Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010824.1 Kokia drynarioides strain JFW-HI SEQ_125791, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 153398
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:4788 original size:22 final size:23
Alignment explanation
Indices: 4758--4802 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
4748 TGATTAATTT
4758 TATTATTATGATAT-AAAAATAAA
1 TATTATTAT-ATATAAAAAATAAA
*
4781 TATT-TTATATTTAAAAAATAAA
1 TATTATTATATATAAAAAATAAA
4803 AAAGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 13 0.65
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATTATTATATATAAAAAATAAA
Found at i:19262 original size:17 final size:17
Alignment explanation
Indices: 19251--19299 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
19241 CAAATGCATT
*
19251 AACAAATAAAATGCAGA
1 AACAAGTAAAATGCAGA
19268 AACAAGTAAAATGCAGA
1 AACAAGTAAAATGCAGA
19285 AACAAGTAAAATGCA
1 AACAAGTAAAATGCA
19300 ATGAGAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.61, C:0.12, G:0.14, T:0.12
Consensus pattern (17 bp):
AACAAGTAAAATGCAGA
Found at i:19493 original size:9 final size:9
Alignment explanation
Indices: 19479--19513 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
19469 GGTTCAACCG
19479 AGGCACATA
1 AGGCACATA
19488 AGGCACATA
1 AGGCACATA
*
19497 AGGCATAATA
1 AGGCA-CATA
19507 AGGCACA
1 AGGCACA
19514 ATAGCCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (9 bp):
AGGCACATA
Found at i:28795 original size:33 final size:33
Alignment explanation
Indices: 28753--28819 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28743 CAAATATGAT
28753 ACAAAGGGAACAAATTATACTCTAATTAGAGAG
1 ACAAAGGGAACAAATTATACTCTAATTAGAGAG
28786 ACAAAGGGAACAAATTATACTCTAATTAGAGAG
1 ACAAAGGGAACAAATTATACTCTAATTAGAGAG
28819 A
1 A
28820 ATTTAATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (33 bp):
ACAAAGGGAACAAATTATACTCTAATTAGAGAG
Found at i:31934 original size:27 final size:27
Alignment explanation
Indices: 31896--31950 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31886 AATATAAAGA
31896 TAAATGCGCATTACAAAAGAATCATTC
1 TAAATGCGCATTACAAAAGAATCATTC
31923 TAAATGCGCATTACAAAAGAATCATTC
1 TAAATGCGCATTACAAAAGAATCATTC
31950 T
1 T
31951 TCACTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (27 bp):
TAAATGCGCATTACAAAAGAATCATTC
Found at i:33974 original size:43 final size:43
Alignment explanation
Indices: 33878--34269 Score: 473
Period size: 43 Copynumber: 9.1 Consensus size: 43
33868 GAAAAATGCT
* *
33878 GCTATAGAACATGGTCTTTAGCGGCGCTTTT-CCACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
33920 GCTAAAAAACATTGTCTTTAGCGACGCTTTTCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
33963 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCGCACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
34006 GCTAAAGAACATGGTCTTTAGAGTCGCTTTTCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * *
34049 GCTAAAGAACATTGTCTTTAGCGGCAC-TTCCCCGCAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * *
34091 GCTAAAGAACATGGTCTTTAGCGGCGCTTCTCCCATAATCACC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
** * *
34134 GCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCACAAACACC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * * * ***
34177 ACTAAAGAACATGATCTTTACCGGCGCTTCTACCACAAACATT
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
34220 GCTAAAGAACATGGTCTTTAGGCGGCGCTTTTCACACAAACACT
1 GCTAAAGAACATGGTCTTTA-GCGGCGCTTTTCCCACAAACGCC
34264 GCTAAA
1 GCTAAA
34270 ATTAACAGAT
Statistics
Matches: 300, Mismatches: 47, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
42 65 0.22
43 211 0.70
44 24 0.08
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:34099 original size:128 final size:127
Alignment explanation
Indices: 33871--34259 Score: 480
Period size: 128 Copynumber: 3.0 Consensus size: 127
33861 TTATGAGGAA
* * * * * *
33871 AAATGCTGCTATAGAACATGGTCTTTAGCGGCGCTTTT-CCACAAATGCCGCTAAAAAACATTGT
1 AAATGCCGCTAAAGAACATGGTCTTTAGAGACGCTTTTCCCACAAACGCCGCTAAAGAACATTGT
* *
33935 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCGCAC
66 CTTTAGCGGCGC-TTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-CAC
*
33999 AAATGCCGCTAAAGAACATGGTCTTTAGAGTCGCTTTTCCCACAAACGCCGCTAAAGAACATTGT
1 AAATGCCGCTAAAGAACATGGTCTTTAGAGACGCTTTTCCCACAAACGCCGCTAAAGAACATTGT
* * *
34064 CTTTAGCGGCACTTCCCCGCAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTCC-C
66 CTTTAGCGGCGCTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
* * * *
34125 ATAATCACCGCTAAAGAACATGGTCTTTAGCA-ACGCTTCTCCCACAAACACCACTAAAGAACA-
1 A-AAT-GCCGCTAAAGAACATGGTCTTTAG-AGACGCTTTTCCCACAAACGCCGCTAAAGAACAT
* * ***
34188 TGATCTTTACCGGCGCTTCTACCACAAACATTGCTAAAGAACATGGTCTTTAGGCGGCGCTTTTC
63 TG-TCTTTAGCGGCGCTTC-CCCACAAACGCCGCTAAAGAACATGGTCTTTA-GCGGCGCTTTTC
34253 ACAC
125 -CAC
34257 AAA
1 AAA
34260 CACTGCTAAA
Statistics
Matches: 228, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
126 2 0.01
127 6 0.03
128 142 0.62
129 62 0.27
130 11 0.05
131 3 0.01
132 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (127 bp):
AAATGCCGCTAAAGAACATGGTCTTTAGAGACGCTTTTCCCACAAACGCCGCTAAAGAACATTGT
CTTTAGCGGCGCTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
Found at i:34184 original size:171 final size:171
Alignment explanation
Indices: 33878--34245 Score: 457
Period size: 171 Copynumber: 2.1 Consensus size: 171
33868 GAAAAATGCT
* * ** * *
33878 GCTATAGAACATGGTCTTTAGCGGCGCTTTTCCACAAATGCCGCTAAAAAACATTGTCTTTAGCG
1 GCTAAAGAACATGGTCTTTAGCGGCACTTCCCCACAAACGCCGCTAAAAAACATGGTCTTTAGCG
* * ** * * ** *
33943 ACGCTTTTCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCGCACAAATGCCGC
66 ACGCTTCTCCCACAAACACCGCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCACAAACACCAC
* * * * * *
34008 TAAAGAACATGGTCTTTAGAGTCGCTTTTCCCACAAACGCC
131 TAAAGAACATGATCTTTACAGGCGCTTCTACCACAAACACC
* * *
34049 GCTAAAGAACATTGTCTTTAGCGGCACTTCCCCGCAAACGCCGCTAAAGAACATGGTCTTTAGCG
1 GCTAAAGAACATGGTCTTTAGCGGCACTTCCCCACAAACGCCGCTAAAAAACATGGTCTTTAGCG
* * *
34114 GCGCTTCTCCCATAATCACCGCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCACAAACACCAC
66 ACGCTTCTCCCACAAACACCGCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCACAAACACCAC
* **
34179 TAAAGAACATGATCTTTACCGGCGCTTCTACCACAAACATT
131 TAAAGAACATGATCTTTACAGGCGCTTCTACCACAAACACC
34220 GCTAAAGAACATGGTCTTTAGGCGGC
