Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 55 of 205
Found at i:16572601 original size:114 final size:114
Alignment explanation
Indices: 16572401--16572616 Score: 351
Period size: 114 Copynumber: 1.9 Consensus size: 114
16572391 AGGTTTTTTT
* *
16572401 GCGGCACTTTCCTAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAACAGTGTCGTTGGGCTTAG
1 GCGGCACTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
16572466 GTTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
66 GTTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
* * * * * *
16572515 GCGGCGCTTTCTTAAAAAGGCCGCTGAATCCCCGGAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCACTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
*
16572580 GTTTTTTTGCGGCGCTTCCTCAAAAACGCCGTTAAAG
66 GTTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAG
16572617 AAAGCGCCGC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (114 bp):
GCGGCACTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCGTCGTTGGGCTTAG
GTTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
Found at i:16573543 original size:31 final size:31
Alignment explanation
Indices: 16573499--16573559 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
16573489 CAATCTAATG
*
16573499 ACTTCAATAAAAACTTTTGAATAGTTCAATA
1 ACTTAAATAAAAACTTTTGAATAGTTCAATA
*
16573530 ACTTAAATGAAAACTTTTGAATAGTTCAAT
1 ACTTAAATAAAAACTTTTGAATAGTTCAAT
16573560 GACCAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTGAATAGTTCAATA
Found at i:16574017 original size:16 final size:16
Alignment explanation
Indices: 16573998--16574029 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
16573988 TTTTAAAGTA
16573998 TTTTTAAAATA-ATTT
1 TTTTTAAAATACATTT
16574013 TTTTTAAAATACATTT
1 TTTTTAAAATACATTT
16574029 T
1 T
16574030 CGAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAAAATACATTT
Found at i:16575380 original size:25 final size:28
Alignment explanation
Indices: 16575352--16575409 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
16575342 AATTTATACT
*
16575352 AATATTTA-A-TAATATTTAACT-TTAA
1 AATATTTAGATTAATATTAAACTCTTAA
16575377 AATA-TTAGATTAATATTAAACTCTTAA
1 AATATTTAGATTAATATTAAACTCTTAA
16575404 AATATT
1 AATATT
16575410 AAACATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 3 0.11
25 5 0.18
26 11 0.39
27 8 0.29
28 1 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
AATATTTAGATTAATATTAAACTCTTAA
Found at i:16578236 original size:26 final size:26
Alignment explanation
Indices: 16578200--16578260 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
16578190 TTCTCACCCC
*
16578200 AATTTTACCCCCAGTAAAATTTTTAT
1 AATTTTACCCCCAGTAAAATTTTGAT
*
16578226 AATTTTACCCCTAGTAAAATTTTGAT
1 AATTTTACCCCCAGTAAAATTTTGAT
*
16578252 GATTTTACC
1 AATTTTACC
16578261 ATCGATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.43
Consensus pattern (26 bp):
AATTTTACCCCCAGTAAAATTTTGAT
Found at i:16578269 original size:26 final size:26
Alignment explanation
Indices: 16578200--16578273 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
16578190 TTCTCACCCC
* *
16578200 AATTTTACCCCCAGTAAAATTTTTAT
1 AATTTTACCCCGAGTAAAATTTTGAT
*
16578226 AATTTTACCCCTAGTAAAATTTTGAT
1 AATTTTACCCCGAGTAAAATTTTGAT
* *
16578252 GATTTTACCATCGA-TAAAATTT
1 AATTTTACC-CCGAGTAAAATTT
16578274 ATAGAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 40 0.95
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (26 bp):
AATTTTACCCCGAGTAAAATTTTGAT
Found at i:16585937 original size:30 final size:30
Alignment explanation
Indices: 16585896--16585970 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
16585886 GATAAAATAA
16585896 GTGACCAAAATGAAAATTTACTAAAGTTAG
1 GTGACCAAAATGAAAATTTACTAAAGTTAG
* *
16585926 GTGACCGAAATGAAAATTTACTAAAGTTGG
1 GTGACCAAAATGAAAATTTACTAAAGTTAG
*
16585956 GTGACTAAAATGAAA
1 GTGACCAAAATGAAA
16585971 GTACAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (30 bp):
GTGACCAAAATGAAAATTTACTAAAGTTAG
Found at i:16587892 original size:26 final size:26
Alignment explanation
Indices: 16587871--16587966 Score: 90
Period size: 25 Copynumber: 3.7 Consensus size: 26
16587861 CATATATATG
16587871 TATATA-TTCTT-TATTTATTATAAA
1 TATATATTTCTTATATTTATTATAAA
* **
16587895 TATATATTTCTTATATTTCATATTTTCTA
1 TATATATTTCTTATA-TT--TATTATAAA
* * *
16587924 CATACATAT-TTATATTTATTATAAA
1 TATATATTTCTTATATTTATTATAAA
16587949 TATATATTTCTTATATTT
1 TATATATTTCTTATATTT
16587967 CATATTTTCT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
24 6 0.11
25 17 0.31
26 10 0.19
27 4 0.07
28 5 0.09
29 12 0.22
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATATTTCTTATATTTATTATAAA
Found at i:16587908 original size:17 final size:17
Alignment explanation
Indices: 16587882--16587963 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
16587872 ATATATTCTT
*
16587882 TATTTATTATAAATATA
1 TATTTCTTATAAATATA
**
16587899 TATTTCTTATATTTCATA
1 TATTTCTTATAAAT-ATA
* *
16587917 T-TTTCTACATACATATTTA
1 TATTTCT-TATA-A-ATATA
*
16587936 TATTTATTATAAATATA
1 TATTTCTTATAAATATA
16587953 TATTTCTTATA
1 TATTTCTTATA
16587964 TTTCATATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 30 0.61
18 8 0.16
19 6 0.12
20 5 0.10
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTCTTATAAATATA
Found at i:16587927 original size:63 final size:57
Alignment explanation
Indices: 16587882--16587991 Score: 192
Period size: 54 Copynumber: 2.0 Consensus size: 57
16587872 ATATATTCTT
16587882 TATTTATTATAAATATATATTTCTTATATTTCATATTTTCTACATACATA-T-T-TA
1 TATTTATTATAAATATATATTTCTTATATTTCATATTTTCTACATACATATTATATA
16587936 TATTTATTATAAATATATATTTCTTATATTTCATATTTTCTACATACATATT-TATA
1 TATTTATTATAAATATATATTTCTTATATTTCATATTTTCTACATACATATTATATA
16587992 CTTATATATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 50 0.93
55 2 0.04
56 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.55
Consensus pattern (57 bp):
TATTTATTATAAATATATATTTCTTATATTTCATATTTTCTACATACATATTATATA
Found at i:16588099 original size:19 final size:21
Alignment explanation
Indices: 16588077--16588132 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
16588067 ATCTCGTATA
16588077 TTTTTACATTTTTA-TAATTT
1 TTTTTACATTTTTATTAATTT
* *
16588097 TTTTTA-AATTTTATTTA-TT
1 TTTTTACATTTTTATTAATTT
* *
16588116 TATTTACATTTTCATTA
1 TTTTTACATTTTTATTA
16588133 TTATCTTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTACATTTTTATTAATTT
Found at i:16595931 original size:27 final size:27
Alignment explanation
Indices: 16595901--16595955 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
16595891 ATTATCAAAA
*
16595901 TTAATTAAAATTCAA-TATTTTAATAAT
1 TTAAGTAAAATTCAATTATTTT-ATAAT
* *
16595928 TTAAGTACAATTTAATTATTTTATAAT
1 TTAAGTAAAATTCAATTATTTTATAAT
16595955 T
1 T
16595956 ATATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAGTAAAATTCAATTATTTTATAAT
Found at i:16599036 original size:22 final size:24
Alignment explanation
Indices: 16598993--16599036 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
16598983 TGATAATATG
16598993 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
16599017 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
16599037 TGAGCATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:16600530 original size:9 final size:9
Alignment explanation
Indices: 16600511--16600547 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
16600501 TGAGTTTTCG
16600511 AATTCGAAT
1 AATTCGAAT
16600520 AACTT-GAAT
1 AA-TTCGAAT
16600529 AATTCGAAT
1 AATTCGAAT
16600538 AATTCGAAT
1 AATTCGAAT
16600547 A
1 A
16600548 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16601427 original size:5 final size:5
Alignment explanation
Indices: 16601417--16601443 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16601407 AAATATATTT
16601417 GATTC GATTC GATTC GATTC GATTC GA
1 GATTC GATTC GATTC GATTC GATTC GA
16601444 ATTCCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (5 bp):
GATTC
Found at i:16602398 original size:24 final size:24
Alignment explanation
Indices: 16602354--16602399 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
16602344 TTTAATAATT
* *
16602354 AGATACAGATGCGTACTCAGATTC
1 AGATACAAATGCGTACACAGATTC
16602378 AGATACAAATGCAG-ACACAGAT
1 AGATACAAATGC-GTACACAGAT
16602400 CCTACCTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
AGATACAAATGCGTACACAGATTC
Found at i:16606184 original size:9 final size:9
Alignment explanation
Indices: 16606170--16606242 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
16606160 TTCCATGCAA
16606170 TTTTTTCTT
1 TTTTTTCTT
16606179 TTTTTTC-T
1 TTTTTTCTT
*
16606187 TTCTTTCTT
1 TTTTTTCTT
*
16606196 TTTGTT-TT
1 TTTTTTCTT
* * *
16606204 TCTCTTCTC
1 TTTTTTCTT
*
16606213 TTATTTCTT
1 TTTTTTCTT
*
16606222 TTCTTTCTT
1 TTTTTTCTT
**
16606231 TCCTTTCTT
1 TTTTTTCTT
16606240 TTT
1 TTT
16606243 CAGCTGCTTC
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
8 13 0.27
9 35 0.73
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:16607542 original size:22 final size:21
Alignment explanation
Indices: 16607493--16607563 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 21
16607483 AGTTCTAAAA
*
16607493 TATATTTAAAATTTAAAATATTTT
1 TATATTT-ATATTTAAAA-A-TTT
*
16607517 TATATTTACTTTTTAAAAATTT
1 TATATTTA-TATTTAAAAATTT
*
16607539 TATAATTTATATTT-AAATTTT
1 TAT-ATTTATATTTAAAAATTT
16607560 TATA
1 TATA
16607564 ATTTTCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.02
21 9 0.22
22 10 0.24
23 7 0.17
24 14 0.34
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATTTATATTTAAAAATTT
