG
25073 TTGTCACCTA
Statistics
Matches: 241, Mismatches: 53, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
31 24 0.10
32 51 0.21
33 56 0.23
34 101 0.42
35 9 0.04
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (34 bp):
ATTTAAGCCCAATTTAGCTGGCACTCATAAAAAG
Found at i:25285 original size:66 final size:66
Alignment explanation
Indices: 25178--25323 Score: 179
Period size: 66 Copynumber: 2.2 Consensus size: 66
25168 TCTATTACTG
* ** * * * *
25178 ATGAAATTTAAG-GTGGTATATCTGGCACTCATGAAACGATTTAAACCCAATTTATCTGGCACCC
1 ATGAAATTTAAGCCTGGTATATCTAACACTCATGAAAAGATTTAAACCAAAATTAGCTGGCACCC
25242 A
66 A
* *
25243 ATGAAATTTAAGCCTGGTTTATCTAACACTCATGAAAAGATTTAAGCCAAAATTAGCTGGCACCC
1 ATGAAATTTAAGCCTGGTATATCTAACACTCATGAAAAGATTTAAACCAAAATTAGCTGGCACCC
25308 A
66 A
25309 AT-AAAGTTTTAAGCC
1 ATGAAA--TTTAAGCC
25324 CAAATTACTT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 15 0.22
66 46 0.67
67 8 0.12
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (66 bp):
ATGAAATTTAAGCCTGGTATATCTAACACTCATGAAAAGATTTAAACCAAAATTAGCTGGCACCC
A
Found at i:25329 original size:33 final size:33
Alignment explanation
Indices: 25215--25454 Score: 148
Period size: 33 Copynumber: 7.3 Consensus size: 33
25205 CTCATGAAAC
* * *
25215 GATTTAAACCCAATTTATCTGGCACCCAATGAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAATAAA
*** * ** *
25248 -ATTTAAGCCTGGTTTATCTAACACTC-ATGAAAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAAT--AAA
* *
25281 GATTTAAGCCAAAATTAGCTGGCACCCAATAAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAATAAA
* * *
25314 GTTTTAAGCCCAAATTA-CTTAGCACCCAATAAA
1 GATTTAAGCCCAATTTAGC-TGGCACCCAATAAA
* * ** * ** *
25347 AATTTAAG-CCAGTTTATTTGGAACATAATGAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAATAAA
* * *
25379 -ATTTAAACCCAATTTAGCTGGCATCCAATTAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAATAAA
* * *
25411 GTTTTAAGCCCAGTTTAGTTGGCACCCAATGAAA
1 GATTTAAGCCCAATTTAGCTGGCACCCAAT-AAA
25445 GATTTAAGCC
1 GATTTAAGCC
25455 TAGTTTAACT
Statistics
Matches: 153, Mismatches: 45, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
31 8 0.05
32 51 0.33
33 63 0.41
34 29 0.19
35 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (33 bp):
GATTTAAGCCCAATTTAGCTGGCACCCAATAAA
Found at i:25726 original size:21 final size:21
Alignment explanation
Indices: 25702--25772 Score: 92
Period size: 21 Copynumber: 3.3 Consensus size: 21
25692 ACAAAATACC
25702 AAAAAAACCAAAAAAGAAAAA
1 AAAAAAACCAAAAAAGAAAAA
*
25723 AAAAAAACC-AAAAGGAAAAA
1 AAAAAAACCAAAAAAGAAAAA
25743 AGAAAAGAACCAAAACAA-AAAAA
1 A-AAAA-AACCAAAA-AAGAAAAA
25766 AAAAAAA
1 AAAAAAA
25773 TTGTCTTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 11 0.25
21 15 0.34
22 8 0.18
23 9 0.20
24 1 0.02
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAACCAAAAAAGAAAAA
Found at i:26116 original size:21 final size:22
Alignment explanation
Indices: 26068--26118 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
26058 TGAAGTTGGC
26068 CATTAAACATAAAAATATATATA
1 CATTAAA-ATAAAAATATATATA
26091 -A-TAAAATAAATAATA-ATA-A
1 CATTAAAATAAA-AATATATATA
26110 CATTAAAAT
1 CATTAAAAT
26119 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 14 0.56
22 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
CATTAAAATAAAAATATATATA
Found at i:26216 original size:15 final size:15
Alignment explanation
Indices: 26188--26230 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
26178 TAATAACATA
*
26188 AAAAATAAATAAATAC
1 AAAAACAAA-AAATAC
* *
26204 AAAACCAAAAAATAG
1 AAAAACAAAAAATAC
26219 AAAAACAAAAAA
1 AAAAACAAAAAA
26231 GCTTGGCCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.79, C:0.09, G:0.02, T:0.09
Consensus pattern (15 bp):
AAAAACAAAAAATAC
Found at i:26230 original size:23 final size:23
Alignment explanation
Indices: 26187--26230 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
26177 CTAATAACAT
* *
26187 AAAAAATAAATAAATACAAAACC
1 AAAAAATAAATAAACAAAAAACC
26210 AAAAAATAGAA-AAACAAAAAA
1 AAAAAATA-AATAAACAAAAAA
26231 GCTTGGCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (23 bp):
AAAAAATAAATAAACAAAAAACC
Found at i:26657 original size:21 final size:21
Alignment explanation
Indices: 26617--26657 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
26607 CAGAAATGTG
* *
26617 AAAAAAAGAAGAGTAGGAAGC
