Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 66 of 182
Found at i:21184271 original size:21 final size:20
Alignment explanation
Indices: 21184247--21184286 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
21184237 AACTTTTTAT
21184247 ATTT-TTTTAATTTTAATTTTG
1 ATTTATTTT-ATTTT-ATTTTG
21184268 ATTTATTTTATTTTATTTT
1 ATTTATTTTATTTTATTTT
21184287 AATAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
ATTTATTTTATTTTATTTTG
Found at i:21188879 original size:41 final size:41
Alignment explanation
Indices: 21188764--21189088 Score: 395
Period size: 41 Copynumber: 8.0 Consensus size: 41
21188754 TTTGGACAGA
* *
21188764 AAGCGCCACTAAAGGT-AGAGCAATAGCAGCGCTTATGGGA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
* * *
21188804 AAGCGACGCTAAAGGT-AGAGCAATAGCAGCGCTTACGGTC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
* * *
21188844 AAGCGCCGCTAAAGGTCAGATCAATAGCAGCGCTTACGGTC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
* * * * * *
21188885 AAGCACCGCTACAGGTCAGATCAATAGCGGCCCTTACGGGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
* * *
21188926 AAACGCCGCTAAAGGTCAGAGTAATAGC-GACACTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAG-CGCTTATGGGC
* *
21188967 AAGCACCTCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
* * * * *
21189008 AAGCGCCGTTAAAGGTCAGAGCAATAACGGCGCTTATGAGA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
*
21189049 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGG
21189089 AAAAACGCAA
Statistics
Matches: 248, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
40 51 0.21
41 196 0.79
42 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGGC
Found at i:21191201 original size:12 final size:12
Alignment explanation
Indices: 21191184--21191213 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21191174 CTGATAGTGT
21191184 GAAGAAGAAGAG
1 GAAGAAGAAGAG
*
21191196 GAAGAAGAAGAT
1 GAAGAAGAAGAG
21191208 GAAGAA
1 GAAGAA
21191214 CCATAAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:21196195 original size:43 final size:42
Alignment explanation
Indices: 21196148--21196405 Score: 241
Period size: 43 Copynumber: 6.3 Consensus size: 42
21196138 TTTGTTAATG
* *
21196148 TTAGCAGCGTTTGTGGGAAAAGTGCCCTTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCC-TAAAGATCATGTTCT
* *
21196191 TTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGATTATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCC-CTAAAGATCATGTTCT
*
21196234 TTAGCGGTGTTTGTGGG---A-------AAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCCTAAAGATCATGTTCT
*
21196266 TTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTT-T
1 TTAGCGGCGTTTGTGGGAAAAGCGCC-CTAAAGATCATGTTCT
* * * *
21196308 TTAGCGGCGTTTGTGGGAAAAGCATCGCTAAAGACCATGTTAT
1 TTAGCGGCGTTTGTGGGAAAAGC-GCCCTAAAGATCATGTTCT
* * * * * *
21196351 TTAGCGGCGTTTGTAGGAAAAACTTCGCTAAAGACCATGATCT
1 TTAGCGGCGTTTGTGGGAAAAGC-GCCCTAAAGATCATGTTCT
*
21196394 TTAGTGGCGTTT
1 TTAGCGGCGTTT
21196406 TTCCTCATAA
Statistics
Matches: 183, Mismatches: 18, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
32 29 0.16
35 1 0.01
40 1 0.01
42 36 0.20
43 115 0.63
44 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (42 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCCTAAAGATCATGTTCT
Found at i:21196263 original size:32 final size:32
Alignment explanation
Indices: 21196220--21196287 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
21196210 AAGCGCCGCT
* *
21196220 AAAGATTATGTTCTTTAGCGGTGTTTGTGGGA
1 AAAGATCATGTTCTTTAGCGGCGTTTGTGGGA
21196252 AAAGATCATGTTCTTTAGCGGCGTTTGTGGGA
1 AAAGATCATGTTCTTTAGCGGCGTTTGTGGGA
21196284 AAAG
1 AAAG
21196288 CGCCGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.35
Consensus pattern (32 bp):
AAAGATCATGTTCTTTAGCGGCGTTTGTGGGA
Found at i:21196300 original size:75 final size:74
Alignment explanation
Indices: 21196177--21196329 Score: 261
Period size: 75 Copynumber: 2.1 Consensus size: 74
21196167 AAGTGCCCTT
* *
21196177 AAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGATTATGTTCTTTAGCGGT
1 AAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTT-TTTAGCGGC
21196242 GTTTGTGGGA
65 GTTTGTGGGA
* *
21196252 AAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTTTTTAGCGGCG
1 AAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTTTTAGCGGCG
21196317 TTTGTGGGA
66 TTTGTGGGA
21196326 AAAG
1 AAAG
21196330 CATCGCTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 22 0.30
75 52 0.70
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (74 bp):
AAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTTTTAGCGGCG
TTTGTGGGA
Found at i:21196355 original size:117 final size:118
Alignment explanation
Indices: 21196148--21196371 Score: 342
Period size: 117 Copynumber: 1.9 Consensus size: 118
21196138 TTTGTTAATG
*
21196148 TTAGCAGCGTTTGTGGGAAAAGTGCCCTTAAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAG
1 TTAGCAGCGTTTGTGGGAAAAGCGCCCTTAAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAG
* ** * * *
21196213 CGCCGCTAAAGATTATGTTCTTTAGCGGTGTTTGTGGGAAAAGATCATGTTCT
66 CACCGCTAAAGACCATGTTATTTAGCGGCGTTTGTAGGAAAAGATCATGTTCT
* * *
21196266 TTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGATCATGTT-TTTAGCGGCGTTTGTGGGAAAAG
1 TTAGCAGCGTTTGTGGGAAAAGCGCCCTTAAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAG
*
21196330 CATCGCTAAAGACCATGTTATTTAGCGGCGTTTGTAGGAAAA
66 CACCGCTAAAGACCATGTTATTTAGCGGCGTTTGTAGGAAAA
21196372 ACTTCGCTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
117 57 0.60
118 38 0.40
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (118 bp):
TTAGCAGCGTTTGTGGGAAAAGCGCCCTTAAAGATCATGTTCTTTAGCGACGTTTGTGGGAAAAG
CACCGCTAAAGACCATGTTATTTAGCGGCGTTTGTAGGAAAAGATCATGTTCT
Found at i:21197998 original size:22 final size:23
Alignment explanation
Indices: 21197948--21197998 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
21197938 AGTATCAGTT
** *
21197948 TTTTTTTAAGTATTTATTATTTA
1 TTTTTTTAAAAATTTATAATTTA
21197971 -TTTTTTAAAAATTTA-AATTTA
1 TTTTTTTAAAAATTTATAATTTA
21197992 TTTTTTT
1 TTTTTTT
21197999 GAAACCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTTAAAAATTTATAATTTA
Found at i:21198082 original size:18 final size:18
Alignment explanation
Indices: 21198059--21198094 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21198049 ATTATATAAT
21198059 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
21198077 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
21198095 TTTTTGAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:21198150 original size:102 final size:103
Alignment explanation
Indices: 21198003--21198232 Score: 367
Period size: 102 Copynumber: 2.2 Consensus size: 103
21197993 TTTTTTGAAA
* *
21198003 CCATTTTAAATTGTGCTAACCAATTGATTTTTGTTTTTTATTATTTATTATATAATATTTAAATA
1 CCATTTTAAATTGCGC-CACCAATTGATTTTTGTTTTTTATTATTTATTATATAATATTTAAATA
21198068 TATAGTTTAATTTAAATGTATATTTTATTTTT-G-AGAG
65 TATAGTTTAATTTAAATGTATATTTTATTTTTGGTAGAG
*
21198105 TCATTTTAAATTGCGCCATCCAATTGATTTTT-TATTTTTATTATTTATTATATAATATTTAAAT
1 CCATTTTAAATTGCGCCA-CCAATTGATTTTTGT-TTTTTATTATTTATTATATAATATTTAAAT
*
21198169 ATATAGTTTAATTTAAATGTATATTTTATTTTTGGTGGAG
64 ATATAGTTTAATTTAAATGTATATTTTATTTTTGGTAGAG
*
21198209 CCATTTTAAATGGCGCCACCAATT
1 CCATTTTAAATTGCGCCACCAATT
21198233 CCCGATGATC
Statistics
Matches: 118, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
101 2 0.02
102 90 0.76
103 7 0.06
104 19 0.16
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (103 bp):
CCATTTTAAATTGCGCCACCAATTGATTTTTGTTTTTTATTATTTATTATATAATATTTAAATAT
ATAGTTTAATTTAAATGTATATTTTATTTTTGGTAGAG
Found at i:21198184 original size:18 final size:18
Alignment explanation
Indices: 21198161--21198196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21198151 ATTATATAAT
21198161 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
21198179 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
21198197 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:21203446 original size:11 final size:11
Alignment explanation
Indices: 21203416--21203440 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21203406 AATCCTTAGC
21203416 TTTAAAATAAA
1 TTTAAAATAAA
21203427 TTTAAAATAAA
1 TTTAAAATAAA
21203438 TTT
1 TTT
21203441 TTAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAATAAA
Found at i:21203898 original size:13 final size:13
Alignment explanation
Indices: 21203880--21203905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21203870 ACCACCTTTC
21203880 CTTCTTCTCTTCT
1 CTTCTTCTCTTCT
21203893 CTTCTTCTCTTCT
1 CTTCTTCTCTTCT
21203906 AATTCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTCTCTTCT
Found at i:21222093 original size:26 final size:26
Alignment explanation
Indices: 21222064--21222113 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
21222054 CCAGAAATTC
21222064 AGCTCATAC-AAGCCCAGACAGAGTTT
1 AGCTCATACGAA-CCCAGACAGAGTTT
* *
21222090 AGCTCTTACGAACCCAGATAGAGT
1 AGCTCATACGAACCCAGACAGAGT
21222114 ATTGCTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (26 bp):
AGCTCATACGAACCCAGACAGAGTTT
Found at i:21222206 original size:52 final size:50
Alignment explanation
Indices: 21222117--21222232 Score: 142
Period size: 52 Copynumber: 2.3 Consensus size: 50
21222107 ATAGAGTATT
* * ** * *
21222117 GCTCTTATGAGCCAGAAAGAATTACGGTCTTGTGAGCCAGAATTAGATTTAC
1 GCTCTTACGAGCCAGAAAGAATTACGCTCTTACGAGCCA-AA-CAGAATTAC