Found at i:16607546 original size:23 final size:22
Alignment explanation
Indices: 16607503--16607567 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
16607493 TATATTTAAA
16607503 ATTTAAAATATTTT-TATATTTACT
1 ATTTAAAA-ATTTTATA-ATTTA-T
*
16607527 TTTTAAAAATTTTATAATTTAT
1 ATTTAAAAATTTTATAATTTAT
*
16607549 ATTT-AAATTTTTATAATTT
1 ATTTAAAAATTTTATAATTT
16607568 TCTATTTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.38
22 4 0.11
23 10 0.27
24 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAAAAATTTTATAATTTAT
Found at i:16607573 original size:22 final size:22
Alignment explanation
Indices: 16607512--16607575 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
16607502 AATTTAAAAT
* *
16607512 ATTTTTAT-ATTTACTTTTTAAA
1 ATTTTTATAATTTTCTATTT-AA
* *
16607534 AATTTTATAA-TTTATATTTAA
1 ATTTTTATAATTTTCTATTTAA
16607555 ATTTTTATAATTTTCTATTTA
1 ATTTTTATAATTTTCTATTTA
16607576 CTTTTTTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 11 0.32
22 22 0.65
23 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTATAATTTTCTATTTAA
Found at i:16609058 original size:15 final size:15
Alignment explanation
Indices: 16609039--16609068 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
16609029 TATACTTAAA
16609039 AAAAACAAAAACCTGC
1 AAAAA-AAAAACCTGC
16609055 AAAAAAAAAACCTG
1 AAAAAAAAAACCTG
16609069 TGGCGGCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAACCTGC
Found at i:16609099 original size:27 final size:27
Alignment explanation
Indices: 16609069--16609131 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
16609059 AAAAAACCTG
* *
16609069 TGGCGGCACCAAAGGTGTCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
*
16609096 TGGCAGCACCAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
16609123 TGGCGGCAC
1 TGGCGGCAC
16609132 AGGACTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.14
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Found at i:16609347 original size:19 final size:19
Alignment explanation
Indices: 16609323--16609385 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
16609313 TCTAATTAAG
16609323 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
16609342 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
16609361 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
16609380 TAATAA
1 TAATAA
16609386 ACTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:16609449 original size:18 final size:17
Alignment explanation
Indices: 16609420--16609454 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16609410 GTAATGTTTC
*
16609420 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
16609437 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
16609455 GAAGTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:16610822 original size:27 final size:27
Alignment explanation
Indices: 16610784--16610845 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
16610774 TTTTAGTCCT
*
16610784 GTGCCGCCAATCTCTTTGACACCTTTG
1 GTGCCGCCAATCACTTTGACACCTTTG
*
16610811 GTGCCGCCAATCACTTTGGCACCTTTG
1 GTGCCGCCAATCACTTTGACACCTTTG
16610838 GTGCCGCC
1 GTGCCGCC
16610846 GCAGGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.13, C:0.35, G:0.23, T:0.29
Consensus pattern (27 bp):
GTGCCGCCAATCACTTTGACACCTTTG
Found at i:16612989 original size:20 final size:20
Alignment explanation
Indices: 16612951--16612988 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16612941 TTGAAATATA
*
16612951 TATATAATATTCATAAAAAT
1 TATAAAATATTCATAAAAAT
16612971 TATAAAATATTC-TAAAAA
1 TATAAAATATTCATAAAAA
16612989 AATCAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAAATATTCATAAAAAT
Found at i:16612997 original size:20 final size:20
Alignment explanation
Indices: 16612956--16612998 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16612946 ATATATATAT
* *
16612956 AATATTCATAAAAATTATAA
1 AATATTCAAAAAAATCATAA
16612976 AATATTCTAAAAAAATCA-AA
1 AATATTC-AAAAAAATCATAA
16612996 AAT
1 AAT
16612999 TTAAAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
AATATTCAAAAAAATCATAA
Found at i:16618602 original size:20 final size:20
Alignment explanation
Indices: 16618577--16618618 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16618567 GTTTGCACAC
*
16618577 GGGCGTGTAGAATTCCATAT
1 GGGCGTGTAGAACTCCATAT
* *
16618597 GGGCGTGTTGAGCTCCATAT
1 GGGCGTGTAGAACTCCATAT
16618617 GG
1 GG
16618619 CCGGGGCACA
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:0.19, C:0.17, G:0.36, T:0.29
Consensus pattern (20 bp):
GGGCGTGTAGAACTCCATAT
Found at i:16630475 original size:3 final size:3
Alignment explanation
Indices: 16630467--16630507 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
16630457 ACATGTTTCC
16630467 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16630508 ATACATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16637716 original size:25 final size:26
Alignment explanation
Indices: 16637688--16637736 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
16637678 TAAATGTCAA
16637688 AAAAGTA-GA-AAGGCCGAAATTTGGG
1 AAAAGTATGAGAA-GCCGAAATTTGGG
16637713 AAAAGTATGAGAAGCCGAAATTTG
1 AAAAGTATGAGAAGCCGAAATTTG
16637737 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.32
26 13 0.59
27 2 0.09
ACGTcount: A:0.45, C:0.08, G:0.29, T:0.18
Consensus pattern (26 bp):
AAAAGTATGAGAAGCCGAAATTTGGG
Found at i:16637742 original size:26 final size:25
Alignment explanation
Indices: 16637686--16637742 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
16637676 TCTAAATGTC
16637686 AAAAAAGTAGAAAGGCCGAAATTTG
1 AAAAAAGTAGAAAGGCCGAAATTTG
**
16637711 GGAAAAGTATGAGAA-GCCGAAATTTG
1 AAAAAAGTA-GA-AAGGCCGAAATTTG
16637737 AAAAAA
1 AAAAAA
16637743 AAAAGATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.27
26 17 0.65
27 2 0.08
ACGTcount: A:0.53, C:0.07, G:0.25, T:0.16
Consensus pattern (25 bp):
AAAAAAGTAGAAAGGCCGAAATTTG
Found at i:16642299 original size:24 final size:24
Alignment explanation
Indices: 16642265--16642321 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
16642255 GATATATCGA
16642265 CTTTTCATTGAGT-TCCTTTTAGAC
1 CTTTTCATTGA-TATCCTTTTAGAC
* * *
16642289 TTTTTCGTTGATATCCTTTTCGAC
1 CTTTTCATTGATATCCTTTTAGAC
16642313 CTTTTCATT
1 CTTTTCATT
16642322 TGTTATCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (24 bp):
CTTTTCATTGATATCCTTTTAGAC
Found at i:16642328 original size:25 final size:24
Alignment explanation
Indices: 16642261--16642335 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
16642251 GGATGATATA
*
16642261 TCGA-CTTTTCATTGAGT-TCCTTT
1 TCGACCTTTTCGTTGA-TATCCTTT
* *
16642284 TAGACTTTTTCGTTGATATCCTTT
1 TCGACCTTTTCGTTGATATCCTTT
* *
16642308 TCGACCTTTTCATTTGTTAT-CTTT
1 TCGACCTTTTC-GTTGATATCCTTT
16642332 TCGA
1 TCGA
16642336 ATGACATCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 4 0.10
24 32 0.76
25 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.12, T:0.53
Consensus pattern (24 bp):
TCGACCTTTTCGTTGATATCCTTT
Found at i:16642345 original size:40 final size:36
Alignment explanation
Indices: 16642301--16642397 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
16642291 TTTCGTTGAT
* **
16642301 ATCCTTTTCGACCTTTTCATTTGTTATCTTTTCGAATGAC
1 ATCCTTTTCAACCTTTTCATTTGTTATC----CGAAAAAC
* *
16642341 ATCCTGTTCAACCTTTTCACTTGTTATCCGAAAAAC
1 ATCCTTTTCAACCTTTTCATTTGTTATCCGAAAAAC
16642377 ATCCTTTTCAACCTTTTCATT
1 ATCCTTTTCAACCTTTTCATT
16642398 GATTCAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 25 0.50
40 25 0.50
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.45
Consensus pattern (36 bp):
ATCCTTTTCAACCTTTTCATTTGTTATCCGAAAAAC
Found at i:16642387 original size:36 final size:37
Alignment explanation
Indices: 16642301--16642395 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 37
16642291 TTTCGTTGAT
* * **
16642301 ATCCTTTTCGACCTTTTCATTTGTTATCTTTTCGAATGAC
1 ATCCTTTTCAACCTTTTCACTTGTTATC---TCGAAAAAC
*
16642341 ATCCTGTTCAACCTTTTCACTTGTTATC-CGAAAAAC
1 ATCCTTTTCAACCTTTTCACTTGTTATCTCGAAAAAC
16642377 ATCCTTTTCAACCTTTTCA
1 ATCCTTTTCAACCTTTTCA
16642396 TTGATTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 24 0.49
40 25 0.51
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (37 bp):
ATCCTTTTCAACCTTTTCACTTGTTATCTCGAAAAAC
Found at i:16651372 original size:3 final size:3
Alignment explanation
Indices: 16651364--16651419 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
16651354 GTAGAAATAT
*
16651364 ATG ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16651412 ATG ATG AT
1 ATG ATG AT
16651420 AAACAATCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:16654944 original size:11 final size:11
Alignment explanation
Indices: 16654925--16654957 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
16654915 AGAACACTAC
*
16654925 AAAATATCTAT
1 AAAAGATCTAT
16654936 AAAAGATCTAT
1 AAAAGATCTAT
16654947 AAAAGATCTAT
1 AAAAGATCTAT
16654958 CGGGAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (11 bp):
AAAAGATCTAT
Found at i:16657221 original size:6 final size:6
Alignment explanation
Indices: 16657210--16657239 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16657200 CCACTCAGAT
16657210 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
16657240 AATATTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:16661286 original size:66 final size:66
Alignment explanation
Indices: 16661164--16661287 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 66
16661154 GTGATTTATG
* **
