Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 69 of 193
Found at i:22245276 original size:28 final size:28
Alignment explanation
Indices: 22245240--22245305 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
22245230 AGTGATTTCA
*
22245240 TTTAGTTTTATATT-TTATTTATTTTTAT
1 TTTA-TTTTATATTGTTAGTTATTTTTAT
*
22245268 TTGTATTTT-TATTGTTAGTTGTTTTTAT
1 TT-TATTTTATATTGTTAGTTATTTTTAT
22245296 TTTATTTTAT
1 TTTATTTTAT
22245306 TATGCATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 10 0.30
28 21 0.64
29 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (28 bp):
TTTATTTTATATTGTTAGTTATTTTTAT
Found at i:22245296 original size:22 final size:23
Alignment explanation
Indices: 22245266--22245323 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
22245256 ATTTATTTTT
22245266 ATTTGTATTTTTATTGTTAGT-TG-
1 ATTT-TATTTTTATT-TTAGTATGC
* *
22245289 TTTTTA-TTTTATTTTATTATGC
1 ATTTTATTTTTATTTTAGTATGC
22245311 ATTTTATTTTTAT
1 ATTTTATTTTTAT
22245324 GGTTTTGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 9 0.31
22 7 0.24
23 9 0.31
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.71
Consensus pattern (23 bp):
ATTTTATTTTTATTTTAGTATGC
Found at i:22253180 original size:18 final size:18
Alignment explanation
Indices: 22253133--22253180 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
22253123 ACTTGTCCTC
*
22253133 AAGCAAACAAAACAAGAA
1 AAGCAAACAAAGCAAGAA
*
22253151 AAGCAAATAAAGCAAGAA
1 AAGCAAACAAAGCAAGAA
22253169 AAGCAAACAAAG
1 AAGCAAACAAAG
22253181 GAGCTTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.02
Consensus pattern (18 bp):
AAGCAAACAAAGCAAGAA
Found at i:22256681 original size:23 final size:22
Alignment explanation
Indices: 22256640--22256700 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
22256630 TTCAAAACGT
*
22256640 TTTAATATATATATATATTACTATA
1 TTTAATAT-T-TATTTATTAC-ATA
22256665 TTTAATATTTATTTATTACATA
1 TTTAATATTTATTTATTACATA
*
22256687 TTTATGTATTTATT
1 TTTA-ATATTTATT
22256701 ACTGATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 7 0.21
23 17 0.52
24 1 0.03
25 8 0.24
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTAATATTTATTTATTACATA
Found at i:22257852 original size:29 final size:29
Alignment explanation
Indices: 22257749--22258104 Score: 159
Period size: 30 Copynumber: 12.1 Consensus size: 29
22257739 TGTTTTATTT
* **
22257749 AAAAATTAAATTTTAACCC-CTAAACTTTGT
1 AAAAATTACATTTT-ACCCTC-AAACTTTCC
*
22257779 AAAAATTATATTTTGACCC-CTAAAC-TTCTC
1 AAAAATTACATTTT-ACCCTC-AAACTTTC-C
* *
22257809 AAAAATCACATTTTTACCCTCGAACTTTCC
1 AAAAATTACA-TTTTACCCTCAAACTTTCC
* *
22257839 AAAAATTACATTTTGAACCTCGAA-TTTCTC
1 AAAAATTACATTTT-ACCCTCAAACTTTC-C
* *
22257869 TAAAATTACATTTTAACCCTTAAACTTTTCC
1 AAAAATTACATTTT-ACCCTCAAAC-TTTCC
* * *
22257900 -AAAATCATATTTGCACCCT-AAACTTTTCC
1 AAAAATTACATTT-TACCCTCAAAC-TTTCC
* * *
22257929 -AAAATTACATTTTTGCTCTCAAAC-ATCC
1 AAAAATTACA-TTTTACCCTCAAACTTTCC
* * *
22257957 AAAAATAACCATTTTGATCC-CGAACTTTTCC
1 AAAAATTA-CATTTT-ACCCTCAAAC-TTTCC
** *
22257988 -AAAATTACATTTTA-CCTCCGAC-ATCC
1 AAAAATTACATTTTACCCTCAAACTTTCC
* * *
22258014 AAAAATTATCATTTTACCCCCGAAC-ATCC
1 AAAAATTA-CATTTTACCCTCAAACTTTCC
* *
22258043 AAAAATTACCCTTTCACCC-CTAAAC-TTCC
1 AAAAATTA-CATTTTACCCTC-AAACTTTCC
* *
22258072 AAAAATCACATTTTGA-CCTCAAATTTTCC
1 AAAAATTACATTTT-ACCCTCAAACTTTCC
22258101 AAAA
1 AAAA
22258105 GTTCGATTTT
Statistics
Matches: 257, Mismatches: 45, Indels: 49
0.73 0.13 0.14
Matches are distributed among these distances:
26 3 0.01
27 9 0.04
28 24 0.09
29 98 0.38
30 107 0.42
31 12 0.05
32 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTACCCTCAAACTTTCC
Found at i:22258029 original size:28 final size:28
Alignment explanation
Indices: 22257988--22258085 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 28
22257978 GAACTTTTCC
*
22257988 AAAATTACATTTTACCTCCG-ACATCCA
1 AAAATTACATTTTACCCCCGAACATCCA
22258015 AAAATTATCATTTTACCCCCGAACATCCA
1 AAAATTA-CATTTTACCCCCGAACATCCA
* * ** *
22258044 AAAATTACCCTTTCACCCCTAAACTTCCA
1 AAAATTA-CATTTTACCCCCGAACATCCA
*
22258073 AAAATCACATTTT
1 AAAATTACATTTT
22258086 GACCTCAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.12
28 16 0.27
29 36 0.61
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTACATTTTACCCCCGAACATCCA
Found at i:22258036 original size:57 final size:59
Alignment explanation
Indices: 22257788--22258038 Score: 160
Period size: 59 Copynumber: 4.3 Consensus size: 59
22257778 TAAAAATTAT
* * * * * * * *
22257788 ATTTTGACCCCTAAACTTCTCAAAAATCACATTTTTACCCTCGAACTTTCCAAAAATTA-C
1 ATTTTGACCCC-GAACTTTTCCAAAATTACATTTTTACTCTCAAAC-ATCCAAAAATAACC
* * * * * *
22257848 ATTTTGAACCTCGAA-TTTCTCTAAAATTACATTTTAACCCTTAAACTTTTCC-AAAAT---C
1 ATTTTG-ACCCCGAACTTT-TCCAAAATTACATTTTTACTCTCAAAC--ATCCAAAAATAACC
** *
22257906 ATATTTGCACCCTAAACTTTTCCAAAATTACATTTTTGCTCTCAAACATCCAAAAATAACC
1 AT-TTTG-ACCCCGAACTTTTCCAAAATTACATTTTTACTCTCAAACATCCAAAAATAACC
* ** * *
22257967 ATTTTGATCCCGAACTTTTCCAAAATTACA-TTTTAC-CTCCGACATCCAAAAATTATC
1 ATTTTGACCCCGAACTTTTCCAAAATTACATTTTTACTCTCAAACATCCAAAAATAACC
22258024 ATTTT-ACCCCCGAAC
1 ATTTTGA-CCCCGAAC
22258039 ATCCAAAAAT
Statistics
Matches: 154, Mismatches: 27, Indels: 23
0.75 0.13 0.11
Matches are distributed among these distances:
56 1 0.01
57 32 0.21
58 13 0.08
59 54 0.35
60 42 0.27
61 12 0.08
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
ATTTTGACCCCGAACTTTTCCAAAATTACATTTTTACTCTCAAACATCCAAAAATAACC
Found at i:22258142 original size:29 final size:29
Alignment explanation
Indices: 22258092--22258148 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
22258082 TTTTGACCTC
*
22258092 AAATTTTCCAAAAGTTCGATTTTAATCCA
1 AAATTTTCCAAAAGTTCAATTTTAATCCA
* *
22258121 AAATTTT-CAAATATTTCAATTTTGATCC
1 AAATTTTCCAAA-AGTTCAATTTTAATCC
22258149 CCAAATTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATTTTCCAAAAGTTCAATTTTAATCCA
Found at i:22270292 original size:38 final size:39
Alignment explanation
Indices: 22270231--22270317 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 39
22270221 GAAGATTCCG
* * *
22270231 ATCTCTTACCCCGAGTCTAGGGCAGATCACAATCATCCA
1 ATCTTTTACCCCGAGCCTAGGGCAGATCACAATCAGCCA
*
22270270 ATCTTTTACCCCGAGCCT-GGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCCTAGGGCAGATCACAATCAGCCA
22270308 ATCTTTTACC
1 ATCTTTTACC
22270318 TTGTGACTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 28 0.64
39 16 0.36
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.25
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCCTAGGGCAGATCACAATCAGCCA
Found at i:22270328 original size:38 final size:39
Alignment explanation
Indices: 22270231--22270334 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 39
22270221 GAAGATTCCG
* * * *
22270231 ATCTCTTACCCCGAGTCTAGGGCAGATCACAATCATCCA
1 ATCTTTTACCCCGAGACTGGGGCAGATCACAATCAGCCA
* *
22270270 ATCTTTTACCCCGAGCCT-GGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGACTGGGGCAGATCACAATCAGCCA
** *
22270308 ATCTTTTACCTTGTGACTGGGGCAGAT
1 ATCTTTTACCCCGAGACTGGGGCAGAT
22270335 TGCAGCCATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 32 0.57
39 24 0.43
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTTTTACCCCGAGACTGGGGCAGATCACAATCAGCCA
Found at i:22270356 original size:39 final size:39
Alignment explanation
Indices: 22270308--22270395 Score: 104
Period size: 39 Copynumber: 2.3 Consensus size: 39
22270298 CCATCAGCCA
* * * *
22270308 ATCTTTTACCTTGTGACTGGGGCAGATTGCAGCCATTAG
1 ATCTTTTACCTCGAGACTAGGACAGATTGCAGCCATTAG
* * * *
22270347 ATCTCTTACCTCGAGCCTAGGATAGATTGCAGCCATTCG
1 ATCTTTTACCTCGAGACTAGGACAGATTGCAGCCATTAG
22270386 ATCTTTTACC
1 ATCTTTTACC
22270396 CCGTGCTTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (39 bp):
ATCTTTTACCTCGAGACTAGGACAGATTGCAGCCATTAG
Found at i:22270495 original size:55 final size:55
Alignment explanation
Indices: 22270408--22270519 Score: 181
Period size: 55 Copynumber: 2.0 Consensus size: 55
22270398 GTGCTTGGGG
* *
22270408 AAGATCACCATTAGCCAATCTCTTACCCCGAGCCAG-GTGCAGATTGCAACCATCC
1 AAGATCACCATCAGCCAATCTCTTACCCCGAGCCAGAG-GCAAATTGCAACCATCC
*
22270463 AAGATCACCATCAGCCAATCTCTTACCTCGAGCCAGAGGCAAATTGCAACCATCC
1 AAGATCACCATCAGCCAATCTCTTACCCCGAGCCAGAGGCAAATTGCAACCATCC
22270518 AA
1 AA
22270520 TATCCTGAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.32, C:0.34, G:0.15, T:0.19
Consensus pattern (55 bp):
AAGATCACCATCAGCCAATCTCTTACCCCGAGCCAGAGGCAAATTGCAACCATCC
Found at i:22271031 original size:18 final size:18
Alignment explanation
Indices: 22271004--22271039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22270994 ATTAAACCCA