1 GCTAAAGAACATGGTCTTTA-GCGGC
34246 GCTTTTCACA
Statistics
Matches: 165, Mismatches: 31, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
171 160 0.97
172 5 0.03
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (171 bp):
GCTAAAGAACATGGTCTTTAGCGGCACTTCCCCACAAACGCCGCTAAAAAACATGGTCTTTAGCG
ACGCTTCTCCCACAAACACCGCTAAAGAACATGGTCTTTAGCAACGCTTCTCCCACAAACACCAC
TAAAGAACATGATCTTTACAGGCGCTTCTACCACAAACACC
Found at i:34588 original size:21 final size:21
Alignment explanation
Indices: 34564--34630 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
34554 TGTTGCCTTT
*
34564 GCTTCCCTCGCTGCTGCCTCC
1 GCTTCCCTAGCTGCTGCCTCC
* * *
34585 GCTTCCCTAGTTGTTGCCTCT
1 GCTTCCCTAGCTGCTGCCTCC
* *
34606 GTTTCCCTTGCTGCTGCCTCC
1 GCTTCCCTAGCTGCTGCCTCC
34627 GCTT
1 GCTT
34631 TAAGTTATAG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.01, C:0.42, G:0.19, T:0.37
Consensus pattern (21 bp):
GCTTCCCTAGCTGCTGCCTCC
Found at i:36646 original size:35 final size:35
Alignment explanation
Indices: 36607--36673 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
36597 CTTTTCAAGT
36607 ACATGGACTAAATCTAAAACTTTATTAAAATATAG
1 ACATGGACTAAATCTAAAACTTTATTAAAATATAG
36642 ACATGGACTAAATCTAAAACTTTATTAAAATA
1 ACATGGACTAAATCTAAAACTTTATTAAAATA
36674 CAGGAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.31
Consensus pattern (35 bp):
ACATGGACTAAATCTAAAACTTTATTAAAATATAG
Found at i:37163 original size:48 final size:46
Alignment explanation
Indices: 37037--37177 Score: 187
Period size: 46 Copynumber: 3.0 Consensus size: 46
37027 GAAATTTAGG
* *
37037 ATTTAGGGTTTTGGGAGAGGAGAAATTAAGAATT-AGTGATTAGAGA
1 ATTTAGGGCTTTGAGAGAGGAGAAATTAAGAATTAAG-GATTAGAGA
*
37083 ATTTTGGGCTTTGAGAGAGGAGAAATTAAGAATTAAGGATT-GCATGA
1 ATTTAGGGCTTTGAGAGAGGAGAAATTAAGAATTAAGGATTAG-A-GA
* *
37130 ATTTGAGGGGTTTGAGAGAGGAGAAATTAAGAATTACGGATTAGAGA
1 ATTT-AGGGCTTTGAGAGAGGAGAAATTAAGAATTAAGGATTAGAGA
37177 A
1 A
37178 ATTTTGGGGT
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
45 1 0.01
46 36 0.43
47 11 0.13
48 35 0.42
49 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.32, T:0.28
Consensus pattern (46 bp):
ATTTAGGGCTTTGAGAGAGGAGAAATTAAGAATTAAGGATTAGAGA
Found at i:37181 original size:48 final size:45
Alignment explanation
Indices: 37037--37190 Score: 193
Period size: 48 Copynumber: 3.3 Consensus size: 45
37027 GAAATTTAGG
* *
37037 ATTTAGGGTTTTGGGAGAGGAGAAATTAAGAATTAGTGATTAGAGA
1 ATTTAGGGGTTTGAGAGAGGAGAAATTAAGAATTAG-GATTAGAGA
* *
37083 ATTTTGGGCTTTGAGAGAGGAGAAATTAAGAATTAAGGATT-GCATGA
1 ATTTAGGGGTTTGAGAGAGGAGAAATTAAGAATT-AGGATTAG-A-GA
37130 ATTTGAGGGGTTTGAGAGAGGAGAAATTAAGAATTACGGATTAGAGAA
1 ATTT-AGGGGTTTGAGAGAGGAGAAATTAAGAATTA-GGATTAGAG-A
*
37178 ATTTTGGGGTTTG
1 ATTTAGGGGTTTG
37191 GGGATAGATC
Statistics
Matches: 95, Mismatches: 6, Indels: 13
0.83 0.05 0.11
Matches are distributed among these distances:
45 1 0.01
46 36 0.38
47 18 0.19
48 39 0.41
49 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.31
Consensus pattern (45 bp):
ATTTAGGGGTTTGAGAGAGGAGAAATTAAGAATTAGGATTAGAGA
Found at i:39054 original size:41 final size:42
Alignment explanation
Indices: 38989--39083 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 42
38979 CTATTGCTTA
** * * *
38989 ACCTTTAGCGGCTTTTTTCTCATAAATGCCGCTATTACTCTG
1 ACCTTTAGCGGCTGCTTTCCCATAAACGCCGCTAATACTCTG
* *
39031 ACCTTTAGCGG-TGCTTTCCCATAAGCGCCGCTAATGCTCTG
1 ACCTTTAGCGGCTGCTTTCCCATAAACGCCGCTAATACTCTG
39072 ACCTTTAGCGGC
1 ACCTTTAGCGGC
39084 GTTTATGTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 34 0.76
42 11 0.24
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (42 bp):
ACCTTTAGCGGCTGCTTTCCCATAAACGCCGCTAATACTCTG
Found at i:39098 original size:41 final size:41
Alignment explanation
Indices: 39053--39164 Score: 206
Period size: 41 Copynumber: 2.7 Consensus size: 41
39043 GCTTTCCCAT
39053 AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGTGG
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGTGG
39094 AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGTGG
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGTGG
* *
39135 AAGTGCCGCTAATGCTCTGACCATTAGCGG
1 AAGCGCCGCTAATGCTCTGACCTTTAGCGG
39165 TGCTTCCCCA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.28
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGTGG
Found at i:39175 original size:123 final size:126
Alignment explanation
Indices: 38953--39195 Score: 287
Period size: 123 Copynumber: 2.0 Consensus size: 126
38943 TTTAAATAAA
* * * * *
38953 TTAGCGGCGTTTATGAGAAAACGTCGCTATTGCTTAACCTTTAGCGGCTTTTTTCTCATAAATGC
1 TTAGCGGCGTTTATGAGAAAACGCCGCTAATGCTTAACCTTTAGCGGCGTTTATCTCAGAAATGC
* * * *
39018 CGCTATTACTCTGACCTTTAGCGGTGCTTTCCCAT-AA-G-CGCCGCTAATGCTCTGACCT
66 CGCTAATACTCTGACCATTAGCGGTGCTTCCCCATAAACGACGCCCCTAATGCTCTGACCT
* * * * * * *
39076 TTAGCGGCGTTTATGTGGAAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTATGT-GGAAGTG
1 TTAGCGGCGTTTATGAGAAAACGCCGCTAATGCT-TAACCTTTAGCGGCGTTTATCTCAGAAATG
* *
39140 CCGCTAATGCTCTGACCATTAGCGGTGCTTCCCCATAAACGNCGCCCCTAATGCTC
65 CCGCTAATACTCTGACCATTAGCGGTGCTTCCCCATAAACGACGCCCCTAATGCTC
39196 CAACTTTTAG
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
123 65 0.66
124 20 0.20
125 1 0.01
126 13 0.13
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (126 bp):
TTAGCGGCGTTTATGAGAAAACGCCGCTAATGCTTAACCTTTAGCGGCGTTTATCTCAGAAATGC
CGCTAATACTCTGACCATTAGCGGTGCTTCCCCATAAACGACGCCCCTAATGCTCTGACCT
Found at i:42871 original size:47 final size:47
Alignment explanation
Indices: 42802--42897 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
42792 CTGCACAAAA
42802 AAAGATTGATGTGCGGAGCGGAGTACTCACTATGGAGTTTGATAGAG
1 AAAGATTGATGTGCGGAGCGGAGTACTCACTATGGAGTTTGATAGAG
42849 AAAGATTGATGTGCGGAGCGGAGTACTCACTATGGAGTTTGATAGAG
1 AAAGATTGATGTGCGGAGCGGAGTACTCACTATGGAGTTTGATAGAG
42896 AA
1 AA
42898 GTGGTGAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.25
Consensus pattern (47 bp):
AAAGATTGATGTGCGGAGCGGAGTACTCACTATGGAGTTTGATAGAG
Found at i:46030 original size:26 final size:27
Alignment explanation
Indices: 46001--46060 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
45991 CAACATCCTT
* *
46001 AACCCAAATAA-AAACTCAACA-CATAA
1 AACCCAAA-AATAAACCCAAAACCATAA
*
46027 AACCCAAAAATAAACCCAAAACCCTAA
1 AACCCAAAAATAAACCCAAAACCATAA
46054 AACCCAA
1 AACCCAA
46061 GTCCACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 16 0.55
