Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015353.1 Kokia drynarioides strain JFW-HI SEQ_130400, 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: 481496
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 571 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:338846 original size:11 final size:10
Alignment explanation
Indices: 338830--338854 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
338820 AAGAGCGGCT
338830 AAAAAAAAAG
1 AAAAAAAAAG
338840 AAAAAAAAAG
1 AAAAAAAAAG
338850 AAAAA
1 AAAAA
338855 GGGTGGAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:339881 original size:50 final size:50
Alignment explanation
Indices: 339736--339881 Score: 159
Period size: 50 Copynumber: 2.9 Consensus size: 50
339726 ATGGCGATAG
* * * * *
339736 AATGACAAATCT-TTTACCCCTAAAGCTATAGAGGTGCAGATTGAAACCGA
1 AATGACAAATCTCATT-CACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGA
* * * * * * *
339786 AAAGGCAAATCTCATACACCTAAAGCTGTAAAGGGGCAAAATGAAGCCGC
1 AATGACAAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGA
*
339836 AATGACAAATCTCATTCACCTAAAACTGTAGAGGGGCAGATTGAAG
1 AATGACAAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAG
339882 TCACAAGGAC
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
50 75 0.99
51 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (50 bp):
AATGACAAATCTCATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGA
Found at i:339897 original size:50 final size:50
Alignment explanation
Indices: 339787--339902 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
339777 TGAAACCGAA
* *
339787 AAGG-CAAATCTCATACACCTAAAGCTGTAAAGGGGCAAAATGAAGCCGC
1 AAGGACAAATCTCATACACCTAAAACTGTAAAGGGGCAAAATGAAGCCAC
* * * * * *
339836 AATGACAAATCTCATTCACCTAAAACTGTAGAGGGGCAGATTGAAGTCAC
1 AAGGACAAATCTCATACACCTAAAACTGTAAAGGGGCAAAATGAAGCCAC
* *
339886 AAGGACGAATCTTATAC
1 AAGGACAAATCTCATAC
339903 TCCTGAGGCT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
49 3 0.06
50 51 0.94
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (50 bp):
AAGGACAAATCTCATACACCTAAAACTGTAAAGGGGCAAAATGAAGCCAC
Found at i:339981 original size:40 final size:40
Alignment explanation
Indices: 339937--340068 Score: 203
Period size: 40 Copynumber: 3.3 Consensus size: 40
339927 TTACAACCTT
* *
339937 CAATCTCTTACCTTAACCAGAGGGCAGATTGAAGACCATC
1 CAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAATC
* *
339977 CAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAATC
1 CAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAATC
*
340017 CAATCTCTTACCCCAACCATG-GGGCAGATTGAAGACAATC
1 CAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAATC
340057 CAATCTCTTACC
1 CAATCTCTTACC
340069 TCGACTATGG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 83 0.99
41 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
CAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAATC
Found at i:340087 original size:80 final size:79
Alignment explanation
Indices: 339937--340108 Score: 206
Period size: 80 Copynumber: 2.2 Consensus size: 79
339927 TTACAACCTT
** * * * *
339937 CAATCTCTTACCTTAACCAGAGGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGGC
1 CAATCTCTTACCCCAACCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCGAATCAGAGGAC
340002 AGATTGAAGACAATC
66 AGATTGAA-ACAATC
*
340017 CAATCTCTTACCCCAACCATG-GGGCAGATTGAAGACAATCCAATCTCTTACCTCGACT-ATG-G
1 CAATCTCTTACCCCAACCA-GAGGGCAGATTGAAGACAATCCAATCTCTTACC-CGAATCA-GAG
*
340079 GACGGATTGAAACAATC
63 GACAGATTGAAACAATC
*
340096 CAATCTTTTACCC
1 CAATCTCTTACCC
340109 TTAAAGTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 18 0.22
80 57 0.71
81 5 0.06
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (79 bp):
CAATCTCTTACCCCAACCAGAGGGCAGATTGAAGACAATCCAATCTCTTACCCGAATCAGAGGAC
AGATTGAAACAATC
Found at i:340107 original size:39 final size:40
Alignment explanation
Indices: 339937--340108 Score: 179
Period size: 40 Copynumber: 4.3 Consensus size: 40
339927 TTACAACCTT
** * *
339937 CAATCTCTTACCTTAACCA-GAGGGCAGATTGAAGACCATC
1 CAATCTCTTACCCCAACCATG-GGACAGATTGAAGACAATC
* * * *
339977 CAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAATC
1 CAATCTCTTACCCCAACCATG-GGACAGATTGAAGACAATC
*
340017 CAATCTCTTACCCCAACCATGGGGCAGATTGAAGACAATC
1 CAATCTCTTACCCCAACCATGGGACAGATTGAAGACAATC
* * * *
340057 CAATCTCTTACCTCGACTATGGGACGGATTGAA-ACAATC
1 CAATCTCTTACCCCAACCATGGGACAGATTGAAGACAATC
*
340096 CAATCTTTTACCC
1 CAATCTCTTACCC
340109 TTAAAGTTAC
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
39 17 0.15
40 99 0.85
41 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
CAATCTCTTACCCCAACCATGGGACAGATTGAAGACAATC
Found at i:340158 original size:50 final size:50
Alignment explanation
Indices: 340097--340213 Score: 207
Period size: 50 Copynumber: 2.3 Consensus size: 50
340087 GAAACAATCC
* * *
340097 AATCTTTTACCCTTAAAGTTACAGAGGGGCAGATTGAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTGAAGCTACAAAAACA
340147 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTGAAGCTACAAAAACA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTGAAGCTACAAAAACA
340197 AATCTTATACCCCTAAA