* *
21222169 GCTCTTACGAGCCAGACAGAATTACGCTCTTACGAGCCAAACAGAATTAT
1 GCTCTTACGAGCCAGAAAGAATTACGCTCTTACGAGCCAAACAGAATTAC
21222219 GCTCTTACGAGCCA
1 GCTCTTACGAGCCA
21222233 AAATCAGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 20 0.36
51 2 0.04
52 34 0.61
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
GCTCTTACGAGCCAGAAAGAATTACGCTCTTACGAGCCAAACAGAATTAC
Found at i:21222233 original size:25 final size:25
Alignment explanation
Indices: 21222117--21222234 Score: 130
Period size: 25 Copynumber: 4.6 Consensus size: 25
21222107 ATAGAGTATT
*
21222117 GCTCTTATGAGCCAGAA-AGAATTAC
1 GCTCTTACGAGCCA-AACAGAATTAC
* ** * *
21222142 GGTCTTGTGAGCCAGAATTAGATTTAC
1 GCTCTTACGAGCCA-AA-CAGAATTAC
*
21222169 GCTCTTACGAGCCAGACAGAATTAC
1 GCTCTTACGAGCCAAACAGAATTAC
*
21222194 GCTCTTACGAGCCAAACAGAATTAT
1 GCTCTTACGAGCCAAACAGAATTAC
21222219 GCTCTTACGAGCCAAA
1 GCTCTTACGAGCCAAA
21222235 ATCAGATTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
25 61 0.76
26 1 0.01
27 18 0.22
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATTAC
Found at i:21228886 original size:17 final size:17
Alignment explanation
Indices: 21228866--21228900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21228856 CAAAATTAAA
21228866 TTTTTATAA-ATGTTTAT
1 TTTTTA-AATATGTTTAT
21228883 TTTTTAAATATGTTTAT
1 TTTTTAAATATGTTTAT
21228900 T
1 T
21228901 AAATTATGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTTTAAATATGTTTAT
Found at i:21230642 original size:9 final size:9
Alignment explanation
Indices: 21230603--21230646 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
21230593 ATTTTATTTT
21230603 TAAAAATTA
1 TAAAAATTA
*
21230612 TTAAAATTA
1 TAAAAATTA
*
21230621 TTAAGAAAGTA
1 -TAA-AAATTA
21230632 TAAAAATTA
1 TAAAAATTA
21230641 TAAAAA
1 TAAAAA
21230647 AACATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 19 0.66
10 5 0.17
11 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:21230728 original size:20 final size:20
Alignment explanation
Indices: 21230699--21230737 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21230689 GTTGATATAT
21230699 CATCCACATGTATGTCATGC
1 CATCCACATGTATGTCATGC
*
21230719 CATCCGCATGTATGTCATG
1 CATCCACATGTATGTCATG
21230738 TCACTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (20 bp):
CATCCACATGTATGTCATGC
Found at i:21234133 original size:45 final size:46
Alignment explanation
Indices: 21234060--21234153 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 46
21234050 GAGCGAAACC
* ** * *
21234060 TTATCACAGAGAGCTCGTATAGGGAGCTTGGC-TGATACATAGCTTA
1 TTATCACAAAGAGCTCACATAGGGAGCTT-GCTTGATACACAACTTA
21234106 TTATCACAAAGAGCTCACATA-GGAGCTTGCTTGATACACAACTTA
1 TTATCACAAAGAGCTCACATAGGGAGCTTGCTTGATACACAACTTA
21234151 TTA
1 TTA
21234154 AAACCGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.05
45 22 0.52
46 18 0.43
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (46 bp):
TTATCACAAAGAGCTCACATAGGGAGCTTGCTTGATACACAACTTA
Found at i:21234873 original size:26 final size:26
Alignment explanation
Indices: 21234810--21234873 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
21234800 AGTTTAGCGT
21234810 TACTTTTGAAAAATATTTTTAAAAAG
1 TACTTTTGAAAAATATTTTTAAAAAG
* ** * *
21234836 T-GTGGTGAAAAAATATTTTTGATAAG
1 TACTTTTG-AAAAATATTTTTAAAAAG
21234862 TACTTTTGAAAA
1 TACTTTTGAAAA
21234874 TTTTGATTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
25 3 0.11
26 22 0.79
27 3 0.11
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (26 bp):
TACTTTTGAAAAATATTTTTAAAAAG
Found at i:21235122 original size:24 final size:23
Alignment explanation
Indices: 21235073--21235122 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
21235063 TTAATATATG
* *
21235073 AAATATTAATTTTAAATATTTTT
1 AAATATTAATATTAAATATTTAT
* *
21235096 AAATAATTAATATTAATTCTTTAT
1 AAAT-ATTAATATTAAATATTTAT
21235120 AAA
1 AAA
21235123 ATCTAATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAT
Found at i:21235256 original size:14 final size:14
Alignment explanation
Indices: 21235222--21235274 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
21235212 AAAAATATTT
*
21235222 TTTATTTTAAATTA
1 TTTATTTTAAAATA
* *
21235236 ATGATTTTAAAATA
1 TTTATTTTAAAATA
21235250 TTTATTTT---AT-
1 TTTATTTTAAAATA
21235260 TTTATTTTAAAATA
1 TTTATTTTAAAATA
21235274 T
1 T
21235275 AATTTGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
10 8 0.27
11 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTATTTTAAAATA
Found at i:21238270 original size:55 final size:54
Alignment explanation
Indices: 21238169--21238280 Score: 127
Period size: 55 Copynumber: 2.1 Consensus size: 54
21238159 TAAATGCATG
* * * *
21238169 GAATAGGGGCACACGGTCGTGTGTCAGCCCGTGTCCCTGCCTGTGTGTGTATAC
1 GAATAGGGGCACACGGTCGTGTATCAGCACGTGTCCCTACCCGTGTGTGTATAC
* * * *
21238223 GAATGGGGGACACACGGTCGTGTATTAGCACGTGCTCCC-ACCCGTGTGTTTATTC
1 GAATAGGGG-CACACGGTCGTGTATCAGCACGTG-TCCCTACCCGTGTGTGTATAC
21238278 GAA
1 GAA
21238281 GTGATGTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
54 8 0.17
55 36 0.75
56 4 0.08
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (54 bp):
GAATAGGGGCACACGGTCGTGTATCAGCACGTGTCCCTACCCGTGTGTGTATAC
Found at i:21240594 original size:31 final size:31
Alignment explanation
Indices: 21240559--21240620 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
21240549 ATTGATAGGT
21240559 GCACTTGCCTTAGTCATAATTTTAGTTAGTA
1 GCACTTGCCTTAGTCATAATTTTAGTTAGTA
21240590 GCACTTGCCTTAGTCATAATTTTAGTTAGTA
1 GCACTTGCCTTAGTCATAATTTTAGTTAGTA
21240621 TCGACTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (31 bp):
GCACTTGCCTTAGTCATAATTTTAGTTAGTA
Found at i:21243446 original size:8 final size:8
Alignment explanation
Indices: 21243425--21243463 Score: 60
Period size: 8 Copynumber: 4.6 Consensus size: 8
21243415 AAATGAAGAA
21243425 AAAAATTC
1 AAAAATTC
21243433 AAAAAAATTC
1 --AAAAATTC
21243443 AAAAATTC
1 AAAAATTC
21243451 AAAAATTC
1 AAAAATTC
21243459 AAAAA
1 AAAAA
21243464 AAAAATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
10 8 0.28
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATTC
Found at i:21243503 original size:18 final size:17
Alignment explanation
Indices: 21243477--21243590 Score: 99
Period size: 17 Copynumber: 6.5 Consensus size: 17
21243467 AATTAGTATA
21243477 TTTATTTTCATTTTCAT
1 TTTATTTTCATTTTCAT
21243494 TTTCATTTTCATTTTCATT
1 TTT-ATTTTCATTTTCA-T
* *
21243513 TTTATTTTTATTTTTAT
1 TTTATTTTCATTTTCAT
* *
21243530 TTTATTTTTATTTTTAT
1 TTTATTTTCATTTTCAT
21243547 GTTTAGTTTT-AGTTTT-AGT
1 -TTTA-TTTTCA-TTTTCA-T
*
21243566 TTTATTTT-ATTTTTATT
1 TTTATTTTCATTTTCA-T
21243583 TTTATTTT
1 TTTATTTT
21243591 AATTATGCAC
Statistics
Matches: 87, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.05
17 36 0.41
18 34 0.39
19 13 0.15
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTATTTTCATTTTCAT
Found at i:21243544 original size:6 final size:6
Alignment explanation
Indices: 21243477--21243590 Score: 133
Period size: 6 Copynumber: 19.3 Consensus size: 6
21243467 AATTAGTATA
* * * * *
21243477 TTTATT TTCATT TTCATT TTCATT TTCATT TTCATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * * *
21243525 TTTA-T TTTATT TTTATT TTTATG TTTAGT TTTAGT TTTAGT TTTA-T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
21243571 TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TT
21243591 AATTATGCAC
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
5 10 0.10
6 91 0.90
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:21247820 original size:22 final size:22
Alignment explanation
Indices: 21247795--21247862 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
21247785 AACATTTGAG
21247795 AATTTATTATTTTTCATTATTT
1 AATTTATTATTTTTCATTATTT
* *
21247817 AATTGAGTTTATTTTAT-ATCTATTA
1 AATTTA--TTATTTT-TCAT-TATTT
*
21247842 AATTTA-TATTTTACATTATTT
1 AATTTATTATTTTTCATTATTT
21247863 TTACATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
21 4 0.11
22 13 0.36
24 9 0.25
25 10 0.28
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (22 bp):
AATTTATTATTTTTCATTATTT
Found at i:21251108 original size:12 final size:13
Alignment explanation
Indices: 21251076--21251115 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
21251066 ATGATGAGTC
*
21251076 TGGCTGAAGCTGA
1 TGGCTGAGGCTGA
*
21251089 TAGCTGAGGCTGA
1 TGGCTGAGGCTGA
21251102 -GGCTGAGGCTGA
1 TGGCTGAGGCTGA
21251114 TG
1 TG
21251116 AGTCTGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (13 bp):
TGGCTGAGGCTGA
Found at i:21253188 original size:6 final size:7
Alignment explanation
Indices: 21253155--21253185 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
21253145 ATGTGACATT
21253155 ATATTAA
1 ATATTAA
21253162 ATATTAA
1 ATATTAA
21253169 ATATTAA
1 ATATTAA
21253176 ATA-TAA
1 ATATTAA
21253182 ATAT
1 ATAT
21253186 AAACATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATTAA
Found at i:21254291 original size:30 final size:27
Alignment explanation
Indices: 21254253--21254318 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 27
21254243 TAAATCTCAA
*
21254253 AATTATACATGAACTTTGATTTAATGTGC
1 AATTATACATGAACTTTAATTT--TGTGC
21254282 AATTGATACATGAACTTTAATTTTGTGC
1 AATT-ATACATGAACTTTAATTTTGTGC
21254310 AATTATACA
1 AATTATACA
21254319 CGTGAAACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 5 0.14
28 9 0.26
29 4 0.11
30 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (27 bp):
