Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 99 of 141
Found at i:28126469 original size:47 final size:47
Alignment explanation
Indices: 28126289--28126461 Score: 267
Period size: 47 Copynumber: 3.7 Consensus size: 47
28126279 TTTCTTCTTC
* *
28126289 CATTTTCTTTGTTTGAAACTATAACTAGTCAAAAGTTTTT-CTTGTCC
1 CATTTTCTTTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTT-TCT
* * *
28126336 CGTTTTCTCTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTCTCT
1 CATTTTCTTTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTTTCT
*
28126383 CGTTTTCTTTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTTTCT
1 CATTTTCTTTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTTTCT
*
28126430 CATTTTCTTTGTTTGAAACTATATCCAGTCAA
1 CATTTTCTTTGTTTGAAACTATAACCAGTCAA
28126462 TTTTTTTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 114 0.98
48 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (47 bp):
CATTTTCTTTGTTTGAAACTATAACCAGTCAAAAGTTTTTCCTTTCT
Found at i:28148015 original size:72 final size:73
Alignment explanation
Indices: 28147885--28148021 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 73
28147875 TAATGAGCTT
* * *
28147885 GATTGAAAAAGTATGTTTATGAAATGAGTTATGTCATTGAGCTTATGAAATGGGAATTGTAATAT
1 GATTGAAAAAGCATGTATATGAAATGAGTTA-GTCATTGAGCTTATGAAATGGAAATTGTAATAT
28147950 GTGTAAAGG
65 GTGTAAAGG
* * *
28147959 GATTGAAAAGGCATGTATATGAAATGAGTTA-TCATTGAGTTTATGAAATGGAAATTGTGATAT
1 GATTGAAAAAGCATGTATATGAAATGAGTTAGTCATTGAGCTTATGAAATGGAAATTGTAATAT
28148022 ATAACTAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 29 0.51
74 28 0.49
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (73 bp):
GATTGAAAAAGCATGTATATGAAATGAGTTAGTCATTGAGCTTATGAAATGGAAATTGTAATATG
TGTAAAGG
Found at i:28149807 original size:54 final size:54
Alignment explanation
Indices: 28149655--28149824 Score: 205
Period size: 54 Copynumber: 3.1 Consensus size: 54
28149645 GTCCTCACCT
* * *** *
28149655 GTGTAACTCACTAAGTTGCCACTCATGCCCGTGTGTTGGGCCATGTGCTAGGTC
1 GTGTAACTCACTAAGTTGCCACACACGCCCGTGTGTCAAGCCGTGTGCTAGGTC
* * *
28149709 GTCTAACTCACTAAGTTGCCACACACGCCTGTGTGTCAAACCGTGTGCTAGGTC
1 GTGTAACTCACTAAGTTGCCACACACGCCCGTGTGTCAAGCCGTGTGCTAGGTC
* * * * *
28149763 GTGTACCTCACTAAGTTGTCACACACGCCCGTGTATCAAGCCGTGTGTTAGGCC
1 GTGTAACTCACTAAGTTGCCACACACGCCCGTGTGTCAAGCCGTGTGCTAGGTC
*
28149817 ATGTAACT
1 GTGTAACT
28149825 GACTGACTTG
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (54 bp):
GTGTAACTCACTAAGTTGCCACACACGCCCGTGTGTCAAGCCGTGTGCTAGGTC
Found at i:28157642 original size:22 final size:21
Alignment explanation
Indices: 28157608--28157648 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28157598 ATTCAACCAA
*
28157608 TAAAAATGAATAAACAAAAAT
1 TAAAAATAAATAAACAAAAAT
*
28157629 TAAAAATAACATAAATAAAA
1 TAAAAATAA-ATAAACAAAA
28157649 TTATCATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAACAAAAAT
Found at i:28174278 original size:28 final size:28
Alignment explanation
Indices: 28174245--28174357 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 28
28174235 TTTTTATTAT
28174245 AATATTTTATTATTTCAGTTTATTTCAC
1 AATATTTTATTATTTCAGTTTATTTCAC
* * *
28174273 AATATTTATTTTAAGTATT-AGATATATTATACATT
1 AATATTT-TATT-A-T-TTCAG-TTTATT-T-CA-C
*
28174308 AATATTTATTTTATTATTTCAGTTCATTTCAC
1 AATA--T--TTTATTATTTCAGTTTATTTCAC
28174340 AATATTTTATTATTTCAG
1 AATATTTTATTATTTCAG
28174358 CTTTTATTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
28 20 0.31
29 3 0.05
30 2 0.03
31 3 0.05
32 11 0.17
33 3 0.05
34 3 0.05
35 10 0.15
36 3 0.05
37 2 0.03
38 3 0.05
39 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (28 bp):
AATATTTTATTATTTCAGTTTATTTCAC
Found at i:28174283 original size:32 final size:32
Alignment explanation
Indices: 28174247--28174346 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 32
28174237 TTTATTATAA
28174247 TATTTTATTATTTCAGTTTATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
* * *
28174279 TATTTTAAGTA-TT-AGATATATTATACATTAATATT
1 TATTTT-ATTATTTCAG-TTTATT-T-CA-CAATATT
*
28174314 TATTTTATTATTTCAGTTCATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
28174346 T
1 T
28174347 TATTATTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
31 2 0.04
32 20 0.37
33 6 0.11
34 6 0.11
35 18 0.33
36 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (32 bp):
TATTTTATTATTTCAGTTTATTTCACAATATT
Found at i:28174364 original size:15 final size:15
Alignment explanation
Indices: 28174344--28174372 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28174334 TTTCACAATA
28174344 TTTTATTATTTCAGC
1 TTTTATTATTTCAGC
28174359 TTTTATTATTTCAG
1 TTTTATTATTTCAG
28174373 TTTATTTCAC
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:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTTATTATTTCAGC
Found at i:28179486 original size:100 final size:100
Alignment explanation
Indices: 28179313--28179511 Score: 353
Period size: 100 Copynumber: 2.0 Consensus size: 100
28179303 TAGATATTGT
*
28179313 TGCACCCATATTTGTTAAGTCGTATGTTGCAAAGGAGAATTGCAGATAAAATTGAAAATTTTTCT
1 TGCACCCATATTTGTTAAGTCGTATGTTGCAAAGGAGAATTGCAGATAAAATTGAAAAGTTTTCT
28179378 ATTCTGGTAAGTTCTTTTTGTAATTAAAGATAAGA
66 ATTCTGGTAAGTTCTTTTTGTAATTAAAGATAAGA
** *
28179413 TGCACCCATATTTGTTAAGTCGTATGTTGCAAAGGAGAATTGTGGATTAAATTGAAAAGTTTTCT
1 TGCACCCATATTTGTTAAGTCGTATGTTGCAAAGGAGAATTGCAGATAAAATTGAAAAGTTTTCT
*
28179478 ATTCTGGTAAGTTCTTTTTGTAATTAAAGTTAAG
66 ATTCTGGTAAGTTCTTTTTGTAATTAAAGATAAG
28179512 TGGCGGGTAG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (100 bp):
TGCACCCATATTTGTTAAGTCGTATGTTGCAAAGGAGAATTGCAGATAAAATTGAAAAGTTTTCT
ATTCTGGTAAGTTCTTTTTGTAATTAAAGATAAGA
Found at i:28180678 original size:22 final size:22
Alignment explanation
Indices: 28180624--28180713 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
28180614 GCACACCTGT
**
28180624 ATATGAGAGCCCCTTGTGCGGGAC
1 ATATGAGAG-CCCTT-TATGGGAC
* *
28180648 GTATAAGAGCCCTTTATGGGAC
1 ATATGAGAGCCCTTTATGGGAC
* * * *
28180670 ATTTGAGAGCCCCTCAGGGGAC
1 ATATGAGAGCCCTTTATGGGAC
*
28180692 GTATGAGAGCCCTTTTATGGGA
1 ATATGAGAGCCC-TTTATGGGA
28180714 TGAATGGAAG
Statistics
Matches: 50, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
22 32 0.64
23 11 0.22
24 7 0.14
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.24
Consensus pattern (22 bp):
ATATGAGAGCCCTTTATGGGAC
Found at i:28206842 original size:46 final size:46
Alignment explanation
Indices: 28206790--28206945 Score: 228
Period size: 46 Copynumber: 3.5 Consensus size: 46
28206780 TGATCAGTGA
*
28206790 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
**
28206836 CAAGTGACAAAGTGATAAGTGACAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* * *
28206882 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCGATACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
28206927 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
28206946 ATCATACGTA
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
43 12 0.12
44 5 0.05
45 17 0.17
46 67 0.66
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:28212486 original size:24 final size:24
Alignment explanation
Indices: 28212439--28212486 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28212429 GATGAATTAT
* *
28212439 AATTTAAAGTATATTGGTTGAATA
1 AATTTAAAGTATAATGATTGAATA
28212463 AATTTAAAGTATGAATGATT-AATA
1 AATTTAAAGTAT-AATGATTGAATA
28212487 TACTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTTAAAGTATAATGATTGAATA
Found at i:28214131 original size:147 final size:147
Alignment explanation
Indices: 28213864--28214152 Score: 533
Period size: 147 Copynumber: 2.0 Consensus size: 147
28213854 GAAAGTTTCG
* *
28213864 AAGAATGTTACTGAAGTGCGGAGTTTTCTAGGATTGGCAGGTTATTATCGCCGATTTGTCAAAGA
1 AAGAATGTTACTGAAGTACGGAGCTTTCTAGGATTGGCAGGTTATTATCGCCGATTTGTCAAAGA
*
28213929 TTTCTCAATGATTACCTTACCGTTGACTCGATTACTACAAAAGAATGTTGAATTTATATGATCCG
66 TTTCTCAATGATTACCTTACCGTTGACTCGATTACTACAAAAGAATGTTGAATTTATATGATCAG
*
28213994 ATGAATGTCAGCCTCCA
131 ACGAATGTCAGCCTCCA
28214011 AAGAATGTTACTGAAGTACGGAGCTTTCTAGGATTGGCAGGTTATTATCGCCGATTTGTCAAAGA
1 AAGAATGTTACTGAAGTACGGAGCTTTCTAGGATTGGCAGGTTATTATCGCCGATTTGTCAAAGA
*
28214076 TTTCTCAATGATTACCTTACCGTTGACTCGATTACTACAAAAGAATGTTGAATTTATATGGTCAG
66 TTTCTCAATGATTACCTTACCGTTGACTCGATTACTACAAAAGAATGTTGAATTTATATGATCAG
28214141 ACGAATGTCAGC
131 ACGAATGTCAGC
28214153 AGAGTTTCGA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 137 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (147 bp):
AAGAATGTTACTGAAGTACGGAGCTTTCTAGGATTGGCAGGTTATTATCGCCGATTTGTCAAAGA
TTTCTCAATGATTACCTTACCGTTGACTCGATTACTACAAAAGAATGTTGAATTTATATGATCAG
ACGAATGTCAGCCTCCA
Found at i:28217049 original size:46 final size:46
Alignment explanation
Indices: 28216982--28217228 Score: 385
Period size: 46 Copynumber: 5.5 Consensus size: 46
28216972 TGATCAGTGA
* *
28216982 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTTCACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
* *
28217028 CAAGTGACAAAGTAATAAGTGGCAGCTTTAGCTACACTAATCTGAT
1 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
*
28217074 CAAGTGACAAAGTGATAAGTGGCAGC-TTAGCTACATTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
28217119 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
* * *
28217165 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTAAT
1 CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
*
28217210 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
28217229 ATCATACGTA
Statistics
Matches: 188, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 61 0.32
46 110 0.59
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGCAGCTTTAGCTACACTTATCTGAT
Found at i:28217138 original size:91 final size:91
Alignment explanation
Indices: 28216982--28217228 Score: 399
Period size: 91 Copynumber: 2.7 Consensus size: 91
28216972 TGATCAGTGA
* *
28216982 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTTCACTTATCTGATCAAGTGACAAAGTAATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
28217047 TGGCAGCTTTAGCTACACTAATCTGAT
65 TGGCAGCTTTAGCTACACTAATCTGAT
* *
28217074 CAAGTGACAAAGTGATAAGTGGCAGCTTAGCTACATTTATCTGATCAAGTGACAAAGTGATAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
28217139 GGCAGCTTTAGCTACACTTATCTGAT
66 GGCAGCTTTAGCTACACTAATCTGAT
* * *
28217165 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTAATC-AGGGAC-AAGTGATAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
28217228 G
66 G
28217229 ATCATACGTA
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
89 12 0.08
90 5 0.03
91 103 0.71
92 25 0.17
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
GGCAGCTTTAGCTACACTAATCTGAT
Found at i:28223780 original size:17 final size:17
Alignment explanation
