Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 85 of 145
Found at i:28786991 original size:27 final size:29
Alignment explanation
Indices: 28786928--28787004 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 29
28786918 AAATATGTTA
*
28786928 CAAGTTCATGCAAATATATGGGACCATAT
1 CAAGTTCATGCAAATATATGTGACCATAT
* *
28786957 CGTA-TTCATGTAAATATATGTGA-CA-AT
1 C-AAGTTCATGCAAATATATGTGACCATAT
28786984 CAAGTTCATGCAAATATATGT
1 CAAGTTCATGCAAATATATGT
28787005 AAATAATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 1 0.02
27 19 0.46
28 2 0.05
29 18 0.44
30 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (29 bp):
CAAGTTCATGCAAATATATGTGACCATAT
Found at i:28789901 original size:23 final size:24
Alignment explanation
Indices: 28789858--28789907 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28789848 AACTACTACT
*
28789858 AAAAAATAACTAATTATACTAA-TA
1 AAAAAATAACT-ATTAAACTAACTA
28789882 AAAAAATAACT-TTAAAACTAACTA
1 AAAAAATAACTATT-AAACTAACTA
28789906 AA
1 AA
28789908 TACACTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 6 0.26
24 15 0.65
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAAATAACTATTAAACTAACTA
Found at i:28797112 original size:15 final size:14
Alignment explanation
Indices: 28797092--28797126 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28797082 TCTCCATCAC
*
28797092 ATCATATCAGTTCAT
1 ATCATATCA-TACAT
28797107 ATCATATCATACAT
1 ATCATATCATACAT
28797121 ATCATA
1 ATCATA
28797127 AGCAGATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (14 bp):
ATCATATCATACAT
Found at i:28805890 original size:11 final size:13
Alignment explanation
Indices: 28805874--28805905 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28805864 TTTACGAGAG
28805874 AAATTTCG-T-GA
1 AAATTTCGTTCGA
28805885 AAATTTCGTTCGA
1 AAATTTCGTTCGA
28805898 AAATTTCG
1 AAATTTCG
28805906 ACGTTTGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 1 0.05
13 10 0.53
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (13 bp):
AAATTTCGTTCGA
Found at i:28807165 original size:51 final size:51
Alignment explanation
Indices: 28807106--28807393 Score: 298
Period size: 51 Copynumber: 5.7 Consensus size: 51
28807096 TATCGATGAA
* * *
28807106 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * * * * *
28807157 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATGTTGGT
* * * *
28807208 TACGTGTGTAGTAC-AGTGTGAAGGCTACTAGGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTA-TGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * *
28807259 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
* * ** *
28807310 CACGTGTGTAGTACTATATGAAGGCTACTACGTTAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
28807360 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
28807394 TATCGAATGA
Statistics
Matches: 192, Mismatches: 37, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 41 0.21
51 148 0.77
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
Found at i:28807283 original size:102 final size:102
Alignment explanation
Indices: 28807106--28807387 Score: 415
Period size: 102 Copynumber: 2.8 Consensus size: 102
28807096 TATCGATGAA
*
28807106 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
28807171 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* *
28807208 TACGTGTGTAGTACAGTGTGAAGGCTACTAGGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
28807273 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * * *** * *
28807310 CACGTGTGTAGTACTA-TATGAAGGCTACTACGTTAACCG-TAAAACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTA
*
28807373 CTATGTGAAGGCTAC
65 CTAAGTGAAGGCTAC
28807388 TACGTGTATC
Statistics
Matches: 163, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
101 33 0.20
102 129 0.79
103 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:28818832 original size:98 final size:98
Alignment explanation
Indices: 28818708--28819091 Score: 439
Period size: 98 Copynumber: 3.9 Consensus size: 98
28818698 TCCTGTACTA
* * ** * *
28818708 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
28818773 AGACATGGTCTTACAGGGGACCTCATCTCGGTG
66 AGACATGGTCTTACAGGGGACCTCATCTCGGTG
* *
28818806 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
** * ** * * *
28818871 AGACACAGTCTTACATGGGATGT-TTC-CTGTACTA
66 AGACATGGTCTTACAGGGGACCTCATCTC-G--GTG
* * * ** * * *
28818905 CCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTGCCCATGCCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
* *
28818970 AAACATGGTCTTACGGGGGACCTCATCTCGGTG
66 AGACATGGTCTTACAGGGGACCTCATCTCGGTG
* * * *
28819003 CCAACGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATCTCGGTGCCAACACCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
**
28819068 AGACATGGTCTTACATAGGACCTC
66 AGACATGGTCTTACAGGGGACCTC
28819092 TCTTAATTTC
Statistics
Matches: 229, Mismatches: 52, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
96 1 0.00
97 3 0.01
98 149 0.65
99 72 0.31
100 3 0.01
101 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (98 bp):
CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
AGACATGGTCTTACAGGGGACCTCATCTCGGTG
Found at i:28818920 original size:147 final size:147
Alignment explanation
Indices: 28818769--28819037 Score: 389
Period size: 147 Copynumber: 1.8 Consensus size: 147
28818759 CCATGCCATG
* *
28818769 TCCCAGACATGGTCTTACA-GGG-GACCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCT
1 TCCCAGACATGGTCTTACATGGGAGACCTCATATCGGTGCCAACGCCATGTCCCAAACATGGTCT
*
28818832 TACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACACAGTCTTACATGGGATGTTTC
66 TACAGGGGA-C-CTCATCTCGGTGCCAACGCCATGTCCCAGACACAGTCTTACATGGGATGTTTC
28818897 CTGTACTACCAATGTCATA
129 CTGTACTACCAATGTCATA
* *** * *
28818916 TCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCT
1 TCCCAGACATGGTCTTACATGGGAGACCTCATATCGGTGCCAACGCCATGTCCCAAACATGGTCT
* ** *
28818981 TACGGGGGACCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTTTTACATGGGA
66 TACAGGGGACCTCATCTCGGTGCCAACGCCATGTCCCAGACACAGTCTTACATGGGA
28819038 CCTCTCATCT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
147 62 0.58
148 4 0.04
149 41 0.38
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (147 bp):
TCCCAGACATGGTCTTACATGGGAGACCTCATATCGGTGCCAACGCCATGTCCCAAACATGGTCT
TACAGGGGACCTCATCTCGGTGCCAACGCCATGTCCCAGACACAGTCTTACATGGGATGTTTCCT
GTACTACCAATGTCATA
Found at i:28818955 original size:99 final size:99
Alignment explanation
Indices: 28818667--28818983 Score: 406
Period size: 99 Copynumber: 3.2 Consensus size: 99
28818657 TGCCAAAGAT
*
28818667 ATGTCCTAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
1 ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
28818732 CTTACATGGGAGTTCTCATATCGGTGCCCATGCC
66 CTTACATGGGAGTTCTCATATCGGTGCCCATGCC
* * ** * * * * * *
28818766 ATGTCCCAGACATGGTCTTACAGGGGACCTCAT-CTCG--GTGCCAACGCCATGTCCCAGACATG
1 ATGTCCCAGACATAGTCTTACATGGGATGT-TTCCT-GTACTACCAATGCCATATCCCAGATATG
** * * *
28818828 GTCTTACATGGGACCTCTCATCTCGGTGCCAACGCC
64 GTCTTACATGGGAGTTCTCATATCGGTGCCCATGCC
* *
28818864 ATGTCCCAGACACAGTCTTACATGGGATGTTTCCTGTACTACCAATGTCATATCCCAGATATGGT
1 ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
*
28818929 CTTACATGGGAGTTTTCATATCGGTGCCCATGCC
66 CTTACATGGGAGTTCTCATATCGGTGCCCATGCC
* *
28818963 ATGTCCCAAACATGGTCTTAC
1 ATGTCCCAGACATAGTCTTAC
28818984 GGGGGACCTC
Statistics
Matches: 176, Mismatches: 37, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
97 2 0.01
98 78 0.44
99 94 0.53
100 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (99 bp):
ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
CTTACATGGGAGTTCTCATATCGGTGCCCATGCC
Found at i:28819015 original size:197 final size:197
Alignment explanation
Indices: 28818667--28819083 Score: 753
Period size: 197 Copynumber: 2.1 Consensus size: 197
28818657 TGCCAAAGAT
*
28818667 ATGTCCTAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
1 ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
*
28818732 CTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC
66 CTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCTTACAGGGGACCTC
*
28818797 ATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
131 ATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
28818862 CC
196 CC
* *
28818864 ATGTCCCAGACACAGTCTTACATGGGATGTTTCCTGTACTACCAATGTCATATCCCAGATATGGT
1 ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
* *
28818929 CTTACATGGGAGTTTTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTC
66 CTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCTTACAGGGGACCTC
*
28818994 ATCTCGGTGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATCTCGGTGCCAACA
131 ATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
28819059 CC
196 CC
*
28819061 ATGTCCCAGACATGGTCTTACAT
1 ATGTCCCAGACATAGTCTTACAT
28819084 AGGACCTCTC
Statistics
Matches: 210, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
197 210 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (197 bp):
ATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTACTACCAATGCCATATCCCAGATATGGT
CTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAAACATGGTCTTACAGGGGACCTC
ATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
CC
Found at i:28819089 original size:50 final size:50
Alignment explanation
Indices: 28818708--28819093 Score: 424
Period size: 50 Copynumber: 7.8 Consensus size: 50
28818698 TCCTGTACTA
* * * ** *
28818708 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
28818758 CCCATGCCATGTCCCAGACATGGTCTTACAGGGGA-C-CTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
28818806 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
** ** * * * *
28818856 CCAACGCCATGTCCCAGACACAGTCTTACATGGGATGTTTCCTGTAC--TA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGGTG
* * * * ** * *