1 AAAAAAAGAAGAGGACGAAGC
26638 AAAAAAAGAAGAGGACGAAG
1 AAAAAAAGAAGAGGACGAAG
26658 ACCAGAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.29, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAGAGGACGAAGC
Found at i:27666 original size:3 final size:3
Alignment explanation
Indices: 27658--27695 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
27648 TGCAACTCAA
*
27658 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27696 ATAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28085 original size:13 final size:13
Alignment explanation
Indices: 28064--28207 Score: 52
Period size: 13 Copynumber: 11.2 Consensus size: 13
28054 TAAATCCTTA
*
28064 AAATTAAAACCCT
1 AAATCAAAACCCT
*
28077 AAATCAAAACCCC
1 AAATCAAAACCCT
**
28090 AAA-CTAAAACATT
1 AAATC-AAAACCCT
*
28103 AAAATCAAAATCCT
1 -AAATCAAAACCCT
*
28117 AAAT-AAAACCCCA
1 AAATCAAAA-CCCT
* *
28130 AAAT-GAAACCTT
1 AAATCAAAACCCT
* *
28142 AAAAT-GAAACCGT
1 -AAATCAAAACCCT
28155 AAATC-AAA-CCT
1 AAATCAAAACCCT
28166 AAA-CTAAAACCCT
1 AAATC-AAAACCCT
* *
28179 GAAAT-GAAACCGT
1 -AAATCAAAACCCT
* *
28192 AAAACAGAACCCT
1 AAATCAAAACCCT
28205 AAA
1 AAA
28208 ACTGAAACTT
Statistics
Matches: 98, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
10 1 0.01
11 5 0.05
12 20 0.20
13 60 0.61
14 11 0.11
15 1 0.01
ACGTcount: A:0.56, C:0.24, G:0.05, T:0.16
Consensus pattern (13 bp):
AAATCAAAACCCT
Found at i:28132 original size:26 final size:27
Alignment explanation
Indices: 28068--28133 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
28058 TCCTTAAAAT
*
28068 TAAAA-CCCTAAATCAAAACCCCAAAC
1 TAAAACCCCAAAATCAAAACCCCAAAC
*** * *
28094 TAAAACATTAAAATCAAAATCCTAAA-
1 TAAAACCCCAAAATCAAAACCCCAAAC
28120 TAAAACCCCAAAAT
1 TAAAACCCCAAAAT
28134 GAAACCTTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.17
Consensus pattern (27 bp):
TAAAACCCCAAAATCAAAACCCCAAAC
Found at i:28158 original size:25 final size:25
Alignment explanation
Indices: 28117--28215 Score: 83
Period size: 26 Copynumber: 3.9 Consensus size: 25
28107 TCAAAATCCT
**
28117 AAATAAAACCCCAAAATGAAACCTTA
1 AAATAAAACCCTGAAATGAAACC-TA
* * *
28143 AAATGAAACCGT-AAATCAAACCTA
1 AAATAAAACCCTGAAATGAAACCTA
*
28167 AACTAAAACCCTGAAATGAAACCGTA
1 AAATAAAACCCTGAAATGAAACC-TA
* * *
28193 AAACAGAACCCTAAAACTGAAAC
1 AAATAAAACCCTGAAA-TGAAAC
28216 TTTAAGTGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
24 11 0.19
25 18 0.31
26 23 0.40
27 6 0.10
ACGTcount: A:0.55, C:0.23, G:0.08, T:0.14
Consensus pattern (25 bp):
AAATAAAACCCTGAAATGAAACCTA
Found at i:28163 original size:12 final size:12
Alignment explanation
Indices: 28130--28194 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
28120 TAAAACCCCA
*
28130 AAATGAAACCTT
1 AAATGAAACCGT
28142 AAAATGAAACCGT
1 -AAATGAAACCGT
*
28155 AAATCAAACC-T
1 AAATGAAACCGT
* *
28166 AAACTAAAACCCT
1 AAA-TGAAACCGT
28179 GAAATGAAACCGT
1 -AAATGAAACCGT
28192 AAA
1 AAA
28195 ACAGAACCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 4 0.09
12 18 0.41
13 19 0.43
14 3 0.07
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (12 bp):
AAATGAAACCGT
Found at i:28253 original size:19 final size:19
Alignment explanation
Indices: 28204--28254 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
28194 AACAGAACCC
*
28204 TAAAAC-TGAAACTTTAAG
1 TAAAACTTGAAACCTTAAG
* *
28222 TGAAACCTT-AAACCTTAGG
1 T-AAAACTTGAAACCTTAAG
28241 TAAAACTTGAAACC
1 TAAAACTTGAAACC
28255 CTAAAATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (19 bp):
TAAAACTTGAAACCTTAAG
Found at i:29881 original size:19 final size:19
Alignment explanation
Indices: 29859--29912 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
29849 ATAATATCAT
*
29859 ATCATGCAGTAAATATAAA
1 ATCATGCAATAAATATAAA
*
29878 ATCATGCAAT-AATA-ATA
1 ATCATGCAATAAATATAAA
29895 ATCATGCAAATAAATATA
1 ATCATGC-AATAAATATA
29913 TTAATAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 13 0.43
20 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (19 bp):
ATCATGCAATAAATATAAA
Found at i:29906 original size:18 final size:17
Alignment explanation
Indices: 29869--29907 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29859 ATCATGCAGT
29869 AAAT-ATAAAATCATGC
1 AAATAATAAAATCATGC
29885 -AATAATAATAATCATGC
1 AAATAATAA-AATCATGC
29902 AAATAA
1 AAATAA
29908 ATATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.15