Indices: 28223758--28223803 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
28223748 GTAAATTGCA
*
28223758 AGCTCACCAGAACTACG
1 AGCTCACCAAAACTACG
28223775 AGCTCACCAAAACTACG
1 AGCTCACCAAAACTACG
28223792 AGCTCACCAAAA
1 AGCTCACCAAAA
28223804 AATGTGAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.41, C:0.35, G:0.13, T:0.11
Consensus pattern (17 bp):
AGCTCACCAAAACTACG
Found at i:28225470 original size:208 final size:208
Alignment explanation
Indices: 28225111--28225525 Score: 740
Period size: 208 Copynumber: 2.0 Consensus size: 208
28225101 CGAAGCCCAA
28225111 CTCGTCACACCTTGCGAACTCTCACTACAGCAAAATAGACTTTTAGCGGCGTTTTTTAGGCCTTT
1 CTCGTCACACCTTGCGAACTCTCACTACAGCAAAATAGACTTTTAGCGGCGTTTTTTAGGCCTTT
28225176 AGCGGCGCTTTTAAGCGTCAGCAAAAAGCATTTATGTGAACAAATGCCGCTAAAGATCATGACCT
66 AGCGGCGCTTTTAAGCGTCAGCAAAAAGCATTTATGTGAACAAATGCCGCTAAAGATCATGACCT
* * *
28225241 TTAGCGGCGCTTTTATCACAAACGCCGTTAAAGATCTTAACCTATAGCGGCGCTAGCGACACAAA
131 TTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATAACCTATAGCGGCGCTAGCGACACAAA
28225306 CGCCGCTAAAGAT
196 CGCCGCTAAAGAT
28225319 CTCGTCACACCTTGCGAACTCTCACTACAGCAAAATAGACTTTTAGCGGCGTTTTTTAGGCCTTT
1 CTCGTCACACCTTGCGAACTCTCACTACAGCAAAATAGACTTTTAGCGGCGTTTTTTAGGCCTTT
28225384 AGCGGCGCTTTTAAGCGTCAGCAAAAAGCATTTATGTGAACAAATGCCGCTAAAGATCATGACCT
66 AGCGGCGCTTTTAAGCGTCAGCAAAAAGCATTTATGTGAACAAATGCCGCTAAAGATCATGACCT
* * * *** *
28225449 TTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTCACAAA
131 TTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATAACCTATAGCGGCGCTAGCGACACAAA
28225514 CGCCGCTAAAGA
196 CGCCGCTAAAGA
28225526 ACATGACCTT
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
208 197 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (208 bp):
CTCGTCACACCTTGCGAACTCTCACTACAGCAAAATAGACTTTTAGCGGCGTTTTTTAGGCCTTT
AGCGGCGCTTTTAAGCGTCAGCAAAAAGCATTTATGTGAACAAATGCCGCTAAAGATCATGACCT
TTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACATAACCTATAGCGGCGCTAGCGACACAAA
CGCCGCTAAAGAT
Found at i:28225488 original size:43 final size:43
Alignment explanation
Indices: 28225423--28225664 Score: 319
Period size: 43 Copynumber: 5.7 Consensus size: 43
28225413 ATTTATGTGA
* *
28225423 ACAAATGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTGTC
1 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
28225466 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
1 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
*
28225509 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTGTC
1 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
* * * * *
28225552 ACAAATGCCGCTAAAGATCTTGACCTTTAGCAGTGCTTTTGTC
1 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
* * *
28225595 ACAAACGCCGCGAAAGAACA-AACCTTTAGCGGTGCTTCTTG-C
1 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT-TTGTC
* * * *
28225637 AAAAACGTCGCTAAA-AACGTAACCTTTA
1 ACAAACGCCGCTAAAGAACATGACCTTTA
28225665 AAAAATATAT
Statistics
Matches: 178, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
41 3 0.02
42 36 0.20
43 139 0.78
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGTC
Found at i:28227282 original size:17 final size:18
Alignment explanation
Indices: 28227244--28227283 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
28227234 CAACCCACAA
28227244 ATTTTTTATTATTTTTCT
1 ATTTTTTATTATTTTTCT
28227262 -TTTTTT-TGTATTTTT-T
1 ATTTTTTAT-TATTTTTCT
28227278 ATTTTT
1 ATTTTT
28227284 GCACTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (18 bp):
ATTTTTTATTATTTTTCT
Found at i:28239589 original size:41 final size:41
Alignment explanation
Indices: 28239498--28239624 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
28239488 TTTAAATAGA
*
28239498 TTCACCGGCACTTAGCCTGCTAGACTTAAAGTCTG-ATTCAG-
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAATT--GT
* * * * *
28239539 TACATCGGCACTTAGCCTTCTAGACATATAGTCTGAAATGT
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAATTGT
* *
28239580 TTCACCGGCAATAAGCCTGCTAGACATAAAGTCTGATATTGT
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGA-ATTGT
28239622 TTC
1 TTC
28239625 TCTGGAAATA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 60 0.86
42 9 0.13
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAATTGT
Found at i:28239636 original size:42 final size:41
Alignment explanation
Indices: 28239552--28239646 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
28239542 ATCGGCACTT
* * *
28239552 AGCCTTCTAGACATATAGTCTGAAATGTTTCACCGGCAATA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGAAATA
* * *
28239593 AGCCTGCTAGACATAAAGTCTGATATTGTTTCTCTGGAAATA
1 AGCCTGCTAGACATAAAGTCTGA-AATGTTTCACCGGAAATA
28239635 AGCCTGCTAGAC
1 AGCCTGCTAGAC
28239647 GCTAAGCCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 21 0.45
42 26 0.55
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGAAATA
Found at i:28249106 original size:41 final size:42
Alignment explanation
Indices: 28249044--28249149 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 42
28249034 AGATTCAATA
* * * *
28249044 CACCGGCACTTAGCCTTCTAGACATATAGTCTGA-AATGTTT
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTGATAATGTTT
* * *
28249085 CACCGGCAATAAGCCTGCTAGACGTAAATTCTGATATTGTTT
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTGATAATGTTT
* *
28249127 CACTGGTAATAAGCCTGCTAGAC
1 CACCGGCAATAAGCCTGCTAGAC
28249150 GCTAAGCCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
41 28 0.51
42 27 0.49
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (42 bp):
CACCGGCAATAAGCCTGCTAGACATAAAGTCTGATAATGTTT
Found at i:28253107 original size:18 final size:19
Alignment explanation
Indices: 28253067--28253110 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
28253057 AAATTACAAA
*
28253067 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTAT
*
28253085 TAAAATTCAAAAT-ATTAT
1 AAAAATTCAAAATAATTAT
28253103 AAAAATTC
1 AAAAATTC
28253111 TCAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATAATTAT
Found at i:28253125 original size:18 final size:18
Alignment explanation
Indices: 28253068--28253125 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
28253058 AATTACAAAA
28253068 AAAATT-AAAATAATTTTT
1 AAAATTCAAAAT-ATTTTT
* *
28253086 AAAATTCAAAATATTATA
1 AAAATTCAAAATATTTTT
** *
28253104 AAAATTCTCAATTTTTTT
1 AAAATTCAAAATATTTTT
28253122 AAAA
1 AAAA
28253126 AAATTACAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTCAAAATATTTTT
Found at i:28254784 original size:20 final size:21
Alignment explanation
Indices: 28254751--28254790 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28254741 ATCTTAACTT
28254751 TTTTATACATTTTTTTAAAAA
1 TTTTATACATTTTTTTAAAAA
28254772 TTTTATA-ATTTTTTTAAAA
1 TTTTATACATTTTTTTAAAA
28254791 CTATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATACATTTTTTTAAAAA
Found at i:28254846 original size:21 final size:21
Alignment explanation
Indices: 28254801--28254850 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
28254791 CTATAAATTT
*
28254801 TAATTTTTTATAAATATTTTG
1 TAATTTTTGATAAATATTTTG
28254822 -AATTTTTGA-AAATTATTTTG
1 TAATTTTTGATAAA-TATTTTG
28254842 TAATTTTTG
1 TAATTTTTG
28254851 TTGAGAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (21 bp):
TAATTTTTGATAAATATTTTG
Found at i:28254991 original size:14 final size:14
Alignment explanation
Indices: 28254972--28255000 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28254962 GAATCGAATA
28254972 ATTCGATTAACTTG
1 ATTCGATTAACTTG
28254986 ATTCGATTAACTTG
1 ATTCGATTAACTTG
28255000 A
1 A
28255001 AATTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (14 bp):
ATTCGATTAACTTG
Found at i:28264059 original size:104 final size:104
Alignment explanation
Indices: 28263898--28264085 Score: 295
Period size: 104 Copynumber: 1.8 Consensus size: 104
28263888 CTCACACAGC
* * * * *
28263898 CTGGGCACACGCCCATATCCCTGGCCGTGTGATTCTAAATCATAAACAGTGAGTTACACGGCTTG
1 CTGGGCACACACCCATATCCCTGACCGTGTGATTCCAAATCATAAACAGTGAGTTACAAGGCCTG
*
28263963 GACACACGTCCATATCCTTTCCCGTTTGGCTTACACGAA
66 GACACACGCCCATATCCTTTCCCGTTTGGCTTACACGAA
* *
28264002 CTGGGCACACATCCATATCCCTGACCGTGTGATTCCAAATCATAAATAGTGAGTTACAAGGCCTG
1 CTGGGCACACACCCATATCCCTGACCGTGTGATTCCAAATCATAAACAGTGAGTTACAAGGCCTG
*
28264067 GACACACGCCCATGTCCTT
66 GACACACGCCCATATCCTT
28264086 GCCCATGAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 75 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.25
Consensus pattern (104 bp):
CTGGGCACACACCCATATCCCTGACCGTGTGATTCCAAATCATAAACAGTGAGTTACAAGGCCTG
GACACACGCCCATATCCTTTCCCGTTTGGCTTACACGAA
Found at i:28274677 original size:18 final size:19
Alignment explanation
Indices: 28274629--28274677 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
28274619 AATTTATATG
*
28274629 AAAATCCTTGAA-AGATTT
1 AAAATCCCTGAAGAGATTT
*
28274647 AAAATCCCAGAAGA-ATTT
1 AAAATCCCTGAAGAGATTT
28274665 AAAATCCCTGAAG
1 AAAATCCCTGAAG
28274678 TATATAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAATCCCTGAAGAGATTT
Found at i:28274685 original size:18 final size:18
Alignment explanation
Indices: 28274623--28274685 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
28274613 TAGTGAAATT
*
28274623 TATATGAAAATCCTTGAAAG
1 TATAT-AAAATCCCTG-AAG
* *
28274643 -ATTTAAAATCCCAGAAG
1 TATATAAAATCCCTGAAG
* *
28274660 AATTTAAAATCCCTGAAG
1 TATATAAAATCCCTGAAG
28274678 TATATAAA
1 TATATAAA
28274686 GTTTCTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.08
18 30 0.83
19 3 0.08
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.29
Consensus pattern (18 bp):
TATATAAAATCCCTGAAG
Found at i:28276154 original size:47 final size:46
Alignment explanation
Indices: 28276093--28276186 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 46
28276083 ATCATTTGAT
* * *
28276093 AAAATGGATGTTCATAACGCCC-AATTCCATTCTATTGTAACCCCTAA
1 AAAATGAATATTCATAAC-CCCTAATT-CATTATATTGTAACCCCTAA
*
28276140 AAAATGAATATTCATAACCCCTAATTCATTATCTTGTAACCCCTAA
1 AAAATGAATATTCATAACCCCTAATTCATTATATTGTAACCCCTAA
28276186 A
1 A
28276187 TAATTTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
46 22 0.52
47 20 0.48
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (46 bp):
AAAATGAATATTCATAACCCCTAATTCATTATATTGTAACCCCTAA
Found at i:28276563 original size:24 final size:24
Alignment explanation
Indices: 28276534--28276579 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
28276524 ATAAGAAAAG
28276534 TAAAAGAACACTTGAATCTCACGA
1 TAAAAGAACACTTGAATCTCACGA
28276558 TAAAAGAACACTTGAATCTCAC
1 TAAAAGAACACTTGAATCTCAC
28276580 CATCCTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
TAAAAGAACACTTGAATCTCACGA
Found at i:28277051 original size:30 final size:28
Alignment explanation
Indices: 28277015--28277079 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
28277005 CTTGAAAATT
*