16661164 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
1 TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
16661229 T
66 T
* * * * *
16661230 TATTGAATTTTCATTCTTGT-TTCAATTTCAATTATTTAGATGA-ACTTGTAAAATATTT
1 TATTGAATTTTCATTATTGTATT-AACTTAAATTATTTACAT-ATACTTGCAAAATATTT
16661288 GAATGAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
65 2 0.04
66 45 0.94
67 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (66 bp):
TATTGAATTTTCATTATTGTATTAACTTAAATTATTTACATATACTTGCAAAATATTTCTATTTT
T
Found at i:16661925 original size:30 final size:30
Alignment explanation
Indices: 16661891--16661953 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
16661881 ACTTATTTTA
*
16661891 TTGTTAATTTTGTTATTATTTTAAAGACGT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
16661921 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
16661951 TTG
1 TTG
16661954 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:16668562 original size:18 final size:18
Alignment explanation
Indices: 16668531--16668568 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16668521 TAAAAATCAC
*
16668531 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
16668549 ATTTTTTA-ATTTTAAAAT
1 ATTTTTTACA-TTTAAAAT
16668567 AT
1 AT
16668569 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:16672644 original size:25 final size:25
Alignment explanation
Indices: 16672581--16672695 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
16672571 ATTCATGTAT
* * * *
16672581 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTGTGAATCGGGAA
*
16672606 GCTCTTACGAGCTGTGAATCGGGAA
1 GCTCATACGAGCTGTGAATCGGGAA
* * * * *
16672631 GCTCATATGAGCTG-CAGTTGAGAA
1 GCTCATACGAGCTGTGAATCGGGAA
* *
16672655 GCTCATACGAGCTATAAATCGGGAA
1 GCTCATACGAGCTGTGAATCGGGAA
16672680 GCTCATACGAGCTGTG
1 GCTCATACGAGCTGTG
16672696 GTGTGTTCGC
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
24 18 0.26
25 52 0.74
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGGAA
Found at i:16680212 original size:21 final size:21
Alignment explanation
Indices: 16680186--16680244 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
16680176 CATGGTTTGC
*
16680186 CCACACGACTGTGTATCTCAG
1 CCACACGACTGTGTACCTCAG
* * *
16680207 CCACACGGCCGTGTCCCTCAG
1 CCACACGACTGTGTACCTCAG
*
16680228 CCATACGACTGTGTACC
1 CCACACGACTGTGTACC
16680245 CTTATCACAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
CCACACGACTGTGTACCTCAG
Found at i:16687610 original size:20 final size:20
Alignment explanation
Indices: 16687564--16687611 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16687554 TGAACTAAAC
*
16687564 TTTAATTTAATTTTTGAGTAT
1 TTTAA-TTAATTTTGGAGTAT
*
16687585 TATAATTAATTTTGGA-TAAT
1 TTTAATTAATTTTGGAGT-AT
16687605 TTTAATT
1 TTTAATT
16687612 TTTATCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTAATTAATTTTGGAGTAT
Found at i:16689153 original size:7 final size:7
Alignment explanation
Indices: 16689122--16689147 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16689112 TCAAGGGATG
16689122 TTTTTTA
1 TTTTTTA
16689129 TTTTTTA
1 TTTTTTA
16689136 TTTTTTA
1 TTTTTTA
16689143 TTTTT
1 TTTTT
16689148 GTTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:16693263 original size:26 final size:26
Alignment explanation
Indices: 16693234--16693293 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
16693224 GCCATATAAT
*
16693234 AAGAAGCTCACGAAGAGCCTTTAAAC
1 AAGAAGCTCACGAAGAGCCATTAAAC
*
16693260 AAGAAGCTCACGAAGAGCCATTAATC
1 AAGAAGCTCACGAAGAGCCATTAAAC
16693286 -AGAAGCTC
1 AAGAAGCTC
16693294 TAGACAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (26 bp):
AAGAAGCTCACGAAGAGCCATTAAAC
Found at i:16696223 original size:20 final size:20
Alignment explanation
Indices: 16696198--16696235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16696188 GACAAAATTG
16696198 TTATTCCCAGAAAATAAAAT
1 TTATTCCCAGAAAATAAAAT
**
16696218 TTATTCTTAGAAAATAAA
1 TTATTCCCAGAAAATAAA
16696236 TTTCCACTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
TTATTCCCAGAAAATAAAAT
Found at i:16700507 original size:23 final size:23
Alignment explanation
Indices: 16700481--16700533 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
16700471 ATAAGTGCCA
*
16700481 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
16700504 CACTAACATGTAGCCGAAGCTAG
1 CACTGATATGTAGCCGAAGCTAC
16700527 CACTGAT
1 CACTGAT
16700534 CAATAACAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:16700568 original size:23 final size:23
Alignment explanation
Indices: 16700542--16700632 Score: 150
Period size: 23 Copynumber: 4.0 Consensus size: 23
16700532 ATCAATAACA
16700542 ATATGTAGCCGAAGCTACCACTG
1 ATATGTAGCCGAAGCTACCACTG
16700565 ATATGTAGCCGAAGCTACCACTG
1 ATATGTAGCCGAAGCTACCACTG
16700588 ATATGTAGCC-ATAGCTACCACTG
1 ATATGTAGCCGA-AGCTACCACTG
16700611 A-ATTGTAGCCGAAGCTACCACT
1 ATA-TGTAGCCGAAGCTACCACT
16700633 AATCAATAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.03
23 62 0.95
24 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (23 bp):
ATATGTAGCCGAAGCTACCACTG
Found at i:16700887 original size:18 final size:17
Alignment explanation
Indices: 16700861--16700899 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16700851 ATTTTCCTTC
16700861 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
16700878 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
16700896 CACA
1 CACA
16700900 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:16710396 original size:3 final size:3
Alignment explanation
Indices: 16710388--16710427 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
16710378 AACGAAAATA
16710388 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16710428 TCCAGATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16712526 original size:19 final size:19
Alignment explanation
Indices: 16712484--16712527 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
16712474 ATATTTTAAC
16712484 TTTATTTAGGTAGATAAAT
1 TTTATTTAGGTAGATAAAT
* *
16712503 CTTATTTAGGTAGATAAGT
1 TTTATTTAGGTAGATAAAT
16712522 TTTATT
1 TTTATT
16712528 CATATTATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (19 bp):
TTTATTTAGGTAGATAAAT
Found at i:16716425 original size:19 final size:19
Alignment explanation
Indices: 16716359--16716417 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
16716349 GTATATATTT
16716359 TAAAT-TTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
16716377 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
16716396 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
16716415 TAA
1 TAA
16716418 GTTTTATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
18 5 0.12
19 35 0.88
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (19 bp):
TAAATCTTATTTAGGTAGA
Found at i:16723906 original size:31 final size:31
Alignment explanation
Indices: 16723868--16723928 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
16723858 TGGGCATTGC
* *
16723868 CATTACATATTTTTATCATTGTAGTCACTTT
1 CATTACATACTTTTATCATTGTAGCCACTTT
*
16723899 CATTACATACTTTTATCATTTTAGCCACTT
1 CATTACATACTTTTATCATTGTAGCCACTT
16723929 GCCATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (31 bp):
CATTACATACTTTTATCATTGTAGCCACTTT
Found at i:16734391 original size:18 final size:17
Alignment explanation
Indices: 16734351--16734392 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
16734341 TTCCTGGTCA
16734351 AGAGGAATCTACTGTTG
1 AGAGGAATCTACTGTTG
16734368 AGGAGGAATCTACTGTTAG
1 A-GAGGAATCTACTGTT-G
16734387 AGAGGA
1 AGAGGA
16734393 GGAAGTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (17 bp):
AGAGGAATCTACTGTTG
Found at i:16735566 original size:9 final size:9
Alignment explanation
Indices: 16735537--16735581 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
16735527 TTAAGATATA
*
16735537 TATAAATAT
1 TATAATTAT
16735546 TAT-ATGTA-
1 TATAAT-TAT
16735554 TATAATTAT
1 TATAATTAT
16735563 TATAATTAT
1 TATAATTAT
16735572 TATAATTAT
1 TATAATTAT
16735581 T
1 T
16735582 TATTTAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TATAATTAT
Found at i:16735745 original size:4 final size:4
Alignment explanation
Indices: 16735736--16735775 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
16735726 AGTAAAAGAT
*
16735736 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTG ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
16735776 TATCATGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:16752469 original size:2 final size:2
Alignment explanation
Indices: 16752462--16752509 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16752452 ACTTGGAGAT
16752462 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16752504 TC TC TC
1 TC TC TC
16752510 CCCTTTCTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16753462 original size:17 final size:16
Alignment explanation
Indices: 16753435--16753479 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
16753425 ATATAAAATG
16753435 TTAAA-ATTATTTATT
1 TTAAATATTATTTATT
16753450 TTCAAATATTA-TT-TT
1 TT-AAATATTATTTATT
*
16753465 TTACATATTATTTAT
1 TTAAATATTATTTAT
16753480 AAAGTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 7 0.28
15 8 0.32
16 6 0.24
17 4 0.16
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATATTATTTATT
Found at i:16754190 original size:5 final size:5
Alignment explanation
Indices: 16754180--16754207 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16754170 TTTATAACAA