1 AATCTTATACCCCTAAA
340214 AGTAATAGAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (50 bp):
AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTGAAGCTACAAAAACA
Found at i:340674 original size:12 final size:11
Alignment explanation
Indices: 340641--340670 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
340631 TACAATCCAA
340641 ATTTATTATTTT
1 ATTTATTA-TTT
340653 ATTTATTATTT
1 ATTTATTATTT
340664 ATTTATT
1 ATTTATT
340671 TATTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTATTT
Found at i:341943 original size:30 final size:30
Alignment explanation
Indices: 341909--342092 Score: 176
Period size: 30 Copynumber: 6.0 Consensus size: 30
341899 TTTTTTACCT
*
341909 CCAAAGTTTTC-AAAAATTCAAATTTGACCC
1 CCAAA-TTTTCAAAAAATTCAAATTTAACCC
* * **
341939 CCAAATTTTCTAAAAATTCAAATTTCACAA
1 CCAAATTTTCAAAAAATTCAAATTTAACCC
* *
341969 CCAAATTTTCCAAAAATTCAAATTTAATCC
1 CCAAATTTTCAAAAAATTCAAATTTAACCC
* *
341999 CCAAAGTTTTCAAAAAAAATCAAATTT-GCCC
1 CCAAA-TTTTC-AAAAAATTCAAATTTAACCC
342030 CCTTAAATTTTCAAAAAATTCAAATTTAACCC
1 CC--AAATTTTCAAAAAATTCAAATTTAACCC
** * *
342062 TTAAAGTTTTC-AAAAATTAAAATCTAACCC
1 CCAAA-TTTTCAAAAAATTCAAATTTAACCC
342092 C
1 C
342093 ATTTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
29 5 0.04
30 71 0.55
31 28 0.22
32 21 0.16
33 3 0.02
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.32
Consensus pattern (30 bp):
CCAAATTTTCAAAAAATTCAAATTTAACCC
Found at i:341962 original size:17 final size:16
Alignment explanation
Indices: 341940--341993 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
341930 ATTTGACCCC
341940 CAAATTTTCTAAAAATT
1 CAAATTTTC-AAAAATT
* *
341957 CAAA-TTTC-ACAA-C
1 CAAATTTTCAAAAATT
341970 CAAATTTTCCAAAAATT
1 CAAATTTT-CAAAAATT
341987 CAAATTT
1 CAAATTT
341994 AATCCCCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 1 0.03
16 7 0.24
17 11 0.38
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
CAAATTTTCAAAAATT
Found at i:342076 original size:93 final size:89
Alignment explanation
Indices: 341909--342093 Score: 225
Period size: 93 Copynumber: 2.0 Consensus size: 89
341899 TTTTTTACCT
* *
341909 CCAAAGTTTTCAAAAATTCAAATTTGACCCCCAAATTTTCTAAAAATTCAAATTTCACAACCAAA
1 CCAAAGTTTTCAAAAAATCAAATTTGACCCCCAAATTTTCAAAAAATTCAAATTTCACAACCAAA
* *
341974 TTTTCCAAAAATTCAAATTTAATCC
66 TTTTCCAAAAATTAAAATCTAA-CC
*
341999 CCAAAGTTTTCAAAAAAAATCAAATTTG-CCCCCTTAAATTTTCAAAAAATTCAAATTT-A-ACC
1 CCAAAGTTTTC--AAAAAATCAAATTTGACCCCC--AAATTTTCAAAAAATTCAAATTTCACAAC
342061 CTTAAAGTTTT-CAAAAATTAAAATCTAACC
62 C--AAA-TTTTCCAAAAATTAAAATCTAACC
342091 CCA
1 CCA
342094 TTTTAATATA
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
90 11 0.13
91 8 0.10
92 20 0.24
93 40 0.48
94 4 0.05
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (89 bp):
CCAAAGTTTTCAAAAAATCAAATTTGACCCCCAAATTTTCAAAAAATTCAAATTTCACAACCAAA
TTTTCCAAAAATTAAAATCTAACC
Found at i:344040 original size:2 final size:2
Alignment explanation
Indices: 344033--344057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
344023 GACAATAATC
344033 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
344058 GGTATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:347000 original size:4 final size:4
Alignment explanation
Indices: 346987--347028 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
346977 AAAATTGAAG
346987 GAAA -AAA GAAA GAAA -AAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
347029 GAAGAGAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 5 0.14
4 28 0.80
5 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:347003 original size:12 final size:12
Alignment explanation
Indices: 346988--347039 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
346978 AAATTGAAGG
346988 AAAAAAGAAAGA
1 AAAAAAGAAAGA
*
347000 AAAAGAGAAAGA
1 AAAAAAGAAAGA
*
347012 AAGAAAGAAAGA
1 AAAAAAGAAAGA
347024 AAGAAGAAGAGAAGA
1 AA-AA-AAGA-AAGA
347039 A
1 A
347040 GGGGTAGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 23 0.70
13 1 0.03
14 4 0.12
15 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:348053 original size:30 final size:30
Alignment explanation
Indices: 348019--348112 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
348009 AAATGGTACA
*
348019 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** * * * * *
348049 AAAT-AAT-GGTGTGTGGATACTATTTTGGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
*
348078 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
348108 AAATA
1 AAATA
348113 GAACATTTTG
Statistics
Matches: 45, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
28 4 0.09
29 16 0.36
30 21 0.47
31 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:349367 original size:43 final size:43
Alignment explanation
Indices: 349285--349369 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
349275 ATTAACATGT
* *
349285 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
*
349328 TAAATTATATTACCTT-ACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTA-CTTGACTCGTATTAATATGCTTG-CATGTTA
349370 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.08
43 31 0.84
44 3 0.08