27 11 0.38
ACGTcount: A:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (27 bp):
AACCCAAAAATAAACCCAAAACCATAA
Found at i:46338 original size:15 final size:17
Alignment explanation
Indices: 46313--46347 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
46303 ACCCAACTCG
46313 AAAAAGAAAGAAAA-AA
1 AAAAAGAAAGAAAAGAA
46329 AAAAAG-AAGAAAAGAA
1 AAAAAGAAAGAAAAGAA
46345 AAA
1 AAA
46348 TATCTAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAGAA
Found at i:67184 original size:18 final size:18
Alignment explanation
Indices: 67161--67203 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
67151 TAATAAGTTT
67161 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
67179 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
67197 TTAATTA
1 TTAATTA
67204 CACATTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:67672 original size:22 final size:24
Alignment explanation
Indices: 67622--67679 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
67612 ATGTCTATTT
*
67622 TTTTA-TATATTTAATATTTAATA
1 TTTTATTATATTGAATATTTAATA
*
67645 TTTTATTATATTGATTATTT-A-A
1 TTTTATTATATTGAATATTTAATA
*
67667 TTTTATTTTATTG
1 TTTTATTATATTG
67680 GTGAATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.42
23 6 0.19
24 12 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTTATTATATTGAATATTTAATA
Found at i:67677 original size:24 final size:23
Alignment explanation
Indices: 67618--67677 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
67608 TAAGATGTCT
*
67618 ATTTTTTTATATATTTAATATTTA
1 ATTTTTTT-TATATTGAATATTTA
* *
67642 ATATTTTATTATATTGATTATTTA
1 AT-TTTTTTTATATTGAATATTTA
67666 ATTTTATTTTAT
1 ATTTT-TTTTAT
67678 TGGTGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 3 0.10
24 22 0.73
25 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTTTTTATATTGAATATTTA
Found at i:75220 original size:14 final size:14
Alignment explanation
Indices: 75201--75227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
75191 ATATTAGGGG
75201 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
75215 TTTTTATTTTTTT
1 TTTTTATTTTTTT
75228 CAGGTTAAGG
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:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:76520 original size:28 final size:31
Alignment explanation
Indices: 76488--76555 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
76478 TATTTAAAAT
*
76488 AAAATATTAA-ATTTAA-A-TTAAAAAATAA
1 AAAATATTAATATTAAATATTTAAAAAATAA
* *
76516 AAAAT-TATAATATTAAATATTTAAATATTAA
1 AAAATAT-TAATATTAAATATTTAAAAAATAA
76547 AAAATATTA
1 AAAATATTA
76556 TTGACTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.25
29 5 0.16
30 1 0.03
31 16 0.50
32 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATATTAATATTAAATATTTAAAAAATAA
Found at i:76534 original size:7 final size:7
Alignment explanation
Indices: 76489--76547 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
76479 ATTTAAAATA
76489 AAATATT
1 AAATATT
76496 AAAT-TT
1 AAATATT
*
76502 AAAT-TA
1 AAATATT
* *
76508 AAAAATA
1 AAATATT
*
76515 AAAAATT
1 AAATATT
76522 ATAATATT
1 A-AATATT
76530 AAATATTT
1 AAATA-TT
76538 AAATATT
1 AAATATT
76545 AAA
1 AAA
76548 AAATATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 10 0.22
7 22 0.49
8 13 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATATT
Found at i:77006 original size:39 final size:37
Alignment explanation
Indices: 76938--77010 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
76928 TATTCCAAAT
*
76938 TATATATATTTATAAAATTTTTATATTTTTAAATGTG
1 TATATATATTTATAAAATATTTATATTTTTAAATGTG
*
76975 TATATATATTTAATAAAAAATATTTGT-TTTTTAAAT
1 TATATATATTT-AT--AAAATATTTATATTTTTAAAT
77011 AAAATCACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 11 0.35
38 2 0.06
39 9 0.29
40 9 0.29
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (37 bp):
TATATATATTTATAAAATATTTATATTTTTAAATGTG
Found at i:85204 original size:16 final size:16
Alignment explanation
Indices: 85171--85217 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
85161 TAGGGTACAA
*
85171 AGAAAATTGAAAGAAT
1 AGAAAATTGAAGGAAT
* *
85187 AGATAATTGAAGGGAT
1 AGAAAATTGAAGGAAT
85203 AGAAAATTAGAAGGA
1 AGAAAATT-GAAGGA
85218 TGAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (16 bp):
AGAAAATTGAAGGAAT
Found at i:85218 original size:16 final size:15
Alignment explanation
Indices: 85171--85224 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
85161 TAGGGTACAA
*
85171 AGAAAATTGAAAGAAT
1 AGAAAATTG-AAGGAT
*
85187 AGATAATTGAAGGGAT
1 AGAAAATTGAA-GGAT
85203 AGAAAATTAGAAGGAT
1 AGAAAATT-GAAGGAT
85219 -GAAAAT
1 AGAAAAT
85225 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 22 0.67
17 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (15 bp):
AGAAAATTGAAGGAT
Found at i:86162 original size:34 final size:34
Alignment explanation
Indices: 86119--86187 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
86109 ATCACAATAT
*
86119 TTTCTATTCAACTTTCCAATAACCTGACATCTCA
1 TTTCTATTCAACTTTCCAATAACATGACATCTCA
**
86153 TTTCTATTCAGTTTTCCAATAACATGACATCTCA
1 TTTCTATTCAACTTTCCAATAACATGACATCTCA
86187 T
1 T
86188 GCTTTCGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.04, T:0.41
Consensus pattern (34 bp):
TTTCTATTCAACTTTCCAATAACATGACATCTCA
Found at i:87080 original size:21 final size:21
Alignment explanation
Indices: 87054--87108 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
87044 ATAATGATAT
87054 GTATCACGATACCAACCATGG
1 GTATCACGATACCAACCATGG
* *
87075 GTATCAGGATACCAGCCATGG
1 GTATCACGATACCAACCATGG
**
87096 GTATTGCGATACC
1 GTATCACGATACC
87109 CAACATCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (21 bp):
GTATCACGATACCAACCATGG
Found at i:87813 original size:12 final size:13
Alignment explanation
Indices: 87785--87813 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
87775 AATCTTATGG
87785 AAATTTTAAATAA
1 AAATTTTAAATAA
87798 AAATTTTAAA-AA
1 AAATTTTAAATAA
87810 AAAT
1 AAAT
87814 GCTTCCAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAATAA
Found at i:89362 original size:30 final size:29
Alignment explanation
Indices: 89328--89390 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
89318 ATTTTTGACG
89328 AATTTGAGATCAAAATTGAAATTATTGAAA
1 AATTTGAGATCAAAATTGAAATT-TTGAAA
* * * *
89358 AATTTGGGATTAAAATTGAACTTTTGGAA
1 AATTTGAGATCAAAATTGAAATTTTGAAA
89387 AATT