* *
22271004 ATTTTTAATTTTAAATTT
1 ATTTTAAATTTAAAATTT
22271022 ATTTTAAATTTAAAATTT
1 ATTTTAAATTTAAAATTT
22271040 GAAAATTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAAATTTAAAATTT
Found at i:22271752 original size:19 final size:21
Alignment explanation
Indices: 22271713--22271777 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
22271703 AAACGTTTTA
* * *
22271713 ATATCTATATATATATATATT
1 ATATATATTTATATATTTATT
22271734 A-ATATATTTA-ATATTTATTT
1 ATATATATTTATATATTTA-TT
*
22271754 ATTATATATTTATGTATTTATT
1 A-TATATATTTATATATTTATT
22271776 AT
1 AT
22271778 TGATTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.17
20 10 0.28
21 2 0.06
22 12 0.33
23 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATATATTTATATATTTATT
Found at i:22271766 original size:8 final size:8
Alignment explanation
Indices: 22271709--22271788 Score: 71
Period size: 8 Copynumber: 10.6 Consensus size: 8
22271699 TTCAAAACGT
22271709 TTTA-ATA
1 TTTATATA
*
22271716 TCTATATA
1 TTTATATA
*
22271724 TATATATA
1 TTTATATA
*
22271732 TTAATATA
1 TTTATATA
22271740 TTTA-ATA
1 TTTATATA
*
22271747 TTTATTTA
1 TTTATATA
22271755 -TTATATA
1 TTTATATA
*
22271762 TTTATGTA
1 TTTATATA
22271770 TTTAT-TA
1 TTTATATA
*
22271777 TTGAT-TA
1 TTTATATA
22271784 TTTAT
1 TTTAT
22271789 TACCCCTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
7 28 0.47
8 32 0.53
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (8 bp):
TTTATATA
Found at i:22271777 original size:11 final size:11
Alignment explanation
Indices: 22271738--22271790 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
22271728 TATATTAATA
*
22271738 TATTTAATATT
1 TATTTATTATT
*
22271749 TATTTATTATA
1 TATTTATTATT
22271760 TATTTATGTATT
1 TATTTAT-TATT
22271772 TA-TTATTGA-T
1 TATTTATT-ATT
22271782 TATTTATTA
1 TATTTATTA
22271791 CCCCTATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.14
11 26 0.72
12 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (11 bp):
TATTTATTATT
Found at i:22272785 original size:30 final size:30
Alignment explanation
Indices: 22272749--22272953 Score: 184
Period size: 30 Copynumber: 6.7 Consensus size: 30
22272739 TATTTTATTT
* *
22272749 AAAAATTATATTTTAACCCTCAAACTTCAC
1 AAAAATTACATTTTAACCCTCAAACTTCTC
*
22272779 AAAAATTACATTTTGACCCTCAAACTTCTC
1 AAAAATTACATTTTAACCCTCAAACTTCTC
* * *
22272809 AAAAATCACATTTTGACCCTCGAACTT-TCC
1 AAAAATTACATTTTAACCCTCAAACTTCT-C
*
22272839 AAAAATAACATTTTGAACCC-CAAACTTCTC
1 AAAAATTACATTTT-AACCCTCAAACTTCTC
* **
22272869 TAAAATTACATTTTAACCCTTGAACTGT-TCC
1 AAAAATTACATTTTAACCCTCAAACT-TCT-C
*
22272900 AAAATCACATAACATTTTGAACCC-CAAACTTCTC
1 -AAA--A-ATTACATTTT-AACCCTCAAACTTCTC
* *
22272934 TAAAATTACATTTTGACCCT
1 AAAAATTACATTTTAACCCT
22272954 TGAACTGTTC
Statistics
Matches: 143, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
29 10 0.07
30 99 0.69
31 8 0.06
32 2 0.01
33 2 0.01
34 3 0.02
35 14 0.10
36 5 0.03
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCAAACTTCTC
Found at i:22272828 original size:60 final size:60
Alignment explanation
Indices: 22272749--22273057 Score: 285
Period size: 60 Copynumber: 5.2 Consensus size: 60
22272739 TATTTTATTT
* * *
22272749 AAAAATTATATTTTAACCCTCAAAC-TTCACAAAAATTACATTTTG-ACCCTCAAACTTCTC
1 AAAAATTACATTTTAACCCTCGAACTTTC-CAAAAATAACATTTTGAACCC-CAAACTTCTC
* *
22272809 AAAAATCACATTTTGACCCTCGAACTTTCCAAAAATAACATTTTGAACCCCAAACTTCTC
1 AAAAATTACATTTTAACCCTCGAACTTTCCAAAAATAACATTTTGAACCCCAAACTTCTC
* *
22272869 TAAAATTACATTTTAACCCTTGAACTGTTCCAAAATCACATAACATTTTGAACCCCAAACTTCTC
1 AAAAATTACATTTTAACCCTCGAACT-TTCC-AAA--A-ATAACATTTTGAACCCCAAACTTCTC
* * * * * ** *
22272934 TAAAATTACATTTTGACCCTTGAACTGTTCC-AAAATCACA-TTTGCACCTTAAACTTTTC
1 AAAAATTACATTTTAACCCTCGAACT-TTCCAAAAATAACATTTTGAACCCCAAACTTCTC
* * * * * *
22272993 CAAAATTGCATTTT-ACCCCCGAAC-ATCCAAAAATAACCA-TTTG-ACCCTAAACATC-C
1 AAAAATTACATTTTAACCCTCGAACTTTCCAAAAATAA-CATTTTGAACCCCAAACTTCTC
22273049 AAAAATTAC
1 AAAAATTAC
22273058 CCTTCCGCCC
Statistics
Matches: 214, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
56 11 0.05
57 15 0.07
58 14 0.07
59 27 0.13
60 73 0.34
61 12 0.06
62 3 0.01
63 2 0.01
64 1 0.00
65 56 0.26
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.31
Consensus pattern (60 bp):
AAAAATTACATTTTAACCCTCGAACTTTCCAAAAATAACATTTTGAACCCCAAACTTCTC
Found at i:22272934 original size:65 final size:65
Alignment explanation
Indices: 22272786--22272974 Score: 291
Period size: 65 Copynumber: 3.0 Consensus size: 65
22272776 CACAAAAATT
* * *
22272786 ACATTTTG-ACCCTCAAACTTCTCAAAAATCACATTTTGACCCTCGAACT-TTCC-AAA--A-AT
1 ACATTTTGAACCC-CAAACTTCTCTAAAATTACATTTTGACCCTTGAACTGTTCCAAAATCACAT
22272845 A
65 A
*
22272846 ACATTTTGAACCCCAAACTTCTCTAAAATTACATTTTAACCCTTGAACTGTTCCAAAATCACATA
1 ACATTTTGAACCCCAAACTTCTCTAAAATTACATTTTGACCCTTGAACTGTTCCAAAATCACATA
22272911 ACATTTTGAACCCCAAACTTCTCTAAAATTACATTTTGACCCTTGAACTGTTCCAAAATCACAT
1 ACATTTTGAACCCCAAACTTCTCTAAAATTACATTTTGACCCTTGAACTGTTCCAAAATCACAT
22272975 TTGCACCTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
60 40 0.34
61 8 0.07
62 3 0.03
64 1 0.01
65 66 0.56
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (65 bp):
ACATTTTGAACCCCAAACTTCTCTAAAATTACATTTTGACCCTTGAACTGTTCCAAAATCACATA
Found at i:22272969 original size:30 final size:29
Alignment explanation
Indices: 22272750--22273010 Score: 183
Period size: 30 Copynumber: 8.6 Consensus size: 29
22272740 ATTTTATTTA
* *
22272750 AAAATTATATTTTAACCCTCAAAC-TTCAC
1 AAAATTACATTTTGACCCTCAAACTTTC-C
*
22272779 AAAAATTACATTTTGACCCTCAAACTTCTCA
1 -AAAATTACATTTTGACCCTCAAACTT-TCC
* *
22272810 AAAATCACATTTTGACCCTCGAACTTTCC
1 AAAATTACATTTTGACCCTCAAACTTTCC
* *
22272839 AAAAATAACATTTTGAACCC-CAAACTTCTCT
1 -AAAATTACATTTTG-ACCCTCAAACTT-TCC
* **
22272870 AAAATTACATTTTAACCCTTGAACTGTTCC
1 AAAATTACATTTTGACCCTCAAACT-TTCC
*
22272900 AAAATCACATAACATTTTGAACCC-CAAACTTCTCT
1 AAAAT----T-ACATTTTG-ACCCTCAAACTT-TCC
**
22272935 AAAATTACATTTTGACCCTTGAACTGTTCC
1 AAAATTACATTTTGACCCTCAAACT-TTCC
* *
22272965 AAAATCACA-TTTG-CACCTTAAACTTTTCC
1 AAAATTACATTTTGAC-CCTCAAAC-TTTCC
*
22272994 AAAATTGCATTTT-ACCC
1 AAAATTACATTTTGACCC
22273011 CCGAACATCC
Statistics
Matches: 186, Mismatches: 25, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
28 1 0.01
29 34 0.18
30 115 0.62
31 10 0.05
32 2 0.01
34 2 0.01
35 18 0.10
36 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTACATTTTGACCCTCAAACTTTCC
Found at i:22278996 original size:24 final size:24
Alignment explanation
Indices: 22278964--22279016 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
22278954 GGAGGAAGGA
22278964 GAAA-GAAACTGCCCCGAAGAAAG
1 GAAAGGAAACTGCCCCGAAGAAAG
22278987 GAAAGGAAACTGCCCCGAAGAAAG
1 GAAAGGAAACTGCCCCGAAGAAAG
22279011 GAAAGG
1 GAAAGG
22279017 GAAAAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.47, C:0.19, G:0.30, T:0.04
Consensus pattern (24 bp):
GAAAGGAAACTGCCCCGAAGAAAG
Found at i:22279365 original size:24 final size:24
Alignment explanation
Indices: 22279324--22279378 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
22279314 GAGTTAAGAG
*
22279324 TAAAATCTATCAGTGCAAATGTAATA
1 TAAAATC-ATCAGAGCAAAT-TAATA
22279350 TAAAATC-TCAGAGCAAATTAATA
1 TAAAATCATCAGAGCAAATTAATA
*
22279373 GAAAAT
1 TAAAAT
22279379 GGATTGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
24 10 0.37
26 7 0.26
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (24 bp):
TAAAATCATCAGAGCAAATTAATA
Found at i:22282005 original size:21 final size:21
Alignment explanation
Indices: 22281979--22282024 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22281969 TTTCTTCTAT
22281979 TTCTTCCTTCTCTTCCT-CTTC
1 TTCTT-CTTCTCTTCCTCCTTC
* *
22282000 TTCTTCTTTTCTTTCTCCTTC
1 TTCTTCTTCTCTTCCTCCTTC
22282021 TTCT
1 TTCT
22282025 GCCTCAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCTTCTTCTCTTCCTCCTTC
Found at i:22289997 original size:21 final size:20
Alignment explanation
Indices: 22289942--22289997 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
22289932 TGAGGAAGAG
22289942 AAAGAAGAAGAGAAAGAGGAA
1 AAAGAAGAAGA-AAAGAGGAA
22289963 AAAGAAGAAGGAAAAGAAGG-A
1 AAAGAAGAA-GAAAAG-AGGAA
*
22289984 GAAGAAGGAAGAAA
1 AAAGAA-GAAGAAA
22289998 TTTTTTTGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGAAAAGAGGAA
Found at i:22306323 original size:23 final size:23
Alignment explanation
Indices: 22306292--22306337 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
22306282 CACCTATATT
*
22306292 ACATGTCAAATAAC-CCAAAATGA
1 ACATATCAAA-AACACCAAAATGA
22306315 ACATATCAAAAACTACCAAAATG