28818905 CCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * **
28818955 CCCATGCCATGTCCCAAACATGGTCTTACGGGGGA-C-CTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
28819003 CCAACGCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
28819053 CCAACACCATGTCCCAGACATGGTCTTACATAGGACCTCTC
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
28819094 TTAATTTCAA
Statistics
Matches: 282, Mismatches: 47, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
48 83 0.29
49 38 0.13
50 160 0.57
51 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:28825974 original size:33 final size:34
Alignment explanation
Indices: 28825909--28825976 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
28825899 GGTTTGGCTT
28825909 TTAATGCCAACGAGGTGCAATTGGGGGGAAAATA
1 TTAATGCCAACGAGGTGCAATTGGGGGGAAAATA
**
28825943 TTAATGCCAGTGAGGTGCAATT-GGGGGAAAATA
1 TTAATGCCAACGAGGTGCAATTGGGGGGAAAATA
28825976 T
1 T
28825977 GGTACTAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Consensus pattern (34 bp):
TTAATGCCAACGAGGTGCAATTGGGGGGAAAATA
Found at i:28836090 original size:11 final size:11
Alignment explanation
Indices: 28836051--28836101 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
28836041 GGCCCATTTT
28836051 TATTTTAAAAA
1 TATTTTAAAAA
28836062 T-TTTT-AAAA
1 TATTTTAAAAA
*
28836071 -A-TTAAAAAA
1 TATTTTAAAAA
28836080 GTATTTTAAAAA
1 -TATTTTAAAAA
28836092 TATTTTAAAA
1 TATTTTAAAA
28836102 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
8 2 0.06
9 8 0.24
10 4 0.12
11 12 0.36
12 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:28836110 original size:31 final size:30
Alignment explanation
Indices: 28836051--28836109 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
28836041 GGCCCATTTT
28836051 TATTTTAAAAATTTTTAAAAATTAAAAAAG
1 TATTTTAAAAATTTTTAAAAATTAAAAAAG
28836081 TATTTTAAAAATATTTT-AAAATTAAAAAA
1 TATTTTAAAAAT-TTTTAAAAATTAAAAAA
28836110 ATAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TATTTTAAAAATTTTTAAAAATTAAAAAAG
Found at i:28836729 original size:38 final size:37
Alignment explanation
Indices: 28836650--28836726 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
28836640 TTTCATATTT
28836650 AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
1 AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
** *
28836687 AAATAAAAAATCAT-ATTTTTTAATAGTT-TATTTTAAA
1 AAATAAAAAA-CATAAAATTTTAATAATTATA-TTTAAA
28836724 AAA
1 AAA
28836727 ATACAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 2 0.06
37 30 0.86
38 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (37 bp):
AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
Found at i:28838148 original size:38 final size:37
Alignment explanation
Indices: 28838069--28838145 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
28838059 TTTCATATTT
28838069 AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
1 AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
** *
28838106 AAATAAAAAATCAT-ATTTTTTAATAGTT-TATTTTAAA
1 AAATAAAAAA-CATAAAATTTTAATAATTATA-TTTAAA
28838143 AAA
1 AAA
28838146 ATACAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 2 0.06
37 30 0.86
38 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (37 bp):
AAATAAAAAACATAAAATTTTAATAATTATATTTAAA
Found at i:28845264 original size:18 final size:18
Alignment explanation
Indices: 28845241--28845280 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
28845231 TTATTATTTT
*
28845241 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
28845259 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
28845277 TAAA
1 TAAA
28845281 GTAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:28848720 original size:22 final size:21
Alignment explanation
Indices: 28848674--28848729 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
28848664 TATTTTTTAA
28848674 AAAATTACCAAAAAATTAAAG
1 AAAATTACCAAAAAATTAAAG
* *
28848695 AAAATTATTCAAAAAA-TAATAT
1 AAAATTA-CCAAAAAATTAA-AG
28848717 AAAATTACACAAA
1 AAAATTAC-CAAA
28848730 TATAAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAATTACCAAAAAATTAAAG
Found at i:28849175 original size:20 final size:19
Alignment explanation
Indices: 28849150--28849223 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 19
28849140 TATAATATAA
*
28849150 AATTTTTAATATTTTCTTTC
1 AATTTTTAATATTTT-TTAC
28849170 AATTTTTAAATTATTTTTTAC
1 AATTTTT-AA-TATTTTTTAC
*
28849191 AATTTAT-ATATTTTTT-C
1 AATTTTTAATATTTTTTAC
* *
28849208 -AGTTATAATATTTTTT
1 AATTTTTAATATTTTTT
28849224 TTATAAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.10
17 10 0.21
18 8 0.17
19 1 0.02
20 7 0.15
21 11 0.23
22 6 0.12
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (19 bp):
AATTTTTAATATTTTTTAC
Found at i:28849303 original size:18 final size:18
Alignment explanation
Indices: 28849282--28849321 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28849272 AAATTTTAAT
*
28849282 TTTTATATAGTTTTATGA
1 TTTTATATAGTTTTATAA
* *
28849300 TTTTCTATATTTTTATAA
1 TTTTATATAGTTTTATAA
28849318 TTTT
1 TTTT
28849322 TAATGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTATATAGTTTTATAA
Found at i:28849337 original size:28 final size:28
Alignment explanation
Indices: 28849280--28849337 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
28849270 AAAAATTTTA
**
28849280 ATTTTTATATAGTTTTATGATTTTCTAT
1 ATTTTTATATAGTTTTATGATTTTAAAT
*
28849308 ATTTTTATA-ATTTTTAATGATTTTAAAT
1 ATTTTTATATAGTTTT-ATGATTTTAAAT
28849336 AT
1 AT
28849338 AAAATATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
ATTTTTATATAGTTTTATGATTTTAAAT
Found at i:28860845 original size:16 final size:16
Alignment explanation
Indices: 28860804--28860846 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28860794 AAAGTTGATA
*
28860804 ATAATTAATATACATT
1 ATAATTAATATAAATT
*
28860820 ATAATAAATATAAA-T
1 ATAATTAATATAAATT
28860835 ATATATTAATAT
1 ATA-ATTAATAT
28860847 TATCACCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTAATATAAATT
Found at i:28866584 original size:16 final size:16
Alignment explanation
Indices: 28866543--28866585 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28866533 AAAGTTGATA
*
28866543 ATAATTAATATACATT
1 ATAATTAATATAAATT
*
28866559 ATAATAAATATAAA-T
1 ATAATTAATATAAATT
28866574 ATATATTAATAT
1 ATA-ATTAATAT
28866586 TATCACCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTAATATAAATT
Found at i:28866673 original size:29 final size:29
Alignment explanation
Indices: 28866631--28866687 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
28866621 TTTAAAAAAA
*
28866631 TATTTACAAAAAGAGACAGCT-AATTTTAG
1 TATTTACAAAAAGA-ACAACTAAATTTTAG
28866660 TATTTACAAAAAGAACAACTAAATTTTA
1 TATTTACAAAAAGAACAACTAAATTTTA
28866688 CAAATAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (29 bp):
TATTTACAAAAAGAACAACTAAATTTTAG
Found at i:28870821 original size:10 final size:10
Alignment explanation
Indices: 28870804--28870846 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
28870794 GTCAAAAATG
28870804 ATCAAAATTA
1 ATCAAAATTA
28870814 ATCAAAATTTA
1 ATCAAAA-TTA
*
28870825 ATATAAAATTA
1 AT-CAAAATTA
*
28870836 ATTAAAATTA
1 ATCAAAATTA
28870846 A
1 A
28870847 ACATGTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 16 0.53
11 10 0.33
12 4 0.13
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (10 bp):
ATCAAAATTA
Found at i:28884299 original size:37 final size:37
Alignment explanation
Indices: 28884256--28884328 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
28884246 ATTCATTGTG
28884256 ATAATATGACAATATTGGAATTGGACTTATTCATACC
1 ATAATATGACAATATTGGAATTGGACTTATTCATACC
*
28884293 ATAATATGACAATGTTGGAATTGGACTTATTCATAC
1 ATAATATGACAATATTGGAATTGGACTTATTCATAC
28884329 TATGTATGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (37 bp):
ATAATATGACAATATTGGAATTGGACTTATTCATACC
Found at i:28887883 original size:931 final size:931
Alignment explanation
Indices: 28886081--28888877 Score: 5326
Period size: 931 Copynumber: 3.0 Consensus size: 931
28886071 TAAAACTAAT
28886081 TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
1 TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
28886146 CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
66 CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
28886211 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
131 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
28886276 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
196 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
28886341 TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
261 TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
28886406 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
326 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
28886471 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
391 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
28886536 TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
456 TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
28886601 AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
521 AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
28886666 TTTTAAATAGAATCTCCTATTAAGAAAACATCTAAGTAAAAACCTAATTTTCTGAAAGATTAAGT
586 TTTTAAATAGAATCTCCTATTAAGAAAACATCTAAGTAAAAACCTAATTTTCTGAAAGATTAAGT
* *
28886731 ACAATTTGTGTAAAAGTCCCCTCAAATTTGATTATAATGTTGTTTATATAGATAAAAGTCAAAAG
651 GCAATTTGTGTAAAAGTCCCATCAAATTTGATTATAATGTTGTTTATATAGATAAAAGTCAAAAG
* *
28886796 ACTAAATTTCCCCTTCATTTATAATTTCAATTAAGGTTTTAAGTTGGAAAAAGACCTCTAATTGC
716 ACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTGC
*
28886861 CTTTAAAATCAGAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAAA
781 CCTTAAAATCAGAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAAA
*