1 AATT
89391 GGGGATCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (29 bp):
AATTTGAGATCAAAATTGAAATTTTGAAA
Found at i:89403 original size:30 final size:29
Alignment explanation
Indices: 89335--89416 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
89325 ACGAATTTGA
* * *
89335 GATCAAAATTGAAATTATTGAAAAATTTGG
1 GATCAAAATTGAACTT-TTGGAAAATTGGG
*
89365 GATTAAAATTGAACTTTTGGAAAATTGGG
1 GATCAAAATTGAACTTTTGGAAAATTGGG
89394 GATCGAAAATATG-ACTTTTGGAA
1 GATC-AAAAT-TGAACTTTTGGAA
89417 GGCAAAATGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 14 0.31
30 29 0.64
31 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
GATCAAAATTGAACTTTTGGAAAATTGGG
Found at i:89462 original size:29 final size:29
Alignment explanation
Indices: 89420--89607 Score: 161
Period size: 29 Copynumber: 6.6 Consensus size: 29
89410 TTTGGAAGGC
*
89420 AAAATGGTAATTTTTGGATGCTCGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* * *
89449 AAAATGGTAATTTTTGAATGTT-GGGGGC
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
** *
89477 AAAATAATAAATTTTGGATGTTC-AGGGAT
1 AAAATGGTAATTTTTGGATGTTCGAGGG-T
* * *
89506 AAAAAT-GTATTTTTTGGATGTTCGAGAGC
1 -AAAATGGTAATTTTTGGATGTTCGAGGGT
* *
89535 AAAATGGTAATTTTTGCATGTTCGGGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
* * * *
89564 AAAAT-GTGATTTTTGAAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGATGTTCGAGGGT
*
89592 GAAAAT-GTGATTTTTG
1 -AAAATGGTAATTTTTG
89608 AAAGTTTGAA
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
28 48 0.38
29 72 0.56
30 8 0.06
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGT
Found at i:89509 original size:57 final size:56
Alignment explanation
Indices: 89417--89607 Score: 179
Period size: 57 Copynumber: 3.3 Consensus size: 56
89407 ACTTTTGGAA
* *
89417 GGCAAAATGGTAATTTTTGGATGCTCGAGGGTAAAATGGTAATTTTTGAATGTT-GGG
1 GGCAAAATGGTAATTTTTGGATGTTC-AGGGTAAAAT-GTAATTTTTGAATGTTCGAG
** * * *
89474 GGCAAAATAATAAATTTTGGATGTTCAGGGATAAAAATGTATTTTTTGGATGTTCGAG
1 GGCAAAATGGTAATTTTTGGATGTTCAGGG-T-AAAATGTAATTTTTGAATGTTCGAG
* * * * * *
89532 AGCAAAATGGTAATTTTTGCATGTTCGGGGGTAAAATGTGATTTTTGAAAGTTTGAG
1 GGCAAAATGGTAATTTTTGGATGTTC-AGGGTAAAATGTAATTTTTGAATGTTCGAG
* *
89589 GGTGAAAAT-GTGATTTTTG
1 GG-CAAAATGGTAATTTTTG
89608 AAAGTTTGAA
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
56 4 0.04
57 67 0.62
58 34 0.31
59 3 0.03
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (56 bp):
GGCAAAATGGTAATTTTTGGATGTTCAGGGTAAAATGTAATTTTTGAATGTTCGAG
Found at i:89597 original size:58 final size:56
Alignment explanation
Indices: 89420--89667 Score: 175
Period size: 57 Copynumber: 4.3 Consensus size: 56
89410 TTTGGAAGGC
* * *
89420 AAAATGGTAATTTTTGGATGCTCGAGGGTAAAATGGTAATTTTTGAATG-TTG-GGGG
1 AAAAT-GTAATTTTTGGATGTTCGAGGGTAAAAT-GTGATTTTTGAAAGTTTGAGGGG
* * * * * * *
89476 CAAAATAATAAATTTTGGATGTTC-AGGGATAAAAATGT-ATTTTTTGGATGTTCGAGAGC
1 -AAAAT-GTAATTTTTGGATGTTCGAGGG-T-AAAATGTGA-TTTTTGAAAGTTTGAGGGG
* *
89535 AAAATGGTAATTTTTGCATGTTCGGGGGTAAAATGTGATTTTTGAAAGTTTGAGGGTG
1 AAAAT-GTAATTTTTGGATGTTCGAGGGTAAAATGTGATTTTTGAAAGTTTGAGGG-G
* * * * * *
89593 AAAATGTGATTTTTGAAAGTTTGAAGGTAAGAACT-TGATTTTTGGAAAGTTT-AGGGTA
1 AAAATGTAATTTTTGGATGTTCGAGGGTAA-AA-TGTGATTTTT-GAAAGTTTGAGGG-G
89651 AAAATGTAATTTTTGGA
1 AAAATGTAATTTTTGGA
89668 AAGTTTAGGG
Statistics
Matches: 153, Mismatches: 27, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
56 5 0.03
57 71 0.46
58 63 0.41
59 14 0.09
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (56 bp):
AAAATGTAATTTTTGGATGTTCGAGGGTAAAATGTGATTTTTGAAAGTTTGAGGGG
Found at i:89606 original size:86 final size:85
Alignment explanation
Indices: 89420--89607 Score: 200
Period size: 86 Copynumber: 2.2 Consensus size: 85
89410 TTTGGAAGGC
* *
89420 AAAATGGTAATTTTTGGATGCTCGAGGGTAAAATGGTAATTTTTGAATGTTGGGGGCAAAATAAT
1 AAAAT-GT-ATTTTTGGATGCTCGAGAGCAAAATGGTAATTTTTGAATGTTGGGGGCAAAATAAT
* *
89485 AAATTTTGGATGTTCAGGGATA
64 AAATTTTGAAAGTTCAGGGATA
* * * *
89507 AAAATGTATTTTTTGGATGTTCGAGAGCAAAATGGTAATTTTTGCATGTTCGGGGGTAAAAT-GT
1 AAAATGTA-TTTTTGGATGCTCGAGAGCAAAATGGTAATTTTTGAATGTT-GGGGGCAAAATAAT
* * * *
89571 GATTTTTGAAAGTTTGAGGG-TG
64 AAATTTTGAAAG-TTCAGGGATA
89593 AAAATGTGATTTTTG
1 AAAATGT-ATTTTTG
89608 AAAGTTTGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
85 1 0.01
86 62 0.73
87 22 0.26
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (85 bp):
AAAATGTATTTTTGGATGCTCGAGAGCAAAATGGTAATTTTTGAATGTTGGGGGCAAAATAATAA
ATTTTGAAAGTTCAGGGATA
Found at i:89682 original size:30 final size:30
Alignment explanation
Indices: 89559--89878 Score: 245
Period size: 29 Copynumber: 10.9 Consensus size: 30
89549 TGCATGTTCG
89559 GGGGT-AAAATGTGATTTTT-GAAAGTTT-
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
*
89586 GAGGGTGAAAATGTGATTTTT-GAAAGTTT-
1 G-GGGTAAAAATGTGATTTTTGGAAAGTTTA
* *
89615 GAAGGTAAGAACT-TGATTTTTGGAAAGTTTA
1 G-GGGTAA-AAATGTGATTTTTGGAAAGTTTA
*
89646 -GGGTAAAAATGTAATTTTTGGAAAGTTTA
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
* *
89675 GGGGTAAAAATGT-AATTTTGAAAAGTTTA
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
** * *
89704 -GGGTCGAAATGTGATTTTTAGAAACTTTA
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
* * * *
89733 AGGGTAAAAATGT-AATTGTGGAAAATTTA
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
* * * ***
89762 AGGGTAAAAGTGT-AATTTCAAAAAGTTT-
1 GGGGTAAAAATGTGATTTTTGGAAAGTTTA
*
89790 GGTGGTCAAAATGTGATTTTTGGAAAGTTTA
1 GG-GGTAAAAATGTGATTTTTGGAAAGTTTA
** * *
89821 GATGTAGAAAATAT-AATTTTGGAAAGTTT-
1 GGGGTA-AAAATGTGATTTTTGGAAAGTTTA
* *
89850 GAGGGTCAAAACGTGATTTTTGGAAAGTT
1 G-GGGTAAAAATGTGATTTTTGGAAAGTT
89879 CAAGGACCTT
Statistics
Matches: 234, Mismatches: 44, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.00
28 18 0.08
29 133 0.57
30 75 0.32
31 7 0.03
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (30 bp):
GGGGTAAAAATGTGATTTTTGGAAAGTTTA
Found at i:91701 original size:17 final size:17
Alignment explanation
Indices: 91669--91748 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 17
91659 TTTTAAAATT
91669 TAAATTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
*
91685 TATATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
91702 TAAATTCAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
91719 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
91736 TAAATTAAAATTT
1 TAAATTTAAATTT