16 4 0.20
17 8 0.40
18 5 0.25
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATAATAAAATCATGC
Found at i:29937 original size:32 final size:32
Alignment explanation
Indices: 29901--29991 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
29891 AATAATCATG
29901 CAAATAAATATATTAATAATCATACAATCACA
1 CAAATAAATATATTAATAATCATACAATCACA
29933 CAAATAAATATATTAATAATCATACAATCACA
1 CAAATAAATATATTAATAATCATACAATCACA
* *
29965 CAAATAAATAAATTAATAATTATACAA
1 CAAATAAATATATTAATAATCATACAA
29992 ATAGACATGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (32 bp):
CAAATAAATATATTAATAATCATACAATCACA
Found at i:30043 original size:41 final size:41
Alignment explanation
Indices: 29997--30249 Score: 332
Period size: 41 Copynumber: 6.2 Consensus size: 41
29987 TACAAATAGA
* *
29997 CATGCAATTAACAATGTAAAACATGTC-ATTAAATATCTAAT
1 CATGCAATTAACAATGTAAAACATG-CAAATAAATATATAAT
* *
30038 CATGCAATTAACAATGTAAAACATGTC-ATTAAATATCTAAT
1 CATGCAATTAACAATGTAAAACATG-CAAATAAATATATAAT
30079 CATGCAATTAACAATGTAAAACATGCAAATAAATATATAAT
1 CATGCAATTAACAATGTAAAACATGCAAATAAATATATAAT
** * * *
30120 TGTGCAATTAACAATATAGATCATGCAAATAAATATATAAT
1 CATGCAATTAACAATGTAAAACATGCAAATAAATATATAAT
* *
30161 CATGTAATTAACAATGTAAATCATGCAAATAAATATATAAT
1 CATGCAATTAACAATGTAAAACATGCAAATAAATATATAAT
* * *
30202 CATGCAATTAACAATATAAATCATGC-AATAAAATTTATAAT
1 CATGCAATTAACAATGTAAAACATGCAAAT-AAATATATAAT
30243 CATGCAA
1 CATGCAA
30250 ATAAATATAT
Statistics
Matches: 195, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.02
41 191 0.98
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (41 bp):
CATGCAATTAACAATGTAAAACATGCAAATAAATATATAAT
Found at i:30260 original size:41 final size:42
Alignment explanation
Indices: 30028--30502 Score: 361
Period size: 41 Copynumber: 11.6 Consensus size: 42
30018 CATGTCATTA
* * *
30028 AATATCTAATCATGCAATTAACA-ATGTAAAACATGTC-ATT-A-
1 AATATATAATCATGCAATTAA-ATATAT-AATCATG-CAATTAAC
* * * *
30069 AATATCTAATCATGCAATTAACA-ATGTAAAACATGCAAAT-A-
1 AATATATAATCATGCAATTAA-ATATAT-AATCATGCAATTAAC
** *
30110 AATATATAATTGTGCAATTAACA-ATATAGATCATGCAAAT-A-
1 AATATATAATCATGCAATTAA-ATATATA-ATCATGCAATTAAC
* * *
30151 AATATATAATCATGTAATTAACA-ATGTAAATCATGCAAAT-A-
1 AATATATAATCATGCAATTAA-ATATAT-AATCATGCAATTAAC
30192 AATATATAATCATGCAATTAACA-ATATAAATCATGCAA-TAA-
1 AATATATAATCATGCAATTAA-ATATAT-AATCATGCAATTAAC
* * *
30233 AATTTATAATCATGCAAATAAATATATAATCATGCAAGTAAC
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
* *
30275 AATATA-AAACATGCAA--ATATATATAATCATGCAATTAAC
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
* * * *
30314 AACATA-AATCATGCAA--ATATATATTATCATGCAATTATC
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
* *
30353 AATATA-AAACATGCAATTAATTATATAATCATGCAATTAAC
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
** * *
30394 AATATA-AATCATATAATAAAATATATTATCATGCAATTAAC
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
* * * * *
30435 AATATA-AAACATGCAAATAAATATATTATCATGCAAATAAT
1 AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
30476 AATATTAATAATCATGCAATTAAATAT
1 AATA-T-ATAATCATGCAATTAAATAT
30503 TAGTTATGCA
Statistics
Matches: 379, Mismatches: 43, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
39 70 0.18
40 14 0.04
41 271 0.72
42 7 0.02
43 1 0.00
44 16 0.04
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (42 bp):
AATATATAATCATGCAATTAAATATATAATCATGCAATTAAC
Found at i:30397 original size:180 final size:182
Alignment explanation
Indices: 30067--30476 Score: 533
Period size: 180 Copynumber: 2.3 Consensus size: 182
30057 AACATGTCAT
* * * **
30067 TAAATATCTAATCATGCAATTAACAATGTAAAACATGCAAATAAATATATAATTGTGCAATTAAC
1 TAAATATATAATCATGCAAGTAACAATATAAAACATGCAAAT-AATATATAATCATGCAATTAAC
* * * * *
30132 AATATAGATCATGCAAATAAATATATAATCATGTAATTAACAATGTAAATCATGCAAATAAATAT
65 AACATAAATCATGCAAAT-AATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATAT
* *
30197 ATAATCATGCAATTAACAATATAAATCATGCAATAAAATTTATAATCATGCAAA
129 ATAATCATGCAATTAACAATATAAATCATACAATAAAATATATAATCATGCAAA
30251 TAAATATATAATCATGCAAGTAACAATATAAAACATGCAAAT-ATATATAATCATGCAATTAACA
1 TAAATATATAATCATGCAAGTAACAATATAAAACATGCAAATAATATATAATCATGCAATTAACA
* * * *
30315 ACATAAATCATGCAAAT-ATATATTATCATGCAATTATCAATATAAAACATGCAATTAATTATAT
66 ACATAAATCATGCAAATAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATAT
* * *
30379 AATCATGCAATTAACAATATAAATCATATAATAAAATATATTATCATGCAAT
131 AATCATGCAATTAACAATATAAATCATACAATAAAATATATAATCATGCAAA
* * * *
30431 TAACA-ATATAAAACATGCAAAT-A-AATATATTATCATGCAAATAATA
1 TAA-ATATAT-AATCATGCAAGTAACAATATA-AAACATGCAAATAATA
30477 ATATTAATAA
Statistics
Matches: 199, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
179 6 0.03
180 105 0.53
181 14 0.07
182 35 0.18
184 39 0.20
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (182 bp):
TAAATATATAATCATGCAAGTAACAATATAAAACATGCAAATAATATATAATCATGCAATTAACA
ACATAAATCATGCAAATAATATATAATCATGCAATTAACAATATAAAACATGCAAATAAATATAT
AATCATGCAATTAACAATATAAATCATACAATAAAATATATAATCATGCAAA
Found at i:30490 original size:24 final size:22
Alignment explanation
Indices: 30075--30499 Score: 225
Period size: 21 Copynumber: 20.7 Consensus size: 22
30065 ATTAAATATC
* *
30075 TAATCATGCAATTAACAATGTAA
1 TAATCATGCAAATAA-AATATAA
30098 -AA-CATGCAAAT-AAATAT-A
1 TAATCATGCAAATAAAATATAA
** *
30116 TAATTGTGCAATTAACAATAT-A
1 TAATCATGCAAATAA-AATATAA
*
30138 -GATCATGCAAAT-AAATAT-A
1 TAATCATGCAAATAAAATATAA
* * *
30157 TAATCATGTAATTAACAATGT-A
1 TAATCATGCAAATAA-AATATAA
30179 -AATCATGCAAAT-AAATAT-A
1 TAATCATGCAAATAAAATATAA
*
30198 TAATCATGCAATTAACAATAT-A
1 TAATCATGCAAATAA-AATATAA
*
30220 -AATCATGC-AATAAAAT-TTA
1 TAATCATGCAAATAAAATATAA
30239 TAATCATGCAAAT-AAATAT-A
1 TAATCATGCAAATAAAATATAA
*
30259 TAATCATGCAAGTAACAATATAA
1 TAATCATGCAAATAA-AATATAA
30282 -AA-CATGCAAAT---ATAT-A
1 TAATCATGCAAATAAAATATAA
* *
30298 TAATCATGCAATTAACAACAT-A
1 TAATCATGCAAATAA-AATATAA
30320 -AATCATGCAAAT---ATAT-A
1 TAATCATGCAAATAAAATATAA
* * *
30337 TTATCATGCAATTATCAATATAA
1 TAATCATGCAAATA-AAATATAA
* *
30360 -AA-CATGC-AATTAATTAT-A
1 TAATCATGCAAATAAAATATAA
*
30378 TAATCATGCAATTAACAATAT-A
1 TAATCATGCAAATAA-AATATAA
30400 -AATCAT--ATAATAAAATAT-A
1 TAATCATGCA-AATAAAATATAA
* *
30419 TTATCATGCAATTAACAATATAA
1 TAATCATGCAAATAA-AATATAA
30442 -AA-CATGCAAAT-AAATAT-A
1 TAATCATGCAAATAAAATATAA
*
30460 TTATCATGCAAATAATAATATTAA
1 TAATCATGCAAATAA-AATA-TAA
*
30484 TAATCATGCAATTAAA
1 TAATCATGCAAATAAA
30500 TATTAGTTAT
Statistics
Matches: 315, Mismatches: 42, Indels: 90
0.70 0.09 0.20
Matches are distributed among these distances:
16 1 0.00
17 10 0.03
18 22 0.07
19 40 0.13
20 84 0.27
21 88 0.28
22 51 0.16
23 5 0.02
24 14 0.04
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (22 bp):
TAATCATGCAAATAAAATATAA
Found at i:31089 original size:20 final size:20
Alignment explanation
Indices: 31065--31102 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
31055 AATCTCACAT
31065 TTTTTTTTA-TTTTTTACTC
1 TTTTTTTTAGTTTTTTACTC
31084 TTTTTTTTAGTTTTTTACT
1 TTTTTTTTAGTTTTTTACT
31103 AACTTGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTTTTAGTTTTTTACTC
Found at i:31523 original size:42 final size:43
Alignment explanation
Indices: 31431--31747 Score: 192
Period size: 42 Copynumber: 7.1 Consensus size: 43
31421 TTTTTTTTGA
* *
31431 AAAATGCTCCCCCATAATTGAGGCTTTGAAACTTTTGAAAAAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
** * *
31474 AAAATGCTCCCTTACAACTGAGGGTTTGAAAC-TTTGAAATAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
* *
31516 AAAATGCTCCCCCACAACTAAGGCATTGAAACTTTTGAAAAAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
* * ** * * ** *** *
31559 AAAAAAGTTTCCAACAAAATGCTCCCCCACAACTTAGGTTTTGAAACTTTTGAAAAAT
1 -AAAATG-CTCCCCCACAA--CT----GA-GGC-T---TTGAAAC--TTTTGAAAAAT
* * *
31617 AAAATGCTCCCCTACAATTGAGGCTTTGGAACTTTT-AAAAAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
* *
31659 AAAATGCTCCCCAACAATTGAGGCTTTGAAAC-TTTGAAAAAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
* * * * * *
31701 AAAATGCTTCCCTATAACTGATGCCTTGGAAC-TTTGAAAAAT
1 AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
31743 AAAAT
1 AAAAT
31748 AAGATTATTC
Statistics
Matches: 209, Mismatches: 48, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
41 3 0.01
42 118 0.56
43 40 0.19
44 5 0.02
45 10 0.05
47 2 0.01
48 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 1 0.00
54 1 0.00
56 9 0.04
57 5 0.02
58 11 0.05
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (43 bp):
AAAATGCTCCCCCACAACTGAGGCTTTGAAACTTTTGAAAAAT
Found at i:31650 original size:143 final size:142
Alignment explanation