28277015 AATTTTATTTAATTATAAAATATATTCAT-A
1 AATTTTATTTAATCA-AAAATAT-TT-ATAA
*
28277045 AATTTTATTTTATCAAAAATATTTATAA
1 AATTTTATTTAATCAAAAATATTTATAA
28277073 AATTTTA
1 AATTTTA
28277080 CAAATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.06
28 10 0.31
29 7 0.22
30 13 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTTTATTTAATCAAAAATATTTATAA
Found at i:28277066 original size:27 final size:28
Alignment explanation
Indices: 28277027--28277079 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28277017 TTTTATTTAA
28277027 TTATAAAATATATTCAT-AAATTTTATT
1 TTATAAAATATATTCATAAAATTTTATT
*
28277054 TTATCAAAA-ATATTTATAAAATTTTA
1 TTAT-AAAATATATTCATAAAATTTTA
28277080 CAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TTATAAAATATATTCATAAAATTTTATT
Found at i:28284437 original size:14 final size:14
Alignment explanation
Indices: 28284418--28284454 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
28284408 TGAGTACTTT
*
28284418 AAATATGTTTATTC
1 AAATATGTGTATTC
28284432 AAATATTGTGTATTC
1 AAATA-TGTGTATTC
28284447 AAATATGT
1 AAATATGT
28284455 CTACCATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (14 bp):
AAATATGTGTATTC
Found at i:28286428 original size:20 final size:20
Alignment explanation
Indices: 28286390--28286431 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28286380 TACAACACAA
* *
28286390 TTCAATTTTATATTTAATAT
1 TTCAATTTTATACTCAATAT
*
28286410 TTCAATTTTTTACTCAATAT
1 TTCAATTTTATACTCAATAT
28286430 TT
1 TT
28286432 GTCTCATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
TTCAATTTTATACTCAATAT
Found at i:28288907 original size:37 final size:37
Alignment explanation
Indices: 28288865--28289021 Score: 197
Period size: 37 Copynumber: 4.2 Consensus size: 37
28288855 TCAGTTTGAT
* * * *
28288865 TAGCTCTTATGAGCATCTAACGTGCTATTGGGTGGAC
1 TAGCTCTTATGAGCATCTAGCATGTTATCGGGTGGAC
*
28288902 TAGCTCTTATGAGCATCTAGCTTGTTATCGGGTGGAC
1 TAGCTCTTATGAGCATCTAGCATGTTATCGGGTGGAC
*
28288939 TAGCTCTTATGAGCATCTAGCATGTTATCGAGTGGAC
1 TAGCTCTTATGAGCATCTAGCATGTTATCGGGTGGAC
* ** * * * *
28288976 TAGCTCTTATTAGCGCCTGGCGTGTTATCGAGTGGAT
1 TAGCTCTTATGAGCATCTAGCATGTTATCGGGTGGAC
28289013 TAGCTCTTA
1 TAGCTCTTA
28289022 CGAGTGATTG
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 108 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (37 bp):
TAGCTCTTATGAGCATCTAGCATGTTATCGGGTGGAC
Found at i:28289034 original size:37 final size:36
Alignment explanation
Indices: 28288896--28289038 Score: 142
Period size: 37 Copynumber: 3.9 Consensus size: 36
28288886 GTGCTATTGG
* * * *
28288896 GTGGACTAGCTCTTATGAGCATCTAGCTTGTTATCGG
1 GTGGACTAGCTCTTATGAGGAT-TGGCGTGTTATCGA
* * *
28288933 GTGGACTAGCTCTTATGAGCATCTAGCATGTTATCGA
1 GTGGACTAGCTCTTATGAGGAT-TGGCGTGTTATCGA
* **
28288970 GTGGACTAGCTCTTATTAGCGCCTGGCGTGTTATCGA
1 GTGGACTAGCTCTTATGAG-GATTGGCGTGTTATCGA
* *
28289007 GTGGATTAGCTCTTACGAGTGATTGGCGTGTT
1 GTGGACTAGCTCTTATGAG-GATTGGCGTGTT
28289039 TCGGTTGGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (36 bp):
GTGGACTAGCTCTTATGAGGATTGGCGTGTTATCGA
Found at i:28299969 original size:51 final size:51
Alignment explanation
Indices: 28299914--28300070 Score: 114
Period size: 51 Copynumber: 3.1 Consensus size: 51
28299904 TTTCAACATG
28299914 ACATAACATCACAAATATTTCAATTACTTATACTTACCTATTTAACTCATT
1 ACATAACATCACAAATATTTCAATTACTTATACTTACCTATTTAACTCATT
* * ** * * * * *
28299965 ACATATC-CCAAGCAAGCA-ATCAA-TAC--A-AGCTAAAACATGTTTTCAA--CATG
1 ACATAACATC-A-CAAATATTTCAATTACTTATA-CT--TACCT-ATTT-AACTCATT
28300015 ACATAACATCACAAATATTTCAATTACTTATACTTACCTATTTAACTCATT
1 ACATAACATCACAAATATTTCAATTACTTATACTTACCTATTTAACTCATT
28300066 ACATA
1 ACATA
28300071 TCCCAAGCAA
Statistics
Matches: 73, Mismatches: 18, Indels: 30
0.60 0.15 0.25
Matches are distributed among these distances:
47 1 0.01
48 3 0.04
49 6 0.08
50 24 0.33
51 29 0.40
52 6 0.08
53 3 0.04
54 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.33
Consensus pattern (51 bp):
ACATAACATCACAAATATTTCAATTACTTATACTTACCTATTTAACTCATT
Found at i:28300038 original size:50 final size:50
Alignment explanation
Indices: 28299883--28300139 Score: 110
Period size: 50 Copynumber: 5.1 Consensus size: 50
28299873 AAGCAATCAA
28299883 TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
1 TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
* * * * * * ** *
28299933 TCAATTACTTATA-CT--TACCT-ATTT-AACTCATTACATATC-CCAAGCAAGCA-A
1 TCAA-TAC--A-AGCTAAAACATGTTTTCAA--CATGACATAACATC-A-CAAATATT
28299984 TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
1 TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
* * * * * * ** *
28300034 TCAATTACTTATA-CT--TACCT-ATTT-AACTCATTACATATC-CCAAGCAAGCAAT
1 TCAA-TAC--A-AGCTAAAACATGTTTTCAA--CATGACATAACATC-A-CAAATATT
28300086 -CAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
1 TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
28300135 TCAAT
1 TCAAT
28300140 TACTTATACT
Statistics
Matches: 141, Mismatches: 36, Indels: 60
0.59 0.15 0.25
Matches are distributed among these distances:
47 2 0.01
48 6 0.04
49 13 0.09
50 52 0.37
51 47 0.33
52 13 0.09
53 6 0.04
54 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.30
Consensus pattern (50 bp):
TCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATATT
Found at i:28300041 original size:101 final size:101
Alignment explanation
Indices: 28299866--28300166 Score: 593
Period size: 101 Copynumber: 3.0 Consensus size: 101
28299856 ATACACCAAT
*
28299866 ATATCCCAAGCAATCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
1 ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
28299931 TTTCAATTACTTATACTTACCTATTTAACTCATTAC
66 TTTCAATTACTTATACTTACCTATTTAACTCATTAC
28299967 ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
1 ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
28300032 TTTCAATTACTTATACTTACCTATTTAACTCATTAC
66 TTTCAATTACTTATACTTACCTATTTAACTCATTAC
28300068 ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
1 ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
28300133 TTTCAATTACTTATACTTACCTATTTAACTCATT
66 TTTCAATTACTTATACTTACCTATTTAACTCATT
28300167 TCATTGATTT
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 199 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.31
Consensus pattern (101 bp):
ATATCCCAAGCAAGCAATCAATACAAGCTAAAACATGTTTTCAACATGACATAACATCACAAATA
TTTCAATTACTTATACTTACCTATTTAACTCATTAC
Found at i:28300708 original size:33 final size:32
Alignment explanation
Indices: 28300671--28300747 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
28300661 ATGCATTGCC
* * *
28300671 ATGGTCTTACATTTGTAGTGCCATAAG-CCAGTT
1 ATGGTCTTACATCTG-AATGCCAT-AGCCCAGCT
*
28300704 ATGGTCTTATCATCTGAATGCCATAGCCCGGCT
1 ATGGTCTTA-CATCTGAATGCCATAGCCCAGCT
28300737 ATGGTCTTACA
1 ATGGTCTTACA
28300748 CATGTATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 4 0.11
33 29 0.76
34 5 0.13
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (32 bp):
ATGGTCTTACATCTGAATGCCATAGCCCAGCT
Found at i:28310666 original size:45 final size:45
Alignment explanation
Indices: 28310603--28310772 Score: 209
Period size: 45 Copynumber: 3.8 Consensus size: 45
28310593 TACACGATGG
* * * *
28310603 ATCAACACATAG-AACCACCCTTATAATCAATTATATTCGGTCGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATGATATTCGGTGGA
**
28310647 ATCAGCACATAGCAACCACCTTTATTTTCAATGAT-TTCCGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATGATATT-CGGTGGA
* * * **
28310692 GTCAGCACATAGCAACCACCTTTATAATCGATGGTACCCGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATGATATTCGGTGGA
*
28310737 ATCAGCACATAGCAACCACCTTTATAATCAACGATA
1 ATCAGCACATAGCAACCACCTTTATAATCAATGATA
28310773 CTCAGTACAC
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 13 0.12
45 93 0.88
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATGATATTCGGTGGA
Found at i:28312482 original size:144 final size:144
Alignment explanation
Indices: 28312255--28312530 Score: 385
Period size: 144 Copynumber: 1.9 Consensus size: 144
28312245 GCACAAATTC
* * * *
28312255 CGTTGGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCTTTGGTTTATTCGACTAGTGTTGA
1 CGTTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATTCGACTAGCGTTGA
* * **
28312320 GCACAACTTTCTTTAATTTATCTGACTAGTGCT-GGTCACACATTCGTCGATTTATCCGGTTAGC
66 GCACAACTTTCATCAATTTATCTGACTAGTGCTAGGT-ACACATTCGTCGATTTATCCGACTAGC
28312384 ACTAGGTGCAAATGT
130 ACTAGGTGCAAATGT
28312399 CGTTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTA-TCTGACTAGCGTTG
1 CGTTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATTC-GACTAGCGTTG
* ** ** * *
28312463 GGTGCAACTTTCATCAATTTATCTGACTAGTTTTAGGTAGACATTCGTCTATTTATCCGACTAGC
65 AGCACAACTTTCATCAATTTATCTGACTAGTGCTAGGTACACATTCGTCGATTTATCCGACTAGC
28312528 ACT
130 ACT
28312531 GTGGGCAAAC
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
143 2 0.02
144 110 0.96
145 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (144 bp):
CGTTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATTCGACTAGCGTTGA
GCACAACTTTCATCAATTTATCTGACTAGTGCTAGGTACACATTCGTCGATTTATCCGACTAGCA
CTAGGTGCAAATGT
Found at i:28312484 original size:75 final size:75
Alignment explanation
Indices: 28312261--28312485 Score: 185
Period size: 75 Copynumber: 3.1 Consensus size: 75
28312251 ATTCCGTTGG
* * * * **
28312261 TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCTTTGGTTTAT-TCGACTAGTGTTGAGCACA
1 TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATCT-GACTAGCGTTGGGTGCA
*
28312325 ACTTTCTTTAA
65 ACTTTCATTAA
** * * * * ** ** *
28312336 TTTATCTGACTAGTGCT-GG-TCAC--A-CA-TTCGTCGATTTATCCGGTTAGCACTAGGTGCAA
1 TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATCTGACTAGCGTTGGGTGCAA
* * * *
28312395 ATGTCGTTAG
66 CTTTCATTAA
28312405 TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATCTGACTAGCGTTGGGTGCAA
1 TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATCTGACTAGCGTTGGGTGCAA
*
28312470 CTTTCATCAA
66 CTTTCATTAA
28312480 TTTATC
1 TTTATC
28312486 TGACTAGTTT
Statistics
Matches: 106, Mismatches: 37, Indels: 14
0.68 0.24 0.09
Matches are distributed among these distances:
69 39 0.37
70 3 0.03
71 5 0.05
73 5 0.05
74 3 0.03
75 51 0.48
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (75 bp):
TTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTCGGTTTATCTGACTAGCGTTGGGTGCAA
CTTTCATTAA
Found at i:28317452 original size:5 final size:5
Alignment explanation
Indices: 28317442--28317480 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
28317432 CAAATATGTT
*
28317442 TTTTA TTTTA TTTTA TTATA TTTT- TGTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTT
28317481 CTCTATCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:28320067 original size:21 final size:21
Alignment explanation