1 ACATATCAAAAAC-ACCAAAATG
22306338 TGTATGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.54, C:0.22, G:0.07, T:0.17
Consensus pattern (23 bp):
ACATATCAAAAACACCAAAATGA
Found at i:22310049 original size:24 final size:24
Alignment explanation
Indices: 22310021--22310077 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
22310011 TACACTAATA
*
22310021 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
22310045 AGAGTGTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
22310069 AAAGTTTAA
1 AGAGTTTAA
22310078 TTGAAAGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:22310078 original size:24 final size:24
Alignment explanation
Indices: 22310033--22310083 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
22310023 AGTTTGACTC
*
22310033 AAACAAATAAACAGAGTGTAATTG
1 AAACAAATAAACAAAGTGTAATTG
*
22310057 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTGTAATTG
22310081 AAA
1 AAA
22310084 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAAAGTGTAATTG
Found at i:22312054 original size:24 final size:24
Alignment explanation
Indices: 22311995--22312057 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
22311985 TAGACTAATA
* *
22311995 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
22312019 TGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
22312043 AGATTTTAATTGAAA
1 AGAGTTTAATTGAAA
22312058 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:22315183 original size:40 final size:40
Alignment explanation
Indices: 22315139--22315219 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22315129 CTATCATGGG
22315139 TGTGTCAAAATCTAGTTTAACATCAGAGGTCGACTAAGAC
1 TGTGTCAAAATCTAGTTTAACATCAGAGGTCGACTAAGAC
22315179 TGTGTCAAAATCTAGTTTAACATCAGAGGTCGACTAAGAC
1 TGTGTCAAAATCTAGTTTAACATCAGAGGTCGACTAAGAC
22315219 T
1 T
22315220 TCAATTAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (40 bp):
TGTGTCAAAATCTAGTTTAACATCAGAGGTCGACTAAGAC
Found at i:22318265 original size:43 final size:42
Alignment explanation
Indices: 22318188--22318314 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 42
22318178 GTACAGGCTA
* * *
22318188 TACTTCAGTTTATCTAATGATACACT-GTAGGTGCTAGTATAAT
1 TACTTCAGTTTATCTGATGGTGCACTCGT--GTGCTAGTATAAT
*
22318231 TACTTCAGTTTATCTGATGGTGCACTACGTGTGCTAGTATATT
1 TACTTCAGTTTATCTGATGGTGCACT-CGTGTGCTAGTATAAT
* * *
22318274 TCCTTCAATTTATCTGATGGTGCGCTGCGTGTGCTAGTATA
1 TACTTCAGTTTATCTGATGGTGCACT-CGTGTGCTAGTATA
22318315 TTTTCTTTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 72 0.97
45 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (42 bp):
TACTTCAGTTTATCTGATGGTGCACTCGTGTGCTAGTATAAT
Found at i:22318315 original size:43 final size:43
Alignment explanation
Indices: 22318218--22318352 Score: 162
Period size: 43 Copynumber: 3.1 Consensus size: 43
22318208 TACACTGTAG
* *
22318218 GTGCTAGTATAATTACTTCAGTTTATCTGATGGTGCACTACGT
1 GTGCTAGTATATTTACTTCAATTTATCTGATGGTGCACTACGT
* * *
22318261 GTGCTAGTATATTTCCTTCAATTTATCTGATGGTGCGCTGCGT
1 GTGCTAGTATATTTACTTCAATTTATCTGATGGTGCACTACGT
* ** ** * *
22318304 GTGCTAGTATATTTTCTTTGATTTATCTGATAATGCACCATGT
1 GTGCTAGTATATTTACTTCAATTTATCTGATGGTGCACTACGT
22318347 GTGCTA
1 GTGCTA
22318353 ATATTTTTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (43 bp):
GTGCTAGTATATTTACTTCAATTTATCTGATGGTGCACTACGT
Found at i:22322369 original size:26 final size:26
Alignment explanation
Indices: 22322343--22322399 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
22322333 TATTCAATTA
* *
22322343 TTATTATTTTTTATCTTATTTTCTTAT
1 TTATTA-TTCTTATATTATTTTCTTAT
* *
22322370 TTATTATTCTTATATTATTTTATAAT
1 TTATTATTCTTATATTATTTTCTTAT
22322396 TTAT
1 TTAT
22322400 ATTTGAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (26 bp):
TTATTATTCTTATATTATTTTCTTAT
Found at i:22322775 original size:31 final size:30
Alignment explanation
Indices: 22322740--22322875 Score: 100
Period size: 31 Copynumber: 4.6 Consensus size: 30
22322730 TTAATATAAT
*
22322740 ATTTAGTATTTAAATTTGATATTTTTTTCTA
1 ATTTAGTATTTAAATTTGACATTTTTTT-TA
* **
22322771 ATTTAATATTTAAATTT----TTTTTGTCCA
1 ATTTAGTATTTAAATTTGACATTTTT-TTTA
* *
22322798 ATTTAATATTCAAATTTGACACTTTTTTTTA
1 ATTTAGTATTTAAATTTGACA-TTTTTTTTA
* * * *
22322829 ATTTGGTATCTAAACTTGACACTTTTTTTA
1 ATTTAGTATTTAAATTTGACATTTTTTTTA
* * *
22322859 AGTTGGTACTTAAATTT
1 ATTTAGTATTTAAATTT
22322876 TTTGGGGTCC
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
27 22 0.27
28 1 0.01
30 21 0.25
31 34 0.41
32 5 0.06
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.55
Consensus pattern (30 bp):
ATTTAGTATTTAAATTTGACATTTTTTTTA
Found at i:22322800 original size:27 final size:26
Alignment explanation
Indices: 22322761--22322814 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
22322751 AAATTTGATA
* *
22322761 TTTTTTTCTAATTTAATATTTAAATT
1 TTTTTTTCCAATTTAATATTCAAATT
22322787 TTTTTTGTCCAATTTAATATTCAAATT
1 TTTTTT-TCCAATTTAATATTCAAATT
22322814 T
1 T
22322815 GACACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTTTTCCAATTTAATATTCAAATT
Found at i:22324269 original size:20 final size:19
Alignment explanation
Indices: 22324235--22324272 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
22324225 TTTTCGTTTA
22324235 TTTTAAAGAGGTTTTATTT
1 TTTTAAAGAGGTTTTATTT
*
22324254 TTTTACAAGAGTTTTTATT
1 TTTTA-AAGAGGTTTTATT
22324273 CCTTTCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (19 bp):
TTTTAAAGAGGTTTTATTT
Found at i:22329826 original size:13 final size:11
Alignment explanation
Indices: 22329797--22329821 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22329787 ATGCTTCATC
22329797 TTCCTCTTTTT
1 TTCCTCTTTTT
22329808 TTCCTCTTTTT
1 TTCCTCTTTTT
22329819 TTC
1 TTC
22329822 TCCTCCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCCTCTTTTT
Found at i:22337347 original size:20 final size:20
Alignment explanation
Indices: 22337322--22337381 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
22337312 TTTTTCAAAA
22337322 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTC
* **
22337342 AAAGTCAACGATCAGTGGTC
1 AAAGTCAACGGTCAACGGTC
*
22337362 AACAGTCAA-AGTCAACGGTC
1 AA-AGTCAACGGTCAACGGTC
22337382 GATCAATGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGTCAACGGTC
Found at i:22337350 original size:13 final size:13
Alignment explanation
Indices: 22337332--22337381 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
22337322 AAAGTCAACG
22337332 GTCAACGGTCAAA
1 GTCAACGGTCAAA
* **
22337345 GTCAACGATCAGTG
1 GTCAACGGTCA-AA
*
22337359 GTCAACAGTCAAA
1 GTCAACGGTCAAA
22337372 GTCAACGGTC
1 GTCAACGGTC
22337382 GATCAATGGA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:22337462 original size:14 final size:15
Alignment explanation
Indices: 22337443--22337477 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22337433 TGGGTTGGAC
*
22337443 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
22337457 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
22337472 TTGGTT
1 TTGGTT
22337478 AGGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:22337520 original size:21 final size:21
Alignment explanation
Indices: 22337452--22337520 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
22337442 CTTGGTTCAA
*
22337452 TTGGTTTGG-TTCAAATGGGT
1 TTGGTTTGGTTTTAAATGGGT
*
22337472 TTGGTTAGGTTTTAAATGGGT
1 TTGGTTTGGTTTTAAATGGGT
22337493 TTGGTTTGGTTTTAAATGGGT
1 TTGGTTTGGTTTTAAATGGGT
22337514 TTGGTTT
1 TTGGTTT
22337521 AAATGAATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 8 0.18
21 37 0.82
ACGTcount: A:0.14, C:0.01, G:0.33, T:0.51
Consensus pattern (21 bp):
TTGGTTTGGTTTTAAATGGGT
Found at i:22337523 original size:15 final size:16
Alignment explanation
Indices: 22337495--22337525 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
22337485 AAATGGGTTT
22337495 GGTTTGGTTTTAAATG
1 GGTTTGGTTTTAAATG
22337511 GGTTTGG-TTTAAATG
1 GGTTTGGTTTTAAATG
22337526 AATGTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (16 bp):
GGTTTGGTTTTAAATG
Found at i:22338028 original size:17 final size:17
Alignment explanation
Indices: 22338006--22338040 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22337996 GTAAGGCAAG
22338006 GAAAAAAGAAAGAAAAA
1 GAAAAAAGAAAGAAAAA
22338023 GAAAAAAGAAAGAAAAA
1 GAAAAAAGAAAGAAAAA
22338040 G
1 G
22338041 GTTTGGGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAGAAAAA
Found at i:22345435 original size:15 final size:16
Alignment explanation
Indices: 22345403--22345447 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
22345393 CAATCGAGGG
*
22345403 TTTTCA-AGAGAAGCA
1 TTTTCACAGAGAAGAA
