Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 182 of 221
Found at i:54189186 original size:27 final size:27
Alignment explanation
Indices: 54189147--54189200 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
54189137 TACGTGCCAA
54189147 GAATCTTCCTCTTCTGGTGAGTTACCC
1 GAATCTTCCTCTTCTGGTGAGTTACCC
*
54189174 GAATCTTCTTCTTCTGGTGAGTTACCC
1 GAATCTTCCTCTTCTGGTGAGTTACCC
54189201 TCTAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.39
Consensus pattern (27 bp):
GAATCTTCCTCTTCTGGTGAGTTACCC
Found at i:54189691 original size:130 final size:130
Alignment explanation
Indices: 54189458--54189718 Score: 450
Period size: 130 Copynumber: 2.0 Consensus size: 130
54189448 TAGCAGACAA
*
54189458 GAATTTAGTAGGATGCAAACGGGTGTTTACTGTGAAACACAAATCTGATGGTTCTATTGAAAGGT
1 GAATTTAGTAGGATGCAAACGGGTGTTTACTGTGAAACACAAATCTGATGGTTCGATTGAAAGGT
* *
54189523 ACAAAGTCAGATTGGTTGCTAAAGGCTTCACTCAAACTTATCGAGTAGACTATCAAAAAACGTTT
66 ACAAAGCCAGATTGGTTACTAAAGGCTTCACTCAAACTTATCGAGTAGACTATCAAAAAACGTTT
* *
54189588 GAATTTGGTAGGATGCAAACGGGTGTTTACTGTGAAACACAAGTCTGATGGTTCGATTGAAAGGT
1 GAATTTAGTAGGATGCAAACGGGTGTTTACTGTGAAACACAAATCTGATGGTTCGATTGAAAGGT
* * *
54189653 ACAAAGCCAGATTGGTTACTAAAGGCTTCACTCAAACTTATGGAGTAGACTATCAAGAGACGTTT
66 ACAAAGCCAGATTGGTTACTAAAGGCTTCACTCAAACTTATCGAGTAGACTATCAAAAAACGTTT
54189718 G
1 G
54189719 CCCCTGTTGC
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 123 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (130 bp):
GAATTTAGTAGGATGCAAACGGGTGTTTACTGTGAAACACAAATCTGATGGTTCGATTGAAAGGT
ACAAAGCCAGATTGGTTACTAAAGGCTTCACTCAAACTTATCGAGTAGACTATCAAAAAACGTTT
Found at i:54194292 original size:19 final size:19
Alignment explanation
Indices: 54194251--54194292 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54194241 CAACATTAAA
* *
54194251 TTTTAACAGTAAAAACTAT
1 TTTTAACAGTAAAAAATAG
*
54194270 TTTTAACAGTAAAAAATGG
1 TTTTAACAGTAAAAAATAG
54194289 TTTT
1 TTTT
54194293 GGATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (19 bp):
TTTTAACAGTAAAAAATAG
Found at i:54195557 original size:23 final size:23
Alignment explanation
Indices: 54195529--54195576 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
54195519 TTATATAGTA
54195529 ATAAATTTT-TATTTAAAAA-ATAT
1 ATAAATTTTGTA--TAAAAATATAT
54195552 ATAAATTTTGTATAAAAATATAT
1 ATAAATTTTGTATAAAAATATAT
54195575 AT
1 AT
54195577 TTAAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 15 0.65
24 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAAATTTTGTATAAAAATATAT
Found at i:54199712 original size:20 final size:20
Alignment explanation
Indices: 54199687--54199734 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
54199677 TGTATGATAA
54199687 TTGATGAAGTATTGATATTC
1 TTGATGAAGTATTGATATTC
*
54199707 TTGATGAATTATTGATATTC
1 TTGATGAAGTATTGATATTC
54199727 TTGATGAA
1 TTGATGAA
54199735 AAGAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGATGAAGTATTGATATTC
Found at i:54203453 original size:27 final size:25
Alignment explanation
Indices: 54203419--54203481 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
54203409 AAAAAATAAT
*
54203419 CAAAATATTATAATTTTTTTTATTTAC
1 CAAAATA-TATAA-TATTTTTATTTAC
54203446 CAAAATATAT-ATATTTTTATTTAC
1 CAAAATATATAATATTTTTATTTAC
*
54203470 TAAAATATATAA
1 CAAAATATATAA
54203482 AACAAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 21 0.64
25 2 0.06
26 3 0.09
27 7 0.21
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (25 bp):
CAAAATATATAATATTTTTATTTAC
Found at i:54203579 original size:27 final size:27
Alignment explanation