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:350001 original size:45 final size:45
Alignment explanation
Indices: 349937--350073 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
349927 TCATAGCTCA
* *
349937 TCAAGCCAAGGATATCAGCCTTAGTTTGACGAGCCACCGCAATAC
1 TCAAGCAAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * *
349982 TCAAGCAAAGGGTATCAGCCTCAATTTGATGAGCTACCGCAATAC
1 TCAAGCAAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * * *
350027 TCAAGGGAAGGATATCAGGCTGAGTTTGACAAGCCACCGCGATAC
1 TCAAGCAAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
350072 TC
1 TC
350074 TATTCCTCCC
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (45 bp):
TCAAGCAAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:350355 original size:14 final size:14
Alignment explanation
Indices: 350338--350405 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
350328 CATTAAACCC
*
350338 TAAAACCTAAAATA
1 TAAAACCTAAACTA
*
350352 TAAACCCTAAACT-
1 TAAAACCTAAACTA
350365 TAAAACCCTAAACTA
1 TAAAA-CCTAAACTA
350380 T-AAACACTAAACT-
1 TAAAAC-CTAAACTA
*
350393 TGAAACTCTAAAC
1 TAAAAC-CTAAAC
350406 CGTAAACACT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.13
14 39 0.85
15 1 0.02
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAAACCTAAACTA
Found at i:350362 original size:28 final size:29
Alignment explanation
Indices: 350326--350391 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
350316 TAAATTTCAT
*
350326 AACATTAAACCCTAAAA-CCTAAAATATA
1 AACACTAAACCCTAAAACCCTAAAATATA
* * *
350354 AACCCTAAA-CTTAAAACCCTAAACTATA
1 AACACTAAACCCTAAAACCCTAAAATATA
350382 AACACTAAAC
1 AACACTAAAC
350392 TTGAAACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.20
Consensus pattern (29 bp):
AACACTAAACCCTAAAACCCTAAAATATA
Found at i:350392 original size:28 final size:28
Alignment explanation
Indices: 350338--350416 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
350328 CATTAAACCC
* *
350338 TAAAA-CCTAAAATATAAACCCTAAACT
1 TAAAACCCTAAACTATAAACACTAAACT
350365 TAAAACCCTAAACTATAAACACTAAACT
1 TAAAACCCTAAACTATAAACACTAAACT
* * **
350393 TGAAACTCTAAACCGTAAACACTA
1 TAAAACCCTAAACTATAAACACTA
350417 GATTGATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.22
Consensus pattern (28 bp):
TAAAACCCTAAACTATAAACACTAAACT
Found at i:354166 original size:4 final size:4
Alignment explanation
Indices: 354121--354186 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
354111 AACACATTAC
* * * * *
354121 CTTT CTTT CATT C-TT CTTT ATTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
354169 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
354187 CCGTTTATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.82
5 6 0.12
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:354381 original size:24 final size:25
Alignment explanation
Indices: 354348--354426 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 25
354338 ATCAAGTGGC
354348 AAAACACCCT-TTAGTGCCGCCACTT
1 AAAA-ACCCTCTTAGTGCCGCCACTT
*
354373 AAAAACCCTTCATTGGTGCCGCCACTT
1 AAAAACCC-TC-TTAGTGCCGCCACTT
354400 AAAAACCCTCCATTAGTGCCGCCACTT
1 AAAAACCCT-C-TTAGTGCCGCCACTT
354427 CGTGTTCCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.08
25 5 0.10
26 1 0.02
27 38 0.79
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.24
Consensus pattern (25 bp):
AAAAACCCTCTTAGTGCCGCCACTT
Found at i:354393 original size:27 final size:27
Alignment explanation
Indices: 354358--354426 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
354348 AAAACACCCT
*
354358 TTAGTGCCGCCACTTAAAAACCCTTCA
1 TTAGTGCCGCCACTTAAAAACCCTCCA
*
354385 TTGGTGCCGCCACTTAAAAACCCTCCA
1 TTAGTGCCGCCACTTAAAAACCCTCCA
354412 TTAGTGCCGCCACTT
1 TTAGTGCCGCCACTT
354427 CGTGTTCCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.26
Consensus pattern (27 bp):
TTAGTGCCGCCACTTAAAAACCCTCCA
Found at i:359981 original size:15 final size:17
Alignment explanation
Indices: 359963--359995 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
359953 CGCTTTTCGA
359963 TTTTTAG-TTTT-TTTT
1 TTTTTAGATTTTATTTT
359978 TTTTTAGATTTTATTTT
1 TTTTTAGATTTTATTTT
359995 T
1 T
359996 ATAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTAGATTTTATTTT
Found at i:360359 original size:16 final size:16
Alignment explanation
Indices: 360314--360364 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
360304 CCCTGAAATA
360314 ATAAAATTTT-AATTT
1 ATAAAATTTTAAATTT
**
360329 A-AACTTTTTATAATTT
1 ATAAAATTTTA-AATTT
*
360345 ATAAAATTTTAAATTA
1 ATAAAATTTTAAATTT
360361 ATAA
1 ATAA
360365 TGGTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.21
15 1 0.04
16 14 0.50
17 7 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTAAATTT
Found at i:360848 original size:5 final size:5
Alignment explanation
Indices: 360838--360883 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
360828 TCAAGTTGTA
360838 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
360884 GTCTAAACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:362799 original size:3 final size:3
Alignment explanation
Indices: 362786--362823 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
362776 TAAACTGAAA
*