16754180 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16754208 GTTAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:16757446 original size:97 final size:97
Alignment explanation
Indices: 16757330--16757547 Score: 314
Period size: 97 Copynumber: 2.2 Consensus size: 97
16757320 AAAATTTTTC
*
16757330 TGGGTGCTGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTT-GGTGCTGACTTGT
1 TGGGTGCTGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGCTGACCTGT
16757394 CAATGGCCGACACCAACACGAAAAAAAAAATTT
66 CAATGGCCGACACCAACA-GAAAAAAAAAATTT
*
16757427 TGGGTGCTGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGCTGGCCTGT
1 TGGGTGCTGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGCTGACCTGT
* * ** * *
16757492 CAATGGCTGGCACCAGTATACAAAAAAAATTT
66 CAATGGCCGACACCAACAGAAAAAAAAAATTT
* *
16757524 TAGATGCTGGCCT-TCTAATGGCCG
1 TGGGTGCTGGCCTGTC-AATGGCCG
16757548 ACATCAAACT
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
96 2 0.02
97 82 0.75
98 25 0.23
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (97 bp):
TGGGTGCTGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGCTGACCTGT
CAATGGCCGACACCAACAGAAAAAAAAAATTT
Found at i:16757489 original size:50 final size:50
Alignment explanation
Indices: 16757277--16757547 Score: 288
Period size: 47 Copynumber: 5.3 Consensus size: 50
16757267 TTTTTGGTTT
* *
16757277 TGGCCTGTCAATGGCCGGCACCACCTAGGAAAACGAAAAAAATAAAATTTTTCTGGGTGC
1 TGGCCTGTCAATGGCCGGCACCACCT----ATACG--AAAAA-AAAA--TTT-TAGGTGC
16757337 TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTT-GGTGC
1 TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGC
* * * * *
16757386 TGACTTGTCAATGGCC-G-A-CACCAACACGAAAAAAAAAATTTTGGGTGC
1 TGGCCTGTCAATGGCCGGCACCACCTATACG-AAAAAAAAATTTTAGGTGC
16757434 TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGC
1 TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGC
* * *
16757484 TGGCCTGTCAATGGCTGGCACCA-GTATAC--AAAAAAAATTTTAGATGC
1 TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGC
16757531 TGGCCT-TCTAATGGCCG
1 TGGCCTGTC-AATGGCCG
16757548 ACATCAAACT
Statistics
Matches: 191, Mismatches: 14, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
46 10 0.05
47 44 0.23
48 20 0.10
49 25 0.13
50 42 0.22
51 11 0.06
53 4 0.02
54 5 0.03
56 4 0.02
60 26 0.14
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (50 bp):
TGGCCTGTCAATGGCCGGCACCACCTATACGAAAAAAAAATTTTAGGTGC
Found at i:16758512 original size:31 final size:31
Alignment explanation
Indices: 16758476--16758547 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
16758466 AATACTAAAA
*
16758476 AACAGAAAAATTTAAAAATAAAAG-AAATATT
1 AACAGAAAAATTTAAAAAT-AAAGTAAAAATT
* * *
16758507 TACAGAACAATTTTAAAATAAAGTAAAAATT
1 AACAGAAAAATTTAAAAATAAAGTAAAAATT
16758538 AACAGAAAAA
1 AACAGAAAAA
16758548 AATTAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (31 bp):
AACAGAAAAATTTAAAAATAAAGTAAAAATT
Found at i:16758554 original size:31 final size:31
Alignment explanation
Indices: 16758476--16758556 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
16758466 AATACTAAAA
*
16758476 AACAG-AAAAATTTAAAAATAAAAGAAATATT
1 AACAGAAAAAATTT-AAAATAAAAGAAAAATT
* * *
16758507 TACAGAACAATTTTAAAAT-AAAGTAAAAATT
1 AACAGAAAAAATTTAAAATAAAAG-AAAAATT
*
16758538 AACAGAAAAAAATTAAAAT
1 AACAGAAAAAATTTAAAAT
16758557 TGTCGCGATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 4 0.10
31 30 0.75
32 6 0.15
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.23
Consensus pattern (31 bp):
AACAGAAAAAATTTAAAATAAAAGAAAAATT
Found at i:16760797 original size:40 final size:39
Alignment explanation
Indices: 16760727--16760854 Score: 204
Period size: 40 Copynumber: 3.2 Consensus size: 39
16760717 ATTTATTTCA
16760727 ATTTCATTTAAAAGG-CTGACACCTTTTTTTTTTCCATTT
1 ATTTCATTTAAAAGGCCTGACACCTTTTTTTTTT-CATTT
16760766 ATTTCATTTAAAAGGCCTGACACCTTTTTTTTTTTCATTT
1 ATTTCATTTAAAAGGCCTGACACC-TTTTTTTTTTCATTT
* *
16760806 ATTTTATTTAAAAGGCCTGGCACCTTTTTTTTTTCATTT
1 ATTTCATTTAAAAGGCCTGACACCTTTTTTTTTTCATTT
16760845 CATTTCATTT
1 -ATTTCATTT
16760855 TTTTATTTCA
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
39 30 0.36
40 43 0.52
41 10 0.12
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.53
Consensus pattern (39 bp):
ATTTCATTTAAAAGGCCTGACACCTTTTTTTTTTCATTT
Found at i:16760845 original size:5 final size:5
Alignment explanation
Indices: 16760837--16760911 Score: 55
Period size: 5 Copynumber: 14.6 Consensus size: 5
16760827 ACCTTTTTTT
* * *
16760837 TTTCA TTTCA TTTCA TTT-- TTTTA TTTCA TTTCA TTCTAA TTTTA TTTCCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TT-TCA TTTCA TTT-CA
* *
16760887 TTACCA TTTCCC TTTCA TTTCA TTT
1 TT-TCA TTT-CA TTTCA TTTCA TTT
16760912 AAAATATTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
3 3 0.05
5 38 0.68
6 15 0.27
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:16760857 original size:18 final size:18
Alignment explanation
Indices: 16760834--16760871 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16760824 GGCACCTTTT
16760834 TTTTTTCATTTCATTTCA
1 TTTTTTCATTTCATTTCA
*
16760852 TTTTTTTATTTCATTTCA
1 TTTTTTCATTTCATTTCA
16760870 TT
1 TT
16760872 CTAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTCATTTCATTTCA
Found at i:16760879 original size:23 final size:23
Alignment explanation
Indices: 16760830--16760879 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
16760820 GCCTGGCACC
* *
16760830 TTTTTTTTTTCATTTCATTTCAT
1 TTTTTTATTTCATTTCATTTCAA
16760853 TTTTTTATTTCATTTCA-TTCTAA
1 TTTTTTATTTCATTTCATTTC-AA
16760876 TTTT
1 TTTT
16760880 ATTTCCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTTATTTCATTTCATTTCAA
Found at i:16761040 original size:53 final size:53
Alignment explanation
Indices: 16760998--16761250 Score: 470
Period size: 53 Copynumber: 4.8 Consensus size: 53
16760988 AACTTTTTTG
16760998 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
*
16761051 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAAATTATTTTTTTCT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
16761104 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTTCT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTA-TTTTTTTCT
*
16761158 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCATATTTATTTTTTTCT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
*
16761211 CATTTCATTTTATATTTAAATTTTCTATTTTCAATTCAAA
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAA
16761251 ATTTTTCTCC
Statistics
Matches: 194, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
53 142 0.73
54 52 0.27
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (53 bp):
CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
Found at i:16761093 original size:107 final size:107
Alignment explanation
Indices: 16760998--16761250 Score: 472
Period size: 107 Copynumber: 2.4 Consensus size: 107
16760988 AACTTTTTTG
16760998 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTA-TTTTTTTCTCATTTCATTTT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTTCTCATTTCATTTT
*
16761062 ATATTTAAATTTTCTATTTTCAATGCAAAATTATTTTTTTCT
66 ATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
16761104 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTTCTCATTTCATTTT
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTTCTCATTTCATTTT
*
16761169 ATATTTAAATTTTCTATTTTCAATGCATATTTATTTTTTTCT
66 ATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
*
16761211 CATTTCATTTTATATTTAAATTTTCTATTTTCAATTCAAA
1 CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAA
16761251 ATTTTTCTCC
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
106 44 0.31
107 99 0.69
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (107 bp):
CATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTTCTCATTTCATTTT
ATATTTAAATTTTCTATTTTCAATGCAAATTTATTTTTTTCT
Found at i:16763766 original size:50 final size:50
Alignment explanation
Indices: 16763609--16763953 Score: 324
Period size: 51 Copynumber: 6.8 Consensus size: 50
16763599 TTGATAAATT
* * * * *
16763609 TGGTACCGGGCATTGACAAGCCAGCACCC--AATTTTTTTTGTATAAAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTCGTATAGAGG
* * *
16763657 TGGTGCCGGCCATTGACAAGCCAGCACCCAAATTTTTTTTTTGTATAGAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAA-ATTTTTTTCGTATAGAGG
*
16763708 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTCATATAGAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTCGTATAGAGG
* * * * **
16763758 TGGTGCCGGCCATTGACAGACCAGCACCTAAATTTTTTTCTTTTCGTTTTCCTAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAA---ATTT-TTTTCG-TAT-AGAGG
16763814 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTCGTAT--AGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAA---TTTTTTTCGTATAGAGG
* * * **
16763865 TGGTGCCGACCATTGACAGGCCAACACCCACAAATTTTTTTCGTTTTCCTAGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCA-AAATTTTTTTCG-TAT-AGAGG
* **
16763918 TGGTGTCGGCCATTGACAGGGTAGCA-CC-AAATTTTT
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
16763954 GTGTGTGTGT
Statistics
Matches: 253, Mismatches: 27, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
48 27 0.11
49 9 0.04
50 56 0.22
51 78 0.31
52 5 0.02
53 27 0.11
54 7 0.03
55 8 0.03
56 36 0.14
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (50 bp):
TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTCGTATAGAGG
Found at i:16763822 original size:56 final size:55
Alignment explanation
Indices: 16763755--16763953 Score: 234
Period size: 56 Copynumber: 3.7 Consensus size: 55
16763745 TTTCATATAG
* *