Indices: 31431--31704 Score: 415
Period size: 143 Copynumber: 1.9 Consensus size: 142
31421 TTTTTTTTGA
* *
31431 AAAATGCTCCCCCATAATTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCTTACAACTGAG
1 AAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGAG
* * *
31496 GGTTTGAAACTTTGAAATATAAAATGCTCCCCCACAACTAAGGCATTGAAACTTTTGAAAAATAA
66 GCTTTGAAACTTTGAAAAATAAAATGCTCCCCAACAACTAAGGCATTGAAAC-TTTGAAAAATAA
31561 AAAAGTTTCCAAC
130 AAAAGTTTCCAAC
* *
31574 AAAATGCTCCCCCACAACTT-AGGTTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAATTGA
1 AAAATGCTCCCCCACAA-TTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGA
* * * * *
31638 GGCTTTGGAACTTTTAAAAATAAAATGCTCCCCAACAATTGAGGCTTTGAAACTTTGAAAAATAA
65 GGCTTTGAAACTTTGAAAAATAAAATGCTCCCCAACAACTAAGGCATTGAAACTTTGAAAAATAA
31703 AA
130 AA
31705 TGCTTCCCTA
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
142 14 0.12
143 102 0.86
144 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (142 bp):
AAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGAG
GCTTTGAAACTTTGAAAAATAAAATGCTCCCCAACAACTAAGGCATTGAAACTTTGAAAAATAAA
AAAGTTTCCAAC
Found at i:31673 original size:100 final size:100
Alignment explanation
Indices: 31474--31675 Score: 255
Period size: 100 Copynumber: 2.0 Consensus size: 100
31464 TTTGAAAAAT
** *
31474 AAAATGCTCCCTTACAACTGAGGGTTTGAAACTTTGAAATATAAAATGCTCCCCCACAACTAAGG
1 AAAATGCTCCCCCACAACTGAGGGTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACTAAGG
**
31539 CATTGAAACTTTTGAAAAATAAAAAAGTTTCCAAC
66 CATTGAAACTTTTGAAAAATAAAAAAGTCCCCAAC
* * * * *
31574 AAAATGCTCCCCCACAACTTAGGTTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAATTGAG
1 AAAATGCTCCCCCACAACTGAGGGTTTGAAAC-TTTGAAAAATAAAATGCTCCCCCACAACTAAG
* * *
31639 GCTTTGGAACTTTT-AAAAAT-AAAATGCTCCCCAAC
65 GCATTGAAACTTTTGAAAAATAAAAAAG-TCCCCAAC
31674 AA
1 AA
31676 TTGAGGCTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
99 5 0.06
100 42 0.48
101 40 0.46
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (100 bp):
AAAATGCTCCCCCACAACTGAGGGTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACTAAGG
CATTGAAACTTTTGAAAAATAAAAAAGTCCCCAAC
Found at i:31730 original size:84 final size:85
Alignment explanation
Indices: 31574--31747 Score: 253
Period size: 84 Copynumber: 2.1 Consensus size: 85
31564 AGTTTCCAAC
* * *
31574 AAAATGCTCCCCCACAACTTAGGTTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAATTGAG
1 AAAATGCTCCCCAACAACTTAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGAG
* *
31639 GCTTTGGAACTTTTAAAAAT
66 GCCTTGGAACTTTGAAAAAT
* *
31659 AAAATGCTCCCCAACAA-TTGAGGCTTTGAAAC-TTTGAAAAATAAAATGCTTCCCTATAACTGA
1 AAAATGCTCCCCAACAACTT-AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGA
*
31722 TGCCTTGGAACTTTGAAAAAT
65 GGCCTTGGAACTTTGAAAAAT
31743 AAAAT
1 AAAAT
31748 AAGATTATTC
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
84 53 0.66
85 27 0.34
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (85 bp):
AAAATGCTCCCCAACAACTTAGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCTACAACTGAG
GCCTTGGAACTTTGAAAAAT
Found at i:33236 original size:15 final size:15
Alignment explanation
Indices: 33219--33259 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
33209 TTCCTCTTTT
33219 TTTTTTGCTTTTTG-
1 TTTTTTGCTTTTTGC
33233 TTTTTTG-TTTTTGCC
1 TTTTTTGCTTTTTG-C
33248 TTTTTTGCTTTT
1 TTTTTTGCTTTT
33260 ATTTACACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.25
14 7 0.29
15 7 0.29
16 4 0.17
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (15 bp):
TTTTTTGCTTTTTGC
Found at i:38020 original size:546 final size:546
Alignment explanation
Indices: 36988--38600 Score: 3109
Period size: 546 Copynumber: 3.0 Consensus size: 546
36978 ATTCACAACA
*
36988 CCTATTTGTGTTCCAATTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
1 CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
*
37053 GAGTGCTTTATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
66 GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
37118 ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
131 ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
37183 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
196 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
37248 TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