28886926 AATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGAAACATTCAATC
846 AATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGCAACATTCAATC
28886991 CAATGTCGCGACATTCAATTC
911 CAATGTCGCGACATTCAATTC
*
28887012 TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCTTATTCCTTGTTTAAACGAGTGAG
1 TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
28887077 CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
66 CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
28887142 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
131 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
*
28887207 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCACTCAGCACAAGCTTAC
196 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
*
28887272 TAAAGGCTTACATAATAGAGCACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
261 TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
28887337 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
326 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
28887402 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
391 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
28887467 TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
456 TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
28887532 AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
521 AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
28887597 TTTTAAATAGAATCTCCTATTAAGAAAACATCTAAGGTAAAAACCT-ATTTTCTGAAAGATTAAG
586 TTTTAAATAGAATCTCCTATTAAGAAAACATCTAA-GTAAAAACCTAATTTTCTGAAAGATTAAG
* *
28887661 TGCAATTTGTGTAAAAGTCCCGTCAAATTTGATTATAATGTTGTTTATATAGATAACAGTCAAAA
650 TGCAATTTGTGTAAAAGTCCCATCAAATTTGATTATAATGTTGTTTATATAGATAAAAGTCAAAA
28887726 GACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTG
715 GACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTG
*
28887791 CCCTTAAAATCAAAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAA
780 CCCTTAAAATCAGAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAA
*
28887856 AAATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTTTAATTTGCAACATTCAAT
845 AAATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGCAACATTCAAT
28887921 CCAATGTCGCGACATTCAATTC
910 CCAATGTCGCGACATTCAATTC
*
28887943 TAAATTAAAATTAAACTAAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
1 TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
* *
28888008 CTACTTATCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAAGCAATATTTACTTCAATTGAAT
66 CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
28888073 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
131 TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
28888138 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
196 TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
* *
28888203 TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGTTATTCTGCTAGGGTTGTCT
261 TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
28888268 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
326 ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
28888333 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
391 AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
*
28888398 TATTCATACAAACATTTAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
456 TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
*
28888463 AATGCTCATTGATAAGTAACGAGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
521 AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
* *
28888528 TTCTAAATAGAATCTCCTATTAAGAAAACATCTAAGTAAAAACCTAATTTTCTAAAAGATTAAGT
586 TTTTAAATAGAATCTCCTATTAAGAAAACATCTAAGTAAAAACCTAATTTTCTGAAAGATTAAGT
*
28888593 GCAATTTGTGTAAAAGTCCCATCAAATTTGATTATAATGTTCTTTATATAGATAAAAGTCAAAAG
651 GCAATTTGTGTAAAAGTCCCATCAAATTTGATTATAATGTTGTTTATATAGATAAAAGTCAAAAG
28888658 ACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTGC
716 ACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTGC
* * * * *
28888723 CCTTGAAATCAGAATCGATGCATGAAGGAAATCTTCGTTGCACAAAGTTAATATCGCGACATAAA
781 CCTTAAAATCAGAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAAA
28888788 AATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGCAACATTCAATC
846 AATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGCAACATTCAATC
28888853 CAATGTCGCGACATTCAATTC
911 CAATGTCGCGACATTCAATTC
28888874 TAAA
1 TAAA
28888878 ATTGCGGCAT
Statistics
Matches: 1830, Mismatches: 34, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
930 10 0.01
931 1810 0.99
932 10 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (931 bp):
TAAATTAAAATTAAACTGAAGGTTAAGACTATTGAAACTTCCTATTCCTTGTTTAAACGAGTGAG
CTACTTAGCCTAAAGTTGGTTGAATTGCTAATTATCAATGAAACCAATATTTACTTCAATTGAAT
TATTTACCACCCGTAACTAAGAATGCCCTCTCGGTGTCATCCTCTCTAAGAGTTACTACCTAAGA
TACCCTTTTGGTCTCCACTAAGCATATGCATACTCTTTCGGTCTCACCGCTCAGCACAAGCTTAC
TAAAGGCTTACATAATAGAGTACCCTTTCGGTCTCATCTATCTAGATATTCTACTAGGGTTGTCT
ATCCTAGTATATTGAGAACTTTAGCAAACTCAAATAAATACCCAATTTTAGATAAACAAGCACTC
AATGAAATAATTAGTTACTCAAACAATCACGCAAGATATTTATGAAAGCATAGGTTTTATTCTCC
TATTCATACAAACATTCAGTTAATTACATTAATGAGGAGATATAAATAAAGAGAATAAAGAATAG
AATGCTCATTGATAAGTAACGCGAATGCACGCGTCTAGAACATTCTCCACTCGCAATGAATAAAC
TTTTAAATAGAATCTCCTATTAAGAAAACATCTAAGTAAAAACCTAATTTTCTGAAAGATTAAGT
GCAATTTGTGTAAAAGTCCCATCAAATTTGATTATAATGTTGTTTATATAGATAAAAGTCAAAAG
ACTAAATTGCCCCTTCATTTATAATTTCAATAAAGGTTTTAAGTTGGAAAAAGACCTCTAATTGC
CCTTAAAATCAGAATCGATGCATGAAGGAAATCATCGTTGTACAAAGTCAATGTCGCGACATAAA
AATCCAATGTTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAATTTGCAACATTCAATC
CAATGTCGCGACATTCAATTC
Found at i:28888848 original size:20 final size:21
Alignment explanation
Indices: 28888814--28888876 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 21
28888804 ATTCAGCCCC
*
28888814 AATGTCGCTACATTCAATTCT
1 AATGTCGCAACATTCAATTCT
* *
28888835 AAT-TTGCAACATTCAA-TCC
1 AATGTCGCAACATTCAATTCT
*
28888854 AATGTCGCGACATTCAATTCT
1 AATGTCGCAACATTCAATTCT
28888875 AA
1 AA
28888877 AATTGCGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.15
20 22 0.65
21 7 0.21
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
AATGTCGCAACATTCAATTCT
Found at i:28888867 original size:40 final size:41
Alignment explanation
Indices: 28888797--28888876 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
28888787 AAATCCAATG
* *
28888797 TTGCAACATTCAGCCCCAATGTCGCTACATTCAATTCTAAT
1 TTGCAACATTCAGACCCAATGTCGCGACATTCAATTCTAAT
*
28888838 TTGCAACATTCA-ATCCAATGTCGCGACATTCAATTCTAA
1 TTGCAACATTCAGACCCAATGTCGCGACATTCAATTCTAA
28888877 AATTGCGGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 24 0.67
41 12 0.33
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (41 bp):
TTGCAACATTCAGACCCAATGTCGCGACATTCAATTCTAAT
Found at i:28889463 original size:210 final size:210
Alignment explanation
Indices: 28889101--28889488 Score: 560
Period size: 210 Copynumber: 1.8 Consensus size: 210
28889091 GTAAATACAT
* * * * *
28889101 AAATTATCATTAAAATAACTTTATTTTACTATTAAACAAGCTAAATTTATATGAAAAGGGATACA
1 AAATTATCATTAAAAGAACTTGATTTTACTATTAAACAAGATAAAATTATACGAAAAGGGATACA
* ** * * * *
28889166 GATAACATGATTGGCTATGGCAGATGACCAACTCACGTATTGGAGAAAGATGTGAGGAAGTTGGA
66 AATAACATGATCAGCTATGGCAGATAACCAACCCACATATTGGAGAAAGATGTGAGGAAGTTGAA
* ** *
28889231 TTTACGGATAAAATTGTGCATGTTTGTGGGATATCCTAAGGGAACAAAGTACGTTTTGAGTAGTT
131 TTCACAAATAAAATTGTGCATGTTTGTGGGATATCCTAAGAGAACAAAGTACGTTTTGAGTAGTT
28889296 AAAATTTAGAAACAG
196 AAAATTTAGAAACAG
* * * *
28889311 AAATTATTATTAAAAGGACTTGATTTTACTATTAAACAAGATAAAATTATGCGGAAAGGGATACA
1 AAATTATCATTAAAAGAACTTGATTTTACTATTAAACAAGATAAAATTATACGAAAAGGGATACA
* * *
28889376 AATAACATGATCAGCTATGGTAGATAACCAACCCACATATTGGATAAATATGTGAGGAAGTTGAA
66 AATAACATGATCAGCTATGGCAGATAACCAACCCACATATTGGAGAAAGATGTGAGGAAGTTGAA
*
28889441 TTCACAAATAGAATTGTGCATGTTTGTGGGATATCCTAAGAGAACAAA
131 TTCACAAATAAAATTGTGCATGTTTGTGGGATATCCTAAGAGAACAAA
28889489 ATGTGGTTTG
Statistics
Matches: 154, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
210 154 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (210 bp):
AAATTATCATTAAAAGAACTTGATTTTACTATTAAACAAGATAAAATTATACGAAAAGGGATACA
AATAACATGATCAGCTATGGCAGATAACCAACCCACATATTGGAGAAAGATGTGAGGAAGTTGAA
TTCACAAATAAAATTGTGCATGTTTGTGGGATATCCTAAGAGAACAAAGTACGTTTTGAGTAGTT
AAAATTTAGAAACAG
Found at i:28897471 original size:26 final size:26
Alignment explanation
Indices: 28897432--28897491 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
28897422 GACAATGAAG
* *
28897432 GGCAAACCTTATGAAATGTGAGTATA
1 GGCAAATCTCATGAAATGTGAGTATA
*
28897458 GGCAAATCTCATGAAATGTGAGTCTA
1 GGCAAATCTCATGAAATGTGAGTATA
28897484 GGCAAATC
1 GGCAAATC
28897492 CCAATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (26 bp):
GGCAAATCTCATGAAATGTGAGTATA
Found at i:28897655 original size:56 final size:55
Alignment explanation
Indices: 28897585--28897700 Score: 135
Period size: 56 Copynumber: 2.1 Consensus size: 55
28897575 GAAAGAAATG
* * * *
28897585 CCTTTATGGGAAAACTTTGGAAAGGTAAG-CTTTGTGGCGAACATGTTAAAGGACAA
1 CCTTTATGGGAAAACTGTAG-AAGGTAAGCCCTCGTGGCGAACATGTTAAAGGA-AA
* * * *
28897641 CCTTTATGGTAAAACTGTAGAGGGTAAGCCCTCGTGGCGAACCTTTTAAAGGAAA
1 CCTTTATGGGAAAACTGTAGAAGGTAAGCCCTCGTGGCGAACATGTTAAAGGAAA
28897696 CCTTT
1 CCTTT
28897701 GTGGCGAGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
55 14 0.27
56 37 0.73
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
CCTTTATGGGAAAACTGTAGAAGGTAAGCCCTCGTGGCGAACATGTTAAAGGAAA
Found at i:28897820 original size:28 final size:28
Alignment explanation
Indices: 28897765--28897820 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
28897755 CATTTGTTGT
* *
28897765 AATCTCTAGTTAATGAAGCATTTGTGGC
1 AATCTCTAGATAATGAAGCATTTATGGC
*
28897793 AATCTCTAGATAA-GAAAGCCTTTATGGC
1 AATCTCTAGATAATG-AAGCATTTATGGC
28897821 TATTTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (28 bp):