Indices: 28320028--28320067 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28320018 AGCAGGAGGT
**
28320028 TGCCTCAACTCAATGACAAAC
1 TGCCTCAACTCAACAACAAAC
*
28320049 TGCCTCAACTCACCAACAA
1 TGCCTCAACTCAACAACAA
28320068 GATGTTACCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.17
Consensus pattern (21 bp):
TGCCTCAACTCAACAACAAAC
Found at i:28322487 original size:23 final size:23
Alignment explanation
Indices: 28322438--28322488 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
28322428 ACCTACTTTC
* * * *
28322438 TTACTGTAGTAATTTTCGGGGTG
1 TTACAGTAGTAATTTTCGAGATA
28322461 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
28322484 TTACA
1 TTACA
28322489 TGCCTTCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:28323500 original size:14 final size:13
Alignment explanation
Indices: 28323481--28323533 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 13
28323471 CATCTCTATT
28323481 TTTTTCTTTTCTCC
1 TTTTTCTTTTCT-C
28323495 TTTTTCTTCTTCTTC
1 TTTTTCTT-TTC-TC
28323510 TTCTCTTCTTTGTCTC
1 TT-T-TTCTTT-TCTC
28323526 TTTTTCTT
1 TTTTTCTT
28323534 CTTTTGCTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 13 0.38
15 7 0.21
16 7 0.21
17 7 0.21
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:28323533 original size:17 final size:16
Alignment explanation
Indices: 28323473--28323538 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
28323463 ACAGTTGGCA
*
28323473 TCTCTATTTTTTTCTTT
1 TCTCT-TTTTCTTCTTT
*
28323490 TCTCCTTTTTCTTCTTC
1 TCT-CTTTTTCTTCTTT
*
28323507 T-TC-TTCTCTTCTTT
1 TCTCTTTTTCTTCTTT
28323521 GTCTCTTTTTCTTCTTT
1 -TCTCTTTTTCTTCTTT
28323538 T
1 T
28323539 GCTGCCTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
16 4 0.10
17 23 0.57
18 2 0.05
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.71
Consensus pattern (16 bp):
TCTCTTTTTCTTCTTT
Found at i:28325686 original size:22 final size:21
Alignment explanation
Indices: 28325656--28325713 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
28325646 ATGCAATCGT
*
28325656 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
28325677 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
28325700 AGATTTGATTTGTA
1 AGATTTGATTTGTA
28325714 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:28325696 original size:23 final size:22
Alignment explanation
Indices: 28325666--28325710 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
28325656 AGATTTGATA
28325666 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
28325689 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
28325711 GTAGATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:28326104 original size:13 final size:13
Alignment explanation
Indices: 28326086--28326112 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28326076 GACAGTATGT
28326086 TTTTAAGTATCTG
1 TTTTAAGTATCTG
28326099 TTTTAAGTATCTG
1 TTTTAAGTATCTG
28326112 T
1 T
28326113 CTTACCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTTAAGTATCTG
Found at i:28326770 original size:18 final size:18
Alignment explanation
Indices: 28326747--28326785 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28326737 TTTACCAACT
28326747 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
28326765 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
28326783 TTA
1 TTA
28326786 AAGATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (18 bp):
TTATGGATAATAATTTAA
Found at i:28326791 original size:18 final size:18
Alignment explanation
Indices: 28326752--28326791 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28326742 CAACTTTATG
**
28326752 GATAATAATTTAATTATG
1 GATAATAATTTAATTAAA
28326770 GATAATAATTTAATTAAA
1 GATAATAATTTAATTAAA
28326788 GATA
1 GATA
28326792 CAACATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
GATAATAATTTAATTAAA
Found at i:28327169 original size:14 final size:15
Alignment explanation
Indices: 28327147--28327223 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
28327137 CAATTAAACA
28327147 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
28327161 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
28327176 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
28327196 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
28327210 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
28327224 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:28327188 original size:20 final size:20
Alignment explanation
Indices: 28327163--28327202 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28327153 AATATTTTCC
*
28327163 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28327183 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28327203 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28327208 original size:34 final size:35
Alignment explanation
Indices: 28327151--28327217 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28327141 TAAACACCAG
*
28327151 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28327186 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28327218 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28327224 original size:14 final size:14
Alignment explanation
Indices: 28327186--28327225 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28327176 ACAGAAAAGT
*
28327186 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
28327200 AAATCATTTTACGG
1 AAAACATTTTACAG
28327214 AAAACATTTTAC
1 AAAACATTTTAC
28327226 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28335910 original size:19 final size:19
Alignment explanation
Indices: 28335886--28335926 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
28335876 TATTTCAAAG
28335886 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
28335905 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
28335924 TTA
1 TTA
28335927 GAATAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:28338896 original size:42 final size:42
Alignment explanation
Indices: 28338758--28338972 Score: 276
Period size: 42 Copynumber: 5.2 Consensus size: 42
28338748 TTTAAACAGA
* * * *
28338758 TTCACTGGCACTT-AGCCTGCTAGACTTAAAGCCTG--ATTCAG
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAAATT-AT
* * * * * *
28338799 TACACTGGCATTTAGCCTGCTAGACATATAGTCTGAAA-TGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
*
28338840 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
28338882 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
*
28338924 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
28338966 TTCACCG
1 TTCACCG
28338973 ACAATAAACC
Statistics
Matches: 157, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.01
41 61 0.39
42 93 0.59
43 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
Found at i:28339509 original size:2 final size:2
Alignment explanation
Indices: 28339502--28339526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28339492 AATCTTAAGT
28339502 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28339527 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28342976 original size:41 final size:41
Alignment explanation
Indices: 28342931--28343025 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
28342921 AGATATTTTA
*
28342931 GGAA-TATTTTATTTTATCTTTTAGTAGTATATCAGAATAAG
1 GGAATTATTTT-TCTTATCTTTTAGTAGTATATCAGAATAAG
* *
28342972 GGAATTATTTTTCTTATCTTTTAGTAGTTTATTAGAATAAG
1 GGAATTATTTTTCTTATCTTTTAGTAGTATATCAGAATAAG
*
28343013 GAAATTATTTTTC
1 GGAATTATTTTTC
28343026 CAATTAGGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 43 0.88
42 6 0.12
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (41 bp):
GGAATTATTTTTCTTATCTTTTAGTAGTATATCAGAATAAG
Found at i:28359262 original size:33 final size:33
Alignment explanation
Indices: 28359225--28359288 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
28359215 AAACACTACT
* *
28359225 ATAAATATAGTAAATGTTTTATTATATTAAAAA
1 ATAAATATAATAAATATTTTATTATATTAAAAA
*
28359258 ATAAATATAATAAATATTTTATTGTATTAAA
1 ATAAATATAATAAATATTTTATTATATTAAA
28359289 TATAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (33 bp):
ATAAATATAATAAATATTTTATTATATTAAAAA
Found at i:28365792 original size:25 final size:25
Alignment explanation
Indices: 28365738--28365809 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
28365728 AGTACTCTCT
*
28365738 CGAGCCATATAATAGGAAGCTCATG
1 CGAGCCATATAATAGGAAGCTCATC
* * *
28365763 TGAGCCATGTAATAGGAAGCTTATC
1 CGAGCCATATAATAGGAAGCTCATC
* *
28365788 CGAG-C-TATAACAGGAAACTCAT
1 CGAGCCATATAATAGGAAGCTCAT
28365810 AAGAGTTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 13 0.34
24 1 0.03
25 24 0.63
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (25 bp):
CGAGCCATATAATAGGAAGCTCATC
Found at i:28381086 original size:14 final size:14
Alignment explanation
Indices: 28381063--28381096 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28381053 TTAAAATTTG
28381063 AGTTTAAGATTTAA
1 AGTTTAAGATTTAA
* *
28381077 GGTTTTAGATTTAA
1 AGTTTAAGATTTAA
28381091 AGTTTA
1 AGTTTA
28381097 GGGTCTCGAA
Statistics
Matches: 16, Mismatches: 4, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
AGTTTAAGATTTAA
Found at i:28381980 original size:47 final size:47
Alignment explanation
Indices: 28381919--28382009 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
28381909 GTAATAAGGC
* * *
28381919 GAATCATTGTTCAATGAGATTGTTTGGGATTATGATCAGTATGTGTA
1 GAATAATTGTTCAATGAAATCGTTTGGGATTATGATCAGTATGTGTA
28381966 GAATAATTGTTCAATGAAATCGTTTGGGATTATGATCAGTATGT
1 GAATAATTGTTCAATGAAATCGTTTGGGATTATGATCAGTATGT
28382010 AAGAACTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.40
Consensus pattern (47 bp):
GAATAATTGTTCAATGAAATCGTTTGGGATTATGATCAGTATGTGTA
Found at i:28390537 original size:13 final size:13
Alignment explanation
Indices: 28390519--28390543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28390509 AAATTATCGA
28390519 GGATAACAAAGAT
1 GGATAACAAAGAT
28390532 GGATAACAAAGA
1 GGATAACAAAGA
28390544 AATTAATTTA
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:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:28394253 original size:16 final size:16
Alignment explanation
Indices: 28394232--28394266 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28394222 TTATATGATG
28394232 AAATGTCATGCAGTCA
1 AAATGTCATGCAGTCA
28394248 AAATGTCATGCAGTCA
1 AAATGTCATGCAGTCA
28394264 AAA
1 AAA
28394267 CAAAACAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (16 bp):
AAATGTCATGCAGTCA
Found at i:28397980 original size:222 final size:222
Alignment explanation
Indices: 28397594--28398040 Score: 876
Period size: 222 Copynumber: 2.0 Consensus size: 222
28397584 CACAGGCTCC
28397594 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