AATTATACATGAACTTTAATTTTGTGC
Found at i:21254552 original size:29 final size:30
Alignment explanation
Indices: 21254507--21254565 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
21254497 GGATTAGATC
21254507 AAATCAAAATTTCATGTATAAAATTATACA
1 AAATCAAAATTTCATGTATAAAATTATACA
* * *
21254537 AAATCAAAGTTT-ATGTATACAATTGTACA
1 AAATCAAAATTTCATGTATAAAATTATACA
21254566 TTAAACCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTATACA
Found at i:21267193 original size:20 final size:18
Alignment explanation
Indices: 21267160--21267204 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 18
21267150 TAAATTGATC
21267160 TAAATTTATTTTTAAATT
1 TAAATTTATTTTTAAATT
21267178 TAAATTTATCTTTTTAAATT
1 TAAATTTA--TTTTTAAATT
21267198 TAAATTT
1 TAAATTT
21267205 GCTTTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTATTTTTAAATT
Found at i:21268989 original size:58 final size:57
Alignment explanation
Indices: 21268915--21269109 Score: 161
Period size: 58 Copynumber: 3.4 Consensus size: 57
21268905 TTTCTAGGGG
*
21268915 TAAAATGGTAATTTTTGTGAAATCGAGGCTAAAAATGGAATTTGGAAAGTTTGGGGAA
1 TAAAATGGTAAATTTTGTGAAATCGAGG-TAAAAATGGAATTTGGAAAGTTTGGGGAA
* * *
21268973 TAAAATGGTAAATTTTG-GCAAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTTGGAGGCAA
1 TAAAATGGTAAATTTTGTG--AAATCGAGGT-AAAAATGGAA-TTTGGAAAGTTTGG-GG-AA
* * * * * * *
21269035 -AACA--GTAAGTTTTGGTGAAATCGGGGTTAAAATGGGATTTAGGGAAGTTTGGGG-G
1 TAAAATGGTAAATTTT-GTGAAATCGAGGTAAAAATGGAATTT-GGAAAGTTTGGGGAA
21269090 TAAAATGGT-AATTTT-TGAAA
1 TAAAATGGTAAATTTTGTGAAA
21269110 GTTTTGGGGT
Statistics
Matches: 109, Mismatches: 16, Indels: 27
0.72 0.11 0.18
Matches are distributed among these distances:
55 5 0.05
56 3 0.03
57 11 0.10
58 36 0.33
59 31 0.28
60 15 0.14
61 6 0.06
62 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (57 bp):
TAAAATGGTAAATTTTGTGAAATCGAGGTAAAAATGGAATTTGGAAAGTTTGGGGAA
Found at i:21269118 original size:30 final size:29
Alignment explanation
Indices: 21269087--21269377 Score: 289
Period size: 30 Copynumber: 9.7 Consensus size: 29
21269077 GGAAGTTTGG
* *
21269087 GGGT-AAAATGGTAATTTTTGAAAGTTTTG
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTTA
* * **
21269116 GGGTCAAAGTATAATTTTCAAAAAGTTTTA
1 GGGTCAAAATGTAATTTT-GGAAAGTTTTA
* *
21269146 GGGTCGAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
*
21269176 GGGTCAAAATATAATTTTGGAAAAG-TTTA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
* * *
21269205 GGGGTTAAAATGTAATTTTTAGAAAGTTTCA
1 -GGGTCAAAATGTAA-TTTTGGAAAGTTTTA
* * *
21269236 AGGTCAAAATATAATTTTCAGAAAGTTTTA
1 GGGTCAAAATGTAATTTT-GGAAAGTTTTA
*
21269266 AGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
21269296 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
* * *
21269326 GGGTCAAAATATAATTTTTAGAAAGTTTTT
1 GGGTCAAAATGTAA-TTTTGGAAAGTTTTA
*
21269356 GGGTCGAAATGTAATTTCTGGA
1 GGGTCAAAATGTAATTT-TGGA
21269378 CAATTTAGGG
Statistics
Matches: 221, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.10
30 186 0.84
31 13 0.06
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTTA
Found at i:21269202 original size:90 final size:90
Alignment explanation
Indices: 21269079--21269377 Score: 352
Period size: 90 Copynumber: 3.3 Consensus size: 90
21269069 GGATTTAGGG
* * * *
21269079 AAGTTTGGGGGT-AAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAGTATAATTTTCAAAAAGT
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGT
* * *
21269142 TTTAGGGTCGAAATGTAATTTT-GGAA
65 TTTAGGGTCAAAATATAATTTTCAG-A
* * * * *
21269168 AAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTT
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTT
* *
21269233 TCAAGGTCAAAATATAATTTTCAGA
66 TTAGGGTCAAAATATAATTTTCAGA
** * **
21269258 AAGTTTTAAGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTT
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTT
*
21269323 TTAGGGTCAAAATATAATTTTTAGA
66 TTAGGGTCAAAATATAATTTTCAGA
* *
21269348 AAGTTTTTGGGTCGAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
21269378 CAATTTAGGG
Statistics
Matches: 177, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
89 19 0.11
90 153 0.86
91 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (90 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTCAAAAAGTT
TTAGGGTCAAAATATAATTTTCAGA
Found at i:21269770 original size:165 final size:164
Alignment explanation
Indices: 21269470--21269782 Score: 450
Period size: 165 Copynumber: 1.9 Consensus size: 164
21269460 ATTTGAAAAT
* *
21269470 CTTGGAAAATTTTCGGACCAATTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAATAA
1 CTTGAAAAATTTTCGGACCAATTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACAA
* * * *
21269535 ATTAAAAATAGAAAGGACTAAATGCATAAATAGGCCAAAAAATGACACGTGGCAACCTCTAGTGC
66 ATTAAAAATAGAAAGGACTAAATGAAGAAATAAGCCAAAAAATGACACGTGGCAACCTCTAGTAC
21269600 AGTCAAACAGTCAAAGGACTTCTTTATAATAAAC
131 AGTCAAACAGTCAAAGGACTTCTTTATAATAAAC
* *
21269634 CTTGAAAAATTGTT-GGACCAATTTTGTAATTAAATAAAAGTTGATTTAAGGATTAAATTAAAAC
1 CTTGAAAAATT-TTCGGACCAA-TTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAAC
* * * * * * *
21269698 AAATTAATAAT-GCCAGGGACTATATGAAGAAATAAGCCAAAACATGACACGTGGCAGCCTCTGG
64 AAATTAAAAATAG-AAAGGACTAAATGAAGAAATAAGCCAAAAAATGACACGTGGCAACCTCTAG
21269762 TACAGTCAAACAGTCAAAGGA
128 TACAGTCAAACAGTCAAAGGA
21269783 TTAAATTGAA
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
164 18 0.14
165 113 0.86
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (164 bp):
CTTGAAAAATTTTCGGACCAATTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACAA
ATTAAAAATAGAAAGGACTAAATGAAGAAATAAGCCAAAAAATGACACGTGGCAACCTCTAGTAC
AGTCAAACAGTCAAAGGACTTCTTTATAATAAAC
Found at i:21270310 original size:17 final size:18
Alignment explanation
Indices: 21270274--21270315 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21270264 TTTCCTCTTT
* *
21270274 TTTTTGTTCTTTTTTCCC
1 TTTTTATTCTATTTTCCC
*
21270292 TTTTTATTCTATTTTCCT
1 TTTTTATTCTATTTTCCC
21270310 TTTTTA
1 TTTTTA
21270316 CTTTCTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTATTCTATTTTCCC
Found at i:21271477 original size:49 final size:48
Alignment explanation
Indices: 21271416--21271511 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 48
21271406 TACTTTGTTA
* *
21271416 TTGAATTTGGGCTAGCCAAATTTAGCCCAATTGGGCTTGTAAAATGGG
1 TTGAATTTGGGCTAACCAAATTTAGCCCAATCGGGCTTGTAAAATGGG
* *
21271464 TTGAACTTTGGGCTAATCAAATTTGGCCCAATCGGGCTTGTAAAATGG
1 TTGAA-TTTGGGCTAACCAAATTTAGCCCAATCGGGCTTGTAAAATGG
21271512 ACTTTGGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 5 0.12
49 38 0.88
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (48 bp):
TTGAATTTGGGCTAACCAAATTTAGCCCAATCGGGCTTGTAAAATGGG
Found at i:21271592 original size:17 final size:16
Alignment explanation
Indices: 21271539--21271594 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
21271529 TAGTTTTAAG
21271539 TTTAAATTTATAATAAA
1 TTTAAA-TTATAATAAA
* *
21271556 TTCAAATT-TTATGCAAA
1 TTTAAATTATAAT--AAA
21271573 TTTAAATTCATAATAAA
1 TTTAAATT-ATAATAAA
21271590 TTTAA
1 TTTAA
21271595 TTTTAAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 23 0.74
19 3 0.10
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATTATAATAAA
Found at i:21272818 original size:30 final size:29
Alignment explanation
Indices: 21272782--21272883 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
21272772 GAACTTTTCC
21272782 AAAATTACATTTTTTACCTCAAAACTTACA
1 AAAATTACATTTTTTACCTCAAAACTT-CA
21272812 AAAATTACA-TTTTTACC-CTAAAACTTTCA
1 AAAATTACATTTTTTACCTC-AAAAC-TTCA
* * * * *
21272841 AAAATTCCATTTTTGACCTCGACACTTCC
1 AAAATTACATTTTTTACCTCAAAACTTCA
21272870 AAAATTACCATTTT
1 AAAATTA-CATTTT
21272884 ACCCCCGGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.02
29 32 0.52
30 27 0.44
31 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTTACCTCAAAACTTCA
Found at i:21272854 original size:59 final size:59
Alignment explanation
Indices: 21272749--21272887 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 59
21272739 CTAAACTATC
* * ** * *
21272749 CAAAAATCATATTTTTGACCCTTGAACTTTTCCAAAATTACATTTTTTACCTCAAAACTT
1 CAAAAATTACATTTTT-ACCCTAAAACTTTTCAAAAATTACATTTTTGACCTCAAAACTT
* * *
21272809 ACAAAAATTACATTTTTACCCTAAAAC-TTTCAAAAATTCCATTTTTGACCTCGACACTT
1 -CAAAAATTACATTTTTACCCTAAAACTTTTCAAAAATTACATTTTTGACCTCAAAACTT
*
21272868 CCAAAATTACCA-TTTTACCC
1 CAAAAATTA-CATTTTTACCC
21272888 CCGGATGTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 16 0.24
59 29 0.43
60 8 0.12
61 14 0.21
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTAAAACTTTTCAAAAATTACATTTTTGACCTCAAAACTT
Found at i:21272903 original size:58 final size:59
Alignment explanation
Indices: 21272841--21272954 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
21272831 AAAACTTTCA
*
21272841 AAAATTCCATTTTTGACCTCGACACTTC-CAAAATTACCATTTTACCCCCGGATGTTCG
1 AAAATTCCATTTTTGACCTCGACACTTCTAAAAATTACCATTTTACCCCCGGATGTTCG
* * ***
21272899 AAAATTCCGTTTTTGATCTCGATTTTTCTAAAAATTACCATTTTACCCCCGGATGT
1 AAAATTCCATTTTTGACCTCGACACTTCTAAAAATTACCATTTTACCCCCGGATGT
21272955 CTGAAACTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 23 0.47
59 26 0.53
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCTCGACACTTCTAAAAATTACCATTTTACCCCCGGATGTTCG
Found at i:21272941 original size:59 final size:58
Alignment explanation
Indices: 21272870--21273121 Score: 226