261 TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
37313 ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
326 ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
37378 CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
391 CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
37443 TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
456 TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
37508 TTGAGGCAAATTCCTTATAGGCATTG
521 TTGAGGCAAATTCCTTATAGGCATTG
37534 CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
1 CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
37599 GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
66 GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
37664 ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
131 ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
37729 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
196 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
*
37794 TCAAGCTCCAATTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
261 TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
37859 ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
326 ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
37924 CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
391 CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
37989 TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
456 TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
38054 TTGAGGCAAATTCCTTATAGGCATTG
521 TTGAGGCAAATTCCTTATAGGCATTG
38080 CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
1 CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
38145 GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
66 GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
*
38210 ACTCATGATTGGTGGATGACTATATGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
131 ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
38275 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
196 CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
*
38340 TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTATTTTAGCAATTTCCACTACCAATAAAGG
261 TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
* *
38405 ATTTAGAAGAGATGATTTTATTGGGCCATTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
326 ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
* *
38470 CTTGCCTATTATTCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
391 CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
* * **
38535 TTTTGAGGCAAATTCCAAGCTTTTAAAGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
456 TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
38600 T
521 T
38601 GAGAACTCTA
Statistics
Matches: 1053, Mismatches: 14, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
546 1053 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (546 bp):
CCTATTTGTGTTCCAGTTTTGACCATTACCCCATTGAGCATTTAGATGTGCTTTTGTGTTTCAAT
GAGTGCTTCATCTTTTTCTTGCATTTTTGCTTGTAATTGTCTATTTTCTTTCAAAAGTTGAGCTA
ACTCATGATTGGTGGATGACTATGTGATGTTAAGATAAAAAAAATATTCTTCCATTCATCATTTT
CTTGTCTAAGTGCTTGAATCCTTTAGCCTATTCTTCCCCCTAACTCTTTTTTTAGCCTTTTGTTT
TCAAGCTCCAGTTCGTCTTTTTCAACTTGGAACTTTCTTTTAGCAATTTCCACTACCAATAAAGG
ATTTAGAAGTGATGATTTTATTGGGCCTTTTGGAGTTATTTCTTCAAGGATTTTAATATCTTTAC
CTTGCCTATTGTGCCACACAAAGTACTCAAGGGTAACCTCATTTGAGCGTCTCCTTTTATCTTCC
TTTTGAGGTAAATTCCAACCTTTTAGGGCTTTGGCTATCTTTATAGAGGCATTGATTTCAATATA
TTGAGGCAAATTCCTTATAGGCATTG
Found at i:39822 original size:13 final size:13
Alignment explanation
Indices: 39804--39869 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
39794 GTTAGCTAAC
*
39804 ATATACAAGGAAT
1 ATATACAAAGAAT
*
39817 ATATACAAAGAACA
1 ATATACAAAGAA-T
*
39831 ATATA-AAAGATT
1 ATATACAAAGAAT
*
39843 AGTATGCAAA-AAT
1 A-TATACAAAGAAT
*
39856 ATATACAAGGAAT
1 ATATACAAAGAAT
39869 A
1 A
39870 ACACAAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 7 0.17
13 26 0.63
14 8 0.20
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (13 bp):
ATATACAAAGAAT
Found at i:41169 original size:24 final size:21
Alignment explanation
Indices: 41108--41180 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 21
41098 ATAATATCAT
41108 ATCATGCAATAA-ATATAA-A
1 ATCATGCAATAATATATAATA
41127 ATCATGCAATAATA-ATAATA
1 ATCATGCAATAATATATAATA