22345418 TTTTCACAGAGAA-AA
1 TTTTCACAGAGAAGAA
22345433 TTTTCACA-AGAAGAA
1 TTTTCACAGAGAAGAA
22345448 GCCACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 17 0.63
16 6 0.22
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (16 bp):
TTTTCACAGAGAAGAA
Found at i:22362290 original size:17 final size:15
Alignment explanation
Indices: 22362277--22362317 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
22362267 ATTATTTAGT
22362277 TTAAAAATAAATTTA
1 TTAAAAATAAATTTA
22362292 TTAAAAATATCAATTT-
1 TTAAAAATA--AATTTA
22362308 TTAAAAATAA
1 TTAAAAATAA
22362318 GGTAAACTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 9 0.38
17 5 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAAATAAATTTA
Found at i:22362298 original size:16 final size:16
Alignment explanation
Indices: 22362279--22362316 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22362269 TATTTAGTTT
22362279 AAAA-ATAAATTTATTA
1 AAAATATAAATTT-TTA
*
22362295 AAAATATCAATTTTTA
1 AAAATATAAATTTTTA
22362311 AAAATA
1 AAAATA
22362317 AGGTAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATAAATTTTTA
Found at i:22368160 original size:17 final size:18
Alignment explanation
Indices: 22368128--22368162 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
22368118 AGGAAAAAGT
*
22368128 AGTTACAAGAATATGAAA
1 AGTTACAAGAAGATGAAA
22368146 AGTTA-AAGAAGATGAAA
1 AGTTACAAGAAGATGAAA
22368163 GCTTAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTACAAGAAGATGAAA
Found at i:22368997 original size:30 final size:30
Alignment explanation
Indices: 22368962--22369024 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
22368952 ACTTATTTTA
*
22368962 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
*
22368992 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
22369022 TTG
1 TTG
22369025 CTTGTTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGACAT
Found at i:22369762 original size:18 final size:18
Alignment explanation
Indices: 22369727--22369776 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
22369717 TATTAAACTT
*
22369727 TATATTATGTTA-TTTTA
1 TATATTATGTAATTTTTA
22369744 TATATTATGTAATTTTTA
1 TATATTATGTAATTTTTA
22369762 TATATTATGTAATTT
1 TATATTATGTAATTT
22369777 AGAACACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TATATTATGTAATTTTTA
Found at i:22369871 original size:27 final size:28
Alignment explanation
Indices: 22369840--22369908 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
22369830 AACATTAAAA
*
22369840 AAATATTAAAATGACTATA-AAAATT-TT
1 AAATATTAAAAT-AATATAGAAAATTATT
* *
22369867 CAATAAATAAAA-AATATAGAAAATTATT
1 AAAT-ATTAAAATAATATAGAAAATTATT
22369895 AAATATTAAAATAA
1 AAATATTAAAATAA
22369909 AATAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 5 0.15
27 15 0.45
28 13 0.39
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
AAATATTAAAATAATATAGAAAATTATT
Found at i:22369929 original size:32 final size:33
Alignment explanation
Indices: 22369871--22369938 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
22369861 AATTTTCAAT
* *
22369871 AAATAAAAAATATAGAAAATTATT-AAATATTA
1 AAATAAAAAAAATAGAAAATTATTAAAAAATTA
* *
22369903 AAATAAAATAAAATA-AATATTTTTAAAAAATTA
1 AAATAAAA-AAAATAGAAAATTATTAAAAAATTA
22369936 AAA
1 AAA
22369939 AATAATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
AAATAAAAAAAATAGAAAATTATTAAAAAATTA
Found at i:22377944 original size:12 final size:12
Alignment explanation
Indices: 22377929--22377953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22377919 ATTAAAGAAT
22377929 TAATAGCATTCA
1 TAATAGCATTCA
22377941 TAATAGCATTCA
1 TAATAGCATTCA
22377953 T
1 T
22377954 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:22378856 original size:16 final size:17
Alignment explanation
Indices: 22378837--22378869 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22378827 ATTTTAATAC
*
22378837 AAATTAATTAT-TTTTT
1 AAATAAATTATATTTTT
22378853 AAATAAATTATATTTTT
1 AAATAAATTATATTTTT
22378870 CGACATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATAAATTATATTTTT
Found at i:22382255 original size:25 final size:23
Alignment explanation
Indices: 22382227--22382272 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
22382217 GTTGGATCCA
22382227 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
22382252 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
22382273 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:22385412 original size:111 final size:112
Alignment explanation
Indices: 22385199--22385414 Score: 389
Period size: 111 Copynumber: 1.9 Consensus size: 112
22385189 TCGATCTCCC
22385199 AATTTAGGTGAATTTTAGTGTCAATGATTTCTGTCAACACATCATCCTCTCTGTCGGCCTTCAAT
1 AATTTAGGTGAATTTTAGTGTCAATGATTTCTGTCAACACATCATCCTCTCTGTCGGCCTTCAAT
*
22385264 AGTTCTTCCAACCATTTCGTCAACTCTTCCTTATTCTCCGCTGCCAA
66 AGTTCCTCCAACCATTTCGTCAACTCTTCCTTATTCTCCGCTGCCAA
*
22385311 AATTTAGGTGAATTTTAGTGTCAATGATTTCTGTCAACACATCAT-CTCTCTGTTGGCCTTCAAT
1 AATTTAGGTGAATTTTAGTGTCAATGATTTCTGTCAACACATCATCCTCTCTGTCGGCCTTCAAT
* *
22385375 AGTTCCTCCAGCCATTTCGTCAACTCTTCCTTCTTCTCCG
66 AGTTCCTCCAACCATTTCGTCAACTCTTCCTTATTCTCCG
22385415 TTATAATAGT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 55 0.55
112 45 0.45
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.38
Consensus pattern (112 bp):
AATTTAGGTGAATTTTAGTGTCAATGATTTCTGTCAACACATCATCCTCTCTGTCGGCCTTCAAT
AGTTCCTCCAACCATTTCGTCAACTCTTCCTTATTCTCCGCTGCCAA
Found at i:22386268 original size:13 final size:13
Alignment explanation
Indices: 22386250--22386277 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22386240 AAATTGAATA
22386250 AAAATGAAATATT
1 AAAATGAAATATT
22386263 AAAATGAAATATT
1 AAAATGAAATATT
22386276 AA
1 AA
22386278 GGGTAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGAAATATT
Found at i:22391086 original size:80 final size:80
Alignment explanation
Indices: 22390944--22391242 Score: 361
Period size: 80 Copynumber: 3.7 Consensus size: 80
22390934 TATGCTATCA
* * *
22390944 GTTTAACTAACTAGAGCTGCGCTCACAATTGCGGTTTATCCGCTAGGCACT-GGATGCTAAGATT
1 GTTTAACCAACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTAGG-TGCCAAGATT
22391008 TGACGGATATTTGTCG
65 TGACGGATATTTGTCG
* * *
22391024 GTTTAACCGACTAGAGCTAGGCTCACAATTGCGGTTTATCCGCTAGGCATTAGGTGCCAAGATTT
1 GTTTAACCAACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTT
22391089 GACGGATATTTGTCG
66 GACGGATATTTGTCG
* ** * * * * * * *
22391104 ATTTAACCGGCTGGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGTGCTAGGACTT
1 GTTTAACCAACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTT
*
22391169 GACGGATATTTGTTG
66 GACGGATATTTGTCG
* ** *
22391184 G-TTAATCCAACTAGAGCTGGGTTCACTTTTGCGG-TTATTCCACTAGGCACTAGGTGCCA
1 GTTTAA-CCAACTAGAGCTGGGCTCACAATTGCGGTTTA-TCCGCTAGGCACTAGGTGCCA
22391243 TAATTGTCGG
Statistics
Matches: 188, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
79 7 0.04
80 179 0.95
81 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (80 bp):
GTTTAACCAACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTT
GACGGATATTTGTCG
Found at i:22392716 original size:21 final size:22
Alignment explanation
Indices: 22392692--22392751 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
22392682 ATGATTTATT
*
22392692 TCGGTAGAAGCTTCACT-TGTA
1 TCGGTAGAAGCTTCACTAGGTA
22392713 TCGGTAGAA-CTGTCA-TAGGTA
1 TCGGTAGAAGCT-TCACTAGGTA
22392734 TCGGTAGAAGCTTGCACT
1 TCGGTAGAAGCTT-CACT
22392752 GTTTCTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 3 0.09
21 25 0.76
22 4 0.12
23 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (22 bp):
TCGGTAGAAGCTTCACTAGGTA
Found at i:22396392 original size:26 final size:26
Alignment explanation
Indices: 22396345--22396399 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
22396335 TTTTTAGAAA
* * *
22396345 AAAAATTTAAATTTTTATATTTTTTT
1 AAAAATATAAATTTTGATATTTTTAT
22396371 AAAAATATAAATTTTGGA-ATTTTTAT
1 AAAAATATAAATTTT-GATATTTTTAT
22396397 AAA
1 AAA
22396400 TATTTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
AAAAATATAAATTTTGATATTTTTAT
Found at i:22396413 original size:18 final size:19
Alignment explanation
Indices: 22396376--22396412 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22396366 TTTTTAAAAA
22396376 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
22396394 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
22396413 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:22396422 original size:19 final size:21
Alignment explanation
Indices: 22396366--22396423 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 21