Indices: 54203541--54203614 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
54203531 CCTTGGTCAG
*
54203541 GCCAATGCCATTGGCGGCACCAAAGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
*
54203568 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCCAAAGCCATTGGCGGCACCAAAGGT
54203595 GCCATACAG--ATTGGCGGCAC
1 GCCA-A-AGCCATTGGCGGCAC
54203615 TACTCGTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 40 0.93
28 1 0.02
29 2 0.05
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (27 bp):
GCCAAAGCCATTGGCGGCACCAAAGGT
Found at i:54203851 original size:3 final size:3
Alignment explanation
Indices: 54203845--54203873 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54203835 ATTATTATTA
54203845 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
54203874 AGTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:54204788 original size:18 final size:18
Alignment explanation
Indices: 54204765--54204802 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54204755 GGTTGGTGGT
*
54204765 GAAGAAGAATGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
54204783 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
54204801 GA
1 GA
54204803 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.45, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:54208733 original size:52 final size:48
Alignment explanation
Indices: 54208714--54208916 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
54208704 TGACAAGTGG
* *
54208714 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
54208760 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
54208812 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
54208858 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
54208904 AAAGTGATAAGTG
1 AAAGTGATAAGTG
54208917 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:54208768 original size:98 final size:98
Alignment explanation
Indices: 54208648--54208916 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
54208638 TTTGAGTACT
*
54208648 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
54208713 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
54208746 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
54208811 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
54208844 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
54208909 GATAAGTG
65 GAAAAGTG
54208917 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:54208952 original size:36 final size:37
Alignment explanation
Indices: 54208880--54209024 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
54208870 GATAGCTTTA
*
54208880 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
54208917 GCTACACTTATCTGATCAAGAAAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
54208953 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
54208990 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
54209025 ATCATACGTA
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
35 11 0.11
36 40 0.39
37 51 0.50
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:54208991 original size:73 final size:72
Alignment explanation
Indices: 54208880--54209024 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 72
54208870 GATAGCTTTA
*
54208880 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAGT
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC-AGAAACAAGT
54208945 GATAAGTG
65 GATAAGTG
* **
54208953 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTGGCTACACTTATCTGATCAGGGACAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG
54209018 ATAAGTG