362786 AAT AA- AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
362824 GTTTAACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:370355 original size:20 final size:21
Alignment explanation
Indices: 370330--370370 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
370320 ATGTTGGGGA
*
370330 TTTTGAAGGTGCT-TTGAAGG
1 TTTTGAAGGTGATGTTGAAGG
*
370350 TTTTGAATGTGATGTTGAAGG
1 TTTTGAAGGTGATGTTGAAGG
370371 GTTGGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.41
Consensus pattern (21 bp):
TTTTGAAGGTGATGTTGAAGG
Found at i:372600 original size:14 final size:15
Alignment explanation
Indices: 372576--372616 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
372566 AATGGAATAA
*
372576 AATAAATTTTTAATT
1 AATAAAATTTTAATT
372591 AA-AAAATTTTAATT
1 AATAAAATTTTAATT
372605 AATTAAAATTTT
1 AA-TAAAATTTT
372617 TAAACCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 13 0.57
15 2 0.09
16 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAAAATTTTAATT
Found at i:382879 original size:50 final size:50
Alignment explanation
Indices: 382752--382879 Score: 166
Period size: 50 Copynumber: 2.6 Consensus size: 50
382742 ATCTTTTACC
* * * * *
382752 CCTAAAGCTGTGGAGGTGCATATTGAAACTGTAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGAGCAGATTGAAGCTGCAATGGCAAATCTCATACA
* * * *
382802 CCTAAAGCTGTAGAGGGGCAGAATGAAGCTGCAATGGTAAATCTCATTCA
1 CCTAAAGCTGTAGAGGAGCAGATTGAAGCTGCAATGGCAAATCTCATACA
*
382852 CCTAAAGCTGTAGAGGAGAAGATTGAAG
1 CCTAAAGCTGTAGAGGAGCAGATTGAAG
382880 TCACAAGGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGAGCAGATTGAAGCTGCAATGGCAAATCTCATACA
Found at i:383125 original size:80 final size:80
Alignment explanation
Indices: 382936--383425 Score: 748
Period size: 80 Copynumber: 6.1 Consensus size: 80
382926 TACAACCTCT
* * * * *
382936 AATCTTTTACCCTAACCAGAAGGCAAAATTAAAGATCATCCGATCGTTTACCCCGATCATGGGAC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
383001 AGATT-AAGAAATTC
66 AGATTGAAGAAATCC
383015 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
383080 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* * * * *
383095 AATCTTTCACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCTCGATCATGGGGT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
383160 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
383175 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
383240 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
** * * * * * *
383255 AATCTTTTACCCTAATTAGAGGGCAAGATGGAAGACCATTCGATCTTTTATCCCGATCATAGAGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
383320 AGATTGAAGAAATCT
66 AGATTGAAGAAATCC
* * * *
383335 AATCTTTTACCCTAACTAAAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCAATCATGGGGT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
383400 AGATTGAAGAAATTC
66 AGATTGAAGAAATCC
383415 AATCTTTTACC
1 AATCTTTTACC
383426 TCGACTATAG
Statistics
Matches: 373, Mismatches: 37, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
79 65 0.17
80 308 0.83
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCC
Found at i:384158 original size:12 final size:12
Alignment explanation
Indices: 384116--384159 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
384106 ACCTAATTCC
*
384116 ATTTTTCTTATT
1 ATTTTTATTATT
384128 ATTTTTATTTATT
1 ATTTTTA-TTATT
*
384141 -TATTTATTATT
1 ATTTTTATTATT
384152 ATTTTTAT
1 ATTTTTAT
384160 AAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:384228 original size:63 final size:63
Alignment explanation
Indices: 384130--384267 Score: 197
Period size: 63 Copynumber: 2.2 Consensus size: 63
384120 TTCTTATTAT
* * *
384130 TTTTATTTATTTATTTATTATTATTTTTATAAATATAAATAAATATAAAATAATATTTATTTTA
1 TTTTA-TTATTTATTTATTATTATTTGTATAAATATAAATAAATATAAAATAATATTAAATTTA
* * *
384194 TTTTATTATTTATTTATTTATTA-TTGTATGAATATAAATAAATGTAAAATAATATTAAATTTG
1 TTTTATTATTTATTTA-TTATTATTTGTATAAATATAAATAAATATAAAATAATATTAAATTTA
384257 TTTTATTATTT
1 TTTTATTATTT
384268 TATGAATATA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 56 0.84
64 11 0.16
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (63 bp):
TTTTATTATTTATTTATTATTATTTGTATAAATATAAATAAATATAAAATAATATTAAATTTA
Found at i:389293 original size:56 final size:56
Alignment explanation
Indices: 389217--389333 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 56
389207 GGTTTTTCCT
* * * *
389217 TATATCATCTTATTTTAAGTTCCGTCCCATGTGAATCTTATCCAAATTTATTTTAG
1 TATAACATCTTATTTTAAGTTCCGTCCCATGAGAATCTTATCCAAATTTATTCTAA
* * ** * *
389273 TATAACATTTTATTTTAAGTTTCGTTTCGTGAGAATGTTATCCAAATTTATTCTAA
1 TATAACATCTTATTTTAAGTTCCGTCCCATGAGAATCTTATCCAAATTTATTCTAA
389329 TATAA
1 TATAA
389334 GTTTAGATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (56 bp):
TATAACATCTTATTTTAAGTTCCGTCCCATGAGAATCTTATCCAAATTTATTCTAA
Found at i:390294 original size:59 final size:58
Alignment explanation
Indices: 390167--390291 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 58
390157 ACTCAACATA
* * *
390167 ATTTTTTTGTCACTCAATTATGAAAATTTTATAAAATAATCACAAACTATTAGTAATTT
1 ATTTTTTTATCACTCAATTATGAAAATGTTACAAAATAATCACAAACTATTA-TAATTT
* * *