AATCTCTAGATAATGAAGCATTTATGGC
Found at i:28903957 original size:16 final size:16
Alignment explanation
Indices: 28903938--28903969 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28903928 TAGTAAAGTA
*
28903938 AAATAAAATTAAAAAT
1 AAATAAAAATAAAAAT
28903954 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
28903970 TGTATCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:28905921 original size:16 final size:16
Alignment explanation
Indices: 28905900--28905930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28905890 ATTGGGCTGA
*
28905900 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
28905916 GAAAATTAATTAATT
1 GAAAATTAATTAATT
28905931 TAAATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:28906516 original size:3 final size:3
Alignment explanation
Indices: 28906508--28906717 Score: 420
Period size: 3 Copynumber: 70.0 Consensus size: 3
28906498 TCGAAAATAA
28906508 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28906556 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28906604 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28906652 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28906700 AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG
28906718 GCGAAACAAC
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 207 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28909198 original size:24 final size:23
Alignment explanation
Indices: 28909149--28909211 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
28909139 AATATTCACA
*
28909149 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCA-TGAACATTAATCG
*
28909172 AACATGTTCATGAACATATAATTG
1 AACATGTTCATGAACAT-TAATCG
* *
28909196 AACACGTTCACGAACA
1 AACATGTTCATGAACA
28909212 ATGTTAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.12
23 11 0.32
24 19 0.56
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (23 bp):
AACATGTTCATGAACATTAATCG
Found at i:28912470 original size:9 final size:9
Alignment explanation
Indices: 28912456--28912485 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28912446 ATAGTTTGAT
28912456 TCACCATCA
1 TCACCATCA
28912465 TCACCATCA
1 TCACCATCA
*
28912474 TCATCATCA
1 TCACCATCA
28912483 TCA
1 TCA
28912486 TCACTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (9 bp):
TCACCATCA
Found at i:28913037 original size:24 final size:24
Alignment explanation
Indices: 28913010--28913057 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28913000 GTAAGTAAGA
28913010 ACTGCTCAATTTTGAAATACAATT
1 ACTGCTCAATTTTGAAATACAATT
28913034 ACTGCTCAATTTTGAAATACAATT
1 ACTGCTCAATTTTGAAATACAATT
28913058 GATTCTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (24 bp):
ACTGCTCAATTTTGAAATACAATT
Found at i:28913780 original size:16 final size:16
Alignment explanation
Indices: 28913741--28913781 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
28913731 GATTGTCATC
*
28913741 GTACCTCCCCCATCAA
1 GTACCTCTCCCATCAA
28913757 GTACCTCTCCCATCAA
1 GTACCTCTCCCATCAA
28913773 GTACCTCTC
1 GTACCTCTC
28913782 AAACTTGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.22, C:0.46, G:0.07, T:0.24
Consensus pattern (16 bp):
GTACCTCTCCCATCAA
Found at i:28914677 original size:18 final size:18
Alignment explanation
Indices: 28914641--28914677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28914631 GAGCAGCAAC
**
28914641 AATTGAAGAAAATGGAAG
1 AATTGAAGAAAATAAAAG
28914659 AATTGAAGAAAATAAAAG
1 AATTGAAGAAAATAAAAG
28914677 A
1 A
28914678 GAAGAGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (18 bp):
AATTGAAGAAAATAAAAG
Found at i:28915711 original size:14 final size:15
Alignment explanation
Indices: 28915694--28915723 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28915684 AAAAATATTC
28915694 AATATT-AATATTTT
1 AATATTAAATATTTT
28915708 AATATTAAATATTTT
1 AATATTAAATATTTT
28915723 A
1 A
28915724 TTACCATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTAAATATTTT
Found at i:28916985 original size:4 final size:4
Alignment explanation
Indices: 28916976--28917006 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
28916966 AGCAACGCTT
28916976 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
28917007 TTTTGACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:28921679 original size:17 final size:17
Alignment explanation
Indices: 28921657--28921689 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28921647 GGTAAGTCTT
*
28921657 TATTTTGGTTTTTTAAA
1 TATTTTGGTTATTTAAA
28921674 TATTTTGGTTATTTAA
1 TATTTTGGTTATTTAA
28921690 TTAAAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
TATTTTGGTTATTTAAA
Found at i:28928844 original size:46 final size:46
Alignment explanation
Indices: 28928742--28928833 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
28928732 GCTAAGCAAA
28928742 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
1 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
28928788 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
1 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
28928834 TACATTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (46 bp):
AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
Found at i:28928866 original size:46 final size:45
Alignment explanation
Indices: 28928742--28928864 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 45
28928732 GCTAAGCAAA
*
28928742 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
1 AAAATATTTTATCTAT-CATTTATTTTATTTTCTTAAATTTATTTT
*
28928788 AAAATATTTTATTTATCCATTTATTTTATTTTCTTAAATTTATTTT
1 AAAATATTTTATCTAT-CATTTATTTTATTTTCTTAAATTTATTTT
* * * *
28928834 TACATTTTTTAATCTAT-TTTTATTTTATTTT
1 AAAATATTTT-ATCTATCATTTATTTTATTTT
28928865 TCATATTTCC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 13 0.18
46 53 0.75
47 5 0.07
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (45 bp):
AAAATATTTTATCTATCATTTATTTTATTTTCTTAAATTTATTTT
Found at i:28934967 original size:21 final size:21
Alignment explanation
Indices: 28934901--28935083 Score: 129
Period size: 21 Copynumber: 8.8 Consensus size: 21
28934891 CAAAAGCCCG
* *
28934901 AAGA-CTGAACAGAAGCTCAT
1 AAGAGCTGAACGGAAACTCAT
* * *
28934921 GAGAGCTAAACGGAAACCCAT
1 AAGAGCTGAACGGAAACTCAT
* * *
28934942 TAGAGTTGAACGGAAACTCGT
1 AAGAGCTGAACGGAAACTCAT
*
28934963 AAGAGCTGAACGAAAACTCAT
1 AAGAGCTGAACGGAAACTCAT
* * * * *
28934984 AAGGGTTAAAC-TAAAGCTCAA
1 AAGAGCTGAACGGAAA-CTCAT
*
28935005 AAGAGCTGAAC-GAAAGCCCAT
1 AAGAGCTGAACGGAAA-CTCAT
* * *
28935026 AAGGGTTGAACGGAAGCTCAT
1 AAGAGCTGAACGGAAACTCAT
* * *
28935047 AAGAGCTAAACGGAAGCTCGT
1 AAGAGCTGAACGGAAACTCAT
*
28935068 AAGAGCTAAACGGAAA
1 AAGAGCTGAACGGAAA
28935084 GTAAACACGA
Statistics
Matches: 126, Mismatches: 34, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
20 6 0.05
21 117 0.93
22 3 0.02
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.15
Consensus pattern (21 bp):
AAGAGCTGAACGGAAACTCAT
Found at i:28934969 original size:42 final size:42
Alignment explanation
Indices: 28934906--28935061 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 42
28934896 GCCCGAAGAC
* * * * *
28934906 TGAACAGAAGCTCATGAGAGCTAAACGGAAACCCATTAGAGT
1 TGAACGGAAACTCATAAGAGCTAAACGGAAACCCATAAGGGT
* * * *
28934948 TGAACGGAAACTCGTAAGAGCTGAACGAAAACTCATAAGGGT
1 TGAACGGAAACTCATAAGAGCTAAACGGAAACCCATAAGGGT
* * * *
28934990 TAAAC-TAAAGCTCAAAAGAGCTGAAC-GAAAGCCCATAAGGGT
1 TGAACGGAAA-CTCATAAGAGCTAAACGGAAA-CCCATAAGGGT
*
28935032 TGAACGGAAGCTCATAAGAGCTAAACGGAA
1 TGAACGGAAACTCATAAGAGCTAAACGGAA
28935062 GCTCGTAAGA
Statistics
Matches: 90, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
41 6 0.07
42 79 0.88
43 5 0.06
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (42 bp):
TGAACGGAAACTCATAAGAGCTAAACGGAAACCCATAAGGGT
Found at i:28935015 original size:63 final size:64
Alignment explanation
Indices: 28934916--28935084 Score: 146
Period size: 63 Copynumber: 2.7 Consensus size: 64
28934906 TGAACAGAAG
* * ** * * *
28934916 CTCATGAGAGCTAAACGGAAA-CCCATTAGAGTTGAACGGAAA-CTCGTAAGAGCTGAACGAAAA
1 CTCATAAGAGCTAAAC-GAAAGCTCAAAAGAGCTGAACGGAAAGCCCATAAGAGCTGAACGAAAA
* * * * * * *
28934979 CTCATAAGGGTTAAACTAAAGCTCAAAAGAGCTGAAC-GAAAGCCCATAAGGGTTGAACGGAAG
1 CTCATAAGAGCTAAACGAAAGCTCAAAAGAGCTGAACGGAAAGCCCATAAGAGCTGAACGAAAA
* ** *
28935042 CTCATAAGAGCTAAACGGAAGCTCGTAAGAGCTAAACGGAAAG
1 CTCATAAGAGCTAAACGAAAGCTCAAAAGAGCTGAACGGAAAG
28935085 TAAACACGAA
Statistics
Matches: 82, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
62 7 0.09
63 70 0.85
64 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (64 bp):
CTCATAAGAGCTAAACGAAAGCTCAAAAGAGCTGAACGGAAAGCCCATAAGAGCTGAACGAAAA
Found at i:28935080 original size:42 final size:42
Alignment explanation
Indices: 28934912--28935082 Score: 153
Period size: 42 Copynumber: 4.1 Consensus size: 42
28934902 AGACTGAACA
* * * *
28934912 GAAGCTCATGAGAGCTAAACGGAAACCCATTAGAGTTGAACG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGAGTTAAACG
* * * * * *
28934954 GAAACTCGTAAGAGCTGAACGAAAACTCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGAGTTAAACG
* * * * * *
28934996 AAAGCTCAAAAGAGCTGAACGAAAGCCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGAGTTAAACG
* * * * *
28935038 GAAGCTCATAAGAGCTAAACGGAAGCTCGTAAGAGCTAAACG
1 GAAGCTCATAAGAGCTAAACGAAAACCCATAAGAGTTAAACG
28935080 GAA
1 GAA
28935083 AGTAAACACG
Statistics
Matches: 102, Mismatches: 27, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 102 1.00
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACGAAAACCCATAAGAGTTAAACG
Found at i:28948900 original size:17 final size:17
Alignment explanation
Indices: 28948878--28948911 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28948868 TTTAGCAGCT
28948878 GATTTATCAAATGTAGG
1 GATTTATCAAATGTAGG
28948895 GATTTATCAAATGTAGG
1 GATTTATCAAATGTAGG