16763755 AGGTGGTGCCGGCCATTGACAGACCAGCACCTAAATTTTTTTCTTTTCGTTTTCCT
1 AGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT-TTTTCGTTTTCCT
* *
16763811 AGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTCG---T-AT
1 AGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTTTCGTTTTCCT
* * *
16763862 AGGTGGTGCCGACCATTGACAGGCCAACACCCACAA---ATTTTTTTCGTTTTCCT
1 AGGTGGTGCCGGCCATTGACAGGCCAGCACCCA-AATTTTTTTTTTTCGTTTTCCT
* **
16763915 AGGTGGTGTCGGCCATTGACAGGGTAGCA-CCAAATTTTT
1 AGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTT
16763954 GTGTGTGTGT
Statistics
Matches: 121, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
49 9 0.07
51 34 0.28
52 7 0.06
53 25 0.21
54 1 0.01
55 6 0.05
56 39 0.32
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (55 bp):
AGGTGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTTTCGTTTTCCT
Found at i:16764622 original size:33 final size:34
Alignment explanation
Indices: 16764585--16764650 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
16764575 GTTCTTCAAC
* * * *
16764585 TTTTATAAATATTAAAA-ATTCAATTAATCTTAG
1 TTTTAAAAATAATAAAATATTAAAATAATCTTAG
16764618 TTTTAAAAATAATAAAATATTAAAATAATCTTA
1 TTTTAAAAATAATAAAATATTAAAATAATCTTA
16764651 TAAAATTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (34 bp):
TTTTAAAAATAATAAAATATTAAAATAATCTTAG
Found at i:16769052 original size:14 final size:15
Alignment explanation
Indices: 16769033--16769065 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16769023 ATTATGTACT
16769033 TATGTGAT-TGTGAA
1 TATGTGATATGTGAA
*
16769047 TATGTGATATGTGGA
1 TATGTGATATGTGAA
16769062 TATG
1 TATG
16769066 ATAACTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.42
Consensus pattern (15 bp):
TATGTGATATGTGAA
Found at i:16774310 original size:42 final size:42
Alignment explanation
Indices: 16774248--16774345 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
16774238 TTTATATGGA
* * ** **
16774248 AAACGCCGCTATAGAACATGACCTTTAGTGGTGCTTTTCCCAC
1 AAACGCCACTA-AAAACATGACCTTTAGCAGCACTTTTCCCAC
16774291 AAACGCCACTAAAAACATGACCTTTAGCAGCACTTTTCCCAC
1 AAACGCCACTAAAAACATGACCTTTAGCAGCACTTTTCCCAC
*
16774333 AAATGCCACTAAA
1 AAACGCCACTAAA
16774346 GGTCATGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 38 0.79
43 10 0.21
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (42 bp):
AAACGCCACTAAAAACATGACCTTTAGCAGCACTTTTCCCAC
Found at i:16779731 original size:40 final size:40
Alignment explanation
Indices: 16779676--16779755 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
16779666 AATGCCGAAG
16779676 GATAGTTTTGAAAATTTCGATCCCTCATAAAGTTCTTCAT
1 GATAGTTTTGAAAATTTCGATCCCTCATAAAGTTCTTCAT
*
16779716 GATAGTTTTGAAAATTTCTATCCCTCATAAAGTTCTTCAT
1 GATAGTTTTGAAAATTTCGATCCCTCATAAAGTTCTTCAT
16779756 TCATTTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (40 bp):
GATAGTTTTGAAAATTTCGATCCCTCATAAAGTTCTTCAT
Found at i:16780593 original size:19 final size:20
Alignment explanation
Indices: 16780565--16780608 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
16780555 TCAAGTTATC
*
16780565 TAAAATTTTAAAAT-AAAAA
1 TAAAAATTTAAAATCAAAAA
* *
16780584 TAAAAATTTAGAATCAAAAC
1 TAAAAATTTAAAATCAAAAA
16780604 TAAAA
1 TAAAA
16780609 TAAATAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAATTTAAAATCAAAAA
Found at i:16783112 original size:21 final size:20
Alignment explanation
Indices: 16783088--16783130 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
16783078 TTTTGCTATG
*
16783088 AAACTGTTGCTGTGAAATCTA
1 AAACTGTTACTGTGAAA-CTA
* *
16783109 AAACTTTTATTGTGAAACTA
1 AAACTGTTACTGTGAAACTA
16783129 AA
1 AA
16783131 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AAACTGTTACTGTGAAACTA
Found at i:16788652 original size:15 final size:16
Alignment explanation
Indices: 16788623--16788656 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
16788613 TCACGTTAGT
*
16788623 TTTCTCTTCTTTTTTC
1 TTTCTCTTCTCTTTTC
16788639 TTTCT-TTCTCTTTTC
1 TTTCTCTTCTCTTTTC
16788654 TTT
1 TTT
16788657 TCCCTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTCTTCTCTTTTC
Found at i:16792963 original size:23 final size:22
Alignment explanation
Indices: 16792920--16792963 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
16792910 TTCTAAGTCA
16792920 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
16792943 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
16792964 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:16793072 original size:45 final size:45
Alignment explanation
Indices: 16793008--16793096 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
16792998 AACAGATACT
* * ** *
16793008 CGGTGGATTCAGCACATAGCAACCATTTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTAGTAATCAATGATGTC
16793053 CGGTGGAATCAACACATAGCAACCACCTTAGTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTAGTAATCAATGATGT
16793097 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTAGTAATCAATGATGTC
Found at i:16793132 original size:26 final size:26
Alignment explanation
Indices: 16793103--16793183 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
16793093 ATGTTCAGTT
16793103 CACATAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCTGCACATAGTACTA
* *
16793129 CACAT-GT-GACCAT-TACCATTCG-A-TA
1 CACATAGTAG-CC-TGCA-CA-TAGTACTA
*
16793154 CACGTAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCTGCACATAGTACTA
16793180 CACA
1 CACA
16793184 CGTGATCNNN
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (26 bp):
CACATAGTAGCCTGCACATAGTACTA
Found at i:16805316 original size:17 final size:16
Alignment explanation
Indices: 16805293--16805343 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
16805283 ATCCATCATC
16805293 CTTTCTTTTTCTTTTT
1 CTTTCTTTTTCTTTTT
* *
16805309 CTTTTCTTTTCCTTCTT
1 C-TTTCTTTTTCTTTTT
*
16805326 CCTTCTTTTTCTTCTTT
1 CTTTCTTTTTCTT-TTT
16805343 C
1 C
16805344 AAGGATTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTCTTTTTCTTTTT
Found at i:16805339 original size:16 final size:17
Alignment explanation
Indices: 16805295--16805341 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
16805285 CCATCATCCT
* *
16805295 TTCTTTTTCTTTTTCTT
1 TTCTTTTTCTTCTTCTC
*
16805312 TTCTTTTCCTTCTTC-C
1 TTCTTTTTCTTCTTCTC
16805328 TTCTTTTTCTTCTT
1 TTCTTTTTCTTCTT
16805342 TCAAGGATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TTCTTTTTCTTCTTCTC
Found at i:16808017 original size:16 final size:16
Alignment explanation
Indices: 16807996--16808028 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16807986 TGAATTATTG
*
16807996 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
16808012 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
16808028 A
1 A
16808029 GTCTAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.33
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:16809970 original size:18 final size:19
Alignment explanation
Indices: 16809935--16809974 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
16809925 TCTTTTACAA
*
16809935 TTTAATCCTTTTAGTTACT
1 TTTAATCCTTTTACTTACT
*
16809954 TTTAAT-CTTTTTCTTACT
1 TTTAATCCTTTTACTTACT
16809972 TTT
1 TTT
16809975 CTTTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.17, C:0.15, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTAATCCTTTTACTTACT
Found at i:16817062 original size:27 final size:27
Alignment explanation
Indices: 16817021--16817073 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
16817011 CTAGGGAGAT
*
16817021 TTGTTAGCTTGTTAGTAAGAGTAGAAG
1 TTGTTAGCTTATTAGTAAGAGTAGAAG
16817048 TTGTTAGCTTATTAGTAAGAGTAGAA
1 TTGTTAGCTTATTAGTAAGAGTAGAA
16817074 ATTTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (27 bp):
TTGTTAGCTTATTAGTAAGAGTAGAAG
Found at i:16822041 original size:14 final size:14
Alignment explanation
Indices: 16822022--16822065 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
16822012 CCACACATTT
*
16822022 GTTCTTCTCTACTG
1 GTTCTTCTCTGCTG
*
16822036 GTTCTTCTATGCTG
1 GTTCTTCTCTGCTG
16822050 GTTCTTCTCTGCTG
1 GTTCTTCTCTGCTG
16822064 GT
1 GT
16822066 GCTGGTGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.05, C:0.25, G:0.20, T:0.50
Consensus pattern (14 bp):
GTTCTTCTCTGCTG
Found at i:16822164 original size:23 final size:24
Alignment explanation
Indices: 16822135--16822191 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
16822125 CTGGTACTGG
16822135 TGTTCCTCTGCT-TG-TTGGTTCTT
1 TGTTCCTCTGCTGTGCTT-GTTCTT
16822158 TGTTCCTCTGCTGGTGCTTGTTCTT
1 TGTTCCTCTGCT-GTGCTTGTTCTT
16822183 TGTTCCTCT
1 TGTTCCTCT
16822192 TCTCCACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 12 0.39
25 17 0.55
26 2 0.06
ACGTcount: A:0.00, C:0.25, G:0.21, T:0.54
Consensus pattern (24 bp):
TGTTCCTCTGCTGTGCTTGTTCTT
Found at i:16824118 original size:18 final size:18
Alignment explanation
Indices: 16824095--16824160 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
16824085 AAAATATGAG
*
16824095 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
16824113 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
16824131 AAATGATGTTCACATCTC
1 AAATGATGTTCACATTTC
16824149 AAATGATGTTCA
1 AAATGATGTTCA
16824161 AATGGACGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:16824698 original size:72 final size:72
Alignment explanation
Indices: 16824577--16824747 Score: 249
Period size: 72 Copynumber: 2.4 Consensus size: 72
16824567 CTGACAATGC
* *
16824577 TAAA-CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 TAAATCTAGTTTTATCAATAGTTATTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTA
*
16824641 TTTATGT
66 TTTATAT
* *
16824648 GT-AATCTAGTTTTATTAATAGTTTTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
1 -TAAATCTAGTTTTATCAATAGTTATTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
*
16824712 ATTTTTAT
65 ATTTATAT
*
16824720 TAAAT-TAGTTTTATCAATAGTTGTTTAT
1 TAAATCTAGTTTTATCAATAGTTATTTAT
16824748 ATATGATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 24 0.27
72 65 0.73
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (72 bp):
TAAATCTAGTTTTATCAATAGTTATTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTA
TTTATAT
Found at i:16826152 original size:21 final size:21
Alignment explanation
Indices: 16826126--16826165 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16826116 TCGAGAAAGT
16826126 GATGAT-GATGATGACGACGAC
1 GATGATAG-TGATGACGACGAC
*
16826147 GATGATAGTGATGATGACG
1 GATGATAGTGATGACGACG
16826166 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.23
Consensus pattern (21 bp):
GATGATAGTGATGACGACGAC
Found at i:16827201 original size:34 final size:35
Alignment explanation
Indices: 16827157--16827223 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16827147 CAGTAAAATA
*
16827157 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
16827191 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
16827224 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:16839478 original size:21 final size:21
Alignment explanation
Indices: 16839441--16839481 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
16839431 GCATATTTTA
16839441 TTTTATTTTTAATAATTGTTAT
1 TTTTATTTTT-ATAATTGTTAT
16839463 TTTTATTTTT-TGAATTGTT
1 TTTTATTTTTAT-AATTGTT
16839482 GTTGACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 7 0.39
22 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TTTTATTTTTATAATTGTTAT
Found at i:16844852 original size:30 final size:29
Alignment explanation
Indices: 16844816--16844910 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 29
16844806 TAACTTTATA
16844816 TGAGCAATTCTGTTAAAATGTCAGCTTGTG
1 TGAGCAATTCTG-TAAAATGTCAGCTTGTG
16844846 TGAGCAA-TCT-TAAAATACTGTCAGCTTGTG
1 TGAGCAATTCTGT-AAA-A-TGTCAGCTTGTG
* *
16844876 TGAGCAATCCTG-AATATTGTCAGCTTGTG
1 TGAGCAATTCTGTAA-AATGTCAGCTTGTG
16844905 TGAGCA
1 TGAGCA
16844911 TTTCATTCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
27 1 0.02
28 3 0.05
29 22 0.39
30 28 0.49
31 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (29 bp):
TGAGCAATTCTGTAAAATGTCAGCTTGTG
Found at i:16844901 original size:29 final size:30
Alignment explanation
Indices: 16844834--16844910 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
16844824 TCTGTTAAAA
*
16844834 TGTCAGCTTGTGTGAGCAATCTTAAAATAC
1 TGTCAGCTTGTGTGAGCAATCCTAAAATAC
* *
16844864 TGTCAGCTTGTGTGAGCAATCCT-GAATAT
1 TGTCAGCTTGTGTGAGCAATCCTAAAATAC
16844893 TGTCAGCTTGTGTGAGCA
1 TGTCAGCTTGTGTGAGCA
16844911 TTTCATTCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (30 bp):
TGTCAGCTTGTGTGAGCAATCCTAAAATAC
Found at i:16847040 original size:12 final size:12
Alignment explanation
Indices: 16847025--16847049 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16847015 AATAACCCAA
16847025 ATTATAAAAAAT
1 ATTATAAAAAAT
16847037 ATTATAAAAAAT
1 ATTATAAAAAAT
16847049 A
1 A
16847050 ACTAAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTATAAAAAAT
Found at i:16847083 original size:29 final size:28
Alignment explanation
Indices: 16847031--16847089 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
16847021 CCAAATTATA
*
16847031 AAAAATATTATAAAAAATAACTAAAGTT
1 AAAAATATTATAAAAAATAACTAAAATT
* * *
16847059 AAAAATATTTTATAAATTAAGCTAAAATT
1 AAAAATATTATAAAAAATAA-CTAAAATT
16847088 AA
1 AA
16847090 TTAGATGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATATTATAAAAAATAACTAAAATT
Found at i:16849654 original size:27 final size:28
Alignment explanation
Indices: 16849602--16849655 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
16849592 GGACAGCCTA
* *
16849602 CTAAGGAGATAGAAGCCCAATTCATCCT
1 CTAAGGAGAGAGAAGCCCAATCCATCCT
16849630 CTAAGGAG-GAGAAGGCCCAA-CCATCC
1 CTAAGGAGAGAGAA-GCCCAATCCATCC
16849656 AAAGAGGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (28 bp):
CTAAGGAGAGAGAAGCCCAATCCATCCT
Found at i:16851555 original size:20 final size:20
Alignment explanation
Indices: 16851530--16851579 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
16851520 ATCCCTCACG
16851530 CCCGTGTGCTACATCACACA
1 CCCGTGTGCTACATCACACA
* * *
16851550 CTCGTGTGCCACATCACACG
1 CCCGTGTGCTACATCACACA
16851570 CCCGTGTGCT
1 CCCGTGTGCT
16851580 TAGGTCGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.40, G:0.20, T:0.22
Consensus pattern (20 bp):
CCCGTGTGCTACATCACACA
Found at i:16853114 original size:14 final size:15
Alignment explanation
Indices: 16853095--16853127 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
16853085 ATTTGCAATA
16853095 TAAATTTT-AAAACT
1 TAAATTTTGAAAACT
16853109 TAAATTTTGAAAACT
1 TAAATTTTGAAAACT
16853124 TAAA
1 TAAA
16853128 AATTTGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
TAAATTTTGAAAACT
Found at i:16853485 original size:54 final size:54
Alignment explanation
Indices: 16853347--16853541 Score: 229
Period size: 57 Copynumber: 3.6 Consensus size: 54
16853337 TACAAATTAC
* * *
16853347 AGAGAAGATTTCCTGTTCACTCGTTTTTTCTTGCAGGGAATTTTTACTATTTTCAT
1 AGAGAATATTTCCTGTTCACTCGTCTTTTCTTGCAGGGAATATTTACTATTTT--T
* *
16853403 CAGAGAATATTTCCTGTTCACTCGTCTTTTCTTGTAAGGAATATTTACTATTTTT
1 -AGAGAATATTTCCTGTTCACTCGTCTTTTCTTGCAGGGAATATTTACTATTTTT
** * *
16853458 AGAGAATATTTCCTGTTCACTTATCTTTTCTTGCAGGGAATATTT-C----GTC
1 AGAGAATATTTCCTGTTCACTCGTCTTTTCTTGCAGGGAATATTTACTATTTTT
* *
16853507 AAAGAATATTTCCTGTTCACTTGTCTTTTCTTGCA
1 AGAGAATATTTCCTGTTCACTCGTCTTTTCTTGCA
16853542 TCATTTTTTC
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
49 34 0.27
53 1 0.01
54 41 0.33
55 1 0.01
57 48 0.38
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (54 bp):
AGAGAATATTTCCTGTTCACTCGTCTTTTCTTGCAGGGAATATTTACTATTTTT
Found at i:16853534 original size:49 final size:49
Alignment explanation
Indices: 16853397--16853541 Score: 182
Period size: 54 Copynumber: 2.9 Consensus size: 49
16853387 TTTTTACTAT
* *
16853397 TTTCATCAGAGAATATTTCCTGTTCACTCGTCTTTTCTTGTAAGGAATA
1 TTTCATCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAAGGAATA
* * *
16853446 TTTACTATTTTTAGAGAATATTTCCTGTTCACTTATCTTTTCTTGCAGGGAATA
1 TTT-C-A---TCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAAGGAATA
* *
16853500 TTTCGTCAAAGAATATTTCCTGTTCACTTGTCTTTTCTTGCA
1 TTTCATCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCA
16853542 TCATTTTTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
49 37 0.45
50 1 0.01
51 1 0.01
53 1 0.01
54 42 0.51
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (49 bp):
TTTCATCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAAGGAATA
Found at i:16856318 original size:21 final size:23
Alignment explanation
Indices: 16856294--16856336 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
16856284 TCAATTTTTT
*
16856294 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTATTTAG
*
16856315 AAAAGAGATTTGCTTCTATTTA
1 AAAACAGATTTGCTTCTATTTA
16856337 TGATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTATTTAG
Found at i:16863870 original size:66 final size:66
Alignment explanation
Indices: 16863786--16864047 Score: 389
Period size: 66 Copynumber: 4.0 Consensus size: 66
16863776 TTACTAATAG
* * *
16863786 AGTTCCTGTCAATTACAGCTCACAACAGGTGAGTAATGCTCAAACAATAATACAAACCAATTTCA
1 AGTTCCTGTCAATCACAGCTCACAACAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTCA
16863851 C
66 C
* * *
16863852 AGTTCCTGTCAACCACAGCTTACAATAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTCA
1 AGTTCCTGTCAATCACAGCTCACAACAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTCA
16863917 C
66 C
* * * *
16863918 AGTTCTTGTCAATCAAAGCTCATAACAGGTGAGTAATGCTCAAAAAATAGTACAAATCAATTTCA
1 AGTTCCTGTCAATCACAGCTCACAACAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTCA
16863983 C
66 C
* * * * *
16863984 AATTCCTATCAATCACAACTCATAACAAGTGAGTAATGCTCAAACAATAGTACAAATCAATTTC
1 AGTTCCTGTCAATCACAGCTCACAACAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTC
16864048 TCACATTTCA
Statistics
Matches: 176, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 176 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (66 bp):
AGTTCCTGTCAATCACAGCTCACAACAGGTGAGTAATGCTCAAACAATAGTACAAATCAATTTCA
C
Found at i:16868616 original size:66 final size:63
Alignment explanation
Indices: 16868522--16868659 Score: 177
Period size: 66 Copynumber: 2.1 Consensus size: 63
16868512 ATGTTTGGTG
* * *
16868522 TGTTGGAGAGTCTAGCTTTATGCTTCACTTATGGGACATGTTTGACTCTATGAGTCTATTTGCTA
1 TGTTGGAGAGTCTAGCTTTATACTTCACTTACGAGACATGTTTGACTC--TGAGTCTATTTGCTA
* * * * *
16868587 TGTTGGAGAGTGTTAGCTTTATACTTCACTTACGAGATATGTTTGACTCTGAGTTTATTTGGTG
1 TGTTGGAGAGT-CTAGCTTTATACTTCACTTACGAGACATGTTTGACTCTGAGTCTATTTGCTA
16868651 TGTTGGAGA
1 TGTTGGAGA
16868660 TTTGTGTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 21 0.33
65 11 0.17
66 32 0.50
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (63 bp):
TGTTGGAGAGTCTAGCTTTATACTTCACTTACGAGACATGTTTGACTCTGAGTCTATTTGCTA
Found at i:16871337 original size:432 final size:431
Alignment explanation
Indices: 16870505--16871357 Score: 1411
Period size: 432 Copynumber: 2.0 Consensus size: 431
16870495 CATCTGAACC
* * *
16870505 TAAACTGTCGTAATTCGGTGTATTAGATTAAACTATTTTTCACATTTAAGGAGTTTAAATACAAG