22396356 TTTTTATATT
22396366 TTTTTAAAAATATAAATTTTGGAA
1 TTTTTAAAAAT-T--ATTTTGGAA
*
22396390 TTTTTATAAA-TATTTT-GAA
1 TTTTTAAAAATTATTTTGGAA
22396409 -TTTTAAAAATTATTT
1 TTTTTAAAAATTATTT
22396424 AGATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 8 0.26
19 8 0.26
20 5 0.16
22 1 0.03
24 9 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTGGAA
Found at i:22396431 original size:19 final size:18
Alignment explanation
Indices: 22396389--22396431 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
22396379 AAATTTTGGA
* *
22396389 ATTTTTATAAATATTTTG
1 ATTTTTAAAAATATTTAG
*
22396407 AATTTTAAAAATTATTTAG
1 ATTTTTAAAAA-TATTTAG
22396426 ATTTTT
1 ATTTTT
22396432 TTGTAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTTTAAAAATATTTAG
Found at i:22396526 original size:9 final size:9
Alignment explanation
Indices: 22396512--22396549 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
22396502 CATCAATCTG
22396512 TTATTTGAA
1 TTATTTGAA
22396521 TTATTTGAA
1 TTATTTGAA
*
22396530 TTATTTGAG
1 TTATTTGAA
*
22396539 TTATTCGAA
1 TTATTTGAA
22396548 TT
1 TT
22396550 GTAAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (9 bp):
TTATTTGAA
Found at i:22398231 original size:21 final size:23
Alignment explanation
Indices: 22398198--22398244 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
22398188 TTCTAAATTA
22398198 TTTAAATATTTTTA-TAAATATT
1 TTTAAATATTTTTATTAAATATT
* *
22398220 TTTAATTA-TTTTATTAATTATT
1 TTTAAATATTTTTATTAAATATT
22398242 TTT
1 TTT
22398245 TTGAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTAAATATTTTTATTAAATATT
Found at i:22398947 original size:15 final size:15
Alignment explanation
Indices: 22398929--22398990 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
22398919 CTATTATGTG
*
22398929 GTATATTATTGTTAT
1 GTATATTACTGTTAT
22398944 GTATATTACTGTTAT
1 GTATATTACTGTTAT
* *
22398959 GTATGTGACTGTTAT
1 GTATATTACTGTTAT
*
22398974 GTATATTATTGTTAT
1 GTATATTACTGTTAT
22398989 GT
1 GT
22398991 TTAATGTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (15 bp):
GTATATTACTGTTAT
Found at i:22398951 original size:45 final size:44
Alignment explanation
Indices: 22398893--22398990 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 44
22398883 TATGTATGTA
*
22398893 TGTTATGGATATTACCG-CATGTATGT-CTATTATGTGGTATATTAT
1 TGTTATGTATATTACCGTCATGTATGTACTATTA--T-GTATATTAT
* * *
22398938 TGTTATGTATATTACTGTTATGTATGTGACTGTTATGTATATTAT
1 TGTTATGTATATTACCGTCATGTATGT-ACTATTATGTATATTAT
22398983 TGTTATGT
1 TGTTATGT
22398991 TTAATGTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 32 0.70
46 9 0.20
48 5 0.11
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.51
Consensus pattern (44 bp):
TGTTATGTATATTACCGTCATGTATGTACTATTATGTATATTAT
Found at i:22400955 original size:72 final size:72
Alignment explanation
Indices: 22400838--22400984 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 72
22400828 GCATTTAGGG
* * *
22400838 ATTGATGGAGAAGATTTCTGAGTTGTTGTCAAGAGTTGAGCATAGAGTCTGTGCAAGATATCTAT
1 ATTGATGGAGAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
22400903 ATGTAAA
66 ATGTAAA
*
22400910 ATTGATGTAGAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
1 ATTGATGGAGAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
22400975 ATGTAAA
66 ATGTAAA
22400982 ATT
1 ATT
22400985 TCTGAGTTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (72 bp):
ATTGATGGAGAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
ATGTAAA
Found at i:22400986 original size:59 final size:60
Alignment explanation
Indices: 22400914--22401040 Score: 229
Period size: 59 Copynumber: 2.1 Consensus size: 60
22400904 TGTAAAATTG
22400914 ATGTAGAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
1 ATGTA-AAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
*
22400975 ATGTAAA-ATTTCTGAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
1 ATGTAAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
22401034 ATGTAAA
1 ATGTAAA
22401041 CTGGAAGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
59 58 0.89
60 2 0.03
61 5 0.08
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (60 bp):
ATGTAAAGATTTCTAAGTTGTTGCCAAGAGTTGAGCATAGAGTCTGTGCAAGACATCTAT
Found at i:22401076 original size:25 final size:25
Alignment explanation
Indices: 22401048--22401095 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
22401038 AAACTGGAAG
22401048 AAAGAAAATCCTAGAGGAGACCTGC
1 AAAGAAAATCCTAGAGGAGACCTGC
22401073 AAAGAAAATCCTAGAGGAGACCT
1 AAAGAAAATCCTAGAGGAGACCT
22401096 ACAACAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (25 bp):
AAAGAAAATCCTAGAGGAGACCTGC
Found at i:22403537 original size:23 final size:23
Alignment explanation
Indices: 22403505--22403548 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
22403495 ACTACCATTT
22403505 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
22403528 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
22403549 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:22403541 original size:13 final size:11
Alignment explanation
Indices: 22403509--22403551 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
22403499 CCATTTTCTA
*
22403509 AATAAAATAAT
1 AATAAAATATT
22403520 AAT-AAATATCT
1 AATAAAATAT-T
22403531 AAGTAAAATATT
1 AA-TAAAATATT
22403543 AATAAAATA
1 AATAAAATA
22403552 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:22403935 original size:3 final size:3
Alignment explanation
Indices: 22403927--22403953 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22403917 CTACTTCTAA
22403927 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
22403954 TTACACTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:22405971 original size:14 final size:13
Alignment explanation
Indices: 22405944--22405968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22405934 TAAAAAACGG
22405944 ATAAAAAAGATTA
1 ATAAAAAAGATTA
22405957 ATAAAAAAGATT
1 ATAAAAAAGATT
22405969 TAAAATCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAAAAAGATTA
Found at i:22406975 original size:14 final size:14
Alignment explanation
Indices: 22406956--22406990 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22406946 TTTTCGATTT
22406956 TAGATCTAAAAAAA
1 TAGATCTAAAAAAA
**
22406970 TAGATCTACTAAAA
1 TAGATCTAAAAAAA
22406984 TAGATCT
1 TAGATCT
22406991 TAGTTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (14 bp):
TAGATCTAAAAAAA
Found at i:22409679 original size:17 final size:17
Alignment explanation
Indices: 22409653--22409685 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22409643 ATAATCCATT
*
22409653 TCATTTTCATTTTCACA
1 TCATTCTCATTTTCACA
22409670 TCATTCTCATTTTCAC
1 TCATTCTCATTTTCAC
22409686 TTTTCTTTCA
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:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (17 bp):
TCATTCTCATTTTCACA
Found at i:22410017 original size:23 final size:24
Alignment explanation
Indices: 22409980--22410032 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
22409970 GAAAGTATCA
*
22409980 ATTTTTCATAATCAATCTCATTTC
1 ATTTCTCATAATCAATCTCATTTC
* *
22410004 CTTTCTCAT-ATCAATTTCATTTC
1 ATTTCTCATAATCAATCTCATTTC
22410027 ATTTCT
1 ATTTCT
22410033 ATTCTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTCTCATAATCAATCTCATTTC
Found at i:22411998 original size:13 final size:11
Alignment explanation
Indices: 22411966--22412008 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
22411956 CCGTTTTTTA
*
22411966 AATAAAATAAT
1 AATAAAATATT
22411977 AAT-AAATATCT
1 AATAAAATAT-T
22411988 AAGTAAAATATT
1 AA-TAAAATATT
22412000 AATAAAATA
1 AATAAAATA
22412009 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:22413615 original size:14 final size:13
Alignment explanation
Indices: 22413581--22413620 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
22413571 ATGGATGGTT
*
22413581 TTATTTTGTTGGA
1 TTATTTTGATGGA
*
22413594 TCATTTTGATGGA
1 TTATTTTGATGGA
22413607 TGTATTTTGATGGA
1 T-TATTTTGATGGA
22413621 CGGTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.53
Consensus pattern (13 bp):
TTATTTTGATGGA
Found at i:22413626 original size:45 final size:45
Alignment explanation
Indices: 22413570--22413666 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 45
22413560 GTTAACATGC
* * *
22413570 GATGGATGGTTTTATTTTGTTGGATCATTTTGATGGATGTATTTT
1 GATGGACGGTTTAATTTTGTTGAATCATTTTGATGGATGTATTTT
*
22413615 GATGGACGGTTTAATTTTGTTGAATCATTTTGATGGTTGTATTTT
1 GATGGACGGTTTAATTTTGTTGAATCATTTTGATGGATGTATTTT
22413660 GATGGAC
1 GATGGAC
22413667 AATTTATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.20, C:0.04, G:0.27, T:0.49