28948912 AACATTGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
GATTTATCAAATGTAGG
Found at i:28951906 original size:19 final size:20
Alignment explanation
Indices: 28951863--28951907 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
28951853 CTTTATTTTC
28951863 CAAATTTTCATGTTTTCTCT
1 CAAATTTTCATGTTTTCTCT
* * *
28951883 AAAATTTTC-TGTTTTGTTT
1 CAAATTTTCATGTTTTCTCT
28951902 CAAATT
1 CAAATT
28951908 GATCCCTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (20 bp):
CAAATTTTCATGTTTTCTCT
Found at i:28966926 original size:58 final size:57
Alignment explanation
Indices: 28966864--28966991 Score: 158
Period size: 57 Copynumber: 2.2 Consensus size: 57
28966854 AGAAATGGTG
28966864 AAATGGAGAAATAGGAAAT-ATTTGGAAAT-GAT-TAAGGTTTTCTCCAAAAT-GAAAATGA
1 AAATGGAGAAAT--GAAATCATTTGGAAATAGATGT--GGTTTTCTCCAAAATAG-AAATGA
*
28966922 AAATGGAGGAATGAAATCATTTGGAAATAGATGTGGTTTTCTCCAAAATAGAAATGA
1 AAATGGAGAAATGAAATCATTTGGAAATAGATGTGGTTTTCTCCAAAATAGAAATGA
*
28966979 AAAT-AAGAAATGA
1 AAATGGAGAAATGA
28966992 GAAATGAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
56 12 0.19
57 35 0.56
58 15 0.24
59 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATGAAATCATTTGGAAATAGATGTGGTTTTCTCCAAAATAGAAATGA
Found at i:28977098 original size:102 final size:103
Alignment explanation
Indices: 28976964--28977174 Score: 406
Period size: 102 Copynumber: 2.0 Consensus size: 103
28976954 AATTTTAATT
28976964 TTTTCTAATAAAAGTGAAAATTAGGGGATTTTATAGGGAATTATCTAGGTTTTTATAGGGAAAAC
1 TTTT-TAATAAAAGTGAAAATTAGGGGATTTTATAGGGAATTATCTAGGTTTTTATAGGGAAAAC
28977029 CATTTATCTTTTTTTTTTTTAAATTAAAGTTAATTTCAG
65 CATTTATCTTTTTTTTTTTTAAATTAAAGTTAATTTCAG
28977068 TTTTTAATAAAAGTG-AAATTAGGGGATTTTATAGGGAATTATCTAGGTTTTTATAGGGAAAACC
1 TTTTTAATAAAAGTGAAAATTAGGGGATTTTATAGGGAATTATCTAGGTTTTTATAGGGAAAACC
28977132 ATTTATCTTTTTTTTTTTTAAATTAAAGTTAATTTCAG
66 ATTTATCTTTTTTTTTTTTAAATTAAAGTTAATTTCAG
28977170 TTTTT
1 TTTTT
28977175 TTAGTAAAAG
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
102 92 0.86
103 11 0.10
104 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (103 bp):
TTTTTAATAAAAGTGAAAATTAGGGGATTTTATAGGGAATTATCTAGGTTTTTATAGGGAAAACC
ATTTATCTTTTTTTTTTTTAAATTAAAGTTAATTTCAG
Found at i:28977538 original size:69 final size:70
Alignment explanation
Indices: 28977452--28977584 Score: 187
Period size: 69 Copynumber: 1.9 Consensus size: 70
28977442 ATTAAATCAA
* * * **
28977452 TGACTAAAATTAAAACTTAATAAGGTTTGGTGACT-AAATGAATGTACAATAACATTGAATTAAC
1 TGACCAAAATGAAAACTTAATAAAGTTTGACGACTAAAATGAATGTACAATAACATTGAATTAAC
28977516 GAGCG
66 GAGCG
* * *
28977521 TGACCAAAATGAAAACTTATTAAAGTTTGACGATTAAAATGAGTGTACAATAACATTGAATTAA
1 TGACCAAAATGAAAACTTAATAAAGTTTGACGACTAAAATGAATGTACAATAACATTGAATTAA
28977585 TGAGAATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
69 28 0.51
70 27 0.49
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (70 bp):
TGACCAAAATGAAAACTTAATAAAGTTTGACGACTAAAATGAATGTACAATAACATTGAATTAAC
GAGCG
Found at i:28982446 original size:17 final size:19
Alignment explanation
Indices: 28982424--28982458 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28982414 TATTTGTATC
28982424 AATATT-TTT-AAATCTAT
1 AATATTGTTTAAAATCTAT
28982441 AATATTGTTTAAAATCTA
1 AATATTGTTTAAAATCTA
28982459 AATCTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (19 bp):
AATATTGTTTAAAATCTAT
Found at i:28983246 original size:3 final size:3
Alignment explanation
Indices: 28983240--28983274 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28983230 TTAGAGAACC
28983240 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28983275 GGTTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28987255 original size:15 final size:15
Alignment explanation
Indices: 28987237--28987266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28987227 AAACCACGAG
28987237 CAAAAATAATTTTAC
1 CAAAAATAATTTTAC
*
28987252 CAAAGATAATTTTAC
1 CAAAAATAATTTTAC
28987267 TATAATGGCA
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:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (15 bp):
CAAAAATAATTTTAC
Found at i:28997703 original size:14 final size:13
Alignment explanation
Indices: 28997677--28997701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28997667 ATTTAAATAT
28997677 TAAATATTTTTTA
1 TAAATATTTTTTA
28997690 TAAATATTTTTT
1 TAAATATTTTTT
28997702 TACTGTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAAATATTTTTTA
Found at i:29005543 original size:14 final size:14
Alignment explanation
Indices: 29005524--29005553 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29005514 GTTGTGTTCA
29005524 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
*
29005538 TAGTTAATTTAGAT
1 TAGTTAAATTAGAT
29005552 TA
1 TA
29005554 AAAACAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:29009203 original size:29 final size:29
Alignment explanation
Indices: 29009170--29009232 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
29009160 TTTCCTATTA
*
29009170 TTATTAT-TTATTTTATCTTCTTTATTTAT
1 TTATTATATTATTTTAT-TCCTTTATTTAT
* *
29009199 TTATTCTATTATTTTATTCCTTTATTTTT
1 TTATTATATTATTTTATTCCTTTATTTAT
29009228 TTATT
1 TTATT
29009233 TTAGTTGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (29 bp):
TTATTATATTATTTTATTCCTTTATTTAT
Found at i:29009214 original size:21 final size:21
Alignment explanation
Indices: 29009165--29009245 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
29009155 CCCATTTTCC
29009165 TATTATTA-TTATTTATTTTAT
1 TATT-TTATTTATTTATTTTAT
*
29009186 CT-TCTTTATTTATTTATTCTAT
1 -TAT-TTTATTTATTTATTTTAT
** *
29009208 TATTTTATTCCTTTATTTTTT
1 TATTTTATTTATTTATTTTAT
* *
29009229 TATTTTAGTTGTTTATT
1 TATTTTATTTATTTATT
29009246 ATCTATTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 33 0.69
22 15 0.31
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTTTATTTATTTATTTTAT
Found at i:29009314 original size:31 final size:31
Alignment explanation
Indices: 29009276--29009339 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
29009266 GCTATTTTCT
* * *
29009276 GTTTTATTATTGA-TATTCTTTATTTTTTTTA
1 GTTTTATTATT-ATTATTATTCATTTTTATTA
29009307 GTTTTATTATTATTATTATTCATTTTTATTA
1 GTTTTATTATTATTATTATTCATTTTTATTA
29009338 GT
1 GT
29009340 ATTTTTTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (31 bp):
GTTTTATTATTATTATTATTCATTTTTATTA
Found at i:29011384 original size:17 final size:17
Alignment explanation
Indices: 29011362--29011394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29011352 TTTAGAATGA
29011362 ATTTTTATCGATTTGTG
1 ATTTTTATCGATTTGTG
*
29011379 ATTTTTATTGATTTGT
1 ATTTTTATCGATTTGT
29011395 TTGGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (17 bp):
ATTTTTATCGATTTGTG
Found at i:29011978 original size:13 final size:13
Alignment explanation
Indices: 29011960--29011984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29011950 TTATTCTCAA
29011960 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
29011973 AAAAAGAAAAAA
1 AAAAAGAAAAAA
29011985 AAGAGTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:29021293 original size:22 final size:22
Alignment explanation
Indices: 29021265--29021421 Score: 102
Period size: 22 Copynumber: 7.1 Consensus size: 22
29021255 GGGATACCGC
29021265 ATACCAGAGGTCCGGTATCGCG
1 ATACCAGAGGTCCGGTATCGCG
*
29021287 ATACCAGAGGTCCAGTATCGCG
1 ATACCAGAGGTCCGGTATCGCG
* * * *
29021309 ATGCTAG-GGGCTTGGTATCGCG
1 ATACCAGAGGTC-CGGTATCGCG
* * * *
29021331 ATGCCAGGGGTCTGGTATCGCC
1 ATACCAGAGGTCCGGTATCGCG
* * ** * *
29021353 ATACTAGGGGTTTGGTATCTCC
1 ATACCAGAGGTCCGGTATCGCG
* * *
29021375 ATACTAG-GTGTTCGCTATCGCG
1 ATACCAGAG-GTCCGGTATCGCG
* *
29021397 ATACCAAAGGTCCCGTATCGCG
1 ATACCAGAGGTCCGGTATCGCG
29021419 ATA
1 ATA
29021422 TCCATAAGAG
Statistics
Matches: 109, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
21 4 0.04
22 101 0.93
23 4 0.04
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (22 bp):
ATACCAGAGGTCCGGTATCGCG
Found at i:29021349 original size:44 final size:44
Alignment explanation
Indices: 29021278--29021371 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
29021268 CCAGAGGTCC
* *
29021278 GGTATCGCGATACCAGAGGTCCAGTATCGCGATGCTAGGGGCTT
1 GGTATCGCGATACCAGAGGTCCAGTATCGCCATACTAGGGGCTT
* * ** *
29021322 GGTATCGCGATGCCAGGGGTCTGGTATCGCCATACTAGGGGTTT
1 GGTATCGCGATACCAGAGGTCCAGTATCGCCATACTAGGGGCTT
29021366 GGTATC
1 GGTATC
29021372 TCCATACTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.18, C:0.21, G:0.35, T:0.26
Consensus pattern (44 bp):
GGTATCGCGATACCAGAGGTCCAGTATCGCCATACTAGGGGCTT
Found at i:29021613 original size:22 final size:22
Alignment explanation
Indices: 29021583--29021658 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
29021573 CATGCAATGA
* *
29021583 GTCTAGTATCGCGATGCTAGGG
1 GTCTGGTATCACGATGCTAGGG
*
29021605 GT-TCGGTATTACGATGCTAGGG
1 GTCT-GGTATCACGATGCTAGGG
* * * *
29021627 GTCTGGTATCTCCATACTAAGG
1 GTCTGGTATCACGATGCTAGGG
29021649 GTCTGGTATC
1 GTCTGGTATC
29021659 GCCATACCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.02
22 42 0.95
23 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (22 bp):
GTCTGGTATCACGATGCTAGGG
Found at i:29021658 original size:287 final size:289
Alignment explanation
Indices: 29021300--29021869 Score: 781
Period size: 287 Copynumber: 2.0 Consensus size: 289
29021290 CCAGAGGTCC
* * *
29021300 AGTATCGCGATGCTAGGGGCTTGGTATCGCGATGCCAGGGGTCTGGTATCGCCATACTAGGGGTT
1 AGTATCGCGATGCTAGGGGCTTGGTATCACGATGCCAGGGGTCTGGTATCGCCATACTAAGGGTC
* * * *
29021365 TGGTATCTCCATACTAGGTGT-TCGCTATCGCGATACCAAAGGTCCCG-TATCGCGATATCCATA
66 TGGTATCGCCATACCAGGGGTCT-GATATCGCGATACCAAAGGT-CCGATATCGCGATATCCATA
* * * *
29021428 AGAGTTTTGGCCTCCCCTCGAAACTATCCAGGATATTGCGATATCCACCCTTGGGTGTCATGATA
129 AAAGTTTTGGCCTCCCCTCAAAACTATCAAGGATATTGCGATATCCACCCTTAGGTGTCATGATA