1 TAAACTGTCGTAATTCGGTGCAGTAGATTAAACTAGTTTTCACATTTAAGGAGTTTAAATACAAG
*
16870570 CATTTTTGTTATGTTTTAATTCACTTTCTTTAGTTTTGTTTACATTCAATAAAATGTACACATTG
66 CATTTTCGTTATGTTTTAATTCACTTTCTTTAGTTTTGTTTACATTCAATAAAATGTACACATTG
* * *
16870635 AGTCTTTTATTAACATAAGGGTCGAATAAGGGGGAGCTAGTGTACATTGTGAGTGTGTAGGAGAC
131 AGTCTTTTATTAACATAAGGGTCAAATAAGGGGGAGCTAGTGTACATTGTGAGTGTGCAAGAGAC
* *
16870700 CATTGACGGCATTTCGGGGCAATACTGGACGCTATGTCACAACAAGGAGGATCCAATGTCGCAAC
196 CATTGAAGGCATTTCGGGGCAATACTGGACGCTATGTCACAACAAGGAGGATCCAATGTCACAAC
* * * *
16870765 ATAGAAATCATAATAAAGAAAGTGAGAAACTGCCTTCAATGCAGCAACACAGGCTGAGGCTGTCA
261 ATAGAAAGCAGAATAAAGAAAGTGAGAAACTGCCTGCAATGCAGCAACACAGGCTAAGGCTGTCA
* * ** *
16870830 CGACATATCCCTAAATATGGCTATAGAGGGACATGTTGGTTGCTACGTCGCGGCACAGGTCTTGG
326 CGACATATCCATAAATATGGCTATAGAGGAACATGTTGGTTGCTACGTCGCAACACAAGTCTTGG
16870895 TGTCGAGACATCGACTTTGTGACGAGAATAAACTAGTAGAT
391 TGTCGAGACATCGACTTTGTGACGAGAATAAACTAGTAGAT
* *
16870936 TAAATTGTCGTAATTTGGTGCAGTAGATTAAACTAGTTTTCACATTTAAGGAGTTTAAATACAAG
1 TAAACTGTCGTAATTCGGTGCAGTAGATTAAACTAGTTTTCACATTTAAGGAGTTTAAATACAAG
* * **
16871001 TATTTTCGTTATGTTTTAATTCAGTTTCTTTAGTTTTGTTTACATTCAATAAAATGTGTACATTG
66 CATTTTCGTTATGTTTTAATTCACTTTCTTTAGTTTTGTTTACATTCAATAAAATGTACACATTG
*
16871066 AGTCTTTTATTAATC-TAAGGGTCAAATAAGGGGGAGGTAGTGTACATTGTGAGTGTGCAAGAGA
131 AGTCTTTTATTAA-CATAAGGGTCAAATAAGGGGGAGCTAGTGTACATTGTGAGTGTGCAAGAGA
*
16871130 CCATTAGAAGGCATTTCGGGGCAATACTGGACGCTATGTCACAACAAGGGGGATCCAATGTCACA
195 CCATT-GAAGGCATTTCGGGGCAATACTGGACGCTATGTCACAACAAGGAGGATCCAATGTCACA
* * *
16871195 ACATAGAAAGCAGAATAGAGAAAGTGAGAAACTGCCTGCAATGCCGTAACACAGGCTAAGGCTGT
259 ACATAGAAAGCAGAATAAAGAAAGTGAGAAACTGCCTGCAATGCAGCAACACAGGCTAAGGCTGT
16871260 CACGACATATCCATAAATATGGCTATAGAGGAACATGTTGGTTGCTACGTCGCAACACAAGTCTT
324 CACGACATATCCATAAATATGGCTATAGAGGAACATGTTGGTTGCTACGTCGCAACACAAGTCTT
*
16871325 GGTGTCGAGACATCGAGTTTGTGACGAGAATAA
389 GGTGTCGAGACATCGACTTTGTGACGAGAATAA
16871358 GACACAAAGT
Statistics
Matches: 390, Mismatches: 30, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
431 183 0.47
432 207 0.53
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (431 bp):
TAAACTGTCGTAATTCGGTGCAGTAGATTAAACTAGTTTTCACATTTAAGGAGTTTAAATACAAG
CATTTTCGTTATGTTTTAATTCACTTTCTTTAGTTTTGTTTACATTCAATAAAATGTACACATTG
AGTCTTTTATTAACATAAGGGTCAAATAAGGGGGAGCTAGTGTACATTGTGAGTGTGCAAGAGAC
CATTGAAGGCATTTCGGGGCAATACTGGACGCTATGTCACAACAAGGAGGATCCAATGTCACAAC
ATAGAAAGCAGAATAAAGAAAGTGAGAAACTGCCTGCAATGCAGCAACACAGGCTAAGGCTGTCA
CGACATATCCATAAATATGGCTATAGAGGAACATGTTGGTTGCTACGTCGCAACACAAGTCTTGG
TGTCGAGACATCGACTTTGTGACGAGAATAAACTAGTAGAT
Found at i:16873545 original size:19 final size:19
Alignment explanation
Indices: 16873521--16873579 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 19
16873511 AGTGTCTTTC
16873521 TTATTTTTCACTTCAACTT
1 TTATTTTTCACTTCAACTT
*
16873540 TTA-TTTT--CTT--TCTT
1 TTATTTTTCACTTCAACTT
16873554 TT-TTTTTCACTTCAACTT
1 TTATTTTTCACTTCAACTT
16873572 TTATTTTT
1 TTATTTTT
16873580 TATTTGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 9 0.28
16 6 0.19
18 9 0.28
19 8 0.25
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTTCACTTCAACTT
Found at i:16873551 original size:31 final size:32
Alignment explanation
Indices: 16873515--16873578 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
16873505 CACATAAGTG
16873515 TCTTTC-TTATTTTTCACTTCAACTTTTATTT
1 TCTTTCTTTATTTTTCACTTCAACTTTTATTT
*
16873546 TCTTTCTTTTTTTTTCACTTCAACTTTTATTT
1 TCTTTCTTTATTTTTCACTTCAACTTTTATTT
16873578 T
1 T
16873579 TTATTTGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (32 bp):
TCTTTCTTTATTTTTCACTTCAACTTTTATTT
Found at i:16874790 original size:5 final size:6
Alignment explanation
Indices: 16874773--16874797 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16874763 GTCCGACTGA
16874773 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
16874798 GGAATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:16886166 original size:109 final size:108
Alignment explanation
Indices: 16885854--16886169 Score: 456
Period size: 108 Copynumber: 2.9 Consensus size: 108
16885844 GATTAAGATA
* *
16885854 TAAAAGGATATTTGGCTATTTGGTCCAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTC
1 TAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTC
* *
16885919 CTCGAATTTCCAAGCGCAAAACATTACATTATTTTAAAATTTT
66 CTCGAATTTCCAAACGCAAAACATTACCTTATTTTAAAATTTT
* *
16885962 TAAAAGGATATTCGGCTATTTA-GTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACATTT
1 TAAAAGGATATTTGGCTA-TTAGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTT
* * *
16886026 CCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAATTTTT
65 CCTCGAATTTCCAAACGCAAAACATTACCTTATTTTAAAATTTT
* *
16886070 TAAAAGGATATTTGGCTATTAGGTTGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGCTT
1 TAAAAGGATATTTGGCTATTAGGTCGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACG-TT
* * * *
16886135 T-CTCGAACTACCAAATGCAAAATATTACCTTATTT
64 TCCTCGAATTTCCAAACGCAAAACATTACCTTATTT
16886170 AGAAAAATTT
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
107 3 0.02
108 122 0.66
109 58 0.31
110 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (108 bp):
TAAAAGGATATTTGGCTATTAGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTC
CTCGAATTTCCAAACGCAAAACATTACCTTATTTTAAAATTTT
Found at i:16888600 original size:44 final size:43
Alignment explanation
Indices: 16888484--16888705 Score: 152
Period size: 44 Copynumber: 5.1 Consensus size: 43
16888474 GTCTAATGCG
* * * *
16888484 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTT-A
1 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGT--TTTTCA
* * * * *
16888528 ATCCGCTTCACTGTAACTTCAG-GAAGATAGGATTCGTTTCTTCA
1 ATCTGCTCCACTGCAACTTTAGAG-AGATAAGATTCGTTT-TTCA
** * *
16888572 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATT-G-GATGCG
1 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGTTTTTCA
*
16888613 ATCTGCTCTACT-CGAACTTTAGAGAGATAAGA-TCTGTGGTTTT-A
1 ATCTGCTCCACTGC-AACTTTAGAGAGATAAGATTC-GT--TTTTCA
* * * *
16888657 ATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCA
1 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGTTT-TTCA
16888701 ATCTG
1 ATCTG
16888706 TTTAACTGCA
Statistics
Matches: 137, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
40 2 0.01
41 31 0.23
42 5 0.04
43 6 0.04
44 89 0.65
45 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTTAGAGAGATAAGATTCGTTTTTCA
Found at i:16888714 original size:129 final size:129
Alignment explanation
Indices: 16888479--16888716 Score: 343
Period size: 129 Copynumber: 1.8 Consensus size: 129
16888469 ATAAAGTCTA
* *
16888479 ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGTAA
1 ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAA
*
16888544 CTTCAGGAAGATAGGATTCGTTTCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTGG
66 CTTCAGGAAGATAGGATTCGTTTCTTCAATCTGCTCAACTGCAACTTTAGAGAGATAAGATTGG
* ** **
16888608 ATGCGATCTGCTCTACT-CGAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCA
1 ATGCGATCTGCTCTACTGC-AACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCCACTGCA
* * * * *
16888672 ACTTTAGGGAGATAGGATTGGTTTCTTCAATCTGTTTAACTGCAA
65 ACTTCAGGAAGATAGGATTCGTTTCTTCAATCTGCTCAACTGCAA
16888717 TGTCGGGGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 1 0.01
129 94 0.99
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (129 bp):
ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAA
CTTCAGGAAGATAGGATTCGTTTCTTCAATCTGCTCAACTGCAACTTTAGAGAGATAAGATTGG
Found at i:16888885 original size:50 final size:49
Alignment explanation
Indices: 16888696--16889283 Score: 259
Period size: 50 Copynumber: 11.8 Consensus size: 49
16888686 GGATTGGTTT
* * * * * *
16888696 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTCGTAG
1 CTTCAATCT-TTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * *** * * * * *
16888746 CTTCAATCTATTCCACTACACCATCAGGAAAAGTAAGATTCGTCATTGTGG
1 CTTCAATCT-TTCAACTGCACTGCCTGG-GAAGTAAGATTCGCCGTTGTAG
* * * * * * * **
16888797 CCTCAATCTTTTAATTGTAATGTCGGGGAAGCGAGATTCGCCGTTGTAG
1 CTTCAATCTTTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * *
16888846 CTTCAATCTATTCCACTGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
1 CTTCAATCT-TTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * * * *
16888896 CTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG
1 CTTCAATC-TTTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * *
16888946 CTTCAATCCGTTCCACTGCACCT-CCTGGGAAAGTAACATCCGCCGTTGTGG
1 CTTCAAT-CTTTCAACTGCA-CTGCCTGGG-AAGTAAGATTCGCCGTTGTAG
* * * * *** *
16888997 CTTCAATCTTTTAATTGCAATGCCGGGGAAAG-AAGATTCGTTATTATAG
1 CTTCAATCTTTCAACTGCACTGCCTGGG-AAGTAAGATTCGCCGTTGTAG
* * * * * *
16889046 CTTCAATCTATTCCACTGTACTGCTTGGAAAGTAAGATTCACCATTGT-G
1 CTTCAATCT-TTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * ** * * *
16889095 ACTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCCATTGT-G
1 -CTTCAATC-TTTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * **
16889145 CTTCAATTTGTTCTACTGCACCGCCTGGGAAGTAAGATTTACCGTTGT-G
1 CTTCAATCT-TTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * * * * * **
16889194 ATTTCAAACTTTTAATTGCAATGTCAGTGAAGCGAGATTCGCCGTTGTAG
1 -CTTCAATCTTTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * *
16889244 CTTCAATCTGTTCCACTGCACCGCTTAGGAAATAAGATTC
1 CTTCAATCT-TTCAACTGCACTGCCTGGGAAGTAAGATTC
16889284 ACTATCTTCG
Statistics
Matches: 379, Mismatches: 144, Indels: 30