91749 TAATTTTAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 9 0.17
17 43 0.83
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:92274 original size:16 final size:15
Alignment explanation
Indices: 92247--92296 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
92237 AGAGAATGTG
92247 TAAA-AAACATAAATA
1 TAAATAAACATAAA-A
*
92262 TAAATAGACATAAAAA
1 TAAATAAACAT-AAAA
*
92278 TAAATAAAGATAAAA
1 TAAATAAACATAAAA
92293 TAAA
1 TAAA
92297 AATAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.40
16 15 0.50
17 3 0.10
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (15 bp):
TAAATAAACATAAAA
Found at i:92308 original size:16 final size:16
Alignment explanation
Indices: 92250--92309 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
92240 GAATGTGTAA
*
92250 AAAACATAAATATAAAT
1 AAAA-ATAAAAATAAAT
* *
92267 AGACATAAAAATAAAT
1 AAAAATAAAAATAAAT
*
92283 AAAGAT-AAAATAAA-
1 AAAAATAAAAATAAAT
92297 AATAAATAAAAAT
1 AA-AAATAAAAAT
92310 TATAAAAGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 20 0.57
17 2 0.06
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:92316 original size:9 final size:10
Alignment explanation
Indices: 92250--92309 Score: 66
Period size: 10 Copynumber: 5.6 Consensus size: 10
92240 GAATGTGTAA
92250 AAAACATAAAT
1 AAAA-ATAAAT
*
92261 ATAAATAGACAT
1 AAAAATA-A-AT
92273 AAAAATAAAT
1 AAAAATAAAT
*
92283 AAAGATAAAAT
1 AAAAAT-AAAT
92294 AAAAATAAAT
1 AAAAATAAAT
92304 AAAAAT
1 AAAAAT
92310 TATAAAAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 20 0.48
11 14 0.33
12 8 0.19
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:92851 original size:22 final size:21
Alignment explanation
Indices: 92823--92864 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
92813 TGGCTGGAAA
92823 TTTTTTTTTTATAAAATCAAAG
1 TTTTTTTTTTATAAAA-CAAAG
*
92845 TTTTTTTTTTTTAAAACAAA
1 TTTTTTTTTTATAAAACAAA
92865 ATAACCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTTTTTTTATAAAACAAAG
Found at i:92935 original size:17 final size:18
Alignment explanation
Indices: 92913--92946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
92903 AATTGTTATG
92913 AAAAA-TCAAACTTTTTT
1 AAAAATTCAAACTTTTTT
*
92930 AAAAATTTAAACTTTTT
1 AAAAATTCAAACTTTTT
92947 CTTTAAACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATTCAAACTTTTTT
Found at i:92983 original size:21 final size:21
Alignment explanation
Indices: 92959--93004 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
92949 TTAAACTGAC
*
92959 TAAAAAAC-AAATTTTTATTTT
1 TAAAAAACTAAACTTTT-TTTT
*
92980 TAAAAATCTAAACTTTTTTTT
1 TAAAAAACTAAACTTTTTTTT
93001 TAAA
1 TAAA
93005 TTACTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAAACTAAACTTTTTTTT
Found at i:93081 original size:31 final size:32
Alignment explanation
Indices: 93018--93084 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
93008 CTATTTTCTT
** *
93018 AAAAATCAAAACTTTTATTTCGAAATAGTTAA
1 AAAAATCAAAACTTTTATTTAAAAAAAGTTAA
* *
93050 AAAAATCAAAA-TTTTGTTTAAAAAAATTTAA
1 AAAAATCAAAACTTTTATTTAAAAAAAGTTAA
93081 AAAA
1 AAAA
93085 TTTCCTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (32 bp):
AAAAATCAAAACTTTTATTTAAAAAAAGTTAA
Found at i:93263 original size:145 final size:143
Alignment explanation
Indices: 92846--93224 Score: 359
Period size: 145 Copynumber: 2.7 Consensus size: 143
92836 AAATCAAAGT
* * * * * * *
92846 TTTTTTTTTTTAAAACAAAATAACCATTTTTTTTAAAATTCAAAACTTTTATTTCAAAATTGTTA
1 TTTTTTTTTTTAAAAAAAAATTACTA-TTTTATTAAAAATCAAAACTTTTATTTCGAAATAGTTA
* ** * * * *
92911 TGAAAAATC-AAACTTT-TTT-AAAAATTT-AAACTTTTTCTTTAAACTGACTAAAAAACAAATT
65 -AAAAAATCAAAACTTTGTTTAAAAAATTTAAAAAATTTCCTTTAAAATAACTAAAAAACATATT
* ****
92972 TTTATTTTTAAAAATC
129 TTTAATTTT-CTTTTC
* *
92988 TAAACTTTTTTTTT------AAATTACTATTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGT
1 T---TTTTTTTTTTAAAAAAAAATTACTATTTTATTAAAAATCAAAACTTTTATTTCGAAATAGT
* * *
93047 TAAAAAAATCAAAATTTTGTTTAAAAAAATTTAAAAAATTTCCTTTAAAATGACTAAAAAACATG
63 TAAAAAAATCAAAACTTTGTTT-AAAAAATTTAAAAAATTTCCTTTAAAATAACTAAAAAACATA
93112 TTTTTAATTTTCTTTTC
127 TTTTTAATTTTCTTTTC
* *
93129 TTTTTTTTTTTAAAAAAAAATTACTACTTTTATTAAAAATCAAAACTTTTATTTTGAAATGGTTA
1 TTTTTTTTTTTAAAAAAAAATTACTA-TTTTATTAAAAATCAAAACTTTTATTTCGAAATAGTT-
93194 AAAAAAATC-AAACTTTGTTT-AAAAATTTAAA
64 AAAAAAATCAAAACTTTGTTTAAAAAATTTAAA
93225 TTTTTTTTAT
Statistics
Matches: 196, Mismatches: 25, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
137 7 0.04
138 49 0.25
139 10 0.05
141 11 0.06
142 37 0.19
143 11 0.06
144 9 0.05
145 53 0.27
146 9 0.05
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (143 bp):
TTTTTTTTTTTAAAAAAAAATTACTATTTTATTAAAAATCAAAACTTTTATTTCGAAATAGTTAA
AAAAATCAAAACTTTGTTTAAAAAATTTAAAAAATTTCCTTTAAAATAACTAAAAAACATATTTT
TAATTTTCTTTTC
Found at i:96789 original size:26 final size:26
Alignment explanation
Indices: 96760--96823 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
96750 GGTAATAACG
96760 TAAAATGATAAATAAAATATGAA-AAC
1 TAAAAT-ATAAATAAAATATGAAGAAC
* * * *
96786 TAAAGTAAAAACAAAATATGAAGTAC
1 TAAAATATAAATAAAATATGAAGAAC
96812 TAAAATATAAAT
1 TAAAATATAAAT
96824 TTTAGATCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (26 bp):
TAAAATATAAATAAAATATGAAGAAC
Found at i:97024 original size:28 final size:30
Alignment explanation
Indices: 96993--97057 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
96983 GTTAAATAAA
*
96993 AAAAATATAAAA-GGATTTTTAAAA-ACAT
1 AAAAATATAAAAGGGAATTTTAAAAGACAT
* *
97021 AAAAAAATAAAAGGGAATTTTAAAAGAGAT
1 AAAAATATAAAAGGGAATTTTAAAAGACAT
97051 AAAAATA
1 AAAAATA
97058 AAAGAATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.35
29 11 0.35
30 9 0.29
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.23
Consensus pattern (30 bp):
AAAAATATAAAAGGGAATTTTAAAAGACAT
Found at i:97041 original size:29 final size:31
Alignment explanation
Indices: 96991--97055 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
96981 GGGTTAAATA
*
96991 AAAAAAATATAAAAGGATTTTTAAAA-ACAT
1 AAAAAAATATAAAAGGAATTTTAAAAGACAT
* *
97021 AAAAAAATA-AAAGGGAATTTTAAAAGAGAT
1 AAAAAAATATAAAAGGAATTTTAAAAGACAT
97051 AAAAA
1 AAAAA
97056 TAAAAGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.22
Consensus pattern (31 bp):
AAAAAAATATAAAAGGAATTTTAAAAGACAT
Found at i:98085 original size:3 final size:3
Alignment explanation