Consensus pattern (45 bp):
GATGGACGGTTTAATTTTGTTGAATCATTTTGATGGATGTATTTT
Found at i:22413770 original size:13 final size:13
Alignment explanation
Indices: 22413752--22413777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22413742 TTATACTTTG
22413752 ACAACAACATTAT
1 ACAACAACATTAT
22413765 ACAACAACATTAT
1 ACAACAACATTAT
22413778 TCAATACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
ACAACAACATTAT
Found at i:22413928 original size:14 final size:16
Alignment explanation
Indices: 22413909--22413940 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22413899 AATTTGTTGT
22413909 TCCTTG-AC-ATTTTA
1 TCCTTGTACAATTTTA
22413923 TCCTTGTACAATTTTA
1 TCCTTGTACAATTTTA
22413939 TC
1 TC
22413941 TTCTCTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TCCTTGTACAATTTTA
Found at i:22418206 original size:20 final size:21
Alignment explanation
Indices: 22418173--22418211 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
22418163 TAAACTTTAG
22418173 AGTTTAGAGTTTAAGATTTGA
1 AGTTTAGAGTTTAAGATTTGA
22418194 AGTTTAG-GTTTAAGATTT
1 AGTTTAGAGTTTAAGATTT
22418212 AAAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
AGTTTAGAGTTTAAGATTTGA
Found at i:22418219 original size:20 final size:21
Alignment explanation
Indices: 22418175--22418219 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
22418165 AACTTTAGAG
* *
22418175 TTTAGAGTTTAAGATTTGAAG
1 TTTAGAGTTTAAGATTTAAAA
22418196 TTTAG-GTTTAAGATTTAAAA
1 TTTAGAGTTTAAGATTTAAAA
22418216 TTTA
1 TTTA
22418220 TAATTTGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (21 bp):
TTTAGAGTTTAAGATTTAAAA
Found at i:22418259 original size:28 final size:28
Alignment explanation
Indices: 22418163--22418260 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
22418153 CCTAAAATCC
* *
22418163 TAAACTTTAGAGTTTAGAGTTTAAGATT
1 TAAAATTTAGGGTTTAGAGTTTAAGATT
* * *
22418191 TGAAGTTTA-GGTTTA-AGATTTAAAATT
1 TAAAATTTAGGGTTTAGAG-TTTAAGATT
* *
22418218 TATAATTT-GAGGTTTAGAGTTTGAGATT
1 TAAAATTTAG-GGTTTAGAGTTTAAGATT
22418246 TAAAATTTAGGGTTT
1 TAAAATTTAGGGTTT
22418261 GAAATTCAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
26 2 0.04
27 18 0.33
28 32 0.58
29 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (28 bp):
TAAAATTTAGGGTTTAGAGTTTAAGATT
Found at i:22418262 original size:35 final size:34
Alignment explanation
Indices: 22418188--22418255 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
22418178 AGAGTTTAAG
*
22418188 ATTTGAAGTTTAGGTTTAAGATTTAAAATTTATA
1 ATTTGAAGTTTAGGTTTAAGATTTAAAATTTAGA
* *
22418222 ATTTGAGGTTTAGAGTTTGAGATTTAAAATTTAG
1 ATTTGAAGTTTAG-GTTTAAGATTTAAAATTTAG
22418256 GGTTTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (34 bp):
ATTTGAAGTTTAGGTTTAAGATTTAAAATTTAGA
Found at i:22418274 original size:21 final size:21
Alignment explanation
Indices: 22418230--22418274 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22418220 TAATTTGAGG
* *
22418230 TTTAGAGTTTGAGATTTAAAA
1 TTTAGAGTTTGAAATTCAAAA
* *
22418251 TTTAGGGTTTGAAATTCAACA
1 TTTAGAGTTTGAAATTCAAAA
22418272 TTT
1 TTT
22418275 GAGATAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTAGAGTTTGAAATTCAAAA
Found at i:22420868 original size:15 final size:17
Alignment explanation
Indices: 22420836--22420868 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22420826 TTGTGGAGAC
22420836 AGAAGAGGAAAAAGAAG
1 AGAAGAGGAAAAAGAAG
22420853 AGAA-AGGAAAAA-AAG
1 AGAAGAGGAAAAAGAAG
22420868 A
1 A
22420869 ACCTGATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AGAAGAGGAAAAAGAAG
Found at i:22421308 original size:17 final size:16
Alignment explanation
Indices: 22421288--22421344 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
22421278 GTTGTCATAA
22421288 CATTTCGTTTGTCATTG
1 CATTTC-TTTGTCATTG
* *
22421305 CATTTTTCTTGTCACTG
1 CATTTCT-TTGTCATTG
*
22421322 CATCTTCATTGTCATTG
1 CAT-TTCTTTGTCATTG
22421339 CATTTC
1 CATTTC
22421345 CATATATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (16 bp):
CATTTCTTTGTCATTG
Found at i:22432047 original size:195 final size:195
Alignment explanation
Indices: 22431651--22432098 Score: 555
Period size: 195 Copynumber: 2.3 Consensus size: 195
22431641 GAAAACGACG
* * * * *
22431651 CGATGGCTAAGGTACCGCATATGTTGCGAGTCCTTGACAGCTCCTGTGAGCAGCATCGTGAGTTG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACTCG
* *
22431716 GGAAATGAGAAAAGAATCTGAGAATGGATTACAGGCCCTACGATGGCTGAGATTTATGCATAAGT
66 AGAAATGAGAAAAGAATCTGAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGT
* * * * *
22431781 GCATATTCTCGACAGCTAGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCATAGATATCGTAT
131 GCATACTCTCGACAGCTAGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGATACCGTAC
* * *
22431846 CGATGGCTGAGGAACCACATATGTTGCGAGTCCTCGACAGCTCATGCGAGCAGCATCGTGACTCG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACTCG
* * * * * *
22431911 AGAAA-GAGATATGGATCCT-A-AATGGATTACAGGCCCTACGATGGCTGGGA-CTATGCTTTA-
66 AGAAATGAGAAAAGAAT-CTGAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAG
* *
22431971 TGCATACTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTTATAGTACAGACAGGTAC
130 TGCATACTCTCGACAGCTAGTGTGAGCAGCATCGTTAGGGAACAG-TTATA-TAC--ACAGATAC
22432036 CGTAC
191 CGTAC
* * * * * *
22432041 CGATGGCTGGGGTATCGCATACGTTGTGAGTCCTCGATAGCTCATGTGAGCAACATCG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCG
22432099 AGTACTGGTA
Statistics
Matches: 216, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
191 43 0.20
192 12 0.06
193 31 0.14
194 9 0.04
195 121 0.56
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACTCG
AGAAATGAGAAAAGAATCTGAGAATGGATTACAGGCCCTACGATGGCTGAGATCTATGCATAAGT
GCATACTCTCGACAGCTAGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGATACCGTAC
Found at i:22441831 original size:3 final size:3
Alignment explanation
Indices: 22441823--22441873 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
22441813 CGGGGTAACG
*
22441823 TCT TCT TCT TCT ACT TCTT TCT TC- TCT TCT T-T TCCT TCT TCT T-T
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT T-CT TCT TCT TCT
22441867 TCT TCT T
1 TCT TCT T
22441874 TTTTATTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 30 0.73
4 5 0.12
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:22441841 original size:12 final size:11
Alignment explanation
Indices: 22441823--22441873 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
22441813 CGGGGTAACG
22441823 TCTTCTTCTTC
1 TCTTCTTCTTC
22441834 TACTTCTTTCTTC
1 T-CTTC-TTCTTC
22441847 TCTTCTT-TTC
1 TCTTCTTCTTC
*
22441857 -CTTCTTCTTT
1 TCTTCTTCTTC
22441867 TCTTCTT
1 TCTTCTT
22441874 TTTTATTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 6 0.17
10 5 0.14
11 9 0.26
12 8 0.23
13 7 0.20
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:22441852 original size:21 final size:20
Alignment explanation
Indices: 22441826--22441873 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22441816 GGTAACGTCT
22441826 TCTTCTTCTACTTCTTTCTTC
1 TCTTCTTCTACTTC-TTCTTC
* * *
22441847 TCTTCTTTTCCTTCTTCTTT
1 TCTTCTTCTACTTCTTCTTC
22441867 TCTTCTT
1 TCTTCTT
22441874 TTTTATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTCTTCTACTTCTTCTTC
Found at i:22441863 original size:24 final size:25
Alignment explanation
Indices: 22441823--22441872 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
22441813 CGGGGTAACG
22441823 TCTTCTTCTTCTACTTC-TTTCTTC
1 TCTTCTTCTTCTACTTCTTTTCTTC
*
22441847 TCTTCTT-TTCCTTCTTCTTTTCTTC
1 TCTTCTTCTT-CTACTTCTTTTCTTC
22441872 T
1 T
22441873 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 13 0.57
25 8 0.35
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (25 bp):
TCTTCTTCTTCTACTTCTTTTCTTC
Found at i:22443684 original size:24 final size:24
Alignment explanation
Indices: 22443639--22443687 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
22443629 TGCAAAAACT
22443639 AAAGAAACAAATTAAAGTAAAATA
1 AAAGAAACAAATTAAAGTAAAATA
*
22443663 AAAGACAA-AAATTAACAGAAAAATA
1 AAAGA-AACAAATTAA-AGTAAAATA
22443688 GTAATGACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (24 bp):
AAAGAAACAAATTAAAGTAAAATA
Found at i:22451993 original size:15 final size:15
Alignment explanation
Indices: 22451973--22452001 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22451963 TTATTGTTTT
22451973 ACAAAATTTGCACTG
1 ACAAAATTTGCACTG
22451988 ACAAAATTTGCACT
1 ACAAAATTTGCACT
22452002 TAATTGCGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (15 bp):
ACAAAATTTGCACTG
Found at i:22456137 original size:11 final size:11