0.69 0.26 0.05
Matches are distributed among these distances:
48 1 0.00
49 115 0.30
50 209 0.55
51 54 0.14
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (49 bp):
CTTCAATCTTTCAACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTAG
Found at i:16888909 original size:100 final size:99
Alignment explanation
Indices: 16888696--16889285 Score: 671
Period size: 100 Copynumber: 5.9 Consensus size: 99
16888686 GGATTGGTTT
* * * *
16888696 CTTCAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGTCGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* ** * * ** *
16888761 CTACACCATCAGGAAAAGTAAGATTCGTCATTGTGG
65 CTGCACCGCCTGG-GAAGTAAGATTCACCGTTGTGG
* * *
16888797 CCTCAATCTTTTAATTGTAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
16888862 TGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
66 TGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
* **
16888896 CTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCCGTTCCA
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* * * *
16888961 CTGCACCTCCTGGGAAAGTAACATCCGCCGTTGTGG
65 CTGCACCGCCTGGG-AAGTAAGATTCACCGTTGTGG
* *** *
16888997 CTTCAATCTTTTAATTGCAATGCCGGGGAAAG-AAGATTCGTTATTATAGCTTCAATCTATTCCA
1 CTTCAATCTTTTAATTGCAATGTCGGGG-AAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* * * * * *
16889061 CTGTACTGCTTGGAAAGTAAGATTCACCATTGTGA
65 CTGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
* * * * *
16889096 CTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCGCCATTGT-GCTTCAATTTGTTCTA
1 CTTCAATC-TTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCA
* *
16889160 CTGCACCGCCTGGGAAGTAAGATTTACCGTTGTGA
65 CTGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
* * * * * *
16889195 TTTCAAACTTTTAATTGCAATGTCAGTGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
* * *
16889260 TGCACCGCTTAGGAAATAAGATTCAC
66 TGCACCGCCTGGGAAGTAAGATTCAC
16889286 TATCTTCGAT
Statistics
Matches: 413, Mismatches: 70, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
98 34 0.08
99 136 0.33
100 207 0.50
101 36 0.09
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (99 bp):
CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
TGCACCGCCTGGGAAGTAAGATTCACCGTTGTGG
Found at i:16889913 original size:132 final size:132
Alignment explanation
Indices: 16889271--16889906 Score: 925
Period size: 132 Copynumber: 4.8 Consensus size: 132
16889261 GCACCGCTTA
* * * * **
16889271 GGAA-ATAAGATTCACTATCTTCGATCTACTCTACTACTTCTTAGGGAGACAGAATCTACAATCT
1 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
** * *
16889335 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTC-CCTTCTACC
66 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCC-ACTATC
*
16889399 TTT
130 TTG
* * *
16889402 GGAAGATAAGATTCACCGTTTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
1 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
** * *
16889467 TCAACCTACTCTACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATAT
66 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
16889532 TG
131 TG
* * *
16889534 AGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAAGGAGACAGAATCTGTAATCT
1 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
* *
16889599 TTGACCTATTCCACTACTACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
66 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
16889664 TG
131 TG
* * * *
16889666 GGAATATAAGATTCACCATCTTCGATCTGCTCTACTACTGCTTAAGGAGACAGAATCTGTAATTT
1 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
* *
16889731 TTGACCTATTCCACTATTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
66 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
16889796 TG
131 TG
* * *
16889798 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGAATCTGCAATTT
1 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
* * * *
16889863 TTAACCTACTCCACTATTGTTTAAGGAGATAGGACTAATGGCTT
66 TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTT
16889907 CGATCTGTTT
Statistics
Matches: 457, Mismatches: 46, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 4 0.01
132 451 0.99
133 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (132 bp):
GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGTAATCT
TTGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATCT
TG
Found at i:16890066 original size:89 final size:89
Alignment explanation
Indices: 16889904--16890486 Score: 796
Period size: 89 Copynumber: 6.6 Consensus size: 89
16889894 GGACTAATGG
* * * * * *
16889904 CTTCGATCTGTTTCGCTGTCAGTACAGGAAGGCAAT-ATTTACTATCTTTAGTCTGCTCCGCTGT
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGC-ATGATCTGCTATCTTCAATCTGCTCCGCTGT
16889968 CAGTACAGGAAGGCAAGACTGGTTT
65 CAGTACAGGAAGGCAAGACTGGTTT
* * * * *
16889993 CTTCAATCTACTTCGCCGTCAGTACAGGAAGGCAAGATCTGCTATCTTTAGTCTGCTCCGCTGTC
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATCTGCTCCGCTGTC
*
16890058 AGTACAGGAAGGCAAAACTGGTTT
66 AGTACAGGAAGGCAAGACTGGTTT
* * * * *
16890082 CTTCGATCTGCTTCACCGTCAATACAGGAACGCATGATCTGCTATCTTCAATTTGCTCCGCTGTT
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATCTGCTCCGCTGTC
16890147 AGTACAGGAAGGCAAGACTGGTTT
66 AGTACAGGAAGGCAAGACTGGTTT
* * * * *
16890171 CTTCAATCTGCTTCGCCGTCAGTACAGGAAGGGATTATCTGCTATCTTCAATCTCCTCCGCTGTT
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATCTGCTCCGCTGTC
16890236 AGTACAGGAAGGCAAGACTGGTTT
66 AGTACAGGAAGGCAAGACTGGTTT
* * * * * *
16890260 CTTCGATCTGCTTCGCCGTTAGTACAAG-AGTGCAAGATCTGCTATCTTTAGTCTGCTCCACTGT
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAG-GCATGATCTGCTATCTTCAATCTGCTCCGCTGT
* *
16890324 CAGTATAGGAAGGTAAGACTGGTTT
65 CAGTACAGGAAGGCAAGACTGGTTT
* *
16890349 CTTCGATCTGCTTCACCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATTTGCTCCGCTGTC
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATCTGCTCCGCTGTC
*
16890414 AGTACAGGAAGGCAAGGA-TGGTGT
66 AGTACAGGAAGGCAA-GACTGGTTT
* *
16890438 CTTCGATCTGCTTCGCCGTCAGTACAGGAATGCATGATCTG-TAACTTCA
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCA
16890487 TTGATCTGTT
Statistics
Matches: 436, Mismatches: 54, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
88 10 0.02
89 422 0.97
90 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (89 bp):
CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATCTGCTCCGCTGTC
AGTACAGGAAGGCAAGACTGGTTT
Found at i:16890396 original size:267 final size:267
Alignment explanation
Indices: 16889904--16890467 Score: 889
Period size: 267 Copynumber: 2.1 Consensus size: 267
16889894 GGACTAATGG
* * * * * *
16889904 CTTCGATCTGTTTCGCTGTCAGTACAGGAAGGCAATATTTACTATCTTTAGTCTGCTCCGCTGTC
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAATATCTACTATCTTCAATCTCCTCCGCTGTC
*
16889969 AGTACAGGAAGGCAAGACTGGTTTCTTCAATCTACTTCGCCGTCAGTACAGGAAGGCAAGATCTG
66 AGTACAGGAAGGCAAGACTGGTTTCTTCAATCTACTTCGCCGTCAGTACAAGAAGGCAAGATCTG
*
16890034 CTATCTTTAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAAACTGGTTTCTTCGATCTGCTTCACC
131 CTATCTTTAGTCTGCTCCACTGTCAGTACAGGAAGGCAAAACTGGTTTCTTCGATCTGCTTCACC
*
16890099 GTCAATACAGGAACGCATGATCTGCTATCTTCAATTTGCTCCGCTGTTAGTACAGGAAGGCAA-G
196 GTCAATACAGGAACGCATGATCTGCTATCTTCAATTTGCTCCGCTGTCAGTACAGGAAGGCAAGG
*
16890163 ACTGGTTT
261 A-TGGTGT
* * * * *
16890171 CTTCAATCTGCTTCGCCGTCAGTACAGGAAGGGATTATCTGCTATCTTCAATCTCCTCCGCTGTT
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAATATCTACTATCTTCAATCTCCTCCGCTGTC
* * *
16890236 AGTACAGGAAGGCAAGACTGGTTTCTTCGATCTGCTTCGCCGTTAGTACAAG-AGTGCAAGATCT
66 AGTACAGGAAGGCAAGACTGGTTTCTTCAATCTACTTCGCCGTCAGTACAAGAAG-GCAAGATCT
* * *
16890300 GCTATCTTTAGTCTGCTCCACTGTCAGTATAGGAAGGTAAGACTGGTTTCTTCGATCTGCTTCAC
130 GCTATCTTTAGTCTGCTCCACTGTCAGTACAGGAAGGCAAAACTGGTTTCTTCGATCTGCTTCAC
* *
16890365 CGTCAGTACAGGAAGGCATGATCTGCTATCTTCAATTTGCTCCGCTGTCAGTACAGGAAGGCAAG
195 CGTCAATACAGGAACGCATGATCTGCTATCTTCAATTTGCTCCGCTGTCAGTACAGGAAGGCAAG
16890430 GATGGTGT
260 GATGGTGT
16890438 CTTCGATCTGCTTCGCCGTCAGTACAGGAA
1 CTTCGATCTGCTTCGCCGTCAGTACAGGAA
16890468 TGCATGATCT
Statistics
Matches: 271, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
266 2 0.01
267 267 0.99
268 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (267 bp):
CTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAATATCTACTATCTTCAATCTCCTCCGCTGTC
AGTACAGGAAGGCAAGACTGGTTTCTTCAATCTACTTCGCCGTCAGTACAAGAAGGCAAGATCTG
CTATCTTTAGTCTGCTCCACTGTCAGTACAGGAAGGCAAAACTGGTTTCTTCGATCTGCTTCACC
GTCAATACAGGAACGCATGATCTGCTATCTTCAATTTGCTCCGCTGTCAGTACAGGAAGGCAAGG
ATGGTGT
Found at i:16891759 original size:11 final size:10
Alignment explanation
Indices: 16891745--16891808 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
16891735 TTGGCCTCTC
16891745 CTTTTTCTTTT
1 CTTTTTC-TTT
16891756 CTTTTTC-TT
1 CTTTTTCTTT
16891765 C--TTTCTTT
1 CTTTTTCTTT
16891773 CTTTTTCTTT
1 CTTTTTCTTT
*
16891783 -TTTTCTCTCT
1 CTTTT-TCTTT
16891793 CTTTTT-TTT
1 CTTTTTCTTT
16891802 CTCTTTT
1 CT-TTTT
16891809 TTTAACAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
9 11 0.24
10 16 0.36
11 11 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:16891761 original size:6 final size:6
Alignment explanation
Indices: 16891745--16891784 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
16891735 TTGGCCTCTC
16891745 CTTTTT C-TTTT CTTTTT CTTCTTT C--TTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT
16891785 TTCTCTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.13
5 5 0.17
6 17 0.57
7 4 0.13
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Done.