66 ATAAGTG
54209025 ATCATACGTA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 16 0.24
73 52 0.76
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (72 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG
ATAAGTG
Found at i:54213218 original size:24 final size:24
Alignment explanation
Indices: 54213190--54213244 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
54213180 TTTAGTGCAT
*
54213190 AATGTTTGAAATTTATTAATTTAG
1 AATGTTAGAAATTTATTAATTTAG
*
54213214 TATGTTAGAAATTTATTAATTTAG
1 AATGTTAGAAATTTATTAATTTAG
54213238 AATGTTA
1 AATGTTA
54213245 TTTAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (24 bp):
AATGTTAGAAATTTATTAATTTAG
Found at i:54213705 original size:162 final size:162
Alignment explanation
Indices: 54213221--54213706 Score: 530
Period size: 159 Copynumber: 3.0 Consensus size: 162
54213211 TAGTATGTTA
* *
54213221 GAAATTTATTAATTTAGAATGTTATTTAAATTAATTTGGTGTAAGAAAATAACCCTTACCCCTTC
1 GAAATTTATTAATTTAGTATGTTATTTAAATTAATTTGGTGTAAGAAAATAACCCTTACCCCTGC
* *
54213286 CCTTTGCTCGTATTATTTTCTTGATTTTTATTACTTTAAATAATAATATATTATTCTCGTATTTT
66 CCTTTGCTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTT
54213351 ATTATTTTATATTATTTCAGTAAATTTTCTTT
131 ATTATTTTATATTATTTCAGTAAATTTTCTTT
* * * * * **** * * *
54213383 GAAATATT-TTGTATTAATTAT-TT-TTGAATTTTAAAAAAGT-T-AG-TAATACACTCTTACTT
1 GAAAT-TTATT-AATTTAGTATGTTATTTAA-ATTAATTTGGTGTAAGAAAATA-ACCCTTAC-C
* * * * * *
54213442 CC-GCCATTTGTTCGTATT-TTTTCTCCGCA-TTTTATTCCTTTGAA-AAATAT-TATAATT-TC
61 CCTGCCCTTTGCTCGTATTATTTTCT-CG-ATTTTTATTACTTTAAATAAAAATATATTATTCTC
* * * ** ** *
54213501 -TAATTTTATAATTTTACATTATTCCAGTGCATAATGTTT
124 GT-ATTTTATTATTTTATATTATTTCAGTAAATTTTCTTT
54213540 GAAATTTATTAATTTAGTATGTTATTTAAATTAATTTGGTGTAAGAAAATAACCCTTACCCCTGC
1 GAAATTTATTAATTTAGTATGTTATTTAAATTAATTTGGTGTAAGAAAATAACCCTTACCCCTGC
54213605 CCTTTGCTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTT
66 CCTTTGCTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTT
*
54213670 ATTATTTTATATTATTTCAGTATATTTTCTTT
131 ATTATTTTATATTATTTCAGTAAATTTTCTTT
54213702 GAAAT
1 GAAAT
54213707 ATTTTGTATT
Statistics
Matches: 247, Mismatches: 56, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
156 10 0.04
157 46 0.19
158 14 0.06
159 52 0.21
160 51 0.21
161 14 0.06
162 51 0.21
163 9 0.04
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (162 bp):
GAAATTTATTAATTTAGTATGTTATTTAAATTAATTTGGTGTAAGAAAATAACCCTTACCCCTGC
CCTTTGCTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTT
ATTATTTTATATTATTTCAGTAAATTTTCTTT
Found at i:54214196 original size:16 final size:15
Alignment explanation
Indices: 54214175--54214204 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54214165 AATAAAAATA
54214175 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
54214191 TATTATTTTATATT
1 TATTATTTTATATT
54214205 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:54214786 original size:36 final size:36
Alignment explanation
Indices: 54214746--54214900 Score: 129
Period size: 36 Copynumber: 4.2 Consensus size: 36
54214736 TTTTCTTTTT
54214746 TTTCCTTCCCTCTTCTTCTTTTTTTTTCTCTTCTCC
1 TTTCCTTCCCTCTTCTTCTTTTTTTTTCTCTTCTCC
* *
54214782 TTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTT-TCTTCTCC
1 TTTCC--TTC---CC-TCTTCTTCTTTTTTTTTCTCTTCTCC
* * *
54214823 TTTCCTCTTCTTCTTCTTCTTTTTTTTTCTCTTCTCA
1 TTTCCT-TCCCTCTTCTTCTTTTTTTTTCTCTTCTCC
** *
54214860 TTTCCTTTTCT-TTCCTTCTTTTTCTTTCT-TTC-CC
1 TTTCCTTCCCTCTT-CTTCTTTTTTTTTCTCTTCTCC
*
54214894 TCTCCTT
1 TTTCCTT
54214901 TTCCCCCCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