* * * *
29021493 CCACTGTATAGTTATCAAAATTTCA-AAAGTTTT-ATCTTCCTCTAAACACAAAATAGGACCCCT
194 CAACTGTATAGTTATCAAAATTTCACAAAATTTTCATCTTCCTCTAAACACAAAACAAGACCCCT
29021556 AAATCCCTAAAATTCAACATGCAATGAGTCT
259 AAATCCCTAAAATTCAACATGCAATGAGTCT
* * *
29021587 AGTATCGCGATGCTAGGGG-TTCGGTATTACGATGCTAGGGGTCTGGTATCTCCATACTAAGGGT
1 AGTATCGCGATGCTAGGGGCTT-GGTATCACGATGCCAGGGGTCTGGTATCGCCATACTAAGGGT
* * * * * *
29021651 CTGGTATCGCCATACCAGGGGTCTGATATCGTGATACCAAGGGTCTGATTTTGTGATATCCATAA
65 CTGGTATCGCCATACCAGGGGTCTGATATCGCGATACCAAAGGTCCGATATCGCGATATCCATAA
* * * * *
29021716 AAGTTTTGGCCTTCCTTCAAAACTATCAAGGGTATTGCGATATCCAGCCTTAGGTGTCGTGATAC
130 AAGTTTTGGCCTCCCCTCAAAACTATCAAGGATATTGCGATATCCACCCTTAGGTGTCATGATAC
* * * *
29021781 AACTGTATAGTTCTGAAAATTTCACAAAATTTTCGTCTTCCTCTAAACACAAAACAAGACCCTTA
195 AACTGTATAGTTATCAAAATTTCACAAAATTTTCATCTTCCTCTAAACACAAAACAAGACCCCTA
29021846 AATCCCTAAAATTCAACATGCAAT
260 AATCCCTAAAATTCAACATGCAAT
29021870 TAATTTAAAA
Statistics
Matches: 245, Mismatches: 33, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
286 4 0.02
287 182 0.74
288 8 0.03
289 51 0.21
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (289 bp):
AGTATCGCGATGCTAGGGGCTTGGTATCACGATGCCAGGGGTCTGGTATCGCCATACTAAGGGTC
TGGTATCGCCATACCAGGGGTCTGATATCGCGATACCAAAGGTCCGATATCGCGATATCCATAAA
AGTTTTGGCCTCCCCTCAAAACTATCAAGGATATTGCGATATCCACCCTTAGGTGTCATGATACA
ACTGTATAGTTATCAAAATTTCACAAAATTTTCATCTTCCTCTAAACACAAAACAAGACCCCTAA
ATCCCTAAAATTCAACATGCAATGAGTCT
Found at i:29021663 original size:22 final size:22
Alignment explanation
Indices: 29021625--29021697 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
29021615 ACGATGCTAG
* *
29021625 GGGTCTGGTATCTCCATACTAA
1 GGGTCTGGTATCGCCATACCAA
*
29021647 GGGTCTGGTATCGCCATACCAG
1 GGGTCTGGTATCGCCATACCAA
* **
29021669 GGGTCTGATATCGTGATACCAA
1 GGGTCTGGTATCGCCATACCAA
29021691 GGGTCTG
1 GGGTCTG
29021698 ATTTTGTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (22 bp):
GGGTCTGGTATCGCCATACCAA
Found at i:29021698 original size:22 final size:22
Alignment explanation
Indices: 29021640--29021708 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
29021630 TGGTATCTCC
* * **
29021640 ATACTAAGGGTCTGGTATCGCC
1 ATACCAAGGGTCTGATATCGTG
*
29021662 ATACCAGGGGTCTGATATCGTG
1 ATACCAAGGGTCTGATATCGTG
* *
29021684 ATACCAAGGGTCTGATTTTGTG
1 ATACCAAGGGTCTGATATCGTG
29021706 ATA
1 ATA
29021709 TCCATAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (22 bp):
ATACCAAGGGTCTGATATCGTG
Found at i:29023470 original size:7 final size:7
Alignment explanation
Indices: 29023458--29023492 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
29023448 TCTTCATCAA
29023458 CACATAT
1 CACATAT
29023465 CACATAT
1 CACATAT
29023472 CACATAT
1 CACATAT
*
29023479 CACGTAT
1 CACATAT
29023486 CACATAT
1 CACATAT
29023493 TGATAGTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (7 bp):
CACATAT
Found at i:29024035 original size:3 final size:3
Alignment explanation
Indices: 29024027--29024073 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
29024017 TTCAAGGAAA
29024027 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29024074 ACAAAACGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29027212 original size:34 final size:34
Alignment explanation
Indices: 29027169--29027239 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
29027159 TCCACAATAG
*
29027169 AGTATGTGTTAGCTTTGCATGTTAGCCACGTGTT
1 AGTATGTGTTAGCTTTGCATGTTAGCCACATGTT
29027203 AGTATGTGTTAGCTTTGCATGTTAGCCACATGTT
1 AGTATGTGTTAGCTTTGCATGTTAGCCACATGTT
29027237 AGT
1 AGT
29027240 TCTACGAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (34 bp):
AGTATGTGTTAGCTTTGCATGTTAGCCACATGTT
Found at i:29040440 original size:15 final size:14
Alignment explanation
Indices: 29040419--29040454 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
29040409 ATAATCCATA
*
29040419 ATAATTATCTTAAT
1 ATAATTATCCTAAT
29040433 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
29040448 ATAATTA
1 ATAATTA
29040455 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:29041007 original size:23 final size:23
Alignment explanation
Indices: 29040980--29041027 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
29040970 ACCCTATTTG
29040980 TTTCCTCCTT-TATTTCTTTTTAT
1 TTTCCT-CTTCTATTTCTTTTTAT
* *
29041003 TTTCCTTTTCTTTTTCTTTTTAT
1 TTTCCTCTTCTATTTCTTTTTAT
29041026 TT
1 TT
29041028 ATTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTCCTCTTCTATTTCTTTTTAT
Found at i:29042165 original size:12 final size:11
Alignment explanation
Indices: 29042126--29042223 Score: 72
Period size: 12 Copynumber: 8.3 Consensus size: 11
29042116 ATTAATATCC
*
29042126 AAATAAGTAAT
1 AAATAAATAAT
*
29042137 AAATAATAAAAT
1 AAATAA-ATAAT
29042149 AAAATAAAGTAAT
1 -AAATAAA-TAAT
29042162 AAATAAAGTAAAGT
1 AAATAAA-T-AA-T
***
29042176 GGTTAAAATAAT
1 AAAT-AAATAAT
29042188 AAATAAATAAAT
1 AAATAAAT-AAT
29042200 AAATAAATAAT
1 AAATAAATAAT
29042211 AAATAAA-AAT
1 AAATAAATAAT
29042221 AAA
1 AAA
29042224 AATTGGGTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
10 6 0.08
11 20 0.28
12 26 0.37
13 13 0.18
14 3 0.04
15 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:29042168 original size:4 final size:4
Alignment explanation
Indices: 29042134--29042217 Score: 59
Period size: 4 Copynumber: 20.5 Consensus size: 4
29042124 CCAAATAAGT
* **
29042134 AATA AAT- AATAA AATAA AATA AAGT- AATA AATA AAGTA AAGTG GTTA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AATA AA-TA AA-TA AATA
29042181 AAATA -ATA AATA AATA AATA AATA AAT- AATA AATA AA
1 -AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
29042218 AATAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
3 10 0.15
4 39 0.59
5 17 0.26
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:29042197 original size:11 final size:11
Alignment explanation
Indices: 29042181--29042223 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
29042171 AAAGTGGTTA
29042181 AAATAATAAAT
1 AAATAATAAAT
29042192 AAATAAATAAAT
1 AAAT-AATAAAT
29042204 AAATAATAAAT
1 AAATAATAAAT
29042215 AAA-AATAAA
1 AAATAATAAA
29042224 AATTGGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.19
11 14 0.45
12 11 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:29042226 original size:12 final size:14
Alignment explanation
Indices: 29042181--29042226 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
29042171 AAAGTGGTTA
29042181 AAATAATAAATAAAT
1 AAATAATAAAT-AAT
29042196 AAATAAATAAATAAT
1 AAAT-AATAAATAAT
29042211 AAATAA-AAATAA-
1 AAATAATAAATAAT
29042223 AAAT
1 AAAT
29042227 TGGGTTGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.13
13 6 0.20
14 2 0.07
15 11 0.37
16 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:29042226 original size:23 final size:23
Alignment explanation
Indices: 29042126--29042226 Score: 71
Period size: 23 Copynumber: 4.2 Consensus size: 23
29042116 ATTAATATCC
*
29042126 AAATAAGTAATAAAT-AATAAAATA
1 AAATAAATAATAAATAAAT-AAA-A
*
29042150 AAATAAAGTAATAAATAAAGTAAAGT
1 AAATAAA-TAATAAATAAA-TAAA-A
*** *
29042176 GGTTAAAATAATAAATAAATAAAT
1 AAAT-AAATAATAAATAAATAAAA
29042200 AAATAAATAATAAATAAA-AATAA
1 AAATAAATAATAAATAAATAA-AA
29042223 AAAT
1 AAAT
29042227 TGGGTTGCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
22 2 0.03
23 19 0.31
24 8 0.13
25 12 0.19
26 17 0.27
27 4 0.06
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (23 bp):
AAATAAATAATAAATAAATAAAA
Found at i:29048708 original size:15 final size:16
Alignment explanation
Indices: 29048688--29048756 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 16
29048678 TAATCTTTAA
29048688 TAATTAT-CTGAATAT
1 TAATTATCCTGAATAT
*
29048703 TAATTATCCTAATATAATT
1 TAATTATCCTGA-AT-A-T
*
29048722 TAATTAT-TTGAATAT
1 TAATTATCCTGAATAT
29048737 TAATTATCCT-AATA-
1 TAATTATCCTGAATAT
29048751 TAATTA
1 TAATTA
29048757 AAATAGAGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
14 6 0.13
15 19 0.42
16 5 0.11
17 4 0.09
18 3 0.07
19 8 0.18
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATTATCCTGAATAT
Found at i:29048726 original size:19 final size:19
Alignment explanation
Indices: 29048702--29048755 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
29048692 TATCTGAATA
29048702 TTAATTATCCTAATATAAT
1 TTAATTATCCTAATATAAT
* *
29048721 TTAATTAT-TTGA-AT-A-
1 TTAATTATCCTAATATAAT
29048736 TTAATTATCCTAATATAAT
1 TTAATTATCCTAATATAAT
29048755 T
1 T
29048756 AAAATAGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 4 0.15
18 3 0.11
19 9 0.33
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (19 bp):
TTAATTATCCTAATATAAT
Found at i:29048727 original size:34 final size:34
Alignment explanation
Indices: 29048688--29048755 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
29048678 TAATCTTTAA
29048688 TAATTATCTGAATATTAATTATCCTAATATAATT
1 TAATTATCTGAATATTAATTATCCTAATATAATT
*
29048722 TAATTATTTGAATATTAATTATCCTAATATAATT
1 TAATTATCTGAATATTAATTATCCTAATATAATT
29048756 AAAATAGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (34 bp):
TAATTATCTGAATATTAATTATCCTAATATAATT
Found at i:29052785 original size:35 final size:35
Alignment explanation
Indices: 29052739--29052825 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
29052729 GATACCGTGA
29052739 AAATGGTATATAGGTC-TTTAGAGGAAACACAATAT
1 AAATGGTATATAGGTCATTT-GAGGAAACACAATAT
* ** ** *
29052774 AAATGGTATATAGGTCATTTGGGGCGACACCGTGT
1 AAATGGTATATAGGTCATTTGAGGAAACACAATAT
29052809 AAATGGTATATAGGTCA
1 AAATGGTATATAGGTCA
29052826 CTGGAATAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 42 0.93
36 3 0.07
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (35 bp):
AAATGGTATATAGGTCATTTGAGGAAACACAATAT
Found at i:29069519 original size:14 final size:14
Alignment explanation
Indices: 29069500--29069528 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29069490 TAATGTTATA