1 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
*
28397659 TAGGGTGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
66 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
28397724 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
131 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
28397789 ACACTATTTGTATAATGAAGGGTGTAT
196 ACACTATTTGTATAATGAAGGGTGTAT
*
28397816 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGGGT
1 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
28397881 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
66 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
28397946 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
131 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
28398011 ACACTATTTGTATAATGAAGGGTGTAT
196 ACACTATTTGTATAATGAAGGGTGTAT
28398038 TAT
1 TAT
28398041 TTACACTAAT
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 223 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (222 bp):
TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
ACACTATTTGTATAATGAAGGGTGTAT
Found at i:28399312 original size:915 final size:915
Alignment explanation
Indices: 28397816--28399607 Score: 3566
Period size: 915 Copynumber: 2.0 Consensus size: 915
28397806 AAGGGTGTAT
*
28397816 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGGGT
1 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
28397881 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
66 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
28397946 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
131 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
28398011 ACACTATTTGTATAATGAAGGGTGTATTATTTACACTAATCACAAGAGCCTTAAATATTTGTTAA
196 ACACTATTTGTATAATGAAGGGTGTATTATTTACACTAATCACAAGAGCCTTAAATATTTGTTAA
28398076 CCCTAAAATAATTAAATCTTCGGTAGCGTTGATAGGTTGAGTTACTCAAAGATTATGATTGCACG
261 CCCTAAAATAATTAAATCTTCGGTAGCGTTGATAGGTTGAGTTACTCAAAGATTATGATTGCACG
28398141 ATAGAATACCATCCGGGTATGGCTAATGTGGTAGCTGATGCCCTCAGCCGTAGAGCGATGACTGA
326 ATAGAATACCATCCGGGTATGGCTAATGTGGTAGCTGATGCCCTCAGCCGTAGAGCGATGACTGA
28398206 TCTGAGAGCAATGTTAGTTCATCTCAGTTTCGTTGAGGATGGAGGGCTGTTGGTTGAATTATTAG
391 TCTGAGAGCAATGTTAGTTCATCTCAGTTTCGTTGAGGATGGAGGGCTGTTGGTTGAATTATTAG
28398271 TAAAATCGATTTGGGTGGAGCAGATTAGAGCTAAAAAGTTGAGTGGTGAGTCGTTAGTTCAGGGT
456 TAAAATCGATTTGGGTGGAGCAGATTAGAGCTAAAAAGTTGAGTGGTGAGTCGTTAGTTCAGGGT
28398336 CTGCAGTATGTTAATTCGAACGAGACTTCTGATTTTAGCTTAAACAGCGATAATGTGTTGTGCTT
521 CTGCAGTATGTTAATTCGAACGAGACTTCTGATTTTAGCTTAAACAGCGATAATGTGTTGTGCTT
28398401 TAAAGGTCAGATTTGTGCACCTAATGATAGAGAACTGAGGCGTTCAATCCTTCAGGAGGCACATA
586 TAAAGGTCAGATTTGTGCACCTAATGATAGAGAACTGAGGCGTTCAATCCTTCAGGAGGCACATA
28398466 GTAGTCCCTATGTTATAGATCCTGGTGGGAAAAAAATGTACCGGGATCTTCGAGAGCTCTATTGG
651 GTAGTCCCTATGTTATAGATCCTGGTGGGAAAAAAATGTACCGGGATCTTCGAGAGCTCTATTGG
28398531 TGGCCCGAACCAAAATGGGAGGTATTTGCTTTTGTGTCCCACTATCTGACTTGTCAAAAGGTTAA
716 TGGCCCGAACCAAAATGGGAGGTATTTGCTTTTGTGTCCCACTATCTGACTTGTCAAAAGGTTAA
28398596 GGCAGAACATCAGTTGCCCTCCGGATTGCTTCAGCCAGTTAAGACTCCTCAGTGGAAGTGGGAGC
781 GGCAGAACATCAGTTGCCCTCCGGATTGCTTCAGCCAGTTAAGACTCCTCAGTGGAAGTGGGAGC
28398661 AGGTAACAATGGATTTTGTTAGTGGGTTGCCTAGTTTTAATATGCTCAAGTCCGTTTTGACACAG
846 AGGTAACAATGGATTTTGTTAGTGGGTTGCCTAGTTTTAATATGCTCAAGTCCGTTTTGACACAG
28398726 GCTCC
911 GCTCC
28398731 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
1 TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
*
28398796 TAGGGTGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
66 TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
28398861 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
131 TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
28398926 ACACTATTTGTATAATGAAGGGTGTATTATTTACACTAATCACAAGAGCCTTAAATATTTGTTAA
196 ACACTATTTGTATAATGAAGGGTGTATTATTTACACTAATCACAAGAGCCTTAAATATTTGTTAA
28398991 CCCTAAAATAATTAAATCTTCGGTAGCGTTGATAGGTTGAGTTACTCAAAGATTATGATTGCACG
261 CCCTAAAATAATTAAATCTTCGGTAGCGTTGATAGGTTGAGTTACTCAAAGATTATGATTGCACG
28399056 ATAGAATACCATCCGGGTATGGCTAATGTGGTAGCTGATGCCCTCAGCCGTAGAGCGATGACTGA
326 ATAGAATACCATCCGGGTATGGCTAATGTGGTAGCTGATGCCCTCAGCCGTAGAGCGATGACTGA
28399121 TCTGAGAGCAATGTTAGTTCATCTCAGTTTCGTTGAGGATGGAGGGCTGTTGGTTGAATTATTAG
391 TCTGAGAGCAATGTTAGTTCATCTCAGTTTCGTTGAGGATGGAGGGCTGTTGGTTGAATTATTAG
28399186 TAAAATCGATTTGGGTGGAGCAGATTAGAGCTAAAAAGTTGAGTGGTGAGTCGTTAGTTCAGGGT
456 TAAAATCGATTTGGGTGGAGCAGATTAGAGCTAAAAAGTTGAGTGGTGAGTCGTTAGTTCAGGGT
28399251 CTGCAGTATGTTAATTCGAACGAGACTTCTGATTTTAGCTTAAACAGCGATAATGTGTTGTGCTT
521 CTGCAGTATGTTAATTCGAACGAGACTTCTGATTTTAGCTTAAACAGCGATAATGTGTTGTGCTT
28399316 TAAAGGTCAGATTTGTGCACCTAATGATAGAGAACTGAGGCGTTCAATCCTTCAGGAGGCACATA
586 TAAAGGTCAGATTTGTGCACCTAATGATAGAGAACTGAGGCGTTCAATCCTTCAGGAGGCACATA
28399381 GTAGTCCCTATGTTATAGATCCTGGTGGGAAAAAAATGTACCGGGATCTTCGAGAGCTCTATTGG
651 GTAGTCCCTATGTTATAGATCCTGGTGGGAAAAAAATGTACCGGGATCTTCGAGAGCTCTATTGG
28399446 TGGCCCGAACCAAAATGGGAGGTATTTGCTTTTGTGTCCCACTATCTGACTTGTCAAAAGGTTAA
716 TGGCCCGAACCAAAATGGGAGGTATTTGCTTTTGTGTCCCACTATCTGACTTGTCAAAAGGTTAA
28399511 GGCAGAACATCAGTTGCCCTCCGGATTGCTTCAGCCAGTTAAGACTCCTCAGTGGAAGTGGGAGC
781 GGCAGAACATCAGTTGCCCTCCGGATTGCTTCAGCCAGTTAAGACTCCTCAGTGGAAGTGGGAGC
28399576 AGGTAACAATGGATTTTGTTAGTGGGTTGCCT
846 AGGTAACAATGGATTTTGTTAGTGGGTTGCCT
28399608 TTAAGCCCCT
Statistics
Matches: 875, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
915 875 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (915 bp):
TATCTTAGTTCAACCGAAATTGGGTCGGGAGTTTATAGTATATAGTGATGCTTCACATATCGAGT
TAGGATGTGTGCTTATGCAAGACGGTAAGGTGGTCGCTTACATGTCGCGGCAGCTCAAGACACGC
TAGGGTAACTACCCTACTTACAATCTTGAGCTAGCTGCAATTGTGTTTGCTTTGAAAATCTAGAG
ACACTATTTGTATAATGAAGGGTGTATTATTTACACTAATCACAAGAGCCTTAAATATTTGTTAA
CCCTAAAATAATTAAATCTTCGGTAGCGTTGATAGGTTGAGTTACTCAAAGATTATGATTGCACG
ATAGAATACCATCCGGGTATGGCTAATGTGGTAGCTGATGCCCTCAGCCGTAGAGCGATGACTGA
TCTGAGAGCAATGTTAGTTCATCTCAGTTTCGTTGAGGATGGAGGGCTGTTGGTTGAATTATTAG
TAAAATCGATTTGGGTGGAGCAGATTAGAGCTAAAAAGTTGAGTGGTGAGTCGTTAGTTCAGGGT
CTGCAGTATGTTAATTCGAACGAGACTTCTGATTTTAGCTTAAACAGCGATAATGTGTTGTGCTT
TAAAGGTCAGATTTGTGCACCTAATGATAGAGAACTGAGGCGTTCAATCCTTCAGGAGGCACATA
GTAGTCCCTATGTTATAGATCCTGGTGGGAAAAAAATGTACCGGGATCTTCGAGAGCTCTATTGG
TGGCCCGAACCAAAATGGGAGGTATTTGCTTTTGTGTCCCACTATCTGACTTGTCAAAAGGTTAA
GGCAGAACATCAGTTGCCCTCCGGATTGCTTCAGCCAGTTAAGACTCCTCAGTGGAAGTGGGAGC
AGGTAACAATGGATTTTGTTAGTGGGTTGCCTAGTTTTAATATGCTCAAGTCCGTTTTGACACAG
GCTCC
Found at i:28403088 original size:2 final size:2
Alignment explanation
Indices: 28403081--28403113 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28403071 TTCTTTTCTT
28403081 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28403114 TACTTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:28408513 original size:30 final size:30
Alignment explanation
Indices: 28408434--28408516 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 30
28408424 TATCACATTT
28408434 AATCTATATTTGATTTAGTGTCCAT-ATATAA
1 AATCT-TATTTGATTTAGTGTCC-TCATATAA
* * *
28408465 ATTCATATTT-AATT-GTGTCCTCATATAA
1 AATCTTATTTGATTTAGTGTCCTCATATAA
28408493 AATCTTATTTGATTTAGTGTCCTC
1 AATCTTATTTGATTTAGTGTCCTC
28408517 GTAAAGATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 1 0.02
28 20 0.47
29 6 0.14
30 13 0.30
31 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (30 bp):
AATCTTATTTGATTTAGTGTCCTCATATAA
Found at i:28408521 original size:28 final size:28
Alignment explanation
Indices: 28408434--28408521 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
28408424 TATCACATTT
28408434 AATCTATATTTGATTTAGTGTCCAT-ATATA
1 AATCT-TATTTGATTTAGTGTCC-TCATA-A
* *
28408464 AATTCATATTT-AATT-GTGTCCTCATATAA
1 AA-TCTTATTTGATTTAGTGTCCTC--ATAA
*
28408493 AATCTTATTTGATTTAGTGTCCTCGTAA
1 AATCTTATTTGATTTAGTGTCCTCATAA
28408521 A
1 A
28408522 GATTTATGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
27 1 0.02
28 17 0.36
29 9 0.19
30 18 0.38
31 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (28 bp):
AATCTTATTTGATTTAGTGTCCTCATAA
Found at i:28408599 original size:64 final size:63
Alignment explanation
Indices: 28408518--28408648 Score: 226
Period size: 64 Copynumber: 2.1 Consensus size: 63
28408508 AGTGTCCTCG
* *
28408518 TAAAGATTTATGTGCTCAACCAATTAAAGAATGGAAAAATATAAAATTTTAAAACATAACTAAA
1 TAAAGATTTATATGCTCAACCAATCAAAGAATGGAAAAATAT-AAATTTTAAAACATAACTAAA
*
28408582 TAAATATTTATATGCTCAACCAATCAAAGAATGGAAAAATATAAATTTTAAAACATAACTAAA
1 TAAAGATTTATATGCTCAACCAATCAAAGAATGGAAAAATATAAATTTTAAAACATAACTAAA
28408645 TAAA
1 TAAA
28408649 ATTAAAGTGT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
63 25 0.39
64 39 0.61
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (63 bp):
TAAAGATTTATATGCTCAACCAATCAAAGAATGGAAAAATATAAATTTTAAAACATAACTAAA
Found at i:28408672 original size:64 final size:64
Alignment explanation
Indices: 28408530--28408663 Score: 195
Period size: 64 Copynumber: 2.1 Consensus size: 64
28408520 AAGATTTATG
* * *
28408530 TGCTCAACCAATTAAAGAATGGAAAAATATAAAATTTTAAAACATAACTAAATAAATATTTATA
1 TGCTAAACCAATCAAAGAATGGAAAAATATAAAATTTTAAAACATAACTAAATAAATATTTAAA
*
28408594 TGCTCAACCAATCAAAGAATGGAAAAATAT-AAATTTTAAAACATAACTAAATAAA-A-TTAAA
1 TGCTAAACCAATCAAAGAATGGAAAAATATAAAATTTTAAAACATAACTAAATAAATATTTAAA
28408655 GTG-TAAACC
1 -TGCTAAACC
28408664 CTAAATCAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
61 9 0.14
62 3 0.05
63 25 0.38
64 29 0.44
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.27
Consensus pattern (64 bp):
TGCTAAACCAATCAAAGAATGGAAAAATATAAAATTTTAAAACATAACTAAATAAATATTTAAA
Found at i:28410967 original size:27 final size:28
Alignment explanation
Indices: 28410928--28410987 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
28410918 ACCCCGAACC
*
28410928 TTAAGGTTCAGGGTT-TGGGTTTGGGAT
1 TTAAGGTTCAGGGTTCGGGGTTTGGGAT
* *
28410955 TTAAGGTTTAGGGTTCGGGGTTTGGGGT
1 TTAAGGTTCAGGGTTCGGGGTTTGGGAT
28410983 TTAAG
1 TTAAG
28410988 ATTTGAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (28 bp):
TTAAGGTTCAGGGTTCGGGGTTTGGGAT
Found at i:28410998 original size:34 final size:34
Alignment explanation
Indices: 28410932--28411005 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
28410922 CGAACCTTAA
**
28410932 GGTTCAGGGTTTGGGTTTGGGATTTAAGGTTTAG
1 GGTTCAGGGTTTGGGTTTAAGATTTAAGGTTTAG
* *
28410966 GGTTCGGGGTTTGGGGTTTAAGATTTGA-GTTTAG
1 GGTTCAGGGTTT-GGGTTTAAGATTTAAGGTTTAG
*
28411000 AGTTCA
1 GGTTCA
28411006 AAGGTTCAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.16, C:0.04, G:0.39, T:0.41
Consensus pattern (34 bp):
GGTTCAGGGTTTGGGTTTAAGATTTAAGGTTTAG
Found at i:28411038 original size:21 final size:23
Alignment explanation
Indices: 28410994--28411040 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
28410984 TAAGATTTGA
*