Indices: 98077--98107 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
98067 CTCTTTATAT
*
98077 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
98108 CGTATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:104610 original size:3 final size:3
Alignment explanation
Indices: 104604--104668 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
104594 ATAAATTCAT
* * * **
104604 TAA TAA TAA TAA TAA TGA TAA TAT TAAA TAA TAA TAA TTA TTT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
104650 TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA
104669 ACACGGAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:105735 original size:30 final size:29
Alignment explanation
Indices: 105666--106017 Score: 271
Period size: 30 Copynumber: 11.9 Consensus size: 29
105656 CCCTGGAGGT
* *
105666 CCTTAAACTGTCAAAAAATTCCGTTTTTAC
1 CCTTAAACT-TCCAAAAATTCCATTTTTAC
** *
105696 CCTCGAACTTCCAAAAATCCCATTTTTACC
1 CCTTAAACTTCCAAAAATTCCATTTTTA-C
* *
105726 CCTTAAACTTTCAAAAATCCCATTTTTGAC
1 CCTTAAACTTCCAAAAATTCCATTTTT-AC
* * * * *
105756 ACTAAAACTTCTAAAACTTCTATTTTTTAC
1 CCTTAAACTTCCAAAAATTCCA-TTTTTAC
* ** *
105786 CCTTGAA-TTTTAAAAAATCTCATTTTTGA-
1 CCTTAAACTTCCAAAAATTC-CATTTTT-AC
* * *
105815 CCTTAAAACTTCTAAAAATTTCATTTTTTC
1 CCTT-AAACTTCCAAAAATTCCATTTTTAC
*
105845 CC-TAAACTTCCAAAAA-TCTCATTTTTAA
1 CCTTAAACTTCCAAAAATTC-CATTTTTAC
* ** *
105873 CCTCAAAACTTTTAAAAATTCTATTTTTAC
1 CCT-TAAACTTCCAAAAATTCCATTTTTAC
* * *
105903 CCCTAAACTTCCAAAAATCCCATTTTTAA
1 CCTTAAACTTCCAAAAATTCCATTTTTAC
*
105932 CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCT-TAAACTTCCAAAAATTCCATTTTTAC
*
105962 CCTTGAACTTCCAAAAATTCCATTTTTAAC
1 CCTTAAACTTCCAAAAATTCCATTTTT-AC
* ** *
105992 CCTGAATTTTCCCAAAATTACCATTT
1 CCTTAAACTTCCAAAAATT-CCATTT
106018 CACTCTTGAG
Statistics
Matches: 253, Mismatches: 54, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.00
28 21 0.08
29 79 0.31
30 129 0.51
31 23 0.09
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
CCTTAAACTTCCAAAAATTCCATTTTTAC
Found at i:105916 original size:59 final size:59
Alignment explanation
Indices: 105701--105992 Score: 313
Period size: 59 Copynumber: 4.9 Consensus size: 59
105691 TTTACCCTCG
* * * * * *
105701 AACTTCCAAAAATCCCATTTTTACCCCTTAAACTTTCAAAAATCCCATTTTTGACACT-AA
1 AACTTCTAAAAATTCTATTTTTACCCC-TAAACTTCCAAAAATCTCATTTTTAAC-CTCAA
* * * * ** * *
105761 AACTTCTAAAACTTCTATTTTTTACCCTTGAATTTTAAAAAATCTCATTTTTGACCTTAA
1 AACTTCTAAAAATTCTA-TTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCAA
*
105821 AACTTCTAAAAATT-TCATTTTT-TCCCTAAACTTCCAAAAATCTCATTTTTAACCTCAA
1 AACTTCTAAAAATTCT-ATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCAA
* * *
105879 AACTTTTAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCGA
1 AACTTCTAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCAA
* * * *
105938 AACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAAT-TCCATTTTTAACC
1 AACTTCTAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATCT-CATTTTTAACC
105993 CTGAATTTTC
Statistics
Matches: 198, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
58 47 0.24
59 90 0.45
60 52 0.26
61 9 0.05
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (59 bp):
AACTTCTAAAAATTCTATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCTCAA
Found at i:106009 original size:59 final size:59
Alignment explanation
Indices: 105666--106017 Score: 302
Period size: 59 Copynumber: 5.9 Consensus size: 59
105656 CCCTGGAGGT
* * ** *
105666 CCTTAAACTGTCAAAAAATTCCGTTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTACC
1 CCTTAAACT-TCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTA-C
* * * * * * *
105726 CCTTAAACTTTCAAAAATCCCATTTTTGACACTAAAACTTCTAAAACTTCTATTTTTTAC
1 CCTTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTTAC
* ** * * * * * *
105786 CCTTGAA-TTTTAAAAAATCTCATTTTTGACCTTAAAACTTCTAAAAATTTCATTTTTTC
1 CCTTAAACTTCCAAAAATTC-CATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTAC
** *
105845 CC-TAAACTTCCAAAAA-TCTCATTTTTAA-CCTCAAAACTTTTAAAAATTCTATTTTTAC
1 CCTTAAACTTCCAAAAATTC-CATTTTTAACCCT-AAAACTTCCAAAAATTCCATTTTTAC
* * *
105903 CCCTAAACTTCCAAAAATCCCATTTTTAA-CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTTAAACTTCCAAAAATTCCATTTTTAACCCT-AAAACTTCCAAAAATTCCATTTTTAC
* * ** *
105962 CCTTGAACTTCCAAAAATTCCATTTTTAACCCTGAATTTTCCCAAAATTACCATTT
1 CCTTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT-CCATTT
106018 CACTCTTGAG
Statistics
Matches: 242, Mismatches: 41, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
57 2 0.01
58 38 0.16
59 126 0.52
60 70 0.29
61 6 0.02
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
CCTTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTAC
Found at i:114645 original size:641 final size:631
Alignment explanation
Indices: 113424--114695 Score: 2454
Period size: 641 Copynumber: 2.0 Consensus size: 631
113414 TATGAGCAAC
113424 CCTGACGCTGACTTAGAACCACACTTCGAGCAAGATACGTGTTTGGAAGAGCTTCAGGACCTTGA
1 CCTGACGCTGACTTAGAACCACACTTCGAGCAAGATACGTGTTTGGAAGAGCTTCAGGACCTTGA
113489 AGATAATCAAGATTGTGATCTGCCTCCGGATTTGTTAAGAATGACGGAATAGGAAGAAAAACAGA
66 AGATAATCAAGATTGTGATCTGCCTCCGGATTTGTTAAGAATGACGGAATAGGAAGAAAAACAGA
113554 TCCTGCCTCAATCGGACCCAGTGGAAGTTATTAATCTGGGGCACGAAGATGAAAAGAAAGAGGTG
131 TCCTGCCTCAATCGGACCCAGTGGAAGTTATTAATCTGGGGCACGAAGATGAAAAGAAAGAGGTG
113619 AAAATTGGGACAAGCATCTCCGTAGAAACCAGAAGAAATCTTATCAAGTTGTTTCAAGAGTTCCA
196 AAAATTGGGACAAGCATCTCCGTAGAAACCAGAAGAAATCTTATCAAGTTGTTTCAAGAGTTCCA
113684 AGATATCTTCACATGGTCTTACCAGGATATGCCTTGCTTGAGCACTGACATTGTGGTGCATAAAC
261 AGATATCTTCACATGGTCTTACCAGGATATGCCTTGCTTGAGCACTGACATTGTGGTGCATAAAC
113749 TCCCTATAAAGAAGAAAGCAGACCTGTGCAGCAAAAACTCCGAAGGATGAGACCGGATGTGTTGT
326 TCCCTATAAAGAAGAAAGCAGACCTGTGCAGCAAAAACTCCGAAGGATGAGACCGGATGTGTTGT
113814 TAAAAATAAAAGAAGAAGTCAAGAAACAATTTGACGTTGGTTTCCTCCAGTGGTTAAATACTCTA
391 TAAAAATAAAAGAAGAAGTCAAGAAACAATTTGACGTTGGTTTCCTCCAGTGGTTAAATACTCTA
113879 AATGGGTAGTTAATATAGTCCCCGTTCCTAAAAAAGACGGAAAGGTGCGCATGTGTGTGGACTAT
456 AATGGGTAGTTAATATAGTCCCCGTTCCTAAAAAAGACGGAAAGGTGCGCATGTGTGTGGACTAT
113944 CGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTCCCTTACCCCATATCGACACTCTAGTCGA
521 CGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTCCCTTACCCCATATCGACACTCTAGTCGA
114009 CAACACGGCAGGACATTCTTTGTTTTCCTTTATGGATGGTTTCTCT
586 CAACACGGCAGGACATTCTTTGTTTTCCTTTATGGATGGTTTCTCT