34 7 0.07
35 5 0.05
36 37 0.38
37 14 0.14
38 3 0.03
39 1 0.01
40 1 0.01
41 15 0.15
42 15 0.15
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (36 bp):
TTTCCTTCCCTCTTCTTCTTTTTTTTTCTCTTCTCC
Found at i:54214808 original size:42 final size:42
Alignment explanation
Indices: 54214745--54214886 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
54214735 TTTTTCTTTT
* *
54214745 TTTTCCTTCCCTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCC
1 TTTTCTTTCCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCC
* *
54214787 TTTTCTTTCCTTCTTTTTCTTTCTTTTT-TCTTCTCCTTTCC
1 TTTTCTTTCCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCC
*
54214828 ---TC-TT-CTTCTTCTTCTTTTTTTTTCTCTTCTCATTTCC
1 TTTTCTTTCCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCC
*
54214865 TTTTCTTTCCTTCTTTTTCTTT
1 TTTTCTTTCCTTCTTCTTCTTT
54214887 CTTTCCCTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
36 17 0.20
37 14 0.16
38 2 0.02
40 2 0.02
41 15 0.17
42 36 0.42
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (42 bp):
TTTTCTTTCCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCC
Found at i:54214811 original size:46 final size:43
Alignment explanation
Indices: 54214756--54214890 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 43
54214746 TTTCCTTCCC
* * * *
54214756 TCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTT-TCCT
1 TCTTTTTCTTTCTTTTTTTCTTCTCCTTTCCTCTTCTTCTCCT
54214798 TCTTTTTCTTTC-TTTTTTCTTCTCCTTTCCTCTTC-T-T-CT
1 TCTTTTTCTTTCTTTTTTTCTTCTCCTTTCCTCTTCTTCTCCT
* *
54214837 TC---TTCTTT-TTTTTTCTCTTCTCATTTCCTTTTCTT-TCCT
1 TCTTTTTCTTTCTTTTTT-TCTTCTCCTTTCCTCTTCTTCTCCT
54214876 TCTTTTTCTTTCTTT
1 TCTTTTTCTTTCTTT
54214891 CCCTCTCCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
36 11 0.14
37 16 0.20
38 2 0.03
39 8 0.10
40 2 0.03
41 21 0.27
42 16 0.20
43 3 0.04
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (43 bp):
TCTTTTTCTTTCTTTTTTTCTTCTCCTTTCCTCTTCTTCTCCT
Found at i:54215024 original size:8 final size:9
Alignment explanation
Indices: 54214999--54215023 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54214989 TTTGCAGGTA
54214999 TTTTTTTTG
1 TTTTTTTTG
54215008 TTTTTTTTG
1 TTTTTTTTG
54215017 TTTTTTT
1 TTTTTTT
54215024 GATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:54218133 original size:16 final size:16
Alignment explanation
Indices: 54218112--54218145 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54218102 TGTGTTTCAC
*
54218112 TTTGACTGCATGGCAT
1 TTTGACTACATGGCAT
*
54218128 TTTGACTACATGGTAT
1 TTTGACTACATGGCAT
54218144 TT
1 TT
54218146 CATTATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTACATGGCAT
Found at i:54218611 original size:19 final size:19
Alignment explanation
Indices: 54218587--54218633 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54218577 AACGTCTATT
*
54218587 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
54218606 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
54218625 TATGCATTA
1 TTTGCATTA
54218634 AAATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:54220530 original size:18 final size:18
Alignment explanation
Indices: 54220507--54220544 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54220497 TGAGCAAATG
54220507 TTCTTTCATTCTTTAAGA
1 TTCTTTCATTCTTTAAGA
*
54220525 TTCTTTCATTCTTTAGGA
1 TTCTTTCATTCTTTAAGA
54220543 TT
1 TT
54220545 TTTTTTTGCC
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:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (18 bp):
TTCTTTCATTCTTTAAGA
Found at i:54222538 original size:22 final size:22