28410994 GTTTAGAGTTCAAAGGTTCAAGG
1 GTTTAGAGTTCAAAGGTCCAAGG
*
28411017 GTTT-GAGTTTAAA-GTCCAAGG
1 GTTTAGAGTTCAAAGGTCCAAGG
28411038 GTT
1 GTT
28411041 CGGAGTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.34
Consensus pattern (23 bp):
GTTTAGAGTTCAAAGGTCCAAGG
Found at i:28426422 original size:58 final size:58
Alignment explanation
Indices: 28426352--28426464 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
28426342 TGATTTGATC
* * * * **
28426352 CAATTTAATACTTAAATTTTATATTTTTTCTTAATTTGGTATTTAAATTTTTTTTTCT
1 CAATTTAATACTTAAACTTGATACTTTTTCCTAATTTGGTACCTAAATTTTTTTTTCT
* * *
28426410 CAATTTAGTACTTGAACTTGGTACTTTTTCCTAATTTGGTACCTAAATTTTTTTT
1 CAATTTAATACTTAAACTTGATACTTTTTCCTAATTTGGTACCTAAATTTTTTTT
28426465 AAGTTTAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (58 bp):
CAATTTAATACTTAAACTTGATACTTTTTCCTAATTTGGTACCTAAATTTTTTTTTCT
Found at i:28433820 original size:54 final size:54
Alignment explanation
Indices: 28433762--28433864 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
28433752 TCTATTGCCC
* * * *
28433762 AAAAGTTAATTCATTGT-GCTTCCACCTCACTCTAAACATGATCACTCTTTTCCA
1 AAAAGTTAATCCATTATAG-TTCAACCTCACTCTAAACAAGATCACTCTTTTCCA
*
28433816 AAAAGTTAATCCATTATAGTTCAACCTCCCTCTAAACAAGATCACTCTT
1 AAAAGTTAATCCATTATAGTTCAACCTCACTCTAAACAAGATCACTCTT
28433865 GCTCAACAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (54 bp):
AAAAGTTAATCCATTATAGTTCAACCTCACTCTAAACAAGATCACTCTTTTCCA
Found at i:28434071 original size:139 final size:139
Alignment explanation
Indices: 28433813--28434063 Score: 360
Period size: 139 Copynumber: 1.8 Consensus size: 139
28433803 TCACTCTTTT
* *
28433813 CCAAAAAGTTAATCCATTATAGTTCAACCTCCCTCTAAACAAGATCACTCTTGCTCAACAAGTCT
1 CCAAAAAGTTAATCCATTATACTTCAACCTCACTCTAAACAAGATCACTCTTGCTCAACAAGTCT
*
28433878 CATATACTCTAAACAACATCACTCTTGCCCAAAAAGTTAATCCATTACACTTCAATTAATTAGAT
66 CATATACTCTAAACAACATCACTCTTGCCCAAAAAGTTAATCCACTACACTTCAATTAATTAGAT
28433943 TATTGTCAC
131 TATTGTCAC
* * * *
28433952 CCAAAAAGTTAATCCATTGTACTTCAACCTCATTCTAAACACGATCACTTTTGCTCAA-AAGGTC
1 CCAAAAAGTTAATCCATTATACTTCAACCTCACTCTAAACAAGATCACTCTTGCTCAACAA-GTC
* ** *** *
28434016 TCATATACTCTAAATAGGATCACTCTTGTGTAGAAAGTTAATCCACTA
65 TCATATACTCTAAACAACATCACTCTTGCCCAAAAAGTTAATCCACTA
28434064 TAGTTCAACC
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
138 2 0.02
139 95 0.98
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (139 bp):
CCAAAAAGTTAATCCATTATACTTCAACCTCACTCTAAACAAGATCACTCTTGCTCAACAAGTCT
CATATACTCTAAACAACATCACTCTTGCCCAAAAAGTTAATCCACTACACTTCAATTAATTAGAT
TATTGTCAC
Found at i:28438510 original size:18 final size:18
Alignment explanation
Indices: 28438477--28438533 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
28438467 TGATGATACG
28438477 AAAATTTGTG-AAACACGA
1 AAAATTT-TGAAAACACGA
* * *
28438495 GAATTTTTTAAAACACGA
1 AAAATTTTGAAAACACGA
*
28438513 AAAATTTTGAAAACGCGA
1 AAAATTTTGAAAACACGA
28438531 AAA
1 AAA
28438534 GTCGAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (18 bp):
AAAATTTTGAAAACACGA
Found at i:28438581 original size:20 final size:19
Alignment explanation
Indices: 28438558--28438662 Score: 58
Period size: 20 Copynumber: 5.5 Consensus size: 19
28438548 AAATACGAGG
28438558 AAATTTTTTTTAAAACACGA
1 AAATTTTTTTTAAAACAC-A
* *
28438578 AAA---TTTCTAAGACACTA
1 AAATTTTTTTTAAAACAC-A
*
28438595 AAA--TTTTTGAAAACACA
1 AAATTTTTTTTAAAACACA
* * *
28438612 GGATTTTTTTTTGAAACACA
1 -AAATTTTTTTTAAAACACA
*
28438632 GAAATTTTTTTTGAAAACACGG
1 -AAATTTTTTTT-AAAACAC-A
28438654 AAATTTTTT
1 AAATTTTTT
28438663 AAACACGAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
17 15 0.23
18 10 0.15
20 25 0.38
21 15 0.23
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AAATTTTTTTTAAAACACA
Found at i:28438624 original size:21 final size:21
Alignment explanation
Indices: 28438598--28438662 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
28438588 GACACTAAAA
* *
28438598 TTTTTGAAAACACAGGATTTT
1 TTTTTGAAAACACAGAAATTT
28438619 TTTTTG-AAACACAGAAATTT
1 TTTTTGAAAACACAGAAATTT
*
28438639 TTTTTGAAAACACGGAAATTT
1 TTTTTGAAAACACAGAAATTT
28438660 TTT
1 TTT
28438663 AAACACGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.45
21 22 0.55
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (21 bp):
TTTTTGAAAACACAGAAATTT
Found at i:28439428 original size:17 final size:17
Alignment explanation
Indices: 28439404--28439442 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28439394 TATTTTTTTA
28439404 TTTCTTTTT-CTCTCTT
1 TTTCTTTTTCCTCTCTT
*
28439420 TTTCTTTTTCCTTTCTT
1 TTTCTTTTTCCTCTCTT
*
28439437 CTTCTT
1 TTTCTT
28439443 CTCTTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTCCTCTCTT
Found at i:28439429 original size:22 final size:23
Alignment explanation
Indices: 28439396--28439442 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
28439386 GCTGTTTTTA
28439396 TTTTTTTATTT-CTTT-TTCTCTC
1 TTTTTTTATTTCCTTTCTTCT-TC
28439418 TTTTTCTT-TTTCCTTTCTTCTTC
1 TTTTT-TTATTTCCTTTCTTCTTC
28439441 TT
1 TT
28439443 CTCTTAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 8 0.36
23 10 0.45
24 4 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTATTTCCTTTCTTCTTC
Found at i:28439572 original size:16 final size:14
Alignment explanation
Indices: 28439551--28439592 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
28439541 CCTTCTATTA
28439551 TTTTCTTCCTTCCTCC
1 TTTTCTT-CTT-CTCC
*
28439567 TTTTCTTCTTTTCC
1 TTTTCTTCTTCTCC
28439581 TTTTC-TCTTCTC
1 TTTTCTTCTTCTC
28439593 TTTCCCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 3 0.12
16 7 0.29
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTCTTCTCC
Found at i:28439603 original size:18 final size:17
Alignment explanation
Indices: 28439560--28439606 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
28439550 ATTTTCTTCC
28439560 TTCCTCCTTT-TCTTCTT
1 TTCC-CCTTTCTCTTCTT
*
28439577 TT-CCTTTTCTCTTCTCT
1 TTCCCCTTTCTCTTCT-T
28439594 TTCCCCTTTCTCT
1 TTCCCCTTTCTCT
28439607 CCTTCCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.16
16 7 0.28
17 5 0.20
18 9 0.36
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCCCCTTTCTCTTCTT
Found at i:28439611 original size:21 final size:19
Alignment explanation
Indices: 28439579--28439628 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 19
28439569 TTCTTCTTTT
*
28439579 CCTTTTCTCTTCTCTTTCC
1 CCTTTTCTCTTCCCTTTCC
28439598 CCTTTCTCTCCTTCCCTTTCC
1 CCTTT-TCT-CTTCCCTTTCC
28439619 TCTCTTTTCT
1 -C-CTTTTCT
28439629 TTCTCTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 10 0.38
22 4 0.15
23 4 0.15
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (19 bp):
CCTTTTCTCTTCCCTTTCC
Found at i:28440219 original size:29 final size:29
Alignment explanation
Indices: 28440180--28440295 Score: 108
Period size: 30 Copynumber: 3.9 Consensus size: 29
28440170 TAGGGCCAAG
*
28440180 ATGTAATTTTTTGAAAGTTTAGGGGTTGAA
1 ATGTAA-TTTTAGAAAGTTTAGGGGTTGAA
* *
28440210 GTGTAATTTTGAGAAAGTTTAGGGTTTGAA
1 ATGTAATTTT-AGAAAGTTTAGGGGTTGAA
* **
28440240 ATGTAATTTTAGAAAAGCTT-GGGGTCAAA
1 ATGTAATTTTAG-AAAGTTTAGGGGTTGAA
* **
28440269 ATGTAAATTTTACAAAGTACAGGGGTT
1 ATGT-AATTTTAGAAAGTTTAGGGGTT
28440296 AAAACATAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
29 20 0.29
30 49 0.71
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
ATGTAATTTTAGAAAGTTTAGGGGTTGAA
Found at i:28452106 original size:132 final size:131
Alignment explanation
Indices: 28451799--28452313 Score: 774
Period size: 132 Copynumber: 4.0 Consensus size: 131
28451789 CTGAATTTAC
* *
28451799 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTTAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* *
28451864 CAAGCCTTGTCTCCCTGAGCAGTAGCGGAGAA----G--GTTATAGATCTTATCTCCCTAAACAG
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGTTATAGATCTTATCTCCCTAAGCAG
28451923 T
131 T
* * *
28451924 AGTGGAGCAGATCGAAGATGGCAAATCTTATCTTTTCAAGATAGTGGGAAGCAGATTTAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
*
28451989 CAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAAGGTTGAAGATTATAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAG-TTATAGATCTTATCTCCCTAAGCA
28452054 GT
130 GT
* * * * *
28452056 AATGAAACAGATCGAAGACGGCGAATTTTATCTTTCCAAGATAGTGGGAAGCAGATTTAGGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* *
28452121 CAAGCCTTGTATCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAG-TTATAGATCTTATCTCCCTAAGCA
28452186 GT
130 GT
* *
28452188 AGTGGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTAAAGCCAC
1 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
* * *
28452253 CAAGCCTTGTCTCCCTGAGCAGCAGCAGAGAAGGTTGAAGCTACA-AGTCTTATCTCCCTAA
66 CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGTTATAGA-TCTTATCTCCCTAA
28452314 AGTTGCAGAG
Statistics
Matches: 351, Mismatches: 31, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
125 90 0.26
129 1 0.00
130 1 0.00
131 17 0.05
132 242 0.69
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (131 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCAC
CAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGTTATAGATCTTATCTCCCTAAGCAG
T
Found at i:28453078 original size:11 final size:11
Alignment explanation
Indices: 28453062--28453086 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28453052 AACCGAAAAG
28453062 TTTCTAGGGTT
1 TTTCTAGGGTT
28453073 TTTCTAGGGTT
1 TTTCTAGGGTT
28453084 TTT
1 TTT
28453087 TTGTCGATTT
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:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTCTAGGGTT
Found at i:28454461 original size:98 final size:98
Alignment explanation
Indices: 28454340--28454536 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
28454330 TTAAAAATAA
* **
28454340 TAAAGGAAATATTCTGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
28454405 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
28454438 TAAAAGAAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
28454503 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
28454536 T
1 T
28454537 TTTATTGCAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAAGAAATATTCCAAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:28468086 original size:107 final size:107
Alignment explanation
Indices: 28467900--28468123 Score: 324
Period size: 107 Copynumber: 2.1 Consensus size: 107
28467890 ACTGAAACTG
* * ** * * *
28467900 TGATCATAAATCAGCAAGCATTAAAAATGTCAATTGTGATCGTAAATCAACGAACTATTTAAATG
1 TGATCATAAACCAGCCAGTTTTAAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATG
* * *
28467965 GAATTGTGGTCGT-AAATCGACGAACTCTTAATGAATTGTTCA
66 GAATTGCGATCGTAAAAT-GACAAACTCTTAATGAATTGTTCA
*
28468007 TGATCGTAAACCAGCCAGTTTTAAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATG
1 TGATCATAAACCAGCCAGTTTTAAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATG
*
28468072 GAGTTGCGATCGTAAAATGACAAACTCTTAATGAATTGTTCA
66 GAATTGCGATCGTAAAATGACAAACTCTTAATGAATTGTTCA
28468114 TGATCATAAA
1 TGATCATAAA
28468124 TAAATGAACT
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 99 0.96
108 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (107 bp):
TGATCATAAACCAGCCAGTTTTAAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATG
GAATTGCGATCGTAAAATGACAAACTCTTAATGAATTGTTCA
Found at i:28468145 original size:134 final size:132
Alignment explanation
Indices: 28468007--28468252 Score: 305
Period size: 134 Copynumber: 1.8 Consensus size: 132
28467997 GAATTGTTCA
* * * * *
28468007 TGATCGTAAACCAGCCAGTTTTAAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATG
1 TGATCGTAAACCAACCAGCTTTAAAAATGACAAATATAATCATAAATCAACAAACTATTTAAATG
* * *
28468072 GAGTTGCGATCGTAAA-ATGACAAACTCTTAATGAATTGTTCATGATCATAAATAAATGAACTGA
66 AAGTTGCGATCATAAATATG--AAA-TCTTAATGAATTATTCATGATCATAAATAAATGAACTGA
28468136 AGCTG
128 AGCTG
* * * * * * *
28468141 TGATCGTAAATCAACGAGCTTTAAAAATGATAAATATGATCGTAAATCAGCAAACTGTTTAAATG
1 TGATCGTAAACCAACCAGCTTTAAAAATGACAAATATAATCATAAATCAACAAACTATTTAAATG
28468206 AAGTTGCGATCATAAATCTATGAAATCTTAATGAATTATTCATGATC
66 AAGTTGCGATCATAAA--TATGAAATCTTAATGAATTATTCATGATC
28468253 GTAAGCACTA
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
134 88 0.94
135 3 0.03
137 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (132 bp):
TGATCGTAAACCAACCAGCTTTAAAAATGACAAATATAATCATAAATCAACAAACTATTTAAATG
AAGTTGCGATCATAAATATGAAATCTTAATGAATTATTCATGATCATAAATAAATGAACTGAAGC
TG
Found at i:28468360 original size:120 final size:120
Alignment explanation
Indices: 28468147--28468368 Score: 291
Period size: 120 Copynumber: 1.9 Consensus size: 120
28468137 GCTGTGATCG
* * * * *
28468147 TAAATCAACGAGCTTTAAAAATGATAAATATGATCGTAAATCAGCAAACTGTTTAAATGAAGTTG
1 TAAATCAACAAGCTTAAAAAATGATAAATATAATCGTAAATCAGCAAACTATTTAAAAGAAGTTG
* * *
28468212 CGATCATAAATCTATGAAATCTTAATGAATTATTCATGATCGTAAGCACTAATCA
66 CAATCATAAATCGACGAAATCTTAATGAATTATTCATGATCGTAAGCACTAATCA
** * * * *
28468267 TAAATCAACAAGCTTAAAAAATGATAGTTGTAATCGTAAATTAGCAAATTATTTAAAAGGAGTTG
1 TAAATCAACAAGCTTAAAAAATGATAAATATAATCGTAAATCAGCAAACTATTTAAAAGAAGTTG
* * *
28468332 CAATCGTAAATCGACGAACTCTTAATGAATTGTTCAT
66 CAATCATAAATCGACGAAATCTTAATGAATTATTCAT
28468369 AATCATAAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 85 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (120 bp):
TAAATCAACAAGCTTAAAAAATGATAAATATAATCGTAAATCAGCAAACTATTTAAAAGAAGTTG
CAATCATAAATCGACGAAATCTTAATGAATTATTCATGATCGTAAGCACTAATCA
Found at i:28468491 original size:254 final size:258
Alignment explanation
Indices: 28468029--28468710 Score: 773
Period size: 254 Copynumber: 2.6 Consensus size: 258
28468019 AGCCAGTTTT
* * * * *
28468029 AAAAATGACAATTGTAATCATAAATCAACGAACTATTTAAATGGAGTTGCGATCGTAAAATGACA
1 AAAAATGACAATTGTAATCATAAATTAGCAAAATATTTAAATGGAGTTGCGATCGT-AAATGACG
* * * *
28468094 AACTCTTAATGAATTGTTCATGATCATAAATAAATGAACTGAAGCTGTGATCGTAAATCAACGAG
65 AACTCTTAATGAATTGTTCATGATCATAAATCAATGAACTGAAGTTGTGATCATAAATCAGCGAG
**
28468159 CTTTAAAAATGATAAATATGATCGTAAATCAGCAAACTGTTTAAATGAAGTTGCGATCATAAATC
130 CTTTAAAAATGATAGTTATGATCGTAAATCAGCAAACTGTTTAAATGAAGTTGCGATCATAAATC
* * * *
28468224 TATGAAATCTTAATGAATTATTCATGATCG-T-AA-GCACT-AA-TCATAAATCAACAAGCTTA
195 GACGAAATCTTAATAAATTATTCATGATCGATCAATGAACTAAAGTCATAAATCAACAAGCTTA
* * * * * *
28468283 AAAAATGATAGTTGTAATCGTAAATTAGCAAATTATTTAAAAGGAGTTGCAATCGTAAATCGACG
1 AAAAATGACAATTGTAATCATAAATTAGCAAAATATTTAAATGGAGTTGCGATCGTAAAT-GACG
* * * *
28468348 AACTCTTAATGAATTGTTCATAATCATAAATCAATGAATTGAAGTTGTGATTATAAATCAGTGAG
65 AACTCTTAATGAATTGTTCATGATCATAAATCAATGAACTGAAGTTGTGATCATAAATCAGCGAG
* * * *
28468413 CTTTAAAAATGACAGTTATGATCGTAAATTAGCAAACTGTTTAAAT-AGAGTTGTGATCGTAAAT
130 CTTTAAAAATGATAGTTATGATCGTAAATCAGCAAACTGTTTAAATGA-AGTTGCGATCATAAAT
* ** *
28468477 CGGCGAGCTCTTAATAAATTATTCATGATCGTAAATCAATGAACTAAAGTTGTGGTCGTAAATCA
194 CGACGAAATCTTAATAAATTATTCATGATCG---ATCAATGAACTAAA------GTCATAAATCA
* *
28468542 ACGAGCTTT
250 ACAAGCTTA
* * * * * * *
28468551 AAAAATGGCAATTTTAATCATAAATTAGCAAAATGTTTAAATGAAGTTACGATCATAAATTGGCG
1 AAAAATGACAATTGTAATCATAAATTAGCAAAATATTTAAATGGAGTTGCGATCGTAAA-TGACG
* *
28468616 AACTCTTAATGAATTGTTCATGATCGTAAATCAATAAACTGAAGTTGTGATCATAAATCAGCGAG
65 AACTCTTAATGAATTGTTCATGATCATAAATCAATGAACTGAAGTTGTGATCATAAATCAGCGAG
** **
28468681 AGTTAAAAATGATAGTTGCGATCGTAAATC
130 CTTTAAAAATGATAGTTATGATCGTAAATC
28468711 GGCGAACTCT
Statistics
Matches: 352, Mismatches: 59, Indels: 20
0.82 0.14 0.05
Matches are distributed among these distances:
253 5 0.01
254 188 0.53
258 1 0.00
259 2 0.01
260 4 0.01
261 2 0.01
268 149 0.42
269 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (258 bp):
AAAAATGACAATTGTAATCATAAATTAGCAAAATATTTAAATGGAGTTGCGATCGTAAATGACGA
ACTCTTAATGAATTGTTCATGATCATAAATCAATGAACTGAAGTTGTGATCATAAATCAGCGAGC
TTTAAAAATGATAGTTATGATCGTAAATCAGCAAACTGTTTAAATGAAGTTGCGATCATAAATCG
ACGAAATCTTAATAAATTATTCATGATCGATCAATGAACTAAAGTCATAAATCAACAAGCTTA
Found at i:28468512 original size:134 final size:134
Alignment explanation
Indices: 28468263--28468709 Score: 529
Period size: 134 Copynumber: 3.3 Consensus size: 134
28468253 GTAAGCACTA
* * * * * *
28468263 ATCATAAATCAACAAGCTTAAAAAATGATAGTTGTAATCGTAAATTAGCAAATTATTTAAA-AGG
1 ATCATAAATCAGCGAGCTTTAAAAATGACAGTTGTAATCGTAAATTAGCAAAATGTTTAAATA-G
* * * * *
28468327 AGTTGCAATCGTAAATCGACGAACTCTTAATGAATTGTTCATAATCATAAATCAATGAATTGAAG
65 AGTTGCGATCGTAAATCGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATGAACTGAAG
28468392 TTGTG
130 TTGTG
* * * * *
28468397 ATTATAAATCAGTGAGCTTTAAAAATGACAGTTATGATCGTAAATTAGCAAACTGTTTAAATAGA
1 ATCATAAATCAGCGAGCTTTAAAAATGACAGTTGTAATCGTAAATTAGCAAAATGTTTAAATAGA
* * * * *
28468462 GTTGTGATCGTAAATCGGCGAGCTCTTAATAAATTATTCATGATCGTAAATCAATGAACTAAAGT
66 GTTGCGATCGTAAATCGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATGAACTGAAGT
28468527 TGTG
131 TGTG
* * * * * * *
28468531 GTCGTAAATCAACGAGCTTTAAAAATGGCAATTTTAATCATAAATTAGCAAAATGTTTAAAT-GA
1 ATCATAAATCAGCGAGCTTTAAAAATGACAGTTGTAATCGTAAATTAGCAAAATGTTTAAATAG-
* * * *
28468595 AGTTACGATCATAAATTGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATAAACTGAAG
65 AGTTGCGATCGTAAATCGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATGAACTGAAG
28468660 TTGTG
130 TTGTG
** * **
28468665 ATCATAAATCAGCGAGAGTTAAAAATGATAGTTGCGATCGTAAAT
1 ATCATAAATCAGCGAGCTTTAAAAATGACAGTTGTAATCGTAAAT
28468710 CGGCGAACTC
Statistics
Matches: 259, Mismatches: 52, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
133 1 0.00
134 257 0.99
135 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (134 bp):
ATCATAAATCAGCGAGCTTTAAAAATGACAGTTGTAATCGTAAATTAGCAAAATGTTTAAATAGA
GTTGCGATCGTAAATCGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATGAACTGAAGT
TGTG
Found at i:28468737 original size:99 final size:98
Alignment explanation
Indices: 28468589--28468776 Score: 304
Period size: 99 Copynumber: 1.9 Consensus size: 98
28468579 CAAAATGTTT
* *
28468589 AAATGAAGTTACGATCATAAATTGGCGAACTCTTAATGAATTGTTCATGATCGTAAATCAATAAA
1 AAATGAAGTTACGATCATAAATCGGCGAACTCTTAATGAATTGTTCATGATCATAAATCAATAAA
* *
28468654 CTGAAGTTGTGATCATAAATCAGCGAGAGTTAA
66 CTAAAGCTGTGATCATAAATCAGCGAGAGTTAA
* * *
28468687 AAATGATAGTTGCGATCGTAAATCGGCGAACTCTTAATGAATTGTTCATGATCATAAATCAATGA
1 AAATGA-AGTTACGATCATAAATCGGCGAACTCTTAATGAATTGTTCATGATCATAAATCAATAA
28468752 ACTAAAGCTGTGATCATAAATCAGC
65 ACTAAAGCTGTGATCATAAATCAGC
28468777 AAGCTTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 6 0.07
99 76 0.93
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (98 bp):
AAATGAAGTTACGATCATAAATCGGCGAACTCTTAATGAATTGTTCATGATCATAAATCAATAAA
CTAAAGCTGTGATCATAAATCAGCGAGAGTTAA
Found at i:28468786 original size:99 final size:98
Alignment explanation
Indices: 28468567--28468779 Score: 302
Period size: 99 Copynumber: 2.2 Consensus size: 98
28468557 GGCAATTTTA
* * * *
28468567 ATCATAAATTAGCAAAATGTT-TAAATGAAGTTACGATCATAAATTGGCGAACTCTTAATGAATT
1 ATCATAAATCAGCAAGA-GTTAAAAATGAAGTTACGATCATAAATCGGCGAACTCTTAATGAATT
* * *
28468631 GTTCATGATCGTAAATCAATAAACTGAAGTTGTG
65 GTTCATGATCATAAATCAATAAACTAAAGCTGTG
* * *
28468665 ATCATAAATCAGCGAGAGTTAAAAATGATAGTTGCGATCGTAAATCGGCGAACTCTTAATGAATT
1 ATCATAAATCAGCAAGAGTTAAAAATGA-AGTTACGATCATAAATCGGCGAACTCTTAATGAATT
*
28468730 GTTCATGATCATAAATCAATGAACTAAAGCTGTG
65 GTTCATGATCATAAATCAATAAACTAAAGCTGTG
28468764 ATCATAAATCAGCAAG
1 ATCATAAATCAGCAAG
28468780 CTTTAAATCT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 3 0.03
98 20 0.20
99 78 0.77
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (98 bp):
ATCATAAATCAGCAAGAGTTAAAAATGAAGTTACGATCATAAATCGGCGAACTCTTAATGAATTG
TTCATGATCATAAATCAATAAACTAAAGCTGTG
Found at i:28471241 original size:292 final size:292
Alignment explanation
Indices: 28470717--28471284 Score: 1109
Period size: 292 Copynumber: 1.9 Consensus size: 292
28470707 CTTAACATCC
28470717 AAATCTGAATGCCACGATTTGGAAGCAACTAGGAGTAATCATGTCACCATAAGAAGTGAAAAAAT
1 AAATCTGAATGCCACGATTTGGAAGCAACTAGGAGTAATCATGTCACCATAAGAAGTGAAAAAAT
28470782 TGAAAGAGGTTGCTAATCCCTCTAAAGTTCATAGCCAATGATCCTAGTAATCAACACTCAAGAGC
66 TGAAAGAGGTTGCTAATCCCTCTAAAGTTCATAGCCAATGATCCTAGTAATCAACACTCAAGAGC
28470847 TGGAAAACTCAAAGAGACTAGCAAGTTCCTTAGCCTTCTTGAGCAAGCTAGCACTTCTCTTAGAA
131 TGGAAAACTCAAAGAGACTAGCAAGTTCCTTAGCCTTCTTGAGCAAGCTAGCACTTCTCTTAGAA
28470912 AATGTGACTTTGATGGAGGAGAGTAAAGGTTATTTTGGTGGGTTTGATCCACGCTCATCACACCA
196 AATGTGACTTTGATGGAGGAGAGTAAAGGTTATTTTGGTGGGTTTGATCCACGCTCATCACACCA
*
28470977 TTGTTTATACAAGATTAAATAGAAATTAATCA
261 TTGTTGATACAAGATTAAATAGAAATTAATCA
*
28471009 AAATCTGAATGCCACGATTTGGAAGCAACTAGGAGTAATCATGTCACCATAAGAAGTGCAAAAAT
1 AAATCTGAATGCCACGATTTGGAAGCAACTAGGAGTAATCATGTCACCATAAGAAGTGAAAAAAT
28471074 TGAAAGAGGTTGCTAATCCCTCTAAAGTTCATAGCCAATGATCCTAGTAATCAACACTCAAGAGC
66 TGAAAGAGGTTGCTAATCCCTCTAAAGTTCATAGCCAATGATCCTAGTAATCAACACTCAAGAGC
*
28471139 TGGAAAACTCAAAGAGACTAGCGAGTTCCTTAGCCTTCTTGAGCAAGCTAGCACTTCTCTTAGAA
131 TGGAAAACTCAAAGAGACTAGCAAGTTCCTTAGCCTTCTTGAGCAAGCTAGCACTTCTCTTAGAA
28471204 AATGTGACTTTGATGGAGGAGAGTAAAGGTTATTTTGGTGGGTTTGATCCACGCTCATCACACCA
196 AATGTGACTTTGATGGAGGAGAGTAAAGGTTATTTTGGTGGGTTTGATCCACGCTCATCACACCA
28471269 TTGTTGATACAAGATT
261 TTGTTGATACAAGATT
28471285 TAATTGGTAG
Statistics
Matches: 273, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
292 273 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (292 bp):
AAATCTGAATGCCACGATTTGGAAGCAACTAGGAGTAATCATGTCACCATAAGAAGTGAAAAAAT
TGAAAGAGGTTGCTAATCCCTCTAAAGTTCATAGCCAATGATCCTAGTAATCAACACTCAAGAGC
TGGAAAACTCAAAGAGACTAGCAAGTTCCTTAGCCTTCTTGAGCAAGCTAGCACTTCTCTTAGAA
AATGTGACTTTGATGGAGGAGAGTAAAGGTTATTTTGGTGGGTTTGATCCACGCTCATCACACCA