114055 NNNNNNNNNNCCTGACGCTGACTTAGAACCACACTTCGAGCAAGATACGTGTTTGGAAGAGCTTC
1 ----------CCTGACGCTGACTTAGAACCACACTTCGAGCAAGATACGTGTTTGGAAGAGCTTC
114120 AGGACCTTGAAGATAATCAAGATTGTGATCTGCCTCCGGATTTGTTAAGAATGACGGAATAGGAA
56 AGGACCTTGAAGATAATCAAGATTGTGATCTGCCTCCGGATTTGTTAAGAATGACGGAATAGGAA
114185 GAAAAACAGATCCTGCCTCAATCGGACCCAGTGGAAGTTATTAATCTGGGGCACGAAGATGAAAA
121 GAAAAACAGATCCTGCCTCAATCGGACCCAGTGGAAGTTATTAATCTGGGGCACGAAGATGAAAA
114250 GAAAGAGGTGAAAATTGGGACAAGCATCTCCGTAGAAACCAGAAGAAATCTTATCAAGTTGTTTC
186 GAAAGAGGTGAAAATTGGGACAAGCATCTCCGTAGAAACCAGAAGAAATCTTATCAAGTTGTTTC
114315 AAGAGTTCCAAGATATCTTCACATGGTCTTACCAGGATATGCCTTGCTTGAGCACTGACATTGTG
251 AAGAGTTCCAAGATATCTTCACATGGTCTTACCAGGATATGCCTTGCTTGAGCACTGACATTGTG
114380 GTGCATAAACTCCCTATAAAGAAGAAAGCAGACCTGTGCAGCAAAAACTCCGAAGGATGAGACCG
316 GTGCATAAACTCCCTATAAAGAAGAAAGCAGACCTGTGCAGCAAAAACTCCGAAGGATGAGACCG
114445 GATGTGTTGTTAAAAATAAAAGAAGAAGTCAAGAAACAATTTGACGTTGGTTTCCTCCAGTGGTT
381 GATGTGTTGTTAAAAATAAAAGAAGAAGTCAAGAAACAATTTGACGTTGGTTTCCTCCAGTGGTT
114510 AAATACTCTAAATGGGTAGTTAATATAGTCCCCGTTCCTAAAAAAGACGGAAAGGTGCGCATGTG
446 AAATACTCTAAATGGGTAGTTAATATAGTCCCCGTTCCTAAAAAAGACGGAAAGGTGCGCATGTG
114575 TGTGGACTATCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTCCCTTACCCCATATCGACA
511 TGTGGACTATCGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTCCCTTACCCCATATCGACA
114640 CTCTAGTCGACAACACGGCAGGACATTCTTTGTTTTCCTTTATGGATGGTTTCTCT
576 CTCTAGTCGACAACACGGCAGGACATTCTTTGTTTTCCTTTATGGATGGTTTCTCT
114696 GGGTATAATC
Statistics
Matches: 631, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
641 631 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (631 bp):
CCTGACGCTGACTTAGAACCACACTTCGAGCAAGATACGTGTTTGGAAGAGCTTCAGGACCTTGA
AGATAATCAAGATTGTGATCTGCCTCCGGATTTGTTAAGAATGACGGAATAGGAAGAAAAACAGA
TCCTGCCTCAATCGGACCCAGTGGAAGTTATTAATCTGGGGCACGAAGATGAAAAGAAAGAGGTG
AAAATTGGGACAAGCATCTCCGTAGAAACCAGAAGAAATCTTATCAAGTTGTTTCAAGAGTTCCA
AGATATCTTCACATGGTCTTACCAGGATATGCCTTGCTTGAGCACTGACATTGTGGTGCATAAAC
TCCCTATAAAGAAGAAAGCAGACCTGTGCAGCAAAAACTCCGAAGGATGAGACCGGATGTGTTGT
TAAAAATAAAAGAAGAAGTCAAGAAACAATTTGACGTTGGTTTCCTCCAGTGGTTAAATACTCTA
AATGGGTAGTTAATATAGTCCCCGTTCCTAAAAAAGACGGAAAGGTGCGCATGTGTGTGGACTAT
CGAGATTTAAATAAAGCTAGCCCAAAGGATAATTTTCCCTTACCCCATATCGACACTCTAGTCGA
CAACACGGCAGGACATTCTTTGTTTTCCTTTATGGATGGTTTCTCT
Found at i:118712 original size:205 final size:203
Alignment explanation
Indices: 118458--119084 Score: 983
Period size: 205 Copynumber: 3.1 Consensus size: 203
118448 NNNNNNNNNN
* *
118458 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAAA
1 GCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGATAAGCAAA
118523 TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGCA
66 TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCG-A
118588 CTCGATGTGAGCAAATCTTCGAA-CTCCAGCTTCCTGATGAGACATCGAGAAGCAGGTCGAAGCA
130 CTCGATGTGAGCAAATCTTCGAATC-CCAGCTTCCTGATGAGACA-CGAGAAGCAGGTCGAAGCA
*
118652 ATAAACGGAGA
193 ATAAACGGTGA
* * *
118663 GCTTCTTGATGAGATATTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACATATAAGCAAA
1 GCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGATAAGCAAA
*
118728 TTGAAACAAATGATGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATG
66 TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC--G
* *
118793 A-TCGAAGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCA
129 ACTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACAC-GAGAAGCAGGTCGAAGCA
118857 ATAAACGGTGA
193 ATAAACGGTGA
*
118868 GCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCATCTTCCTGATGAGATACAGATAAGCAAA
1 GCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGATAAGCAAA
*
118933 TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATGCTGAGAAGAAGACCAAATCAAACCC-AT
66 TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGA-
* * * *
118997 GCTCGATGTGGGCAAATCTTCGAATCCCAGCTTCTTGATGAGGCACCGAGAAGC-GAGTCGAAAC
130 -CTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACA-CGAGAAGCAG-GTCGAAGC
*
119061 AATAAAACGGTTA
192 AAT-AAACGGTGA
119074 GCTTCCTGATG
1 GCTTCCTGATG
119085 CAATACAGAG
Statistics
Matches: 390, Mismatches: 22, Indels: 19
0.90 0.05 0.04
Matches are distributed among these distances:
202 1 0.00
204 1 0.00
205 365 0.94
206 22 0.06
207 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (203 bp):
GCTTCCTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGATAAGCAAA
TTGAAACAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCGAC
TCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGACACGAGAAGCAGGTCGAAGCAATA
AACGGTGA
Found at i:120370 original size:3 final size:3
Alignment explanation
Indices: 120364--120452 Score: 115
Period size: 3 Copynumber: 29.0 Consensus size: 3
120354 ATAAATTCAT
* *
120364 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAT TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* **
120413 TAA TAA TAA TTA TTT TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
120453 ACACGGAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 71 0.93
4 5 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:121509 original size:29 final size:29
Alignment explanation
Indices: 121467--121745 Score: 273
Period size: 29 Copynumber: 9.5 Consensus size: 29
121457 TACACTGTTC
* *
121467 AAAAATTTCATTTTTACCCTCGAACTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCT
* * *
121496 AAAAATCCCA-TTTTACCACTCGAACTTTT
1 AAAAATTCCATTTTTACC-CTCAAACTTCT
* * *
121525 AAAAATCCCATTTTAACCCTAAAACTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCT
*
121554 AAAAATTCCATTTTTACCC-CTATACTT-T
1 AAAAATTCCATTTTTACCCTC-AAACTTCT
* *
121582 CAAAAA-TCTCATTTTTAACCTTGAAACTTCT
1 -AAAAATTC-CATTTTT-ACCCTCAAACTTCT
* *
121613 AAAAATTCTATTTTTACCC-CAAAACTTCC
1 AAAAATTCCATTTTTACCCTC-AAACTTCT
*
121642 AAAAATTCCATTTTTAACCC-CAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTC-AAACTTCT
*
121672 AAAAATTCCATTTTTACCCTCAAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCT
*
121701 AAAAATTCCATTTTTAACCTCGAAACTTCT
1 AAAAATTCCATTTTTACCCTC-AAACTTCT
*
121731 AAAAAATACCATTTT
1 -AAAAATTCCATTTT
121746 ATCCTCGGAT
Statistics
Matches: 214, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.05
29 126 0.59
30 62 0.29
31 16 0.07
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCAAACTTCT
Found at i:121746 original size:59 final size:58
Alignment explanation