Alignment explanation
Indices: 54222483--54222543 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
54222473 CATTCTCGAA
* *
54222483 AAAATGACATTCTGCATTCATT
1 AAAATGTCATTCTACATTCATT
* *
54222505 AAAATATTATTCTACATTCATT
1 AAAATGTCATTCTACATTCATT
*
54222527 CAAATGTCATTCATACA
1 AAAATGTCATTC-TACA
54222544 CGTCTAGTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAATGTCATTCTACATTCATT
Found at i:54222746 original size:45 final size:45
Alignment explanation
Indices: 54222689--54222834 Score: 133
Period size: 45 Copynumber: 3.3 Consensus size: 45
54222679 GCAGCAGTAG
* *
54222689 AGTAGGTTAAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGA
1 AGTAGATTAAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGAGA
* * * * *
54222734 AGTAGATTAAAGATACCAG-CCTTGTC-TCCT-TGAGC-AGCAGTGG
1 AGTAGATTAAAGATAGCAGATCTTGTCTTCCTGT-A-CTGGCAGAGA
*
54222777 AGTAGATTGAAA-AT-GACAGATCTTGCCTTCCTGTACTGGCAGAGA
1 AGTAGATT-AAAGATAG-CAGATCTTGTCTTCCTGTACTGGCAGAGA
*
54222822 AGTAGATTGAAGA
1 AGTAGATTAAAGA
54222835 CACCAGTCTT
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
42 1 0.01
43 23 0.29
44 18 0.23
45 36 0.46
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (45 bp):
AGTAGATTAAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGAGA
Found at i:54222774 original size:88 final size:88
Alignment explanation
Indices: 54222662--54222854 Score: 255
Period size: 88 Copynumber: 2.2 Consensus size: 88
54222652 GGTGAGACCT
* * * *
54222662 CAGCTTTATCTCCCTGAGCAGCAGTAGAGTAGGTT-AAAGAT-AGCAGATCTTGTCTTCCTGTAC
1 CAGCCTTATCTCCTTGAGCAGCAGTAGAGTAGATTGAAA-ATGA-CAGATCTTGCCTTCCTGTAC
* *
54222725 TGGCAGCGAAGTAGATTAAAGATAC
64 TGGCAGAGAAGTAGATTAAAGACAC
* *
54222750 CAGCCTTGTCTCCTTGAGCAGCAGTGGAGTAGATTGAAAATGACAGATCTTGCCTTCCTGTACTG
1 CAGCCTTATCTCCTTGAGCAGCAGTAGAGTAGATTGAAAATGACAGATCTTGCCTTCCTGTACTG
*
54222815 GCAGAGAAGTAGATTGAAGACAC
66 GCAGAGAAGTAGATTAAAGACAC
* *
54222838 CAGTCTTATCGCCTTGA
1 CAGCCTTATCTCCTTGA
54222855 CGTTGCAATG
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 87 0.96
89 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
CAGCCTTATCTCCTTGAGCAGCAGTAGAGTAGATTGAAAATGACAGATCTTGCCTTCCTGTACTG
GCAGAGAAGTAGATTAAAGACAC
Found at i:54223248 original size:44 final size:43
Alignment explanation
Indices: 54223207--54223571 Score: 233
Period size: 44 Copynumber: 8.4 Consensus size: 43
54223197 TCCTATCTTC
* *
54223207 CTGAAGTTGCAGTGGAGCGGATTAAAACCACAGGTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCGGATTAAAACCACA-ATCTTATCTCT
* ** * ** * *
54223251 CTGAAGTTGCAGTAGAGCAAATAGAAAAAAATTAATCCTATCTCT
1 CTGAAGTTGCAGTGGAGCGGAT-TAAAACCA-CAATCTTATCTCT
* ** *
54223296 TTGAAGTTATAGTGGAGCGGATTAAAACCACAGATATTATCTCT
1 CTGAAGTTGCAGTGGAGCGGATTAAAACCACA-ATCTTATCTCT
* ** * *** * *
54223340 TTGAAGTTGCAGCAGAGCAGA-TCGCATC-CAGTCTTATCTCT
1 CTGAAGTTGCAGTGGAGCGGATTAAAACCACAATCTTATCTCT
* * * *
54223381 CTGAAGTTGCAGTGGAGCAGAGA-GAAGAAAC-CAATCCTATCTCC
1 CTGAAGTTGCAGTGGAGC-G-GATTAA-AACCACAATCTTATCTCT
*
54223425 CTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCGGATTAAAACCACA-ATCTTATCTCT
* * * *** * *
54223469 CTAAAGTTACAGTAGAGC--ATATCGCATC-CAATCCTATCT-T
1 CTGAAGTTGCAGTGGAGCGGAT-TAAAACCACAATCTTATCTCT
*
54223509 CTTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCT
1 C-TGAAGTTGCAGTGGAGCGGATTAAAACCACA-ATCTTATCTCT
*
54223554 CTGAAGTTGCAGTAGAGC
1 CTGAAGTTGCAGTGGAGC
54223572 AGATCGCATC
Statistics
Matches: 235, Mismatches: 70, Indels: 32
0.70 0.21 0.09
Matches are distributed among these distances:
40 2 0.01
41 45 0.19
42 14 0.06