TTGTTGATACAAGATTAAATAGAAATTAATCA
Found at i:28479625 original size:13 final size:13
Alignment explanation
Indices: 28479607--28479632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28479597 GTATACTAAC
28479607 TTATGAGTTTGAT
1 TTATGAGTTTGAT
28479620 TTATGAGTTTGAT
1 TTATGAGTTTGAT
28479633 GGTGTTATAT
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
TTATGAGTTTGAT
Found at i:28480759 original size:42 final size:42
Alignment explanation
Indices: 28480668--28480765 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
28480658 GGTTCAATTT
* * * * * * *
28480668 AGAGAGTTACACGGCCTGGCACATGGGCGTGTGGCGCAACTT
1 AGAGAGTTACACGGCCTAGCACACGGCCATGTGACCCAACTC
*
28480710 AGAGAGTTACACGGCCTAGCACACGGCCATGTGACCCTACTC
1 AGAGAGTTACACGGCCTAGCACACGGCCATGTGACCCAACTC
*
28480752 AGTGAGTTACACGG
1 AGAGAGTTACACGG
28480766 GTGAGGACAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.18
Consensus pattern (42 bp):
AGAGAGTTACACGGCCTAGCACACGGCCATGTGACCCAACTC
Found at i:28484695 original size:14 final size:14
Alignment explanation
Indices: 28484676--28484705 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28484666 ATCGATTGCA
28484676 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
28484690 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
28484704 GC
1 GC
28484706 TAGTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:28487740 original size:20 final size:20
Alignment explanation
Indices: 28487715--28487754 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28487705 AATATTTTCT
*
28487715 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28487735 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
28487755 TCATTTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28488761 original size:10 final size:11
Alignment explanation
Indices: 28488729--28488767 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
28488719 TGTTTAAAAA
28488729 TATATATTATT
1 TATATATTATT
28488740 T-TATATTATT
1 TATATATTATT
28488750 TATATA-TATT
1 TATATATTATT
28488760 TATA-ATTA
1 TATATATTA
28488768 AATTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 20 0.77
11 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:28488991 original size:30 final size:30
Alignment explanation
Indices: 28488957--28489022 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
28488947 AATAAACACC
* *
28488957 AAAAATTTATTTTAAAAATA-AAAAAGTAA
1 AAAAAATTATTTTAAAAATATAAAAAATAA
28488986 AAAAAA-TATTTTAAAAATATTAAAAAATAA
1 AAAAAATTATTTTAAAAATA-TAAAAAATAA
28489016 AAAAAAT
1 AAAAAAT
28489023 AAAAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 13 0.41
29 5 0.16
30 14 0.44
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAAATTATTTTAAAAATATAAAAAATAA
Found at i:28488996 original size:28 final size:29
Alignment explanation
Indices: 28488964--28489023 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
28488954 ACCAAAAATT
*
28488964 TATTTTAAAAATA-AAAAAGTAAAAAAAA
1 TATTTTAAAAATATAAAAAATAAAAAAAA
28488992 TATTTTAAAAATATTAAAAAATAAAAAAAA
1 TATTTTAAAAATA-TAAAAAATAAAAAAAA
28489022 TA
1 TA
28489024 AAAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 13 0.45
30 16 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (29 bp):
TATTTTAAAAATATAAAAAATAAAAAAAA
Found at i:28492371 original size:36 final size:42
Alignment explanation
Indices: 28492314--28492400 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 42
28492304 AAATTCACAT
*
28492314 TTCAATTC-AATTTCACTTTTT-CA-CTTTCAA-TC-ATA-A
1 TTCAATTCAAAATTCACTTTTTCCATCTTTCAAGTCAATATA
*
28492350 TTCAATTCAAAATTCAC-TTTTCCATTTTTCAAGTCAATATA
1 TTCAATTCAAAATTCACTTTTTCCATCTTTCAAGTCAATATA
28492391 TTCAATTCAA
1 TTCAATTCAA
28492401 TTCCACACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
36 12 0.28
37 9 0.21
38 6 0.14
39 2 0.05
40 3 0.07
41 11 0.26
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.45
Consensus pattern (42 bp):
TTCAATTCAAAATTCACTTTTTCCATCTTTCAAGTCAATATA
Found at i:28499035 original size:114 final size:114
Alignment explanation
Indices: 28498835--28499061 Score: 445
Period size: 114 Copynumber: 2.0 Consensus size: 114
28498825 GGGAGTCGCC
*
28498835 ACCAATCCTTTTTTGACGAGGTGTGATCGGGTCACCTCAAAACAGTGGTTGTTTTTAATAAATGA
1 ACCAATCCTTTTTTGACGAGGTGTGATCGGGTCACCTCAAAAAAGTGGTTGTTTTTAATAAATGA
28498900 TTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAGAAAAATG
66 TTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAGAAAAATG
28498949 ACCAATCCTTTTTTGACGAGGTGTGATCGGGTCACCTCAAAAAAGTGGTTGTTTTTAATAAATGA
1 ACCAATCCTTTTTTGACGAGGTGTGATCGGGTCACCTCAAAAAAGTGGTTGTTTTTAATAAATGA
28499014 TTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAGAAAAAT
66 TTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAGAAAAAT
28499062 AAGTTCGGGA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (114 bp):
ACCAATCCTTTTTTGACGAGGTGTGATCGGGTCACCTCAAAAAAGTGGTTGTTTTTAATAAATGA
TTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAGAAAAATG
Found at i:28499527 original size:109 final size:107
Alignment explanation
Indices: 28499344--28499541 Score: 279
Period size: 109 Copynumber: 1.8 Consensus size: 107
28499334 AAGCTTTAAG
* *
28499344 AGGATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
1 AGGATATTTAGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCCTCGA
*
28499409 GTTTCCAAACTCGAAATATTGCCTGATTTTGAAATTTTTGAA
66 GTTTCCAAACGCGAAATATTGCCTGATTTTGAAATTTTTGAA
* ** * * * *
28499451 AGGATATTTAGCTATTTGGTGGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTT
1 AGGATATTTAGCTATTTAGTCAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACGTTTCCTC
*
28499516 GAGTTTCCAAACGCTAAATATTGCCT
64 GAGTTTCCAAACGCGAAATATTGCCT
28499542 CCATCGAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 24 0.31
109 54 0.69
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (107 bp):
AGGATATTTAGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCCTCGA
GTTTCCAAACGCGAAATATTGCCTGATTTTGAAATTTTTGAA
Found at i:28500512 original size:52 final size:52
Alignment explanation
Indices: 28500434--28500537 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
28500424 TACAGAAGGA
28500434 CCAAAGCTGCAAATAGCCCCTCCAGTATGGAAACACGCGGACCTTCCTCGGG
1 CCAAAGCTGCAAATAGCCCCTCCAGTATGGAAACACGCGGACCTTCCTCGGG
*
28500486 CCAAAGCTGCAAATAGCCCCTCCAGTATGGAAACACGCGGATCTTCCTCGGG
1 CCAAAGCTGCAAATAGCCCCTCCAGTATGGAAACACGCGGACCTTCCTCGGG
28500538 TCGGGTCGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (52 bp):
CCAAAGCTGCAAATAGCCCCTCCAGTATGGAAACACGCGGACCTTCCTCGGG
Found at i:28509622 original size:34 final size:33
Alignment explanation
Indices: 28509545--28509627 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
28509535 TTTTATTCTA
* **
28509545 AATATTATTATTTCTTAGCATGTAAAATTTATAT
1 AATA-TATTATTTTTTAAAATGTAAAATTTATAT
*
28509579 TATGA-ATTATTTTTTAAAATGTAAAATTATATAT
1 AAT-ATATTATTTTTTAAAATGTAAAATT-TATAT
*
28509613 AATATATTATCTTTT
1 AATATATTATTTTTT
28509628 CATGTGTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
33 21 0.52
34 18 0.45
35 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.52
Consensus pattern (33 bp):
AATATATTATTTTTTAAAATGTAAAATTTATAT
Found at i:28509908 original size:22 final size:23
Alignment explanation
Indices: 28509877--28509920 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28509867 TATTTTCTAA
* *
28509877 TATATAAATATTTATTTTATATT
1 TATATAAATATGTAATTTATATT
28509900 TATAT-AATATGTAATTTATAT
1 TATATAAATATGTAATTTATAT
28509921 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATAAATATGTAATTTATATT
Found at i:28511583 original size:27 final size:26
Alignment explanation
Indices: 28511539--28511594 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
28511529 AAATAAAAAA
*
28511539 AAACAAAAAAAAATTTTCTTCTAC-T
1 AAACAAAAAAAAAATTTCTTCTACAT
28511564 AAACAAAAATAAAAAATTTCTTCTACAT
1 AAAC-AAAA-AAAAAATTTCTTCTACAT
28511592 AAA
1 AAA
28511595 ATNCCGGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 15 0.56
28 4 0.15
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (26 bp):
AAACAAAAAAAAAATTTCTTCTACAT
Found at i:28511902 original size:13 final size:13
Alignment explanation
Indices: 28511840--28511910 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 13
28511830 CCAAACAAGC
* *
28511840 AAAGCAAAAAGCA
1 AAAGAAAAAAGAA
28511853 AAAGAGAAAAAGAA
1 AAAGA-AAAAAGAA
* *
28511867 ATAAAAAAAAACAA
1 A-AAGAAAAAAGAA
*
28511881 CAACCGAAAAAAGAA
1 -AA-AGAAAAAAGAA
28511896 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
28511909 AA
1 AA
28511911 GAAGACAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
13 16 0.35
14 18 0.39
15 12 0.26
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.01
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:28512011 original size:17 final size:17
Alignment explanation
Indices: 28511989--28512022 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28511979 GAATGAGAAG
28511989 AGAAGAAAGG-AGAAAAA
1 AGAAG-AAGGAAGAAAAA
28512006 AGAAGAAGGAAGAAAAA
1 AGAAGAAGGAAGAAAAA
28512023 GGGGGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAGAAGGAAGAAAAA
Found at i:28512338 original size:13 final size:13
Alignment explanation
Indices: 28512320--28512392 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
28512310 ACAGCCCAGC
28512320 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
28512333 AGAAAAAAGAAGAAA
1 AGAAAAAAG-A-AAA
28512348 AGGAAAAAAGAAAGA
1 A-GAAAAAAGAAA-A
*
28512363 A-AAAAAGGAAAA
1 AGAAAAAAGAAAA
* *
28512375 AAAAGAAAAAAAAA
1 AGAA-AAAAGAAAA
28512389 AGAA
1 AGAA
28512393 GAAGGGGCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.04
13 20 0.40
14 13 0.26
15 7 0.14
16 8 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:28512361 original size:20 final size:19
Alignment explanation
Indices: 28512320--28512387 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
28512310 ACAGCCCAGC
*
28512320 AGAAAAAAGAAAAAGAAAAA
1 AGAAAAAAGGAAAA-AAAAA
*
28512340 AGAAGAAAAGGAAAAAAGAA
1 AGAA-AAAAGGAAAAAAAAA
28512360 AGAAAAAAAGGAAAAAAAAGA
1 AG-AAAAAAGGAAAAAAAA-A
28512381 A-AAAAAA
1 AGAAAAAA
28512388 AAGAAGAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.14
20 23 0.55
21 13 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AGAAAAAAGGAAAAAAAAA
Found at i:28512367 original size:29 final size:30
Alignment explanation
Indices: 28512320--28512395 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
28512310 ACAGCCCAGC
*
28512320 AGAAAAAAGAAA-AAGAAAAAAGAAGAAAA
1 AGAAAAAAGAAAGAAGAAAAAAGAAAAAAA
* *
28512349 GGAAAAAAGAAAGAA-AAAAAGGAAAAAAA
1 AGAAAAAAGAAAGAAGAAAAAAGAAAAAAA
*
28512378 AGAAAAAAAAAAGAAGAA
1 AGAAAAAAGAAAGAAGAA
28512396 GGGGCCCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (30 bp):
AGAAAAAAGAAAGAAGAAAAAAGAAAAAAA
Done.