29069500 TTTAAATAATTCAT
1 TTTAAATAATTCAT
29069514 TTTAAATAATTCAT
1 TTTAAATAATTCAT
29069528 T
1 T
29069529 AATAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAATAATTCAT
Found at i:29069999 original size:16 final size:17
Alignment explanation
Indices: 29069974--29070008 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29069964 CAGGCATTCA
29069974 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
29069990 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
29070007 TC
1 TC
29070009 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:29075016 original size:10 final size:10
Alignment explanation
Indices: 29075001--29075025 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29074991 CTTACGCTTA
29075001 TGTGAAGAAC
1 TGTGAAGAAC
29075011 TGTGAAGAAC
1 TGTGAAGAAC
29075021 TGTGA
1 TGTGA
29075026 TAAGTGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (10 bp):
TGTGAAGAAC
Found at i:29076448 original size:16 final size:16
Alignment explanation
Indices: 29076424--29076457 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29076414 TTAATTATTT
29076424 TTTAGTTCTTTAGGAA
1 TTTAGTTCTTTAGGAA
* *
29076440 TTTATTTCTTTAGTAA
1 TTTAGTTCTTTAGGAA
29076456 TT
1 TT
29076458 AGGATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTAGTTCTTTAGGAA
Found at i:29078610 original size:16 final size:16
Alignment explanation
Indices: 29078588--29078625 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29078578 TTTTCAGGCA
29078588 TCTCTCATCCCTCATCC
1 TCTCTCATCCC-CATCC
*
29078605 -CTCTCATCTCCATCC
1 TCTCTCATCCCCATCC
29078620 TCTCTC
1 TCTCTC
29078626 TCAACTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.37
Consensus pattern (16 bp):
TCTCTCATCCCCATCC
Found at i:29084460 original size:18 final size:19
Alignment explanation
Indices: 29084434--29084471 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29084424 AATTGATGAA
*
29084434 ATTTGGTTTTGTTA-TTTT
1 ATTTGGTTTTCTTAGTTTT
*
29084452 ATTTTGTTTTCTTAGTTTT
1 ATTTGGTTTTCTTAGTTTT
29084471 A
1 A
29084472 GCTAACTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.71
Consensus pattern (19 bp):
ATTTGGTTTTCTTAGTTTT
Found at i:29089504 original size:12 final size:13
Alignment explanation
Indices: 29089458--29089514 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
29089448 TCTAATACTC
29089458 TGTTTTCAAA-ATA
1 TGTTTT-AAAGATA
* *
29089471 TGTTTTCAAGTTA
1 TGTTTTAAAGATA
* *
29089484 TGTTTTTAAGCTA
1 TGTTTTAAAGATA
29089497 TGTTTTAAAGATA
1 TGTTTTAAAGATA
29089510 TGTTT
1 TGTTT
29089515 CACGCATGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
12 2 0.05
13 35 0.95
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (13 bp):
TGTTTTAAAGATA
Found at i:29091234 original size:39 final size:39
Alignment explanation
Indices: 29091174--29091296 Score: 147
Period size: 40 Copynumber: 3.1 Consensus size: 39
29091164 ATGTTATACT
* *
29091174 TTCTATTTGGTGTGATTCGGGTGGATCAGCTCTTATGAGC
1 TTCTA-TTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGC
*
29091214 TTCTATTGGCGTGTTTCGGGTGGACCAGCTCTTATGAGC
1 TTCTATTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGC
* * * ** *
29091253 TTTTGTTTGGCGTATTTCGATTGGATCAGCTCTTATGAGT
1 TTCT-ATTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGC
29091293 TTCT
1 TTCT
29091297 GTTTGGTGTG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 34 0.48
40 37 0.52
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (39 bp):
TTCTATTGGCGTGTTTCGGGTGGATCAGCTCTTATGAGC
Found at i:29101588 original size:17 final size:17
Alignment explanation
Indices: 29101568--29101605 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
29101558 ACAAATCTCG
*
29101568 CCAAAACACATAATTCA
1 CCAAAACACAGAATTCA
*
29101585 CCAAAACACAGGATTCA
1 CCAAAACACAGAATTCA
29101602 CCAA
1 CCAA
29101606 TTAGTTCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.32, G:0.05, T:0.13
Consensus pattern (17 bp):
CCAAAACACAGAATTCA
Found at i:29105102 original size:140 final size:140
Alignment explanation
Indices: 29104850--29105130 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
29104840 TGCATTTCTT
29104850 TAATCATAGTTTGGACTCATATAATTGTTTATATCTTTCCTCGAAGTTTCTCGTGTTCAATCAGC
1 TAATCATAGTTTGGACTCATATAATTGTTTATATCTTTCCTCGAAGTTTCTCGTGTTCAATCAGC
29104915 ATGACCCTGTTGAGAATTAATAAATGCGTATTAGGTGCTGACATGTAGTGCAGATGGTACACTAC
66 ATGACCCTGTTGAGAATTAATAAATGCGTATTAGGTGCTGACATGTAGTGCAGATGGTACACTAC
29104980 TTGCCAGTGC
131 TTGCCAGTGC
29104990 TAATCATAGTTTGGACTCATATAATTGTTTATATCTTTCCTCGAAGTTTCTCGTGTTCAATCAGC
1 TAATCATAGTTTGGACTCATATAATTGTTTATATCTTTCCTCGAAGTTTCTCGTGTTCAATCAGC
*
29105055 ATGACCCTGTTGAGAATTAATAAATGCGTATTAGGTGCTGACATGTAGTTCAGATGGTACACTAC
66 ATGACCCTGTTGAGAATTAATAAATGCGTATTAGGTGCTGACATGTAGTGCAGATGGTACACTAC
29105120 TTGCCAGTGC
131 TTGCCAGTGC
29105130 T
1 T
29105131 GTCAAGGTGT
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (140 bp):
TAATCATAGTTTGGACTCATATAATTGTTTATATCTTTCCTCGAAGTTTCTCGTGTTCAATCAGC
ATGACCCTGTTGAGAATTAATAAATGCGTATTAGGTGCTGACATGTAGTGCAGATGGTACACTAC
TTGCCAGTGC
Found at i:29108689 original size:3 final size:3
Alignment explanation
Indices: 29108681--29108708 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29108671 CCTTTTCCTT
29108681 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
29108709 CTCTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:29110246 original size:15 final size:15
Alignment explanation
Indices: 29110226--29110266 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
29110216 TATACAATAA
29110226 ACAACAAGATTATCC
1 ACAACAAGATTATCC
* *
29110241 ACAACACGATTATCT
1 ACAACAAGATTATCC
29110256 ACAACAAGATT
1 ACAACAAGATT
29110267 TGAACAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (15 bp):
ACAACAAGATTATCC
Found at i:29111142 original size:214 final size:212
Alignment explanation
Indices: 29110775--29111195 Score: 743
Period size: 214 Copynumber: 2.0 Consensus size: 212
29110765 ATGCCAAAGG
*
29110775 ACCCAATAAAATTTGGGTATCAAAATCCGAAGTTAGACACCACAAAGTTGGATGTTGCACTAGAG
1 ACCCAATAAAATTTGGGTATCAAAATCCAAAGTTAGACACCACAAAGTTGGATGTTGCACTAGAG
*
29110840 AGTGTCAATTTGAGACGGGAGATGCTTGAGATGTTGGATTTCATCAAAAGAAAAAATCTTAGTAG
66 AGTGTCAATTTGAGACAGGAGATGCTTGAGATGTTGGATTTCATCAAAAGAAAAAATCTTAGTAG
29110905 AAGTTGTCTCCTTAGATGACTATAATTTTTGTCAAATTTGCTTGAGCCCTTGTAGACTTGACTCT
131 AAGTTGTCTCCTTAGATGACTATAATTTTTGTCAAATTTGCTTGAGCCCTTGTAGACTTGACTCT
29110970 TTTCCCACCATGCCCAA
196 TTTCCCACCATGCCCAA
** *
29110987 ACCCAATAAAATTTGGGTATCAAAATCCAAAGTTAGACTTCACAAAGTTGGATGTTGGACTAGAG
1 ACCCAATAAAATTTGGGTATCAAAATCCAAAGTTAGACACCACAAAGTTGGATGTTGCACTAGAG
*
29111052 AAAGTGTCAATTTGAGACAGGAGATGGTTGAGATGTTGGATTTCATCAAAAGAAAAAATCTTAGT
66 --AGTGTCAATTTGAGACAGGAGATGCTTGAGATGTTGGATTTCATCAAAAGAAAAAATCTTAGT
* *
29111117 AGAAGTTGTCTCCTTAGGTGACTATAATTTTTGTCAAATTTGCTTGAGCCCTTGTTGACTTGACT
129 AGAAGTTGTCTCCTTAGATGACTATAATTTTTGTCAAATTTGCTTGAGCCCTTGTAGACTTGACT
*
29111182 CTTTTCCCTCCATG
194 CTTTTCCCACCATG
29111196 TCCTCTAGTG
Statistics
Matches: 198, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
212 61 0.31
214 137 0.69
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (212 bp):
ACCCAATAAAATTTGGGTATCAAAATCCAAAGTTAGACACCACAAAGTTGGATGTTGCACTAGAG
AGTGTCAATTTGAGACAGGAGATGCTTGAGATGTTGGATTTCATCAAAAGAAAAAATCTTAGTAG
AAGTTGTCTCCTTAGATGACTATAATTTTTGTCAAATTTGCTTGAGCCCTTGTAGACTTGACTCT
TTTCCCACCATGCCCAA
Found at i:29114242 original size:18 final size:19
Alignment explanation
Indices: 29114207--29114244 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29114197 GACTAATTGG
29114207 TATAGCAGATTATTTGGGA
1 TATAGCAGATTATTTGGGA
29114226 TATAGCAGATT-TTTGGGA
1 TATAGCAGATTATTTGGGA
29114244 T
1 T
29114245 GTAATTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.39
Consensus pattern (19 bp):
TATAGCAGATTATTTGGGA
Found at i:29132972 original size:12 final size:12
Alignment explanation
Indices: 29132955--29132979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29132945 TGCAAATGAA
29132955 TCATTTCCATTT
1 TCATTTCCATTT
29132967 TCATTTCCATTT
1 TCATTTCCATTT
29132979 T
1 T
29132980 GGAAGCATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:29139538 original size:26 final size:26
Alignment explanation
Indices: 29139496--29139546 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
29139486 ATTCACCTTT
*
29139496 ATTTACTTAC-AATTTTTTTCTTTAGA
1 ATTTACTTACAAATTTTATT-TTTAGA
29139522 ATTTACTTA-AACATTTTATTTTTAG
1 ATTTACTTACAA-ATTTTATTTTTAG
29139547 TTCCATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (26 bp):
ATTTACTTACAAATTTTATTTTTAGA
Found at i:29142820 original size:20 final size:20
Alignment explanation
Indices: 29142789--29142854 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
29142779 GAAGTTTATA
29142789 AAAATATTCAAAAAAATTAAG
1 AAAAT-TTCAAAAAAATTAAG
*
29142810 AAAATTTCAAAATAAAAATAA-
1 AAAATTTC-AAA-AAAATTAAG
*
29142831 AAAA-TTCATAAAAATTCAAG
1 AAAATTTCAAAAAAATT-AAG
29142851 AAAA
1 AAAA
29142855 AGTACATGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.13
19 4 0.11
20 10 0.26
21 12 0.32
22 7 0.18
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATTTCAAAAAAATTAAG
Found at i:29143171 original size:34 final size:32
Alignment explanation
Indices: 29143126--29143190 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 32
29143116 TATATTTGAT
* *
29143126 TGAAAATTAAAAAAAAATTGAAAATGAAAATATG
1 TGAAAACTAAAAAAAAAATGAAAA--AAAATATG
29143160 TGAAAACTAAAAAAAAAATGAAAAAAAATAT
1 TGAAAACTAAAAAAAAAATGAAAAAAAATAT
29143191 TTTCATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.24
34 22 0.76
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (32 bp):
TGAAAACTAAAAAAAAAATGAAAAAAAATATG
Found at i:29154101 original size:14 final size:14
Alignment explanation