43 18 0.08
44 124 0.53
45 31 0.13
46 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
CTGAAGTTGCAGTGGAGCGGATTAAAACCACAATCTTATCTCT
Found at i:54223303 original size:89 final size:89
Alignment explanation
Indices: 54223194--54223358 Score: 242
Period size: 89 Copynumber: 1.9 Consensus size: 89
54223184 TTGAGGCCAA
* * *
54223194 TAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGGTCTTATCTCCCTGAAGTT
1 TAATCCTATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATATTATCTCCCTGAAGTT
*
54223259 GCAGTAGAGCAAATAGAAAAAAAT
66 GCAGCAGAGCAAATAGAAAAAAAT
* * **
54223283 TAATCCTATC-TCTTTGAAGTTATAGTGGAGCGGATTAAAACCACAGATATTATCTCTTTGAAGT
1 TAATCCTATCTTC-CTGAAGTTACAGTGGAGCGGATTAAAACCACAGATATTATCTCCCTGAAGT
54223347 TGCAGCAGAGCA
65 TGCAGCAGAGCA
54223359 GATCGCATCC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 2 0.03
89 65 0.97
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (89 bp):
TAATCCTATCTTCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATATTATCTCCCTGAAGTT
GCAGCAGAGCAAATAGAAAAAAAT
Found at i:54223451 original size:129 final size:130
Alignment explanation
Indices: 54223240--54223526 Score: 371
Period size: 129 Copynumber: 2.2 Consensus size: 130
54223230 AAAACCACAG
* * * ** **
54223240 GTCTTATCTCCCTGAAGTTGCAGTAGAGCAAATAGAAAAAAATTAATCCTATCTCTTTGAAGTTA
1 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAAAGAGAAAAAAACCAATCCTATCTCCCTGAAGTTA
* * * *
54223305 TAGTGGAGCGGATTAAAACCACAGATATTATCTCTTTGAAGTTGCAGCAGAGCAGATCGCATCCA
66 CAGTGGAGCGGATTAAAACCACAGATATTATCTCTCTAAAGTTACAGCAGAGCAGATCGCATCCA
* * * *
54223370 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGAGAG-AAGAAACCAATCCTATCTCCCTGAGGTTG
1 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAAAGAGAAAAAAACCAATCCTATCTCCCTGAAGTTA
* * *
54223434 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTACAGTAGAGCATATCGCATCCA
66 CAGTGGAGCGGATTAAAACCACAGATATTATCTCTCTAAAGTTACAGCAGAGCAGATCGCATCCA
* *
54223499 ATCCTATCT-TCTTGAAGTTGCAGTGGAG
1 GTCTTATCTCTC-TGAAGTTGCAGTGGAG
54223527 TGGATTAAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
128 2 0.01
129 103 0.76
130 31 0.23
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (130 bp):
GTCTTATCTCTCTGAAGTTGCAGTGGAGCAAAGAGAAAAAAACCAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAACCACAGATATTATCTCTCTAAAGTTACAGCAGAGCAGATCGCATCCA
Found at i:54223504 original size:85 final size:85
Alignment explanation
Indices: 54223411--54223581 Score: 279
Period size: 85 Copynumber: 2.0 Consensus size: 85
54223401 AGAGAAGAAA
*
54223411 CCAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGT
*
54223476 TACAGTAGAGCATATCGCAT
66 TACAGTAGAGCAGATCGCAT
* * * *
54223496 CCAATCCTATCTTCTTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGT
1 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGT
*
54223561 TGCAGTAGAGCAGATCGCAT
66 TACAGTAGAGCAGATCGCAT
54223581 C
1 C
54223582 AGACTTATCT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (85 bp):
CCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGT
TACAGTAGAGCAGATCGCAT
Found at i:54224407 original size:19 final size:20
Alignment explanation
Indices: 54224369--54224407 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
54224359 GGAAAGAAGG
54224369 TTCTTATTTTCTTCTATTTT
1 TTCTTATTTTCTTCTATTTT
54224389 TTCTATATTTT-TT-TATTTT
1 TTCT-TATTTTCTTCTATTTT
54224408 ATTTTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (20 bp):
TTCTTATTTTCTTCTATTTT
Found at i:54225461 original size:36 final size:36
Alignment explanation