Period size: 59 Copynumber: 4.3 Consensus size: 58
21272860 CGACACTTCC
*
21272870 AAAATTACCATTTTACCCCCGGATGTTCGAAAATTCCGTTTTTGATCTCGATTTTTCTA
1 AAAATTACCATTTTACCCCCGGATG-TCGAAAATTCAGTTTTTGATCTCGATTTTTCTA
* * * * *
21272929 AAAATTACCATTTTACCCCCGGATGTCTGAAACTTCAGTTTTTAATCTTGATATTTCTT
1 AAAATTACCATTTTACCCCCGGATGTC-GAAAATTCAGTTTTTGATCTCGATTTTTCTA
* * * * * * *
21272988 AAAATTATCATTTGACCCTCGAATATCTAAAACTCTA-TTTTTGATCTCGATTTTT-TCA
1 AAAATTACCATTTTACCCCCGGATGTCGAAAATTC-AGTTTTTGATCTCGATTTTTCT-A
** * ** * * *
21273046 AAAATTACCATTTTACCCTTGGACGTATAAAATTTCA--TTTTAACCTCGAATTTTCCT-
1 AAAATTACCATTTTACCCCCGGATGTCGAAAA-TTCAGTTTTTGATCTCG-ATTTTTCTA
21273103 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
21273122 TCGACAGTCC
Statistics
Matches: 157, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
57 28 0.18
58 53 0.34
59 76 0.48
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGGATGTCGAAAATTCAGTTTTTGATCTCGATTTTTCTA
Found at i:21272971 original size:117 final size:114
Alignment explanation
Indices: 21272848--21273121 Score: 282
Period size: 117 Copynumber: 2.4 Consensus size: 114
21272838 TCAAAAATTC
* * * * * *
21272848 CATTTTTGACCTCGACACTTCCAAAATTACCATTTTACCCCCGGATGTTCGAAAATTCCGTTTTT
1 CATTTTTAACCTCGA-ATTTCCAAAATTACCATTTTACCCCCGAAT-ATCGAAAACTCCATTTTT
* * *
21272913 GATCTCGA-TTTTTCTAAAAATTACCATTTTACCCCCGGATGTCTGAAACTT
64 GATCTCGATTTTTTC-AAAAATTACCATTTTACCCCCGGACGTATAAAACTT
* * * * * * * *
21272964 CAGTTTTTAATCTTGATATTTCTTAAAATTATCATTTGACCCTCGAATATCTAAAACTCTATTTT
1 CA-TTTTTAACCTCGA-ATTTC-CAAAATTACCATTTTACCCCCGAATATCGAAAACTCCATTTT
** *
21273029 TGATCTCGATTTTTTCAAAAATTACCATTTTACCCTTGGACGTATAAAATTT
63 TGATCTCGATTTTTTCAAAAATTACCATTTTACCCCCGGACGTATAAAACTT
21273081 CA-TTTTAACCTCGAATTTTCCTAAAATTACCATTTTACCCC
1 CATTTTTAACCTCGAA-TTTCC-AAAATTACCATTTTACCCC
21273122 TCGACAGTCC
Statistics
Matches: 126, Mismatches: 27, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
114 1 0.01
115 30 0.24
116 2 0.02
117 67 0.53
118 26 0.21
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (114 bp):
CATTTTTAACCTCGAATTTCCAAAATTACCATTTTACCCCCGAATATCGAAAACTCCATTTTTGA
TCTCGATTTTTTCAAAAATTACCATTTTACCCCCGGACGTATAAAACTT
Found at i:21274079 original size:18 final size:18
Alignment explanation
Indices: 21274034--21274088 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
21274024 TTTGACATAC
21274034 ATCATCAATCATAATTCATA
1 ATCAT-AATCATAATT-ATA
*
21274054 ACTCATAATTATAATTATA
1 A-TCATAATCATAATTATA
21274073 ATCATAATCATAATTA
1 ATCATAATCATAATTA
21274089 ATATATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.44
19 4 0.12
20 10 0.31
21 4 0.12
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCATAATCATAATTATA
Found at i:21278360 original size:27 final size:27
Alignment explanation
Indices: 21278321--21278374 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21278311 TATAAGGGGG
*
21278321 TGGTGCCTACCTGACAGGCGGCACCAA
1 TGGTGCCTACCTGACAAGCGGCACCAA
* *
21278348 TGGTGCCTTCCTGTCAAGCGGCACCAA
1 TGGTGCCTACCTGACAAGCGGCACCAA
21278375 CCCGTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.19
Consensus pattern (27 bp):
TGGTGCCTACCTGACAAGCGGCACCAA
Found at i:21278416 original size:15 final size:15
Alignment explanation
Indices: 21278392--21278446 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21278382 TTTTATTACC
21278392 AAAATAATACAAAAA
1 AAAATAATACAAAAA
* ** *
21278407 AAAATTATACACCAG
1 AAAATAATACAAAAA
*
21278422 AATATAATACAAAAA
1 AAAATAATACAAAAA
21278437 AAAATTAATA
1 AAAA-TAATA
21278447 ACTTAAATAA
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.69, C:0.09, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATAATACAAAAA
Found at i:21278558 original size:21 final size:20
Alignment explanation
Indices: 21278532--21278576 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
21278522 ATAAGAATTA
21278532 TAAAAAA-TAATATTATAAAAT
1 TAAAAAATTAA-ATTA-AAAAT
*
21278553 TAAAAAATTAAATTAAATAT
1 TAAAAAATTAAATTAAAAAT
21278573 TAAA
1 TAAA
21278577 TAAGAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 11 0.50
22 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAAATTAAATTAAAAAT
Found at i:21282506 original size:6 final size:6
Alignment explanation
Indices: 21282495--21282535 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
21282485 ATATTTGCAT
*
21282495 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
21282536 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:21285785 original size:17 final size:17
Alignment explanation
Indices: 21285763--21285796 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21285753 CTTACAATAA
*
21285763 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
21285780 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
21285797 AAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:21288067 original size:4 final size:4
Alignment explanation
Indices: 21288058--21288084 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21288048 AATTATCGAA
21288058 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
21288085 CGGGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:21288325 original size:29 final size:29
Alignment explanation
Indices: 21288293--21288422 Score: 145
Period size: 30 Copynumber: 4.4 Consensus size: 29
21288283 GAAAATTTGA
21288293 GGGTCAAAACATAATTTTTGAAAGTTTAG
1 GGGTCAAAACATAATTTTTGAAAGTTTAG
* *
21288322 GGGTCAAAACATAATTTTAAGAAAG-TTCG
1 GGGTCAAAACATAATTTT-TGAAAGTTTAG
*
21288351 AGAGTCAAAACATAATTTTTGGAAAGTTTAG
1 -GGGTCAAAACATAATTTTT-GAAAGTTTAG
* * * *
21288382 GGGTGAAAACATTATTTGTGGAAAGTTTGG
1 GGGTCAAAACATAATTT-TTGAAAGTTTAG
*
21288412 GGGTTAAAACA
1 GGGTCAAAACA
21288423 CCATTTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
29 21 0.25
30 60 0.71
31 4 0.05
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (29 bp):
GGGTCAAAACATAATTTTTGAAAGTTTAG
Found at i:21288348 original size:30 final size:29
Alignment explanation
Indices: 21288190--21288422 Score: 156
Period size: 29 Copynumber: 8.0 Consensus size: 29
21288180 GTAAAAATGA
* *
21288190 AATTTTGAAAAGTTT--GGGCCAAAACAT
1 AATTTTGGAAAGTTTAGGGGTCAAAACAT
* * * * **
21288217 AGTTTTTGGAAAATTTA-GGGACCAAATTT
1 A-ATTTTGGAAAGTTTAGGGGTCAAAACAT
* * *
21288246 GAATTTTGGGAAGTTTA-AGGTC-AAATAT
1 -AATTTTGGAAAGTTTAGGGGTCAAAACAT
*
21288274 GAATTATTGGAAAATTT-GAGGGTCAAAACAT
1 -AATT-TTGGAAAGTTTAG-GGGTCAAAACAT
*
21288305 AATTTTTGAAAGTTTAGGGGTCAAAACAT
1 AATTTTGGAAAGTTTAGGGGTCAAAACAT
* * *
21288334 AATTTTAAGAAAG-TTCGAGAGTCAAAACAT
1 AATTTT-GGAAAGTTTAG-GGGTCAAAACAT
*
21288364 AATTTTTGGAAAGTTTAGGGGTGAAAACAT
1 AA-TTTTGGAAAGTTTAGGGGTCAAAACAT
* * *
21288394 TATTTGTGGAAAGTTTGGGGGTTAAAACA
1 AATTT-TGGAAAGTTTAGGGGTCAAAACA
21288423 CCATTTTTAA
Statistics
Matches: 164, Mismatches: 29, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 21 0.13
29 65 0.40
30 65 0.40
31 12 0.07
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (29 bp):
AATTTTGGAAAGTTTAGGGGTCAAAACAT
Found at i:21288430 original size:60 final size:58
Alignment explanation
Indices: 21288275--21288422 Score: 188
Period size: 60 Copynumber: 2.5 Consensus size: 58
21288265 GTCAAATATG
*
21288275 AATTATTGGAAAATTTGAGGGTCAAAACATAATTTTTGAAAGTTTAGGGGTCAAAACAT
1 AATT-TTGGAAAGTTTGAGGGTCAAAACATAATTTTTGAAAGTTTAGGGGTCAAAACAT
* * * *
21288334 AATTTTAAGAAAGTTCGAGAGTCAAAACATAATTTTTGGAAAGTTTAGGGGTGAAAACAT
1 AATTTT-GGAAAGTTTGAGGGTCAAAACATAATTTTT-GAAAGTTTAGGGGTCAAAACAT
* * *
21288394 TATTTGTGGAAAGTTTGGGGGTTAAAACA
1 AATTT-TGGAAAGTTTGAGGGTCAAAACA
21288423 CCATTTTTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
58 2 0.03
59 30 0.40
60 42 0.56
61 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (58 bp):
AATTTTGGAAAGTTTGAGGGTCAAAACATAATTTTTGAAAGTTTAGGGGTCAAAACAT
Found at i:21294606 original size:22 final size:22
Alignment explanation
Indices: 21294578--21294662 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
21294568 TACACCACAC
21294578 TAGAGAGCACCGAAGTGCTAAG
1 TAGAGAGCACCGAAGTGCTAAG
** * *
21294600 TAGAGAGCACTAAAATGCTGA-
1 TAGAGAGCACCGAAGTGCTAAG
21294621 TCAGAGAGCACCGAAGTGCTAAG
1 T-AGAGAGCACCGAAGTGCTAAG
* *
21294644 TAGAGAACATCGAAGTGCT
1 TAGAGAGCACCGAAGTGCT
21294663 GAACAGAGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 49 0.96
23 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.16
Consensus pattern (22 bp):
TAGAGAGCACCGAAGTGCTAAG
Found at i:21294663 original size:44 final size:44
Alignment explanation
Indices: 21294579--21294672 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
21294569 ACACCACACT
* *
21294579 AGAGAGCACCGAAGTGCTAAGTAGAGAGCACTAAAATGCTGATC
1 AGAGAGCACCGAAGTGCTAAGTAGAGAACACTAAAATGCTGAAC
* *
21294623 AGAGAGCACCGAAGTGCTAAGTAGAGAACA-TCGAAGTGCTGAAC
1 AGAGAGCACCGAAGTGCTAAGTAGAGAACACT-AAAATGCTGAAC
21294667 AGAGAG
1 AGAGAG
21294673 AACATAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 44 0.98
ACGTcount: A:0.39, C:0.17, G:0.30, T:0.14
Consensus pattern (44 bp):
AGAGAGCACCGAAGTGCTAAGTAGAGAACACTAAAATGCTGAAC
Found at i:21302533 original size:21 final size:23
Alignment explanation
Indices: 21302502--21302548 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
21302492 TAAAAAAAAT
21302502 TAAATAAAATT-ATCATT-TTAAA
1 TAAATAAAATTAAT-ATTGTTAAA
21302524 TAAA-AAAATTAATATTGTTAAA
1 TAAATAAAATTAATATTGTTAAA
21302546 TAA
1 TAA
21302549 TTTTCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAATAAAATTAATATTGTTAAA
Found at i:21303179 original size:23 final size:23
Alignment explanation
Indices: 21303153--21303222 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
21303143 TTCATTTAAC
21303153 TTAATCGAACATGTTCACGAATA
1 TTAATCGAACATGTTCACGAATA
* * *
21303176 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAATA
* *
21303199 TATAATTGAACATGTTCACAAATA
1 T-TAATCGAACATGTTCACGAATA
21303223 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.55
24 17 0.45
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAATA
Found at i:21303617 original size:23 final size:23
Alignment explanation
Indices: 21303591--21303635 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21303581 AATTTTAAAT
**
21303591 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
21303614 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
21303636 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:21303701 original size:18 final size:18
Alignment explanation
Indices: 21303680--21303717 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
21303670 TGAATTTTCG
21303680 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
21303698 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
21303716 AA
1 AA
21303718 AATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:21305585 original size:23 final size:23
Alignment explanation
Indices: 21305557--21305618 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
21305547 AGTTAAAAAT
21305557 AAAATAAAATA-AAATACCAAGTA
1 AAAATAAAA-AGAAATACCAAGTA
* *
21305580 AAAATAAAAAGTAGTACCAAGTAA
1 AAAATAAAAAGAAATACCAAGT-A
*
21305604 AAAATTAAAAGAAAT
1 AAAATAAAAAGAAAT
21305619 TGTAGGTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.56
24 13 0.41
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAATAAAAAGAAATACCAAGTA
Found at i:21305668 original size:2 final size:2
Alignment explanation
Indices: 21305661--21305694 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
21305651 TTGCAAGTGA
21305661 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
21305695 ACATATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21305700 original size:16 final size:17
Alignment explanation
Indices: 21305665--21305707 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
21305655 AAGTGAATAT
*
21305665 ATATAT-ATATATATAT
1 ATATATCATATATATAC
21305681 ATATATCATATATA-AC
1 ATATATCATATATATAC
*
21305697 ATATAACATAT
1 ATATATCATAT
21305708 TTAATGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATCATATATATAC
Found at i:21305759 original size:19 final size:18
Alignment explanation
Indices: 21305722--21305784 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
21305712 TGTAAATAAT
21305722 ATTTAAAATAATATAGAA
1 ATTTAAAATAATATAGAA
*
21305740 ATTTAAAATTATATTAGAA
1 ATTTAAAATAATA-TAGAA
* * *
21305759 AGTAAAATATAATATA-AT
1 ATTTAAA-ATAATATAGAA
21305777 ATTTAAAA
1 ATTTAAAA
21305785 ATAAAAATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 18 0.50
19 12 0.33
20 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
ATTTAAAATAATATAGAA
Found at i:21306986 original size:13 final size:13
Alignment explanation
Indices: 21306970--21306994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21306960 AATATATATT
21306970 ATTAATTAAAAAC
1 ATTAATTAAAAAC
21306983 ATTAATTAAAAA
1 ATTAATTAAAAA
21306995 AAATCTTGAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:21307047 original size:13 final size:13
Alignment explanation
Indices: 21307029--21307053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21307019 AAAAATACAA
21307029 ATTAATTAAAAAC
1 ATTAATTAAAAAC
21307042 ATTAATTAAAAA
1 ATTAATTAAAAA
21307054 AGTTTGAAAT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:21307831 original size:9 final size:10
Alignment explanation
Indices: 21307808--21307836 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
21307798 GGTGCACCAC
21307808 CTTTCTTTTT
1 CTTTCTTTTT
21307818 CTTTCTTTTT
1 CTTTCTTTTT
21307828 -TTTCTTTTT
1 CTTTCTTTTT
21307837 AAATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:21308917 original size:28 final size:28
Alignment explanation
Indices: 21308866--21308920 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
21308856 TGTCTACTTC
* *
21308866 TTCCAAATTGGTAGATAAAATTTTTTTA
1 TTCCAAATTGGTACACAAAATTTTTTTA
* *
21308894 TTCCAAATTGGTACCCAAACTTTTTTT
1 TTCCAAATTGGTACACAAAATTTTTTT
21308921 CTGTCCACTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (28 bp):
TTCCAAATTGGTACACAAAATTTTTTTA
Found at i:21310301 original size:13 final size:13
Alignment explanation
Indices: 21310283--21310316 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
21310273 ACAAGCTTAA
21310283 ATTGGGGGGAGAG
1 ATTGGGGGGAGAG
21310296 ATTGGGGGGAGAG
1 ATTGGGGGGAGAG
21310309 ATTGGGGG
1 ATTGGGGG
21310317 TAGAAGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.62, T:0.18
Consensus pattern (13 bp):
ATTGGGGGGAGAG
Found at i:21313159 original size:22 final size:23
Alignment explanation
Indices: 21313116--21313196 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 23
21313106 AATAAACACA
* * **
21313116 TAGGGTTCGTATATTATTACATG
1 TAGGGTTTGCATATTACAACATG
* * *
21313139 TAAGGTTTGCATTTTA-AACATA
1 TAGGGTTTGCATATTACAACATG
* *
21313161 TAGGGTTTACATATTACAATATG
1 TAGGGTTTGCATATTACAACATG
21313184 TAGGGTTTGCATA
1 TAGGGTTTGCATA
21313197 AATGACATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
22 17 0.38
23 28 0.62
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (23 bp):
TAGGGTTTGCATATTACAACATG
Found at i:21313219 original size:45 final size:44
Alignment explanation
Indices: 21313043--21313235 Score: 131
Period size: 45 Copynumber: 4.3 Consensus size: 44
21313033 ACAAGTTCGC
* *
21313043 ACATCTAGGGTTTGCATGATAAGTA-A-ATAGGGTTCACACATTACA
1 ACATGTAGGGTTTGCAT-A-AA-TACATATAGGGTTCACATATTACA
*** * ** **
21313088 ACATGTAGGGTTCATATAAATAAACACATAGGGTTCGTATATTATT
1 ACATGTAGGGTTTGCATAAAT--ACATATAGGGTTCACATATTACA
* * *
21313134 ACATGTAAGGTTTGCATTTTAA-ACATATAGGGTTTACATATTACA
1 ACATGTAGGGTTTGCA--TAAATACATATAGGGTTCACATATTACA
* * ***
21313179 ATATGTAGGGTTTGCATAAATGACATATAGGGTTCGCATATTGGT
1 ACATGTAGGGTTTGCATAAAT-ACATATAGGGTTCACATATTACA
21313224 ACATGTAGGGTT
1 ACATGTAGGGTT
21313236 CACATGTTAA
Statistics
Matches: 111, Mismatches: 29, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
42 1 0.01
43 5 0.05
44 2 0.02
45 74 0.67
46 26 0.23
48 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (44 bp):
ACATGTAGGGTTTGCATAAATACATATAGGGTTCACATATTACA
Found at i:21313265 original size:90 final size:91
Alignment explanation
Indices: 21313069--21313265 Score: 225
Period size: 90 Copynumber: 2.2 Consensus size: 91
21313059 TGATAAGTAA
* * * *
21313069 ATAGGGTTCACACATTACAACATGTAGGGTTCATATAAATAAACACATAGGGTTCGTATATTATT
1 ATAGGGTTCACATATTACAACATGTAGGGTTCACATAAATAAACACATAGGGTTCGCATATTAGT
** * *
21313134 ACATGTAAGGTTTGCATTTTAAACAT
66 ACATGTAAGGTTCACATGTTAAACAG
* * ** * * *
21313160 ATAGGGTTTACATATTACAATATGTAGGGTTTGCATAAAT-GACATATAGGGTTCGCATATTGGT
1 ATAGGGTTCACATATTACAACATGTAGGGTTCACATAAATAAACACATAGGGTTCGCATATTAGT
* *
21313224 ACATGTAGGGTTCACATGTTAAATAG
66 ACATGTAAGGTTCACATGTTAAACAG
*
21313250 ATAGGGTTCATATATT
1 ATAGGGTTCACATATT
21313266 TAAACAAATA
Statistics
Matches: 87, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
90 53 0.61
91 34 0.39
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (91 bp):
ATAGGGTTCACATATTACAACATGTAGGGTTCACATAAATAAACACATAGGGTTCGCATATTAGT
ACATGTAAGGTTCACATGTTAAACAG
Found at i:21314757 original size:46 final size:46
Alignment explanation
Indices: 21314688--21314780 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
21314678 ATTCAATTTT
* * *
21314688 TTTGTTGTTTGGGTATAATTCCATGTGTTATGTTTTTTAGTGCACA
1 TTTGTTGTTTGGGTATAACTCCATGTGTTATATTTTTGAGTGCACA
21314734 TTTGTTGTTTGGGTATAACTCCATGTGTTATATTTTTGAGTGCACA
1 TTTGTTGTTTGGGTATAACTCCATGTGTTATATTTTTGAGTGCACA
21314780 T
1 T
21314781 ATGATATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.18, C:0.10, G:0.22, T:0.51
Consensus pattern (46 bp):
TTTGTTGTTTGGGTATAACTCCATGTGTTATATTTTTGAGTGCACA
Found at i:21317941 original size:21 final size:23
Alignment explanation
Indices: 21317905--21317957 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
21317895 ATCATGTAAT
*
21317905 TTAAAAAAAAATTATC-ATGCAAA
1 TTAAATAAAAATTATCAATG-AAA
21317928 -TAAATAAAAA-TATCAATGAAA
1 TTAAATAAAAATTATCAATGAAA
21317949 TTAAATAAA
1 TTAAATAAA
21317958 TGCAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (23 bp):
TTAAATAAAAATTATCAATGAAA
Found at i:21318127 original size:15 final size:15
Alignment explanation
Indices: 21318109--21318145 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21318099 ATAACTTACG
21318109 AATAAATAAATAAGA
1 AATAAATAAATAAGA
*
21318124 AATAAATAAATAATA
1 AATAAATAAATAAGA
21318139 AA-AAATA
1 AATAAATA
21318146 CTAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AATAAATAAATAAGA
Found at i:21318150 original size:10 final size:11
Alignment explanation
Indices: 21318113--21318159 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
21318103 CTTACGAATA
21318113 AATAAATAAGA-
1 AATAAATAA-AT
21318124 AATAAATAAAT
1 AATAAATAAAT
21318135 AATAAA-AAAT
1 AATAAATAAAT
*
21318145 ACTAAATAAAAT
1 AATAAAT-AAAT
21318157 AAT
1 AAT
21318160 GCAAATGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.32
11 15 0.48