390226 AATTTTTTATCACTCAATTATGAAAA-GTTACAAATTGATCACTAAACTATT-TAATTTT
1 ATTTTTTTATCACTCAATTATGAAAATGTTACAAAATAATCAC-AAACTATTATAA-TTT
*
390284 GTTTTTTT
1 ATTTTTTT
390292 TATATTTTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 3 0.05
58 21 0.38
59 32 0.57
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
ATTTTTTTATCACTCAATTATGAAAATGTTACAAAATAATCACAAACTATTATAATTT
Found at i:392547 original size:17 final size:17
Alignment explanation
Indices: 392525--392557 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
392515 TATTTAAACA
392525 TATATTTATAATTATAC
1 TATATTTATAATTATAC
*
392542 TATATTTATATTTATA
1 TATATTTATAATTATA
392558 AACTCTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTATAATTATAC
Found at i:393702 original size:71 final size:71
Alignment explanation
Indices: 393583--393722 Score: 262
Period size: 71 Copynumber: 2.0 Consensus size: 71
393573 GCATAAGTGA
393583 GACTCGAACTTAAGTACGCAATGACCAAAGACCTCAACTTTTAGTATAATGTCAATGCTTCATTA
1 GACTCGAACTTAAGTACGCAATGACCAAAGACCTCAACTTTTAGTATAATGTCAATGCTTCATTA
393648 GCAAGG
66 GCAAGG
* *
393654 GACTCGAACTTAAGTACTCAATGACCAAAGACCTCAACTTTTATTATAATGTCAATGCTTCATTA
1 GACTCGAACTTAAGTACGCAATGACCAAAGACCTCAACTTTTAGTATAATGTCAATGCTTCATTA
393719 GCAA
66 GCAA
393723 CCCAAAGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (71 bp):
GACTCGAACTTAAGTACGCAATGACCAAAGACCTCAACTTTTAGTATAATGTCAATGCTTCATTA
GCAAGG
Found at i:395224 original size:107 final size:108
Alignment explanation
Indices: 395029--395243 Score: 378
Period size: 107 Copynumber: 2.0 Consensus size: 108
395019 TTAATGTAAA
395029 TCGCTGTCCTTTAACTCGTAAGTAATGTAAACATCATCAAACTTTTCCCTCTCAGGTGGTAGCAG
1 TCGCTGTCCTTTAACTCGTAAGTAATGTAAACATCATCAAACTTTTCCCTCTCAGGTGGTAGCAG
*
395094 AATGTCCTTGATTTTGACAATCTGTAAAAAGATTACTGCAAGT
66 AATGTCCTTGATTTTGACAATCTGTAAAAAGATTAATGCAAGT
* * * *
395137 TCGCTGTCCTTTAACTCGTAAGTAATGTAAACATCATCAAGC-TTTCCCTCTCCGGTGGTGGCAT
1 TCGCTGTCCTTTAACTCGTAAGTAATGTAAACATCATCAAACTTTTCCCTCTCAGGTGGTAGCAG
395201 AATGTCCTTGATTTTGACAATCTGTAAAAAGATTAATGCAAGT
66 AATGTCCTTGATTTTGACAATCTGTAAAAAGATTAATGCAAGT
395244 ATGCAACACT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 61 0.60
108 41 0.40
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (108 bp):
TCGCTGTCCTTTAACTCGTAAGTAATGTAAACATCATCAAACTTTTCCCTCTCAGGTGGTAGCAG
AATGTCCTTGATTTTGACAATCTGTAAAAAGATTAATGCAAGT
Found at i:404018 original size:16 final size:19
Alignment explanation
Indices: 403974--404010 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
403964 TGTTAACTCG
403974 ATTGATATAA-ATATTATT
1 ATTGATATAATATATTATT
403992 ATTGATATAATATATTATT
1 ATTGATATAATATATTATT
404011 TTATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTGATATAATATATTATT
Found at i:404566 original size:29 final size:30
Alignment explanation
Indices: 404529--404589 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
404519 AAATTTGGAT
* **
404529 TTTAGTCCCTATA-TTTTTATTTTTAAAAA
1 TTTAATCCCTATACTTTTTAGATTTAAAAA
*
404558 TTTAATCCCTTTACTTTTTAGATTTAAAAA
1 TTTAATCCCTATACTTTTTAGATTTAAAAA
404588 TT
1 TT
404590 AAGTCCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTAATCCCTATACTTTTTAGATTTAAAAA
Found at i:409617 original size:122 final size:120
Alignment explanation
Indices: 409483--409706 Score: 412
Period size: 122 Copynumber: 1.9 Consensus size: 120
409473 TAGTATTCAC
*
409483 ATTCGAATTCGAGTAAATTATAATCTTTATCAAGAGTTGTTTATAGTAAATTTTGATTAGTTTAT
1 ATTCGAATTCGAGTAAATTATAATCTTTATCAAGAGTTGTTCATAGTAAATTTTGATTAGTTTAT
409548 TTGTTAAATTTGAAAAGTCAGAGTTGGATTTAGCTCAATCTAATTTAGATTGGATCA
66 TTGTTAAATTTGAAAAGTC--AGTTGGATTTAGCTCAATCTAATTTAGATTGGATCA
409605 ATTCGAATTCGAGTAAATTATAATCTTTATCAAGAGTTGTTCATAGTAAATTTTGATTAGTTTAT
1 ATTCGAATTCGAGTAAATTATAATCTTTATCAAGAGTTGTTCATAGTAAATTTTGATTAGTTTAT
*
409670 TTGTTATATTTGAAAAGTCAGTTGGATTTAGCTCAAT
66 TTGTTAAATTTGAAAAGTCAGTTGGATTTAGCTCAAT
409707 TCGAATTCGA
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 18 0.18
122 82 0.82
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (120 bp):
ATTCGAATTCGAGTAAATTATAATCTTTATCAAGAGTTGTTCATAGTAAATTTTGATTAGTTTAT
TTGTTAAATTTGAAAAGTCAGTTGGATTTAGCTCAATCTAATTTAGATTGGATCA
Found at i:410747 original size:21 final size:21
Alignment explanation
Indices: 410723--410764 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
410713 TTTTTAATAG
* *
410723 GATAAATGAATGAATTTTTTT
1 GATAAAAGAATCAATTTTTTT
410744 GATAAAAGAATCAATTTTTTT
1 GATAAAAGAATCAATTTTTTT
410765 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
GATAAAAGAATCAATTTTTTT
Found at i:410767 original size:27 final size:29
Alignment explanation
Indices: 410736--410799 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
410726 AAATGAATGA
410736 ATTTTTTTGATA-AAAGAATCAATTT-TTT
1 ATTTTTTTGATATAAAG-ATCAATTTGTTT
* *
410764 -TTTTTTTTATATAAAGATTAATTTGTTT
1 ATTTTTTTGATATAAAGATCAATTTGTTT
410792 ATTTTTTT
1 ATTTTTTT
410800 TAGTAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 17 0.55
28 7 0.23
29 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (29 bp):
ATTTTTTTGATATAAAGATCAATTTGTTT
Found at i:410777 original size:29 final size:29
Alignment explanation