Alignment explanation
Indices: 22456102--22456192 Score: 94
Period size: 11 Copynumber: 8.1 Consensus size: 11
22456092 AGCCCAAACC
22456102 ATTTAAATTTA
1 ATTTAAATTTA
* *
22456113 CTTTGAAATTAA
1 ATTT-AAATTTA
*
22456125 ATTT-ATTTTAA
1 ATTTAAATTT-A
22456136 ATTTAAATTTA
1 ATTTAAATTTA
* *
22456147 TTTTAAATTCA
1 ATTTAAATTTA
22456158 ATTTAAATTTAA
1 ATTTAAATTT-A
*
22456170 ATTTGAATTTA
1 ATTTAAATTTA
22456181 ATTTAAATTTA
1 ATTTAAATTTA
22456192 A
1 A
22456193 CATCATTGTA
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
10 3 0.05
11 38 0.59
12 23 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:22456142 original size:6 final size:6
Alignment explanation
Indices: 22456102--22456192 Score: 86
Period size: 6 Copynumber: 16.0 Consensus size: 6
22456092 AGCCCAAACC
* *
22456102 ATTTAA ATTT-A CTTTGAA A-TTAA ATTT-A TTTTAA ATTTAA ATTT-A
1 ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
22456147 TTTTAA A-TTCA ATTTAA ATTTAA ATTTGA ATTT-A ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
22456193 CATCATTGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
5 24 0.35
6 44 0.64
7 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:22456190 original size:17 final size:17
Alignment explanation
Indices: 22456102--22456192 Score: 105
Period size: 17 Copynumber: 5.4 Consensus size: 17
22456092 AGCCCAAACC
*
22456102 ATTTAAATTTACTTTGAA
1 ATTTAAATTTAATTT-AA
*
22456120 A-TTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
*
22456136 ATTTAAATTTATTTTAA
1 ATTTAAATTTAATTTAA
*
22456153 A-TTCAATTTAAATTTAA
1 ATTTAAATTT-AATTTAA
*
22456170 ATTTGAATTTAATTTAA
1 ATTTAAATTTAATTTAA
22456187 ATTTAA
1 ATTTAA
22456193 CATCATTGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.15
17 47 0.72
18 8 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:22456952 original size:10 final size:10
Alignment explanation
Indices: 22456929--22456984 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
22456919 TAATAAAGGC
22456929 ATTAATAA-T
1 ATTAATAATT
*
22456938 ATTAATATTT
1 ATTAATAATT
22456948 ATTAATAATT
1 ATTAATAATT
*
22456958 AATAATAA-T
1 ATTAATAATT
22456967 AGTTAAT-ATT
1 A-TTAATAATT
22456977 A-TAATAAT
1 ATTAATAAT
22456985 AAAAAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.10
9 12 0.31
10 23 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (10 bp):
ATTAATAATT
Found at i:22457339 original size:26 final size:23
Alignment explanation
Indices: 22457299--22457346 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
22457289 ATCTGGATTC
*
22457299 GATTTTTTTTTAAGAATGAAAAA
1 GATTTTTTTTTAAGAAAGAAAAA
22457322 GATTGTTTTTTTAAAAGAAAGAAAA
1 GATT-TTTTTTT--AAGAAAGAAAA
22457347 GAAAAGGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 7 0.33
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (23 bp):
GATTTTTTTTTAAGAAAGAAAAA
Found at i:22458151 original size:29 final size:30
Alignment explanation
Indices: 22458072--22458242 Score: 190
Period size: 29 Copynumber: 5.8 Consensus size: 30
22458062 GAAGGTACCT
22458072 AAACTGTCCAAAAATTACA-TTTTGA-CCTCA
1 AAACT-TCCAAAAATTACATTTTTGACCCT-A
*
22458102 AAACTTCTCCAAAATTACATTTTTGACCCTA
1 AAACTTC-CAAAAATTACATTTTTGACCCTA
*
22458133 AAACTTCC-AAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTACATTTTTGACCCTA
* *
22458162 AAACTTCCAAAAACTACATTTTT-ACCCTT
1 AAACTTCCAAAAATTACATTTTTGACCCTA
* * * *
22458191 AAATTTCCTAAAATTCCATTTTTGACCC-C
1 AAACTTCCAAAAATTACATTTTTGACCCTA
* *
22458220 GAACTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTACATTTTT
22458243 AACCTCGAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
29 74 0.60
30 32 0.26
31 14 0.11
32 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTGACCCTA
Found at i:22458182 original size:59 final size:59
Alignment explanation
Indices: 22458072--22458243 Score: 199
Period size: 59 Copynumber: 2.9 Consensus size: 59
22458062 GAAGGTACCT
* *
22458072 AAACTGTCCAAAAATTACA-TTTTGA-CCTCAAAACTTCTCCAAAATTACATTTTTGACCCTA
1 AAACT-TCCAAAAATTCCATTTTTGACCCT-AAAACTTC-CAAAAATTACATTTTT-ACCCTA
* *
22458133 AAACTTCC-AAAATTCCATTTTTGACCCTAAAACTTCCAAAAACTACATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCTA
* * ** *
22458191 AAATTTCCTAAAATTCCATTTTTGACCC-CGAACTTCCAAAAATTCCATTTTTA
1 AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTA
22458244 ACCTCGAAAC
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
58 33 0.33
59 41 0.41
60 17 0.17
61 8 0.08
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCTA
Found at i:22458251 original size:29 final size:29
Alignment explanation
Indices: 22458072--22458289 Score: 169
Period size: 29 Copynumber: 7.4 Consensus size: 29
22458062 GAAGGTACCT
* *
22458072 AAACTGTCCAAAAATTACATTTTGA-CCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* * *
22458101 AAAACTTCTCCAAAATTACATTTTTGACCCTA
1 -AAACTTC-CAAAAATTCCATTTTT-ACCCTC
*
22458133 AAACTTCC-AAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* * *
22458162 AAACTTCCAAAAACTACATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
22458191 AAATTTCCTAAAATTCCATTTTTGACCC-C
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
* *
22458220 GAACTTCCAAAAATTCCATTTTTAACCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
*
22458249 GAAAC-TCTC-GAAATTACCA-TTTTACCCTC
1 -AAACTTC-CAAAAATT-CCATTTTTACCCTC
* *
22458278 GAGCTTCCAAAA
1 AAACTTCCAAAA
22458290 GGTCCCATTT
Statistics
Matches: 155, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
28 6 0.04
29 95 0.61
30 43 0.28
31 8 0.05
32 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:22465194 original size:12 final size:13
Alignment explanation
Indices: 22465177--22465209 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22465167 CGGATTCAAT
*
22465177 AAAAAAAGAAGA-
1 AAAAAAAAAAGAG
22465189 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
22465202 AAAAAAAA
1 AAAAAAAA
22465210 CCTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:22465197 original size:15 final size:14
Alignment explanation
Indices: 22465177--22465209 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
22465167 CGGATTCAAT
22465177 AAAAAAAGAAGAAAA
1 AAAAAAAG-AGAAAA
22465192 AAAAAAAGAGAAAA
1 AAAAAAAGAGAAAA
22465206 AAAA
1 AAAA
22465210 CCTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAGAAAA
Found at i:22466764 original size:21 final size:21
Alignment explanation
Indices: 22466738--22466781 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
22466728 ATGAAACTTC
22466738 TACCTTGAAGTCATGGTGGGT
1 TACCTTGAAGTCATGGTGGGT
22466759 TACCTTGAAGTCATGGTGGGT
1 TACCTTGAAGTCATGGTGGGT
22466780 TA
1 TA
22466782 GATAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TACCTTGAAGTCATGGTGGGT
Found at i:22466899 original size:92 final size:92
Alignment explanation
Indices: 22466788--22467480 Score: 1224
Period size: 92 Copynumber: 7.5 Consensus size: 92
22466778 GTTAGATAAA
* *
22466788 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCTAGATGAAGCATCAAACATCAATTTC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
22466853 TATCCTCTTGAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
*
22466880 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCCAGATGAAGCATCAAACATCAATTCC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
22466945 TATCCTCTTGAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
*
22466972 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGGTGAAGCATCAAACATCAATTCC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
22467037 TATCCTCTTGAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
* *
22467064 GATTGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATTAAGCATCAAACATCAATTCC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
22467129 TATCCTCTTGAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
* *
22467156 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGGTGAAGCATCAAACATCAATTCT
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
*
22467221 TATCCTCTTAAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
*
22467248 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
*
22467313 TATCCTCTTGAAGTTGTAGTAAAATTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
* ** *
22467340 GATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTTC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
22467405 TATCCTCTTGAAGTTGTAGTAAAGTTG
66 TATCCTCTTGAAGTTGTAGTAAAGTTG
* * *
22467432 GATAGCAAGTCTTTATCTCTCTAAAGTTGTAGTGAGAGTAAGATGAAGC
1 GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
22467481 CTTGACATCA
Statistics