12 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:21319595 original size:43 final size:43
Alignment explanation
Indices: 21319503--21319755 Score: 255
Period size: 43 Copynumber: 5.9 Consensus size: 43
21319493 GGTGTTGTAA
* * *
21319503 CTTCAATTTGCCCTTTTGGATTAGGGTTAAGATATTGGATGA-TG
1 CTTCAATTTGCCC-TCTGGATTAGGG-TAAAAGATTGGATGATTG
* * *
21319547 ACTTCAATCTGCCTTCTAGATTAGGGTAAAAGATTGGATGATTG
1 -CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGATTG
** *
21319591 CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGGCTA
1 CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGATTG
* *
21319634 CTTCAATTTACCCTCTGGATTAGGATAAAAGATTGGATGATTG
1 CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGATTG
* ** * ** *
21319677 CTTCAATCTGCCC-CATGG-TCGGGGTAAGAGATTAAATG-GTG
1 CTTCAATTTGCCCTC-TGGATTAGGGTAAAAGATTGGATGATTG
*
21319718 TCTTCAATCTGCCCTCTGG-TTAGGGTAAAAGATTGGAT
1 -CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGAT
21319756 TTTCTTTAAT
Statistics
Matches: 173, Mismatches: 31, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
41 2 0.01
42 45 0.26
43 103 0.60
44 12 0.07
45 11 0.06
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGATTG
Found at i:21319655 original size:86 final size:86
Alignment explanation
Indices: 21319503--21319797 Score: 309
Period size: 86 Copynumber: 3.5 Consensus size: 86
21319493 GGTGTTGTAA
* * * * *
21319503 CTTCAATTTGCCCTTTTGGATTAGGGTTAAGATATTGGATGATGACTTCAATCTGCCTTCTAGAT
1 CTTCAATTTGCCC-TCTGGATTAGGG-TAAGAGATTGGATGGTGACTTCAATCTGCCCTCTGGAT
21319568 TAGGGTAAAAGATTGGATGATTG
64 TAGGGTAAAAGATTGGATGATTG
* * *
21319591 CTTCAATTTGCCCTCTGGATTAGGGTAAAAGATTGGATGGCT-ACTTCAATTTACCCTCTGGATT
1 CTTCAATTTGCCCTCTGGATTAGGGTAAGAGATTGGATGG-TGACTTCAATCTGCCCTCTGGATT
*
21319655 AGGATAAAAGATTGGATGATTG
65 AGGGTAAAAGATTGGATGATTG
* ** ** *
21319677 CTTCAATCTGCCC-CATGG-TCGGGGTAAGAGATTAAATGGTGTCTTCAATCTGCCCTCTGG-TT
1 CTTCAATTTGCCCTC-TGGATTAGGGTAAGAGATTGGATGGTGACTTCAATCTGCCCTCTGGATT
*
21319739 AGGGTAAAAGATTGGAT--TTT
65 AGGGTAAAAGATTGGATGATTG
* * * *
21319759 CTTTAATCTGCCC-CATGG-TTGGGGTAAGAGATTTGATGG
1 CTTCAATTTGCCCTC-TGGATTAGGGTAAGAGATTGGATGG
21319798 GATAGTGTAA
Statistics
Matches: 180, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
82 37 0.21
84 19 0.11
85 33 0.18
86 66 0.37
87 12 0.07
88 13 0.07
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (86 bp):
CTTCAATTTGCCCTCTGGATTAGGGTAAGAGATTGGATGGTGACTTCAATCTGCCCTCTGGATTA
GGGTAAAAGATTGGATGATTG
Found at i:21319723 original size:42 final size:40
Alignment explanation
Indices: 21319673--21319791 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 40
21319663 AGATTGGATG
*
21319673 ATTG-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTAA
1 ATTGTCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTAA
* * **
21319712 ATGGTGTCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGG
1 AT--TGTCTTCAATCTGCCC-CATGGTTGGGGTAAGAGATTAA
* *
21319754 ATTTTCTTTAATCTGCCCCATGGTTGGGGTAAGAGATT
1 ATTGTCTTCAATCTGCCCCATGGTTGGGGTAAGAGATT
21319792 TGATGGGATA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
39 3 0.05
40 30 0.45
41 2 0.03
42 30 0.45
43 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (40 bp):
ATTGTCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTAA
Found at i:21320023 original size:99 final size:99
Alignment explanation
Indices: 21319806--21320033 Score: 252
Period size: 99 Copynumber: 2.3 Consensus size: 99
21319796 GGGATAGTGT
* * * * *
21319806 AACTTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCCTTTCTGTAGTTTTAATCCGCT
1 AACTTCACTCTATTCCACTGCAACTTCAGGAAGATTGAGATCCCTTACTGTAGTTTTAATACGAT
*
21319871 TCACTCAACTTCAGGAAGATAGGATTTGGTGTTG
66 CCACTCAACTTCAGGAAGATAGGATTTGGTGTTG
* *
21319905 AAGCTTCA-TCT-TGCTCCACTGCAACTTCAGGAAGATTGAGATCCGTTACT-T-GTTTTAATAT
1 AA-CTTCACTCTAT--TCCACTGCAACTTCAGGAAGATTGAGATCCCTTACTGTAGTTTTAATAC
* * *
21319966 GATCCACTGTAACTTCAGGGATATAGGATTTAAGGT-TATG
63 GATCCACT-CAACTTCAGGAAGATAGGATTT--GGTGT-TG
21320006 -ACTTCACTCTATTCCACTGCAACTTCAG
1 AACTTCACTCTATTCCACTGCAACTTCAG
21320034 TGGAGGTTGA
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
98 15 0.14
99 45 0.41
100 43 0.39
101 6 0.06
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (99 bp):
AACTTCACTCTATTCCACTGCAACTTCAGGAAGATTGAGATCCCTTACTGTAGTTTTAATACGAT
CCACTCAACTTCAGGAAGATAGGATTTGGTGTTG
Found at i:21321070 original size:14 final size:14
Alignment explanation
Indices: 21321051--21321092 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
21321041 TCCTTTTTTG
21321051 TTTTCTTCTCCTTT
1 TTTTCTTCTCCTTT
* *
21321065 TTTTCTTTTTCTTT
1 TTTTCTTCTCCTTT
21321079 TTTTC-TCTCCTTT
1 TTTTCTTCTCCTTT
21321092 T
1 T
21321093 CTTTTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTCTCCTTT
Found at i:21321079 original size:25 final size:23
Alignment explanation
Indices: 21321045--21321102 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
21321035 GGCCCTTCCT
**
21321045 TTTTTGTTTTCTTCTCCTTTTTTTC
1 TTTTT-TTTTCTTCT-CTCCTTTTC
*
21321070 TTTTTCTTTTTTTCTCTCCTTTTC
1 TTTTT-TTTTCTTCTCTCCTTTTC
21321094 TTTTTTTTT
1 TTTTTTTTT
21321103 AGTTTAAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.14
24 12 0.41
25 13 0.45
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTTTTTTCTTCTCTCCTTTTC
Found at i:21328714 original size:22 final size:21
Alignment explanation
Indices: 21328659--21328718 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
21328649 TATATAATAA
*
21328659 ATCATGTAATTAAA-AAAAAT
1 ATCATGAAATTAAATAAAAAT
* *
21328679 ATCATGCAAGTAAATAAAAAT
1 ATCATGAAATTAAATAAAAAT
21328700 ATCAATGAAATTAAATAAA
1 ATC-ATGAAATTAAATAAA
21328719 TGCAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.35
21 9 0.26
22 13 0.38
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
ATCATGAAATTAAATAAAAAT
Found at i:21348081 original size:17 final size:17
Alignment explanation
Indices: 21348059--21348092 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21348049 CACCAAAGAA
21348059 GAAAGAAAAAGGAAAAG
1 GAAAGAAAAAGGAAAAG
*
21348076 GAAAGAAGAAGGAAAAG
1 GAAAGAAAAAGGAAAAG
21348093 AAATCAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAGGAAAAG
Found at i:21353228 original size:31 final size:31
Alignment explanation
Indices: 21353190--21353254 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
21353180 TAAGGGGCCT
*
21353190 AATTTTTTTTTACCAACTTTT-AAGAGATCTAA
1 AATTTTTTTCT-CCAACTTTTAAAGA-ATCTAA
21353222 AATTTTTTTCTCCAACTTTTAAAGAATCTAA
1 AATTTTTTTCTCCAACTTTTAAAGAATCTAA
21353253 AA
1 AA
21353255 CCCTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.45
Consensus pattern (31 bp):
AATTTTTTTCTCCAACTTTTAAAGAATCTAA
Found at i:21353851 original size:26 final size:26
Alignment explanation
Indices: 21353818--21353868 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
21353808 ACTCCTCGTG
21353818 ATCACATAGAACAATCCATTTTGATA
1 ATCACATAGAACAATCCATTTTGATA
21353844 ATCACATAGAACAATCCATTTTGAT
1 ATCACATAGAACAATCCATTTTGAT
21353869 GAAACTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCACATAGAACAATCCATTTTGATA
Found at i:21354452 original size:105 final size:105
Alignment explanation
Indices: 21354268--21354609 Score: 429
Period size: 105 Copynumber: 3.3 Consensus size: 105
21354258 ATCTTGTGAT
* * **
21354268 TAAATTTATTTGAGTTAGTTGATTTAAGATTGA-AACTCCTAAACAACTCGCTGACCTGTGTTCA
1 TAAATTTATTTGAGTTAGCTGATTTAAGA-TCACAACTCCTAAACAACTCGCTGACCTACGTTCA
* *
21354332 CAGCTGATATCATTAAGGTTAGCTGATTTAAGATTGCAACC
65 CAGCTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACC
* * * * *
21354373 TGAATTTATTTGAGTTAGCTGATTCAAGATCACAACTCCTAAGCAATTCGTTGACCTACGTTCAC
1 TAAATTTATTTGAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTCGCTGACCTACGTTCAC
* * *
21354438 AACGGACATTATTAAGGTTAGTTGATTTAAGATCGTGC--CC
66 AGCTGATATTATTAAGGTTAGTTGATTTAAGAT--TGCAACC
* * * *
21354478 TAAATTTATTTGAGTTAGCTGATTTAATATCACAACTCCTAAACAGCTCGCTGACGTACATTCAC
1 TAAATTTATTTGAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTCGCTGACCTACGTTCAC
* * *
21354543 AGCTGATATTATTAATGTTAGTTGATTTAATATCGCAACC
66 AGCTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACC
* *
21354583 TAAATTTATTTAAGTTAGTTGATTTAA
1 TAAATTTATTTGAGTTAGCTGATTTAA
21354610 AATCGCAATT
Statistics
Matches: 201, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
103 2 0.01
104 2 0.01
105 194 0.97
107 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (105 bp):
TAAATTTATTTGAGTTAGCTGATTTAAGATCACAACTCCTAAACAACTCGCTGACCTACGTTCAC
AGCTGATATTATTAAGGTTAGTTGATTTAAGATTGCAACC
Found at i:21355848 original size:7 final size:7
Alignment explanation
Indices: 21355838--21355867 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
21355828 GAGATTGGAG
*
21355838 AAGAACA
1 AAGAGCA
21355845 AAGAGCA
1 AAGAGCA
21355852 AAGAGCA
1 AAGAGCA
21355859 AAGAGCA
1 AAGAGCA
21355866 AA
1 AA
21355868 AAGACAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.63, C:0.13, G:0.23, T:0.00
Consensus pattern (7 bp):
AAGAGCA
Found at i:21364264 original size:10 final size:10
Alignment explanation
Indices: 21364239--21364270 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
21364229 TTTTTTGTCA
21364239 TTTCA-TATT
1 TTTCATTATT
21364248 TTT-ATTATT
1 TTTCATTATT
21364257 TTTCATTATT
1 TTTCATTATT
21364267 TTTC
1 TTTC
21364271 TATCATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 10 0.48
10 10 0.48
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTCATTATT
Found at i:21368247 original size:23 final size:23
Alignment explanation
Indices: 21368221--21368566 Score: 296
Period size: 23 Copynumber: 14.8 Consensus size: 23
21368211 TTTACACATT
* *
21368221 AATCACATTATCATTTGAGCATA
1 AATCACATTATCTTTTAAGCATA
* * *
21368244 AATCATATTAACTTTTAA-CAAAA
1 AATCACATTATCTTTTAAGC-ATA
*
21368267 AATCACATTAAT-TTTTTAGCATA
1 AATCACATT-ATCTTTTAAGCATA
* *
21368290 AGTCACA-TATACTTTCAAGCATA
1 AATCACATTAT-CTTTTAAGCATA
* *
21368313 AATTACATTAACTTTTAAGCATA
1 AATCACATTATCTTTTAAGCATA
*
21368336 AATCACA-TATACTTTTAAGCAAA
1 AATCACATTAT-CTTTTAAGCATA
21368359 AATCACATTAAAATTAACTTTTAAGCATA
1 AATCACATT---A-T--CTTTTAAGCATA
*
21368388 AATCACA-TATACTTTTAAGCAAA
1 AATCACATTAT-CTTTTAAGCATA
*
21368411 AATCACATTAACTTTTAAGCATA
1 AATCACATTATCTTTTAAGCATA
* *
21368434 AATAACA-TATACTTTTAAGCAAA
1 AATCACATTAT-CTTTTAAGCATA
* * *
21368457 AATCATATTAACCTTTAAGCATA
1 AATCACATTATCTTTTAAGCATA
21368480 AATCACA-TATACTTTTAAGCA-A
1 AATCACATTAT-CTTTTAAGCATA
*
21368502 AAGTCACATTAACTTTTAAGCATA
1 AA-TCACATTATCTTTTAAGCATA
* *
21368526 AATCACA-TATACTTTTTAGCAAA
1 AATCACATTAT-CTTTTAAGCATA
*
21368549 AATCACATTAACTTTTAA
1 AATCACATTATCTTTTAA
21368567 CACATTTAAT
Statistics
Matches: 261, Mismatches: 40, Indels: 44
0.76 0.12 0.13
Matches are distributed among these distances:
21 2 0.01
22 13 0.05
23 206 0.79
24 17 0.07
25 1 0.00
27 1 0.00
28 2 0.01
29 19 0.07
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (23 bp):
AATCACATTATCTTTTAAGCATA
Found at i:21368288 original size:46 final size:46
Alignment explanation
Indices: 21368221--21368566 Score: 471
Period size: 46 Copynumber: 7.4 Consensus size: 46
21368211 TTTACACATT
* * * *
21368221 AATCACATTATCATTTGAGCATAAATCATAT-TAACTTTTAA-CAAAA
1 AATCACATTAACTTTTAAGCATAAATCACATAT-ACTTTTAAGC-AAA
* * * * *
21368267 AATCACATTAATTTTTTAGCATAAGTCACATATACTTTCAAGCATA
1 AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
*
21368313 AATTACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
1 AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
21368359 AATCACATTAAAATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
1 AATCAC------ATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
*
21368411 AATCACATTAACTTTTAAGCATAAATAACATATACTTTTAAGCAAA
1 AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
* *
21368457 AATCATATTAACCTTTAAGCATAAATCACATATACTTTTAAGCAAA
1 AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
* *
21368503 AGTCACATTAACTTTTAAGCATAAATCACATATACTTTTTAGCAAA
1 AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
21368549 AATCACATTAACTTTTAA
1 AATCACATTAACTTTTAA
21368567 CACATTTAAT
Statistics
Matches: 268, Mismatches: 24, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
46 220 0.82
47 2 0.01
52 46 0.17
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (46 bp):
AATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGCAAA
Found at i:21369002 original size:36 final size:36
Alignment explanation
Indices: 21368954--21369112 Score: 219
Period size: 36 Copynumber: 4.4 Consensus size: 36
21368944 TTAGCACAAT
*
21368954 ATATTCATTGTCACATGGCATGAATAACATACCCAC
1 ATATTCACTGTCACATGGCATGAATAACATACCCAC
* *
21368990 ATATTCACTGTCACATGGCATGAATAACATGCTCAC
1 ATATTCACTGTCACATGGCATGAATAACATACCCAC
* *
21369026 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
1 ATATTCACTGTCACATGGCATGAATAACATACCCAC
* * *
21369062 ATATTTACTATCACATGGCATGAATAGCATACCCAC
1 ATATTCACTGTCACATGGCATGAATAACATACCCAC
* * *
21369098 GTATCCACTTTCACA
1 ATATTCACTGTCACA
21369113 GCAGTCATCA
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 109 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (36 bp):
ATATTCACTGTCACATGGCATGAATAACATACCCAC
Found at i:21371198 original size:30 final size:29
Alignment explanation
Indices: 21371164--21371220 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
21371154 GAAAATATGA
21371164 AATAAAAGAAAATAAAGGTATTGAAAATTT
1 AATAAAAGAAAATAAAGGTATT-AAAATTT
* * *
21371194 AATAACAGAATATAACGGTATTAAAAT
1 AATAAAAGAAAATAAAGGTATTAAAAT
21371221 AAAAAAGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (29 bp):
AATAAAAGAAAATAAAGGTATTAAAATTT
Found at i:21374269 original size:11 final size:11
Alignment explanation
Indices: 21374246--21374278 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
21374236 GGGTTAAGGG
21374246 TTTTTTTTGTA
1 TTTTTTTTGTA
21374257 TTTTATTTT-TA
1 TTTT-TTTTGTA
21374268 TTTTTTTTGTA
1 TTTTTTTTGTA
21374279 AATGGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.20
11 12 0.60
12 4 0.20
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTTTTTGTA
Found at i:21375746 original size:15 final size:15
Alignment explanation
Indices: 21375728--21375761 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
21375718 TTCAAGTTTT
*
21375728 TTTTTTGAATTTGAG
1 TTTTTTAAATTTGAG
21375743 TTTTTTAAATTTGAG
1 TTTTTTAAATTTGAG
21375758 TTTT
1 TTTT
21375762 CTCAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (15 bp):
TTTTTTAAATTTGAG
Found at i:21383104 original size:25 final size:24
Alignment explanation
Indices: 21383047--21383105 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
21383037 AAAAAAAAGT
* *
21383047 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
21383070 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
21383094 TATTTTAATAAT
1 TATATT-ATAAT
21383106 CATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:21383147 original size:15 final size:15
Alignment explanation
Indices: 21383117--21383160 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21383107 ATTATATTAA
*
21383117 AAATATTATTAAATT
1 AAATATTATTTAATT
* *
21383132 ATATATTATTTTATT
1 AAATATTATTTAATT
*
21383147 AAATTTTATTTAAT
1 AAATATTATTTAAT
21383161 AATAATTATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATTATTTAATT
Found at i:21383162 original size:58 final size:58
Alignment explanation
Indices: 21383079--21383224 Score: 172
Period size: 58 Copynumber: 2.5 Consensus size: 58
21383069 ATATATTATA
* * ** *
21383079 ATTTTTACT-AATTCATATTTTAATAATCATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATAGAATTAAATTAAT-TAAT
* *
21383139 A-TTTTATTAAATTTTATTTAATAATAATTATGTTAAAATAGAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATAGAATTAAATTAATTAAT
21383196 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
21383225 CATTAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
57 18 0.24
58 44 0.59
59 8 0.11
60 5 0.07
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATAGAATTAAATTAATTAAT
Found at i:21383423 original size:16 final size:16
Alignment explanation
Indices: 21383394--21383465 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
21383384 TGAATTCCTA
*
21383394 ATTACAG-TCCTATTTC
1 ATTACAGCT-CTATTCC
*
21383410 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
21383426 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
*
21383442 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
21383458 ATTACAGC
1 ATTACAGC
21383466 GAACCAAACG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 47 0.98
17 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:21383991 original size:19 final size:20
Alignment explanation
Indices: 21383962--21384020 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
21383952 TTTAATATTA
* *
21383962 CATACCATAACATATCTTAT
1 CATATCATAACATATCATAT
*
21383982 CA-ATCATAACATGTCATAT
1 CATATCATAACATATCATAT
* *
21384001 CATATCATATCATGTCATAT
1 CATATCATAACATATCATAT
21384021 AATGTCCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (20 bp):
CATATCATAACATATCATAT
Found at i:21384005 original size:5 final size:5
Alignment explanation
Indices: 21383962--21384020 Score: 57
Period size: 5 Copynumber: 12.0 Consensus size: 5
21383952 TTTAATATTA
* * * * *
21383962 CATAC CATAA CATAT CTTAT CA-AT CATAA CATGT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
*
21384011 CATGT CATAT
1 CATAT CATAT
21384021 AATGTCCTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
4 4 0.09
5 39 0.91
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (5 bp):
CATAT
Found at i:21384020 original size:15 final size:15
Alignment explanation
Indices: 21383984--21384026 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
21383974 TATCTTATCA
*
21383984 ATCATAACATGTCAT
1 ATCATATCATGTCAT
*
21383999 ATCATATCATATCAT
1 ATCATATCATGTCAT
* *
21384014 GTCATATAATGTC
1 ATCATATCATGTC
21384027 CTACCCTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (15 bp):
ATCATATCATGTCAT
Found at i:21384025 original size:10 final size:10
Alignment explanation
Indices: 21383985--21384026 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
21383975 ATCTTATCAA
*
21383985 TCATAACATG
1 TCATATCATG
*
21383995 TCATATCATA
1 TCATATCATG
21384005 TCATATCATG
1 TCATATCATG
*
21384015 TCATATAATG
1 TCATATCATG
21384025 TC
1 TC
21384027 CTACCCTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (10 bp):
TCATATCATG
Found at i:21391774 original size:37 final size:37
Alignment explanation
Indices: 21391701--21391808 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 37
21391691 ATTCTTTGAT
* * * * * *
21391701 CACCGGCACAAAGCCTGCTAGGTACGTAGGCTGAATA
1 CACCAGCACGAAGCCTGCTAGGCACATAGCCCGAATA
* *
21391738 CACTAGCACGAAGCTTGCTAGGCACATAGCCCGAATA
1 CACCAGCACGAAGCCTGCTAGGCACATAGCCCGAATA
* * *
21391775 CACCGGAACGAAGCCTACTAGGCACATAGCCCGA