Indices: 410737--410806 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
410727 AATGAATGAA
410737 TTTTTTT-GATAAAAGAATCAATTT-TTT-T
1 TTTTTTTAGAT-AAAG-ATCAATTTGTTTAT
* *
410765 TTTTTTTATATAAAGATTAATTTGTTTAT
1 TTTTTTTAGATAAAGATCAATTTGTTTAT
410794 TTTTTTTAG-TAAA
1 TTTTTTTAGATAAA
410807 TGAAATAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 7 0.19
28 18 0.50
29 11 0.31
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTTTTAGATAAAGATCAATTTGTTTAT
Found at i:413976 original size:3 final size:3
Alignment explanation
Indices: 413968--414012 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
413958 CAAACCGGAT
* * *
413968 TAA TAA TAA TAA TAA TCA TAG TCA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
414013 ACAGTTGAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:427017 original size:31 final size:28
Alignment explanation
Indices: 426999--427052 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
426989 ACTATACTAA
426999 TTTTCTCA-AATTGGTACCTAAACT-TT
1 TTTTCTCAGAATTGGTACCTAAACTATT
*
427025 TTTTGTCAGAATTGGTACCTAAACTATT
1 TTTTCTCAGAATTGGTACCTAAACTATT
427053 AAACCGTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.28
27 16 0.64
28 2 0.08
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (28 bp):
TTTTCTCAGAATTGGTACCTAAACTATT
Found at i:428554 original size:105 final size:105
Alignment explanation
Indices: 428366--428556 Score: 274
Period size: 105 Copynumber: 1.8 Consensus size: 105
428356 CCGTCAGCAA
* * *
428366 AGTTTGCCGCACCAGTTCGGATTGTCACCTACACCATCAATTGGTACATTATCGGATACACCTAT
1 AGTTTGCCACACCAATTCGGATTGTCACCTACACCATCAATTGGCACATTATCGGATACACCTAT
* * *
428431 GATGGGGCAGAAACGAGATGCATTTGAGAAGAGTATTGAG
66 GACGGGACAGAAAAGAGATGCATTTGAGAAGAGTATTGAG
* * * * *
428471 AGTTTGCCACAGCAATTTGGATTGTCACCTACCCCATCTATTGGCACGTTATCGGATACACCTAT
1 AGTTTGCCACACCAATTCGGATTGTCACCTACACCATCAATTGGCACATTATCGGATACACCTAT
*
428536 GACGGGACGGAAAAGAGATGC
66 GACGGGACAGAAAAGAGATGC
428557 TCAAGATGCA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (105 bp):
AGTTTGCCACACCAATTCGGATTGTCACCTACACCATCAATTGGCACATTATCGGATACACCTAT
GACGGGACAGAAAAGAGATGCATTTGAGAAGAGTATTGAG
Found at i:429339 original size:69 final size:69
Alignment explanation
Indices: 429258--429396 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
429248 TGCAAGCATT
429258 ATCTATGGGAATGCAATAATATTTGCTTTTAAACCCTGCATAATGAGAATTCATGTGCCAAAATT
1 ATCTATGGGAATGCAATAATATTTGCTTTTAAACCCTGCATAATGAGAATTCATGTGCCAAAATT
429323 ACAA
66 ACAA
429327 ATCTATGGGAATGCAATAATATTTGCTTTTAAACCCTGCATAATGAGAATTCATGTGCCAAAATT
1 ATCTATGGGAATGCAATAATATTTGCTTTTAAACCCTGCATAATGAGAATTCATGTGCCAAAATT
429392 ACAA
66 ACAA
429396 A
1 A
429397 CAACTAGTTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (69 bp):
ATCTATGGGAATGCAATAATATTTGCTTTTAAACCCTGCATAATGAGAATTCATGTGCCAAAATT
ACAA
Found at i:433132 original size:36 final size:33
Alignment explanation
Indices: 433064--433140 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
433054 TTTGTTAGGA
433064 TTATTTAATAAAATAATATAAAAAATAATTATT
1 TTATTTAATAAAATAATATAAAAAATAATTATT
* **
433097 TTATTTGATATAAATAATAT-TTAAA-AATTA-T
1 TTATTTAATA-AAATAATATAAAAAATAATTATT
433128 TTATTTAATAAAA
1 TTATTTAATAAAA
433141 ATTAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 3 0.08
31 10 0.26
32 5 0.13
33 12 0.31
34 9 0.23
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
TTATTTAATAAAATAATATAAAAAATAATTATT
Found at i:433154 original size:32 final size:32
Alignment explanation
Indices: 433064--433159 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 32
433054 TTTGTTAGGA
* *
433064 TTATTTAAT-AAAATAATATAAAAAATAATTATT
1 TTATTTAATAAAAATAATATTATAAA-AATTA-T
* *
433097 TTATTTGATATAAATAATATT-TAAAAATTAT
1 TTATTTAATAAAAATAATATTATAAAAATTAT
433128 TTATTTAATAAAAATTAA-ATTATAAAAATTAT
1 TTATTTAATAAAAA-TAATATTATAAAAATTAT
433160 AAAATTAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
31 16 0.30
32 18 0.33
33 11 0.20
34 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
TTATTTAATAAAAATAATATTATAAAAATTAT
Found at i:435994 original size:16 final size:16
Alignment explanation
Indices: 435973--436023 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
435963 AGTGGAAAAG
435973 AAATTGGAAGGATGGA
1 AAATTGGAAGGATGGA
* * *
435989 AAATTGAAAGGGTAGA
1 AAATTGGAAGGATGGA
* *
436005 AAACTAGAAGGATGGA
1 AAATTGGAAGGATGGA
436021 AAA
1 AAA
436024 CATAATTTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.31, T:0.16
Consensus pattern (16 bp):
AAATTGGAAGGATGGA
Found at i:439720 original size:30 final size:31
Alignment explanation
Indices: 439668--439730 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
439658 GGTTAGACCT
*
439668 ATTCATCATAATTCATGCAATATCAAAGAAC
1 ATTCATCATAAGTCATGCAATATCAAAGAAC
439699 ATTCATCATAAGTCA-GCAATATCAAAGAAC
1 ATTCATCATAAGTCATGCAATATCAAAGAAC
439729 AT
1 AT
439731 CTTCAACTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (31 bp):
ATTCATCATAAGTCATGCAATATCAAAGAAC
Found at i:444950 original size:15 final size:15
Alignment explanation
Indices: 444930--444959 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
444920 AAAAATAACA
444930 CAAGTACAATATCTT