Indices: 121466--121836 Score: 312
Period size: 59 Copynumber: 6.3 Consensus size: 58
121456 TTACACTGTT
* * * * *
121466 CAAAAATTTCATTTTTACCCTCG-AACTTCTAAAAATCCCA-TTTTACCACTCGAACTTT
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTCCATTTTTACC-C-CAAACTTC
* * * * *
121524 TAAAAATCCCA-TTTTAACC-CTAAAACTTCTAAAAATTCCATTTTTACCCCTATACTTT
1 CAAAAATTCCATTTTTAACCTC-GAAACTTCTAAAAATTCCATTTTTACCCC-AAACTTC
* *
121582 CAAAAA-TCTCATTTTTAACCTTGAAACTTCTAAAAATTCTATTTTTACCCCAAAACTTC
1 CAAAAATTC-CATTTTTAACCTCGAAACTTCTAAAAATTCCATTTTTACCCC-AAACTTC
* * *
121641 CAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTCCATTTTTACCC-CAAACTTC
* * **
121700 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAAATACCA-TTTTATCCTCGGA-TGTC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCT-AAAAATTCCATTTTTA-CCCCAAACT-TC
* * ** * * *
121759 CAAAAACTCCATTTTTGATTTCGAAAC-TCTTAAAATTACC-CTTTTACTCCCGAA-TATC
1 CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATT-CCATTTTTAC-CCCAAACT-TC
*
121817 TAAAAATTCCATTTTTAACC
1 CAAAAATTCCATTTTTAACC
121837 CTAAATTTTC
Statistics
Matches: 256, Mismatches: 42, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.00
57 15 0.06
58 70 0.27
59 156 0.61
60 14 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
CAAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTCCATTTTTACCCCAAACTTC
Found at i:121832 original size:29 final size:29
Alignment explanation
Indices: 121554--121861 Score: 129
Period size: 29 Copynumber: 10.4 Consensus size: 29
121544 TAAAACTTCT
* *
121554 AAAAATTCCATTTTTACCCC-TATACTTTC
1 AAAAATTCCATTTTTACCCCGAATAC-TCC
** *
121583 AAAAA-TCTCATTTTTAACCTTGAA-ACTTCT
1 AAAAATTC-CATTTTT-ACCCCGAATAC-TCC
* *
121613 AAAAATTCTATTTTTACCCC-AAAACTTCC
1 AAAAATTCCATTTTTACCCCGAATAC-TCC
*
121642 AAAAATTCCATTTTTAACCCC-AAAACTTCC
1 AAAAATTCCATTTTT-ACCCCGAATAC-TCC
121672 AAAAATTCCATTTTTACCCTC-AA-ACTTCC
1 AAAAATTCCATTTTTACCC-CGAATAC-TCC
* *
121701 AAAAATTCCATTTTTAACCTCGAA-ACTTCTA
1 AAAAATTCCATTTTT-ACCCCGAATAC-TC-C
* * * *
121732 AAAAATACCA-TTTTATCCTCGGAT-GTCC
1 AAAAATTCCATTTTTA-CCCCGAATACTCC
* *** *
121760 AAAAACTCCATTTTTGATTTCGAA-ACTCT
1 AAAAATTCCATTTTT-ACCCCGAATACTCC
* * *
121789 TAAAATTACC-CTTTTACTCCCGAATA-TCT
1 AAAAATT-CCATTTTTAC-CCCGAATACTCC
** **
121818 AAAAATTCCATTTTTAACCCTAAATTTTCC
1 AAAAATTCCATTTTT-ACCCCGAATACTCC
121848 AAAAATTACCATTT
1 AAAAATT-CCATTT
121862 CACTCCCGAG
Statistics
Matches: 222, Mismatches: 35, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
28 15 0.07
29 104 0.47
30 85 0.38
31 18 0.08
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCGAATACTCC
Found at i:143321 original size:38 final size:38
Alignment explanation
Indices: 143248--143399 Score: 117
Period size: 38 Copynumber: 4.0 Consensus size: 38
143238 GATTGCTTTA
* ** * *
143248 AGAGCGATACTAGCTCGTTAGAGCGATACTAGCTCGTT
1 AGAGCAATACTAGCTCGCAAGAGAGATACTGGCTCGTT
* * * *
143286 AGAGCGATACTGGCTCGCAAGAGAGATATTGGCTCGTA
1 AGAGCAATACTAGCTCGCAAGAGAGATACTGGCTCGTT
** * *
143324 AGAGCAAATACTAGCTCATAAGAGTGATACTGGCTCATT
1 AGAGC-AATACTAGCTCGCAAGAGAGATACTGGCTCGTT
* * * * *
143363 CGAGCAATATTGGCTAGCAAGAGCA-ATATTGGCTCGT
1 AGAGCAATACTAGCTCGCAAGAG-AGATACTGGCTCGT
143400 AAAAGAGATA
Statistics
Matches: 88, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
38 59 0.67
39 29 0.33
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (38 bp):
AGAGCAATACTAGCTCGCAAGAGAGATACTGGCTCGTT
Found at i:143361 original size:19 final size:19
Alignment explanation
Indices: 143246--143359 Score: 120
Period size: 19 Copynumber: 5.9 Consensus size: 19
143236 TCGATTGCTT
143246 TAAGAGCGATACTAGCTCG
1 TAAGAGCGATACTAGCTCG
*
143265 TTAGAGCGATACTAGCTCG
1 TAAGAGCGATACTAGCTCG
* *
143284 TTAGAGCGATACTGGCTCG
1 TAAGAGCGATACTAGCTCG
* * * *
143303 CAAGAGAGATATTGGCTCG
1 TAAGAGCGATACTAGCTCG
* *
143322 TAAGAGCAAATACTAGCTCA
1 TAAGAGC-GATACTAGCTCG
* *
143342 TAAGAGTGATACTGGCTC
1 TAAGAGCGATACTAGCTC
143360 ATTCGAGCAA
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 65 0.82
20 14 0.18
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (19 bp):
TAAGAGCGATACTAGCTCG
Found at i:143377 original size:77 final size:77
Alignment explanation
Indices: 143246--143415 Score: 211
Period size: 77 Copynumber: 2.2 Consensus size: 77
143236 TCGATTGCTT
* * * * *
143246 TAAGAGC-GATACTAGCTCGTTAGAGCGATACTAGCTCGTTAGAGCGATACTGGCTCGCAAGAG-
1 TAAGAGCAGATACTAGCTCATAAGAGCGATACTAGCTCATTAGAGCAATACTGGCTAGCAAGAGC
143309 AGATATTGGCTCG
66 A-ATATTGGCTCG
* * * * *
143322 TAAGAGCAAATACTAGCTCATAAGAGTGATACTGGCTCATTCGAGCAATATTGGCTAGCAAGAGC
1 TAAGAGCAGATACTAGCTCATAAGAGCGATACTAGCTCATTAGAGCAATACTGGCTAGCAAGAGC
143387 AATATTGGCTCG
66 AATATTGGCTCG
*
143399 TAAAAG-AGATACTAGCT
1 TAAGAGCAGATACTAGCT
143416 TGTGAGAGCA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
76 17 0.21
77 62 0.77
78 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (77 bp):
TAAGAGCAGATACTAGCTCATAAGAGCGATACTAGCTCATTAGAGCAATACTGGCTAGCAAGAGC
AATATTGGCTCG
Found at i:147921 original size:22 final size:22
Alignment explanation
Indices: 147878--147922 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
147868 TCTTAATCCA
* **
147878 TTTTATTTTGGGTCTTTTTTTT
1 TTTTATTTTAGGTCTTAGTTTT
*
147900 TTTTGTTTTAGGTCTTAGTTTT
1 TTTTATTTTAGGTCTTAGTTTT
147922 T
1 T
147923 CGTTGTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.73
Consensus pattern (22 bp):
TTTTATTTTAGGTCTTAGTTTT
Found at i:148727 original size:9 final size:8
Alignment explanation
Indices: 148702--148726 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
148692 ATTTTTAAAT
148702 ATTAAAAA
1 ATTAAAAA
148710 ATTAAAAA
1 ATTAAAAA
148718 ATTAAAAA
1 ATTAAAAA
148726 A
1 A
148727 AACACGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTAAAAA
Found at i:149533 original size:50 final size:50
Alignment explanation
Indices: 149479--149573 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
149469 TAATTTAAGC
* *
149479 ATGTTCAATAATTTTAA-AAAAATGTTATGACCA-AAGAATTTGAAAACACT
1 ATGTTCAAT-ACTTTAAGAAAAAAGTTATGA-CAGAAGAATTTGAAAACACT
* *
149529 ATGTTCAATGCTTTAAGAAAAAAGTTATGATAGAAGAATTTGAAA
1 ATGTTCAATACTTTAAGAAAAAAGTTATGACAGAAGAATTTGAAA
149574 TGACAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 6 0.15
50 33 0.85
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (50 bp):
ATGTTCAATACTTTAAGAAAAAAGTTATGACAGAAGAATTTGAAAACACT
Done.