41147 ATCATGCAAATAAATATATTAATA
1 ATCATGC-AAT-AATATA-TAATA
*
41171 ATCATACAAT
1 ATCATGCAAT
41181 CACACAAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
19 16 0.34
20 9 0.19
21 3 0.06
22 4 0.09
23 4 0.09
24 11 0.23
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (21 bp):
ATCATGCAATAATATATAATA
Found at i:41244 original size:20 final size:20
Alignment explanation
Indices: 41217--41644 Score: 270
Period size: 20 Copynumber: 20.8 Consensus size: 20
41207 TACAAATAGA
*
41217 CATGCAATTAAACATATAAT
1 CATGCAATTAAATATATAAT
* * *
41237 CATACAATTAACGATGTA-AAA
1 CATGCAATTAA--ATATATAAT
* *
41258 CATGCTATTAAATATCTAAT
1 CATGCAATTAAATATATAAT
* *
41278 CATGCAATTAACA-ATGTAAAA
1 CATGCAATTAA-ATATAT-AAT
*
41299 CATGCAAATAAATATATAAT
1 CATGCAATTAAATATATAAT
41319 CATGCAATTAACA-ATATAAAT
1 CATGCAATTAA-ATATAT-AAT
* *
41340 CACGCAAATAAATATATAAT
1 CATGCAATTAAATATATAAT
* *
41360 CATACAATTAAATACA-AAT
1 CATGCAATTAAATATATAAT
**
41379 CATGCAAAAAAATATATAAT
1 CATGCAATTAAATATATAAT
*
41399 CATGCAATTAACA-ATATAAAA
1 CATGCAATTAA-ATATAT-AAT
*
41420 CATG--A-T--ATATATGAT
1 CATGCAATTAAATATATAAT
41435 CATGCAATTAACA-ATATAAAT
1 CATGCAATTAA-ATATAT-AAT
*
41456 TATGCATATATATATATATATATATT
1 CATGCA-AT-TA-A-ATATATA-A-T
*
41482 CATGCAATTAACA-ATATGAAA
1 CATGCAATTAA-ATATAT-AAT
*
41503 CATGCAATTAAATATATAAC
1 CATGCAATTAAATATATAAT
41523 CATGCAATTAACA-ATATAAAT
1 CATGCAATTAA-ATATAT-AAT
* * *
41544 CATGTAATAAAATATATTAT
1 CATGCAATTAAATATATAAT
* * *
41564 CATGCAATTAACAATAAAAAAA
1 CATGCAATT-A-AATATATAAT
* *
41586 CATGCAAATAAATATATCAT
1 CATGCAATTAAATATATAAT
*
41606 CATGCAAATAATAATATTAATAAT
1 CATGC-AATTA-AATA-T-ATAAT
41630 CATGCAATTAAATAT
1 CATGCAATTAAATAT
41645 TAGTTATGCA
Statistics
Matches: 314, Mismatches: 57, Indels: 73
0.71 0.13 0.16
Matches are distributed among these distances:
15 6 0.02
16 4 0.01
17 1 0.00
18 2 0.01
19 19 0.06
20 117 0.37
21 96 0.31
22 32 0.10
23 10 0.03
24 14 0.04
25 7 0.02
26 6 0.02
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (20 bp):
CATGCAATTAAATATATAAT
Found at i:41261 original size:41 final size:41
Alignment explanation
Indices: 41216--41644 Score: 449
Period size: 41 Copynumber: 10.4 Consensus size: 41
41206 ATACAAATAG
* * * *
41216 ACATGCAATTAAACATATAATCATACAATTAACGATGTAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* * *
41257 ACATGCTATTAAATATCTAATCATGCAATTAACAATGTAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
*
41298 ACATGCAAATAAATATATAATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* * * * *
41339 TCACGCAAATAAATATATAATCATACAATT-A-AATACAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* **
41378 TCATGCAAAAAAATATATAATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
*
41419 ACATG--A-T--ATATATGATCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
** *
41455 TTATGCATATATATATATATATATATTCATGCAATTAACAATATGAA
1 ACATGCA-AT-TA-A-ATATATA-A-TCATGCAATTAACAATATAAA
*
41502 ACATGCAATTAAATATATAACCATGCAATTAACAATATAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
* * * * *
41543 TCATGTAATAAAATATATTATCATGCAATTAACAATAAAAAA
1 ACATGCAATTAAATATATAATCATGCAATTAACAAT-ATAAA
* * * *
41585 ACATGCAAATAAATATATCATCATGCAAATAATAATATTAATA
1 ACATGCAATTAAATATATAATCATGCAATTAACAATA-TAA-A
41628 ATCATGCAATTAAATAT
1 A-CATGCAATTAAATAT
41645 TAGTTATGCA
Statistics
Matches: 328, Mismatches: 43, Indels: 31
0.82 0.11 0.08
Matches are distributed among these distances:
36 31 0.09
39 36 0.11
40 2 0.01
41 163 0.50
42 36 0.11
43 9 0.03
44 15 0.05
45 8 0.02
46 3 0.01
47 25 0.08
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATCATGCAATTAACAATATAAA
Found at i:42313 original size:20 final size:20
Alignment explanation
Indices: 42271--42313 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
42261 TCTTTTGACT
**
42271 AAAAAAGTAAAAATTAAACA
1 AAAAAAGTAAAAAACAAACA
* *
42291 AAAAAATTAAAAAACAAATA
1 AAAAAAGTAAAAAACAAACA
42311 AAA
1 AAA
42314 TTTAAGGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAGTAAAAAACAAACA
Found at i:47199 original size:23 final size:23
Alignment explanation
Indices: 47149--47201 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
47139 ATGGAGCTTG
47149 GAAA-AAAATGAAAAAAAAAAGA
1 GAAACAAAATGAAAAAAAAAAGA
47171 GAAAACAAAA-GAAAAGAAAGAAA-A
1 G-AAACAAAATGAAAA-AAA-AAAGA
47195 GAAACAA
1 GAAACAA