Matches: 577, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 577 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (92 bp):
GATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCC
TATCCTCTTGAAGTTGTAGTAAAGTTG
Found at i:22467767 original size:11 final size:11
Alignment explanation
Indices: 22467751--22467805 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
22467741 TACTTTGATA
*
22467751 TTAAATTTATT
1 TTAAATTTAAT
22467762 TTAAATTTAAT
1 TTAAATTTAAT
22467773 TTAAATTTAAAT
1 TTAAATTT-AAT
*
22467785 TTGAATTTAAT
1 TTAAATTTAAT
22467796 TTAAATTTAA
1 TTAAATTTAA
22467806 CATCATTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 30 0.75
12 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:22467771 original size:17 final size:17
Alignment explanation
Indices: 22467732--22467805 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
22467722 GGCCCAAACC
* *
22467732 ATTTAAATTTACTTT-G
1 ATTTAAATTTAATTTAA
*
22467748 ATATTAAATTTATTTTAA
1 AT-TTAAATTTAATTTAA
22467766 ATTT-AATTTAAATTTAA
1 ATTTAAATTT-AATTTAA
*
22467783 ATTTGAATTTAATTTAA
1 ATTTAAATTTAATTTAA
22467800 ATTTAA
1 ATTTAA
22467806 CATCATTGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.14
17 36 0.72
18 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:22467779 original size:6 final size:6
Alignment explanation
Indices: 22467751--22467805 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
22467741 TACTTTGATA
* *
22467751 TTAAAT TT-ATT TTAAAT TT-AAT TTAAAT TTAAAT TTGAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
22467796 TTAAAT TTAA
1 TTAAAT TTAA
22467806 CATCATTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
5 14 0.33
6 29 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:22468583 original size:10 final size:9
Alignment explanation
Indices: 22468543--22468596 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 9
22468533 TAATAAAGGC
22468543 ATTAATAAT
1 ATTAATAAT
22468552 ATTAAT-AT
1 ATTAATAAT
*
22468560 -TTATTAAT
1 ATTAATAAT
22468568 AATTAATAAT
1 -ATTAATAAT
*
22468578 AGTTAATATT
1 A-TTAATAAT
22468588 A-TAATAAT
1 ATTAATAAT
22468596 A
1 A
22468597 AAAAATTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
7 4 0.11
8 11 0.30
9 7 0.19
10 15 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (9 bp):
ATTAATAAT
Found at i:22468952 original size:23 final size:22
Alignment explanation
Indices: 22468908--22468951 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22468898 ATCTGGATTC
* * *
22468908 GATTTTTTTTTAAGAATGAAAA
1 GATTGTTTTTTAAAAAAGAAAA
22468930 GATTGTTTTTTAAAAAAGAAAA
1 GATTGTTTTTTAAAAAAGAAAA
22468952 AATAAAAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (22 bp):
GATTGTTTTTTAAAAAAGAAAA
Found at i:22469809 original size:29 final size:29
Alignment explanation
Indices: 22469737--22469928 Score: 128
Period size: 29 Copynumber: 6.6 Consensus size: 29
22469727 TCGAAACTTC
* *
22469737 TCCAAAATTACA--TTTTAACCTCGAAACTT
1 TCCAAAATTCCATTTTTTACCCT-GAAAC-T
*
22469766 CTCCAAAATTACATTTTTTACCCTGAAACT
1 -TCCAAAATTCCATTTTTTACCCTGAAACT
* * *
22469796 TCCAAAATTCCATTTCTGACCCTAAAACT
1 TCCAAAATTCCATTTTTTACCCTGAAACT
* * *
22469825 TCTAAAAATTACA-TTTTTGCCCT-AAACT
1 TC-CAAAATTCCATTTTTTACCCTGAAACT
*
22469853 TCCTAAAATTCCATTTTTGA-CCTCG-AACT
1 TCC-AAAATTCCATTTTTTACCCT-GAAACT
* * *
22469882 TCCAAAAAATCCATTTTTAACCCTAAAAC-
1 TCC-AAAATTCCATTTTTTACCCTGAAACT
*
22469911 TCCTGAAATTACCATTTT
1 TCC-AAAATT-CCATTTT
22469929 ACCCTTGAGC
Statistics
Matches: 131, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
28 18 0.14
29 66 0.50
30 34 0.26
31 5 0.04
32 8 0.06
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAATTCCATTTTTTACCCTGAAACT
Found at i:22469840 original size:30 final size:30
Alignment explanation
Indices: 22469696--22469928 Score: 148
Period size: 30 Copynumber: 7.9 Consensus size: 30
22469686 CCTTGGAGGT
*
22469696 CCCT-AAACTGTCCAAAAATTACA-TTTTGA
1 CCCTGAAACT-TCTAAAAATTACATTTTTGA
* *
22469725 -CATCGAAACTTCTCCAAAATTACA-TTTT-A
1 CCCT-GAAACTTCT-AAAAATTACATTTTTGA
* * *
22469754 ACCTCGAAACTTCTCCAAAATTACATTTTTTA
1 CCCT-GAAACTTCT-AAAAATTACATTTTTGA
* * *
22469786 CCCTGAAACTTC-CAAAATTCCATTTCTGA
1 CCCTGAAACTTCTAAAAATTACATTTTTGA
*
22469815 CCCTAAAACTTCTAAAAATTACATTTTTG-
1 CCCTGAAACTTCTAAAAATTACATTTTTGA
*
22469844 CCCT-AAACTTCCT-AAAATTCCATTTTTGA
1 CCCTGAAACTT-CTAAAAATTACATTTTTGA
* * * *
22469873 -CCTCG-AACTTCCAAAAAATCCATTTTTAA
1 CCCT-GAAACTTCTAAAAATTACATTTTTGA
* * *
22469902 CCCTAAAACTCCT-GAAATTACCATTTT
1 CCCTGAAACTTCTAAAAATTA-CATTTT
22469929 ACCCTTGAGC
Statistics
Matches: 167, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
28 26 0.16
29 57 0.34
30 68 0.41
31 12 0.07
32 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
CCCTGAAACTTCTAAAAATTACATTTTTGA
Found at i:22469874 original size:58 final size:58
Alignment explanation
Indices: 22469760--22469928 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 58
22469750 TTTAACCTCG
* * *
22469760 AAACTTCTCCAAAATTACATTTTTTACCCTGAAACTTCC-AAAATTCCATTTCTGACCCTA
1 AAACTTCT-AAAAATTACA-TTTTTACCCTAAAACTTCCTAAAATTCCATTTTTGA-CCTA
* *
22469820 AAACTTCTAAAAATTACATTTTTGCCCT-AAACTTCCTAAAATTCCATTTTTGACCTC
1 AAACTTCTAAAAATTACATTTTTACCCTAAAACTTCCTAAAATTCCATTTTTGACCTA
* * * * *
22469877 GAACTTCCAAAAAATCCATTTTTAACCCTAAAAC-TCCTGAAATTACCATTTT
1 AAACTTCTAAAAATTACATTTTT-ACCCTAAAACTTCCTAAAATT-CCATTTT
22469929 ACCCTTGAGC
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
57 30 0.32
58 37 0.39
59 20 0.21
60 8 0.08
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (58 bp):
AAACTTCTAAAAATTACATTTTTACCCTAAAACTTCCTAAAATTCCATTTTTGACCTA
Found at i:22475713 original size:17 final size:17
Alignment explanation
Indices: 22475674--22475714 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22475664 ATATATACGG
* *
22475674 AAATGCAATGACAATGA
1 AAATGCAAAGACAATAA
*
22475691 AGATGCAAAGACAATAA
1 AAATGCAAAGACAATAA
22475708 AAATGCA
1 AAATGCA
22475715 GTGATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (17 bp):
AAATGCAAAGACAATAA
Found at i:22486673 original size:13 final size:13
Alignment explanation
Indices: 22486655--22486679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22486645 TTCATTTAAT
22486655 TAATTAATTATTC
1 TAATTAATTATTC
22486668 TAATTAATTATT
1 TAATTAATTATT
22486680 TTCTCTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTAATTATTC
Found at i:22486686 original size:17 final size:16
Alignment explanation
Indices: 22486637--22486683 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
22486627 TGCCCAAAAT
*
22486637 ATTATTTATTCATT-TA
1 ATTAATTATT-ATTCTA
22486653 ATTAATTAATTATTCTA
1 ATTAATT-ATTATTCTA
22486670 ATTAATTATT-TTCT
1 ATTAATTATTATTCT
22486684 CTATTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 12 0.43
17 12 0.43
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTAATTATTATTCTA
Found at i:22488273 original size:36 final size:35
Alignment explanation
Indices: 22488226--22488298 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 35
22488216 AATCACTTTA
*
22488226 AAATTAAATTAATA-AAATACTATTAAGATAAGTATT
1 AAATTAAATTAATATAAAT-CTATTAAAATAA-TATT
22488262 AAATTAAATTAATATTAAATCTATTAAAATAATATT
1 AAATTAAATTAATA-TAAATCTATTAAAATAATATT
22488298 A
1 A
22488299 TTTTTGGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 19 0.56
37 11 0.32
38 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (35 bp):
AAATTAAATTAATATAAATCTATTAAAATAATATT
Found at i:22488724 original size:9 final size:9
Alignment explanation
Indices: 22488710--22488739 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22488700 AAAATATCAT
22488710 ATTAATTTA
1 ATTAATTTA
*
22488719 ATTAATTTG
1 ATTAATTTA
22488728 ATTAATTTA
1 ATTAATTTA
22488737 ATT
1 ATT
22488740 TTACTTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:22492462 original size:36 final size:36
Alignment explanation
Indices: 22492411--22492539 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 36
22492401 AATGTGAGCT
* *
22492411 CAGCTCTAATCGGATATACCAACAATGTTTTGCGCC
1 CAGCGCTAGTCGGATATACCAACAATGTTTTGCGCC
* * * * *
22492447 CAGCGCTAGTCGGATAAACCGACAAATATAAAATGTGAGCC
1 CAGCGCTAGTCGGATATACCAAC-AATGT----TTTGCGCC
* * * *
22492488 CAACTCTAGTTGAATATACCAACAATGTTTTGCGCC
1 CAGCGCTAGTCGGATATACCAACAATGTTTTGCGCC
*
22492524 CAGCGCTAGTTGGATA
1 CAGCGCTAGTCGGATA
22492540 AACCGACGAA
Statistics
Matches: 69, Mismatches: 19, Indels: 10
0.70 0.19 0.10
Matches are distributed among these distances:
36 38 0.55
37 4 0.06
40 4 0.06
41 23 0.33
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (36 bp):
CAGCGCTAGTCGGATATACCAACAATGTTTTGCGCC
Done.