1 CAAGTACAATATCTT
*
444945 CAAGTATAATATCTT
1 CAAGTACAATATCTT
444960 GTTGTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (15 bp):
CAAGTACAATATCTT
Found at i:446340 original size:21 final size:21
Alignment explanation
Indices: 446297--446339 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
446287 TGTTTCAATG
* *
446297 TTCACTTTGATATCTGAGTTT
1 TTCAATTTAATATCTGAGTTT
446318 TTCAATTTAATAT-TGAGTTT
1 TTCAATTTAATATCTGAGTTT
446338 TT
1 TT
446340 TTTTTGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (21 bp):
TTCAATTTAATATCTGAGTTT
Found at i:447663 original size:20 final size:22
Alignment explanation
Indices: 447638--447677 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
447628 AAGAATGACT
447638 TTATTT-TATGT-TATTTTAAA
1 TTATTTATATGTATATTTTAAA
*
447658 TTATTTATATTTATATTTTA
1 TTATTTATATGTATATTTTA
447678 TAATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTATTTATATGTATATTTTAAA
Found at i:449844 original size:106 final size:106
Alignment explanation
Indices: 449659--449942 Score: 541
Period size: 106 Copynumber: 2.7 Consensus size: 106
449649 TTAATACCCA
449659 AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
1 AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
449724 TGTCATATAATAAAACACCTACTATATGGACCGTTGTATAT
66 TGTCATATAATAAAACACCTACTATATGGACCGTTGTATAT
449765 AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
1 AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
449830 TGTCATATAATAAAACACCTACTATATGGACCGTTGTATAT
66 TGTCATATAATAAAACACCTACTATATGGACCGTTGTATAT
* * *
449871 AACAATATGTACCAAACATTAGCCCTTGATGGTAGGTAGGGGTGGCTTCGTGGCTGAAAACAACA
1 AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
449936 TGTCATA
66 TGTCATA
449943 CACACACTAA
Statistics
Matches: 175, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 175 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (106 bp):
AACAATATGTACCAAACATTAGCCCTTGATGGTAAGTAGGGTTGGCTTCGTGGCCGAAAACAACA
TGTCATATAATAAAACACCTACTATATGGACCGTTGTATAT
Found at i:454325 original size:17 final size:17
Alignment explanation
Indices: 454303--454336 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
454293 TTCAGACCTC
*
454303 AAATATAATGGACCAAA
1 AAATATAAAGGACCAAA
454320 AAATATAAAGGACCAAA
1 AAATATAAAGGACCAAA
454337 TTGAAAAATG
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:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATATAAAGGACCAAA
Found at i:454931 original size:4 final size:4
Alignment explanation
Indices: 454922--454950 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
454912 TAGTATAAAT
454922 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
454951 CAGTTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:455091 original size:142 final size:139
Alignment explanation
Indices: 454922--455329 Score: 476
Period size: 142 Copynumber: 3.0 Consensus size: 139
454912 TAGTATAAAT
*
454922 ATACATACATACATACATACATACATACACAGTTTGAATAATACACTGTTTTGGTTTACATAATT
1 ATACAT-CAT-CATACATACATACATACACAGTTTGAATAATATACTGTTTTGGTTTACATAATT
* * * *
454987 GGGATGATGGTAGCTGCAGAATGGATAATAATTTTGGTTTTGATTCCAAGTCACTGATTTACCAT
64 GGGATGATGGTAGCTGCAGAATGGATATTGATTTGGGTTTTGATTCCAAGTCACTGATTCACCAT
455052 ATTTTTTATCAG
129 -TTTTTTATCAG
* * * * *
455064 ATACATGCATGCATGCATACATACATACATAGTTTGAATAATATACTGTTGTGGTTTACGTGATT
1 ATACAT-CAT-CATACATACATACATACACAGTTTGAATAATATACTGTTTTGGTTTACATAATT
* *
455129 GGGATGATGGTAGCTGCTGAATGGATATTGATTTGGGTTTTGATTCCAAGTCTCTGATTCACC-T
64 GGGATGATGGTAGCTGCAGAATGGATATTGATTTGGGTTTTGATTCCAAGTCACTGATTCACCAT
* **
455193 TTTTTTTTTTG
129 TTTTTTATCAG
* * * * *
455204 -T---T-AT-ATACGT--ATACATATACAGTTTGAATAATATGCT-TTTGTGGGTTACATAACTG
1 ATACATCATCATACATACATACATACACAGTTTGAATAATATACTGTTT-TGGTTTACATAATTG
* * * *
455260 GGATGATGGTAGCTGCAGAATGGACATTGGTTTGGGGTTTGAGTCCAAGTCACTGATTCACCATT
65 GGATGATGGTAGCTGCAGAATGGATATTGATTTGGGTTTTGATTCCAAGTCACTGATTCACCATT
455325 TTTTT
130 TTTTT
455330 TGTTATATAC
Statistics
Matches: 231, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
129 2 0.01
130 91 0.39
131 7 0.03
132 4 0.02
134 2 0.01
136 1 0.00
139 1 0.00
140 8 0.03
141 1 0.00
142 114 0.49
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (139 bp):
ATACATCATCATACATACATACATACACAGTTTGAATAATATACTGTTTTGGTTTACATAATTGG
GATGATGGTAGCTGCAGAATGGATATTGATTTGGGTTTTGATTCCAAGTCACTGATTCACCATTT
TTTTATCAG
Found at i:455262 original size:130 final size:128
Alignment explanation
Indices: 455084--455344 Score: 360
Period size: 130 Copynumber: 2.0 Consensus size: 128
455074 GCATGCATAC
* * * * * *
455084 ATACATACATAGTTTGAATAATATACTGTTGTGGTTTACGTGATTGGGATGATGGTAGCTGCTGA
1 ATACATACACAGTTTGAATAATATACTGTTGTGGGTTACATAACTGGGATGATGGTAGCTGCAGA
* * * * * *
455149 ATGGATATTGATTTGGGTTTTGATTCCAAGTCTCTGATTCACCTTTTTTTTTTTGTTATATACGT
66 ATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACC--ATTTTTTTTGTTATATACAT
* * *
455214 ATACATATACAGTTTGAATAATATGCTTTTGTGGGTTACATAACTGGGATGATGGTAGCTGCAGA
1 ATACATACACAGTTTGAATAATATACTGTTGTGGGTTACATAACTGGGATGATGGTAGCTGCAGA
*
455279 ATGGACATTGGTTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATATACAT
66 ATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATATACAT
455342 ATA
1 ATA
455345 TGTGTATGAT
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 21 0.18
130 94 0.82
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (128 bp):
ATACATACACAGTTTGAATAATATACTGTTGTGGGTTACATAACTGGGATGATGGTAGCTGCAGA
ATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATATACAT
Found at i:460970 original size:20 final size:22
Alignment explanation
Indices: 460928--460970 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
460918 CAGTAAGTAC
*
460928 ACACGTGTTTACAATTTGATAT
1 ACACGTGTTTACAATATGATAT
*
460950 ACACGT-TTTA-AATATGCTAT
1 ACACGTGTTTACAATATGATAT
460970 A
1 A
460971 TGCTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (22 bp):
ACACGTGTTTACAATATGATAT
Found at i:463803 original size:31 final size:31
Alignment explanation
Indices: 463767--463829 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
463757 AATGATCCTC
463767 GAACTATTCGAAAGTTTTCATTTAAGTCACT
1 GAACTATTCGAAAGTTTTCATTTAAGTCACT
* * *
463798 GAACTATTTGAAAGTTTTTATTTAAGTTACT
1 GAACTATTCGAAAGTTTTCATTTAAGTCACT
463829 G
1 G
463830 GATTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (31 bp):
GAACTATTCGAAAGTTTTCATTTAAGTCACT
Found at i:465538 original size:31 final size:31
Alignment explanation
Indices: 465503--465562 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
465493 ATTATAAAAT
* * * *
465503 AATCATTAAACTATTCGAAAGTTTTTATTTA
1 AATCATCAAAATATTCAAAAGCTTTTATTTA
465534 AATCATCAAAATATTCAAAAGCTTTTATT
1 AATCATCAAAATATTCAAAAGCTTTTATT
465563 GAAGTCACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (31 bp):
AATCATCAAAATATTCAAAAGCTTTTATTTA
Found at i:467917 original size:23 final size:24
Alignment explanation
Indices: 467890--467940 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
467880 TGATTTGATG
*
467890 CTTTTTTGGTGC-ATTTTGGTACT
1 CTTTTTTGGTGCTATTTTAGTACT
* *
467913 -GTTTTTGGTTCTATTTTAGTACT
1 CTTTTTTGGTGCTATTTTAGTACT
467936 CTTTT
1 CTTTT
467941 CAATGCTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
22 9 0.41
23 10 0.45
24 3 0.14
ACGTcount: A:0.10, C:0.12, G:0.18, T:0.61
Consensus pattern (24 bp):
CTTTTTTGGTGCTATTTTAGTACT
Found at i:468215 original size:28 final size:28
Alignment explanation
Indices: 468160--468215 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
468150 GTTTTACGAA
* *
468160 TTGTTTTAATATTTTTTTAATTTGTTTG
1 TTGTTTTAATATTTTTTTAATGTATTTG
468188 TTGTTTTAATA-TTTTTTAAGTGTATTTG
1 TTGTTTTAATATTTTTTTAA-TGTATTTG
468216 ATATATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (28 bp):
TTGTTTTAATATTTTTTTAATGTATTTG
Found at i:469503 original size:2 final size:2
Alignment explanation
Indices: 469496--469528 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
469486 TTGGTTGTAA
469496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469529 TTTGATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:476091 original size:37 final size:38
Alignment explanation
Indices: 476050--476125 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
476040 TACTGAGTAC
476050 CACTTTA-CTTC-AACTAGGCCGATGAGACACTGGGTGT
1 CACTTTATCTTCGAACTA-GCCGATGAGACACTGGGTGT
* *
476087 CACTTTATTGCTTCGAACTATCCGATGAGGCACTGGGTG
1 CACTTTA-T-CTTCGAACTAGCCGATGAGACACTGGGTG
476126 CCATTCTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 7 0.21
40 21 0.64
41 5 0.15
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (38 bp):
CACTTTATCTTCGAACTAGCCGATGAGACACTGGGTGT
Found at i:477894 original size:37 final size:38
Alignment explanation
Indices: 477853--477928 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
477843 TACTGAGTAC
477853 CACTTTA-CTTC-AACTAGGCCGATGAGACACTGGGTGT
1 CACTTTATCTTCGAACTA-GCCGATGAGACACTGGGTGT
* *
477890 CACTTTATTGCTTCGAACTATCCGATGAGGCACTGGGTG
1 CACTTTA-T-CTTCGAACTAGCCGATGAGACACTGGGTG
477929 CCATTCTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 7 0.21
40 21 0.64
41 5 0.15
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (38 bp):
CACTTTATCTTCGAACTAGCCGATGAGACACTGGGTGT
Found at i:479484 original size:17 final size:18
Alignment explanation
Indices: 479459--479492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
479449 CTCTTTTATT
479459 TTTATATTTGTTTTGAAA
1 TTTATATTTGTTTTGAAA
*
479477 TTTA-ATTTTTTTTGAA
1 TTTATATTTGTTTTGAA
479493 TAATTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
TTTATATTTGTTTTGAAA
Found at i:480458 original size:17 final size:18
Alignment explanation
Indices: 480436--480473 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
480426 CCGGGTCCCT
480436 TTTAAATTAATTTT-AAA
1 TTTAAATTAATTTTCAAA
*
480453 TTTAAATTTATTTTCAAA
1 TTTAAATTAATTTTCAAA
480471 TTT
1 TTT
480474 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTAATTTTCAAA
Found at i:480524 original size:13 final size:14
Alignment explanation
Indices: 480504--480538 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
480494 CCAATTACAA
480504 AAGTCCAAA-TTAC
1 AAGTCCAAATTTAC
*
480517 ATGTCCAAATTTAC
1 AAGTCCAAATTTAC
480531 AAGTCCAA
1 AAGTCCAA
480539 TTGGGCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (14 bp):
AAGTCCAAATTTAC
Done.