47202 GCTAAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 1 0.04
23 14 0.52
24 9 0.33
25 3 0.11
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (23 bp):
GAAACAAAATGAAAAAAAAAAGA
Found at i:55833 original size:39 final size:39
Alignment explanation
Indices: 55751--55835 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
55741 AAATAAGAAA
* * *
55751 AAAAAAAGAATTGCAAAAGCCAAAAGTAAGTTAAAGAAC
1 AAAAAAAGAATTGCAAAAGCCAAAAATAAGTAAAAAAAC
* *
55790 AAAAAAATAATATG-AAAAGCCAAAAAT-AGCTAAAAAAAG
1 AAAAAAAGAAT-TGCAAAAGCCAAAAATAAG-TAAAAAAAC
55829 AAAAAAA
1 AAAAAAA
55836 ACCCCAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
38 2 0.05
39 35 0.90
40 2 0.05
ACGTcount: A:0.68, C:0.08, G:0.12, T:0.12
Consensus pattern (39 bp):
AAAAAAAGAATTGCAAAAGCCAAAAATAAGTAAAAAAAC
Found at i:57197 original size:17 final size:18
Alignment explanation
Indices: 57171--57217 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
57161 TTTATTTTCT
57171 CAAG-TTATTTTCAAT-A
1 CAAGTTTATTTTCAATCA
*
57187 CAAGTTTATTTTTAATCA
1 CAAGTTTATTTTCAATCA
* *
57205 AAAGTTTTTTTTC
1 CAAGTTTATTTTC
57218 TTTACTTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 4 0.16
17 10 0.40
18 11 0.44
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
CAAGTTTATTTTCAATCA
Found at i:60992 original size:23 final size:24
Alignment explanation
Indices: 60955--60999 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
60945 CAAGGTTAAA
*
60955 TTTTAGTTTTCTTTTAAATTCATG
1 TTTTAGTTTTATTTTAAATTCATG
*
60979 TTTTA-TTTTATTTTTAATTCA
1 TTTTAGTTTTATTTTAAATTCA
61000 ATTCAAGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTAGTTTTATTTTAAATTCATG
Found at i:67826 original size:22 final size:22
Alignment explanation
Indices: 67798--67840 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
67788 TCACGTTACG
67798 ATCAAATTAATGAGTACAGTAC
1 ATCAAATTAATGAGTACAGTAC
*
67820 ATCAAATTAATGAGTAGAGTA
1 ATCAAATTAATGAGTACAGTA
67841 TAGAACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (22 bp):
ATCAAATTAATGAGTACAGTAC
Found at i:71899 original size:16 final size:16
Alignment explanation
Indices: 71838--71868 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
71828 ATTTGTAAAA
71838 ATACTTGTAAAAATAC
1 ATACTTGTAAAAATAC
71854 ATACTTGTAAAAATA
1 ATACTTGTAAAAATA
71869 TTTTTAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
ATACTTGTAAAAATAC
Found at i:73568 original size:16 final size:16
Alignment explanation
Indices: 73544--73578 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
73534 TTTGATGACA
*
73544 TATCTTTAACAATTGG
1 TATCCTTAACAATTGG
73560 TATCCTTAACAATTGG
1 TATCCTTAACAATTGG
73576 TAT
1 TAT
73579 GAGCTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (16 bp):
TATCCTTAACAATTGG
Found at i:74987 original size:20 final size:20
Alignment explanation
Indices: 74941--75027 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
74931 AAATCCAGAA
*
74941 AAGGGATCGATCCCCCCA-C
1 AAGGGATCGATCCCCCAAGC
*
74960 ATAGGGGATCGATCACCCAAGC
1 A-A-GGGATCGATCCCCCAAGC
* *
74982 AAGGGATCAATCCCCTCAAGG
1 AAGGGATCGATCCCC-CAAGC
* *
75003 AAGGGATCAATCCCCTCAAGG
1 AAGGGATCGATCCCC-CAAGC
75024 AAGG
1 AAGG
75028 CTTTTCAAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.02
20 12 0.20
21 44 0.75
22 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.13
Consensus pattern (20 bp):
AAGGGATCGATCCCCCAAGC
Found at i:75001 original size:21 final size:21
Alignment explanation
Indices: 74964--75027 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
74954 CCCCACATAG
* * *
74964 GGGATCGATCACC-CAAGCAA
1 GGGATCAATCCCCTCAAGGAA
74984 GGGATCAATCCCCTCAAGGAA
1 GGGATCAATCCCCTCAAGGAA
75005 GGGATCAATCCCCTCAAGGAA
1 GGGATCAATCCCCTCAAGGAA
75026 GG
1 GG
75028 CTTTTCAAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 11 0.28
21 29 0.73
ACGTcount: A:0.33, C:0.28, G:0.27, T:0.12
Consensus pattern (21 bp):
GGGATCAATCCCCTCAAGGAA
Found at i:75300 original size:10 final size:10
Alignment explanation
Indices: 75285--75320 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
75275 CACCAAGAAG
*
75285 CAAGAGGAAA
1 CAAGAGGAAT
75295 CAAGAGGAAT
1 CAAGAGGAAT
*
75305 CAAGATGAAT
1 CAAGAGGAAT
75315 CAAGAG
1 CAAGAG
75321 AGTAAGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.53, C:0.11, G:0.28, T:0.08
Consensus pattern (10 bp):
CAAGAGGAAT
Done.