Indices: 29154082--29154108 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29154072 CATTTCTTGG
29154082 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
29154096 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
29154109 ACTAGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:29161561 original size:16 final size:15
Alignment explanation
Indices: 29161540--29161579 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
29161530 ATATTTTTAC
29161540 ATTTAAATTAACAATA
1 ATTTAAATTAAC-ATA
29161556 ATTT-AATTAACATA
1 ATTTAAATTAACATA
29161570 ATATTAAATT
1 AT-TTAAATT
29161580 TTAAAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 8 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAATTAACATA
Found at i:29167741 original size:114 final size:115
Alignment explanation
Indices: 29167589--29167817 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 115
29167579 CTATGGATCA
29167589 AGACACAAGTGAATACGTCGTTTAATTCAAATTCATAATAATAAGCGAAGTCTAGGTGGATTCTT
1 AGACACAAGTGAATACGTCGTTTAATTCAAATTCATAATAATAAGCGAAGTCTAGGTGGATTCTT
29167654 TCCTAGGTATTGTCTATCTCATTGGTTAATATTTGATTATTTATTTGATT
66 TCCTAGGTATTGTCTATCTCATTGGTTAATATTTGATTATTTATTTGATT
29167704 AGACACAAGT-AATACGTCGTTTAATTCAAATTCATAATAATAAGCGAAGTCTAGGTGGATTCTT
1 AGACACAAGTGAATACGTCGTTTAATTCAAATTCATAATAATAAGCGAAGTCTAGGTGGATTCTT
29167768 TCCTAGGTATTGTCTATCTCATTGGTTAATATTTGATTATTTATTTGATT
66 TCCTAGGTATTGTCTATCTCATTGGTTAATATTTGATTATTTATTTGATT
29167818 CATTCTCTAT
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 104 0.91
115 10 0.09
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (115 bp):
AGACACAAGTGAATACGTCGTTTAATTCAAATTCATAATAATAAGCGAAGTCTAGGTGGATTCTT
TCCTAGGTATTGTCTATCTCATTGGTTAATATTTGATTATTTATTTGATT
Found at i:29168933 original size:21 final size:20
Alignment explanation
Indices: 29168904--29168942 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29168894 ATGCCTACGA
29168904 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
29168924 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
29168943 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:29169895 original size:59 final size:61
Alignment explanation
Indices: 29169831--29169948 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 61
29169821 ATCACTTTAA
* * *
29169831 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTATATTAAATTTAATATTAAGTCT
1 TATTAAATTAATAGAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAGTCT
*
29169890 TATTAACTTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAG
1 TATTAAATTAATAGAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAAG
29169949 ATAATCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.38
61 1 0.02
62 31 0.60
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAGTCT
Found at i:29169973 original size:20 final size:18
Alignment explanation
Indices: 29169926--29169974 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
29169916 CAAGATAAAC
29169926 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
29169943 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
29169963 ATTAAATTAATA
1 ATTAAATTAATA
29169975 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:29171535 original size:59 final size:61
Alignment explanation
Indices: 29171471--29171588 Score: 177
Period size: 62 Copynumber: 2.0 Consensus size: 61
29171461 ATCACTTTAA
* * *
29171471 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTATATTAAATTTAATATTAAGTCT
1 TATTAAATTAATAGAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAGTCT
*
29171530 TATTAACTTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAG
1 TATTAAATTAATAGAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAAG
29171589 ATAATCACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.38
61 1 0.02
62 31 0.60
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAGTCT
Found at i:29171613 original size:20 final size:18
Alignment explanation
Indices: 29171566--29171614 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
29171556 CAAGATAAAC
29171566 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
29171583 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
29171603 ATTAAATTAATA
1 ATTAAATTAATA
29171615 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:29175252 original size:20 final size:20
Alignment explanation
Indices: 29175229--29175266 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29175219 ATAATTAATC
*
29175229 TAGTTTAATTATCTTAAACT
1 TAGTTTAATTAACTTAAACT
*
29175249 TAGTTTTATTAACTTAAA
1 TAGTTTAATTAACTTAAA
29175267 GCAACTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (20 bp):
TAGTTTAATTAACTTAAACT
Found at i:29175693 original size:17 final size:17
Alignment explanation
Indices: 29175671--29175710 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
29175661 ATAAATATTT
29175671 AAAATTAACATTAAA-TA
1 AAAATTAA-ATTAAATTA
29175688 AAAATTAAATTAAATTA
1 AAAATTAAATTAAATTA
29175705 AAAATT
1 AAAATT
29175711 TTATCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAAATTAAATTA
Found at i:29190292 original size:56 final size:56
Alignment explanation
Indices: 29190229--29190433 Score: 383
Period size: 56 Copynumber: 3.7 Consensus size: 56
29190219 GGGAATGAGA
*
29190229 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
29190285 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
29190341 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
* *
29190397 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29190434 CCAAGATAAG
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 146 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (56 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
Found at i:29190331 original size:46 final size:51
Alignment explanation
Indices: 29190229--29190581 Score: 265
Period size: 56 Copynumber: 6.7 Consensus size: 51
29190219 GGGAATGAGA
*
29190229 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC--TATTGA-G-TAT-AGAGG
29190285 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC--TATTGA-G-TAT-AGAGG
29190341 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC--TATTGA-G-TAT-AGAGG
* * ***
29190397 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGC-ACCAAG-ATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTATTGAGTAT-AGAGG
** * * ** **
29190447 TCCCCCGTAAGACCATGTCTGAGACATGGCATGGGC-ACCGA-TATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTATTGAGTAT-AGAGG
* * ** * **
29190497 TCCCAATGTAAGACC-TATCTGGGATATGAAATTGG-TAGTAT-AGGA-A-ACA
1 TCCC-ATGTAAGACCATGTCTGGGACATGGCATTGGCTA-T-TGAGTATAGAGG
*
29190546 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC
29190582 ATGTTATTAT
Statistics
Matches: 256, Mismatches: 33, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
48 10 0.04
49 20 0.08
50 68 0.27
51 9 0.04
52 2 0.01
53 2 0.01
56 145 0.57
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTATTGAGTATAGAGG
Found at i:29190467 original size:50 final size:53
Alignment explanation
Indices: 29190229--29190485 Score: 277
Period size: 56 Copynumber: 4.7 Consensus size: 53
29190219 GGGAATGAGA
* * **
29190229 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AGG-TATGAGAGG
* **
29190285 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AGG-TATGAGAGG
* **
29190341 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AGG-TATGAGAGG
* *
29190397 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-A-G-ATAAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATGAGAGG
* * *
29190447 TCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACC
29190486 GATATGAGAA
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
50 42 0.22
52 1 0.01
53 1 0.01
56 147 0.77
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (53 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATGAGAGG
Found at i:29196974 original size:56 final size:50
Alignment explanation
Indices: 29196908--29197045 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
29196898 GGGAATGAGA
* ** *
29196908 TCCCATGTAAGACCATGTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTG-CA--ACCGA-G--ATAAGAGG
* *
29196964 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGAACCGAGATAAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGCAACCGAGATAAGAGG
*
29197014 TCCCCCGTAAGACCATGTCTGGGACATGGCAT
1 TCCCACGTAAGACCATGTCTGGGACATGGCAT
29197046 GGGCACCATA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 37 0.50
52 1 0.01
53 3 0.04
55 1 0.01
56 32 0.43
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGCAACCGAGATAAGAGG
Found at i:29199212 original size:20 final size:20
Alignment explanation
Indices: 29199184--29199221 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29199174 AATTTTTCTC
*
29199184 CTAAATTTTAATTTTATTAT
1 CTAAATTTTAAATTTATTAT
*
29199204 CTAATTTTTAAATTTATT
1 CTAAATTTTAAATTTATT
29199222 GAATTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
CTAAATTTTAAATTTATTAT
Found at i:29199251 original size:25 final size:25
Alignment explanation
Indices: 29199199--29199251 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
29199189 TTTTAATTTT
* *
29199199 ATTATCTAATTTTTAAATTTATTGA
1 ATTATCTAATTTTTAAATTAATTAA
*
29199224 ATTAT-TAATATTTTATATTAATTAA
1 ATTATCTAAT-TTTTAAATTAATTAA
29199249 ATT
1 ATT
29199252 TTTGAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTATCTAATTTTTAAATTAATTAA
Found at i:29224352 original size:8 final size:8
Alignment explanation
Indices: 29224339--29224380 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
29224329 GGCTATATAA
29224339 AAAATTAT
1 AAAATTAT
29224347 AAAATTAT
1 AAAATTAT
29224355 AAAATTAT
1 AAAATTAT
*
29224363 AAAATGAT
1 AAAATTAT
*
29224371 ATAA-TAT
1 AAAATTAT
29224378 AAA
1 AAA
29224381 TATATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Done.