1 CACCAGCACGAAGCCTGCTAGGCACATAGCCCGA
21391809 TTTACTTGAA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (37 bp):
CACCAGCACGAAGCCTGCTAGGCACATAGCCCGAATA
Found at i:21398066 original size:37 final size:36
Alignment explanation
Indices: 21398002--21398127 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 36
21397992 ATTCTTTGAT
*
21398002 CACCGGCACAAAGCCTGCTAGGTACATAAGCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACAT-AGCTGAATA
* *
21398039 CACCAGCACGAAGCCTGCTAGGCACATAGCTTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGC-TGAATA
* ** * *
21398076 CACTGGCATGAAGTCTACTAGGCACATAGCTCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCT-GAATA
*
21398113 CCCCGGCACAAAGCC
1 CACCGGCACAAAGCC
21398128 CGATTTACTT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
36 4 0.05
37 70 0.95
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (36 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCTGAATA
Found at i:21399401 original size:75 final size:75
Alignment explanation
Indices: 21399322--21399470 Score: 208
Period size: 75 Copynumber: 2.0 Consensus size: 75
21399312 ATTCCTCTCA
* * **
21399322 AAAATTTTACTTCCCCTCAAACCCCAAAAACTTTTTTCTTTTTATTTTTTTCCCAAAACTTTTAC
1 AAAATTTTACTTCCCCTCAAACCCCAAAAACTTTTTTCATTTTACTTTTCCCCCAAAACTTTTAC
*
21399387 TTCTCCCAAC
66 TTCCCCCAAC
* * * * *
21399397 AAAATTTTACTTCCCCTTAAACTCCTAAAACTTTTTTCATTTTACTTTTCCCCCAAATCTTTTAT
1 AAAATTTTACTTCCCCTCAAACCCCAAAAACTTTTTTCATTTTACTTTTCCCCCAAAACTTTTAC
21399462 TTCCCCCAA
66 TTCCCCCAA
21399471 ACCCCCCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (75 bp):
AAAATTTTACTTCCCCTCAAACCCCAAAAACTTTTTTCATTTTACTTTTCCCCCAAAACTTTTAC
TTCCCCCAAC
Found at i:21401033 original size:6 final size:6
Alignment explanation
Indices: 21401022--21401049 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21401012 TGTCTTGGAG
21401022 ATGGGC ATGGGC ATGGGC ATGGGC ATGG
1 ATGGGC ATGGGC ATGGGC ATGGGC ATGG
21401050 CAGTTTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.50, T:0.18
Consensus pattern (6 bp):
ATGGGC
Found at i:21403941 original size:14 final size:14
Alignment explanation
Indices: 21403904--21403945 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
21403894 CTATATTTTA
21403904 AATATTTAAATA-T
1 AATATTTAAATATT
21403917 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
21403931 TATATTTAAATATT
1 AATATTTAAATATT
21403945 A
1 A
21403946 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:21405044 original size:14 final size:15
Alignment explanation
Indices: 21405015--21405047 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
21405005 TTTATATGAA
*
21405015 AATTTTGAATTGGTG
1 AATTTTGAATTAGTG
21405030 AATTTT-AATTAGTG
1 AATTTTGAATTAGTG
21405044 AATT
1 AATT
21405048 AGAAGTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
AATTTTGAATTAGTG
Found at i:21406203 original size:53 final size:53
Alignment explanation
Indices: 21406113--21406430 Score: 467
Period size: 53 Copynumber: 6.0 Consensus size: 53
21406103 TAAATGAGAA
* * * * * * *
21406113 ATGAATCCCATCATGGATTAAATGTCCGATAATTCTGTGTCATCCTGAGTTAT
1 ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
*
21406166 ATGAATCCTATCACGGATTAAAGG-CTCGATGACTCTGTGTCATCGTGAGTTAT
1 ATGAATCCTATTACGGATTAAAGGTC-CGATGACTCTGTGTCATCGTGAGTTAT
* *
21406219 TTGAATCCTATTATGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
* * *
21406272 TTGAATCCTATTTCAGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
*
21406325 TTGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
* * *
21406378 ATGAATCCTATTTCAGATTAAAGGTCCGATGACTCTGTGTCATCGTGATTTAT
1 ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
21406431 CAAATGAGAA
Statistics
Matches: 245, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
52 1 0.00
53 243 0.99
54 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (53 bp):
ATGAATCCTATTACGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
Found at i:21409733 original size:52 final size:52
Alignment explanation
Indices: 21409655--21409756 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
21409645 CAAAAGGTTC
*
21409655 GATGATTATGTGTCATCGTGAGTATATTAATCCTTTACGGATTATGAGGTCT
1 GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCT
21409707 GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
1 GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGT
21409757 GTCATCGTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (52 bp):
GATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCT
Found at i:21409761 original size:39 final size:39
Alignment explanation
Indices: 21409716--21409795 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
21409706 TGATGATTAT
* * *
21409716 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAG
21409755 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAG
1 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAG
21409794 GT
1 GT
21409796 CCGATGACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (39 bp):
GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAG
Found at i:21409819 original size:91 final size:91
Alignment explanation
Indices: 21409664--21409847 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
21409654 CGATGATTAT
* * * * * *
21409664 GTGTCATCGTGAGTATATTAATCCTTTACGGATTATGAGGTCTGATGATTATGTGTCATCGTGAG
1 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAGGTCCGATGACTATGTGTCATCGTGAG
* *
21409729 TATATGAATCCTTTACGGATTATGAG
66 TATATGAATCATTTACGGATTATAAG
*
21409755 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAGGTCCGATGACTATGTGTTATCGTGAG
1 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAGGTCCGATGACTATGTGTCATCGTGAG
21409820 TATATGAATCATTTACGGATTATAAG
66 TATATGAATCATTTACGGATTATAAG
21409846 GT
1 GT
21409848 CTGATGACTA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (91 bp):
GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAGGTCCGATGACTATGTGTCATCGTGAG
TATATGAATCATTTACGGATTATAAG
Found at i:21409841 original size:52 final size:52
Alignment explanation
Indices: 21409755--21409925 Score: 236
Period size: 52 Copynumber: 3.3 Consensus size: 52
21409745 GGATTATGAG
* *
21409755 GTGTCATCGTGAGTATATGAAACCTTTACAGATTATAAGGTCCGATGACTAT
1 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTAT
* * *
21409807 GTGTTATCGTGAGTATATGAATCATTTACGGATTATAAGGTCTGATGACTAT
1 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTAT
** * * *
21409859 GTGTCATCGTGACCATATGAATCCTTT-CGGATTATGAGGTTCGATGATTAT
1 GTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTAT
*
21409910 TTGTCATCGTGAGTAT
1 GTGTCATCGTGAGTAT
21409926 CAAATGAGAA
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 33 0.32
52 70 0.68
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (52 bp):
GTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTAT
Found at i:21414022 original size:16 final size:16
Alignment explanation
Indices: 21414001--21414033 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21413991 TTATGATTTT
*
21414001 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
21414017 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
21414033 A
1 A
21414034 TTTGTAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:21415100 original size:52 final size:52
Alignment explanation
Indices: 21415021--21415258 Score: 363
Period size: 52 Copynumber: 4.6 Consensus size: 52
21415011 ATAAATGCAA
*
21415021 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
21415073 GAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
21415125 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* ** *
21415177 AAGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTTTGTATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
21415229 GACGTTCGATGAC--TGTGCCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
21415259 CAAATGAGAA
Statistics
Matches: 172, Mismatches: 14, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
50 15 0.09
52 157 0.91
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:21417640 original size:72 final size:71
Alignment explanation
Indices: 21417531--21417722 Score: 314
Period size: 72 Copynumber: 2.7 Consensus size: 71
21417521 TACAAATTTT
* *
21417531 ATATCCAAAATCAAATATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATA
1 ATATCCAAAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATA
21417596 AATTCA
66 AATTCA
**
21417602 ATATCCAAAACCCAAACATAAACAACTATTGATAAAACTGGATTACACATAAATAAGTAGAACAT
1 ATATCCAAAA-CCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
21417667 AAATTCA
65 AAATTCA
*
21417674 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAATTTA-ACAT
1 ATATCC-AAAACCAAACATAAACAACTATTGATAAAACTAAATTACACAT
21417723 TGTTGCTTAT
Statistics
Matches: 112, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
71 14 0.12
72 94 0.84
73 4 0.04
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (71 bp):
ATATCCAAAACCAAACATAAACAACTATTGATAAAACTAAATTACACATAAATAAGTAGAACATA
AATTCA
Found at i:21418192 original size:18 final size:18
Alignment explanation
Indices: 21418144--21418192 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
21418134 CATTTCCATC
*
21418144 AATGTTAACATCATTTGA
1 AATGTTAACATCAATTGA
*
21418162 AAT-TTGAATATCAATTGA
1 AATGTT-AACATCAATTGA
*
21418180 AGTGTTAACATCA
1 AATGTTAACATCA
21418193 TTTCCTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (18 bp):
AATGTTAACATCAATTGA
Done.