Indices: 54225414--54225486 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
54225404 TTTTAGAAAA
54225414 TATATATTTTGGTTTCGTCAAAACATTAAAATCATT
1 TATATATTTTGGTTTCGTCAAAACATTAAAATCATT
*
54225450 TATATATTTTGGTTTTGTCAAAACATTAAAATCATT
1 TATATATTTTGGTTTCGTCAAAACATTAAAATCATT
54225486 T
1 T
54225487 TCTTTTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.47
Consensus pattern (36 bp):
TATATATTTTGGTTTCGTCAAAACATTAAAATCATT
Found at i:54226667 original size:29 final size:30
Alignment explanation
Indices: 54226625--54226686 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
54226615 AGACATTAGT
*
54226625 ATGCTTCAGCTGTGTTCC-TGGTTACTTGC
1 ATGCTTCAGATGTGTTCCATGGTTACTTGC
*
54226654 ATGCTTCAGATGTGTTCCATGGTTTCTTGC
1 ATGCTTCAGATGTGTTCCATGGTTACTTGC
54226684 ATG
1 ATG
54226687 TTGCTGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (30 bp):
ATGCTTCAGATGTGTTCCATGGTTACTTGC
Found at i:54235680 original size:21 final size:20
Alignment explanation
Indices: 54235647--54235686 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
54235637 TTTATGGAAC
54235647 TTTTATATATTTTGATATTAA
1 TTTTATATATTTTGA-ATTAA
54235668 TTTTATA-ATTTTTGAATTA
1 TTTTATATA-TTTTGAATTA
54235687 TTTGTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATATATTTTGAATTAA
Found at i:54242996 original size:42 final size:42
Alignment explanation
Indices: 54242948--54243029 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
54242938 CTTAGGTGCT
* *
54242948 ATTTCTTATTTTATAATTGTTAATTAATCCAATTGCATCTGA
1 ATTTCTTATTTGATAATTGTTAATTAAACCAATTGCATCTGA
*
54242990 ATTTCTTATTTGATAGTTGTTAATTAAACCAATTGCATCT
1 ATTTCTTATTTGATAATTGTTAATTAAACCAATTGCATCT
54243030 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (42 bp):
ATTTCTTATTTGATAATTGTTAATTAAACCAATTGCATCTGA
Found at i:54250802 original size:46 final size:46
Alignment explanation
Indices: 54250731--54250823 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
54250721 TCAATTAACG
* *
54250731 AAGTGAAAACTCATTCTCTGTTTCCAACCTTTTAAGGTTTAATCTC
1 AAGTGAAAACTCACTCTCTGATTCCAACCTTTTAAGGTTTAATCTC
*
54250777 AAGTGAAAACTCACTCTCTGATTCCACCCTTTTAAGGTTTAATCTC
1 AAGTGAAAACTCACTCTCTGATTCCAACCTTTTAAGGTTTAATCTC
54250823 A
1 A
54250824 CTTCCTTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (46 bp):
AAGTGAAAACTCACTCTCTGATTCCAACCTTTTAAGGTTTAATCTC
Found at i:54254466 original size:31 final size:30
Alignment explanation
Indices: 54254405--54254473 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
54254395 TCTTAATAAA
*
54254405 TTATTATATAATAAATATTTTTATAATTTAT
1 TTATAATA-AATAAATATTTTTATAATTTAT
* *
54254436 TTTTAATAAATATAATTTTTTTA-AATTTTAT
1 TTATAATAAATA-AATATTTTTATAA-TTTAT
54254467 TTATAAT
1 TTATAAT
54254474 CTAGGATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATAATAAATAAATATTTTTATAATTTAT
Found at i:54268548 original size:22 final size:22
Alignment explanation
Indices: 54268499--54268556 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
54268489 CCCAGAAGTA
*
54268499 TGTCTCGAGACATATTGAGTTT
1 TGTCTCGAGACATATTGAGCTT
* *
54268521 TATCTCGAGACATA-TGTTGCTT
1 TGTCTCGAGACATATTG-AGCTT
*
54268543 TGTCTCAAGACATA
1 TGTCTCGAGACATA
54268557 GTTCATTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (22 bp):
TGTCTCGAGACATATTGAGCTT
Found at i:54268567 original size:20 final size:22
Alignment explanation
Indices: 54268523--54268578 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
54268513 TTGAGTTTTA
* *
54268523 TCTCGAGACATATGTTGCTTTG
1 TCTCAAGACATATGTTGCATTG
54268545 TCTCAAGACATA-GTT-CATTG
1 TCTCAAGACATATGTTGCATTG
*
54268565 TCTTAAGAC-TATGT
1 TCTCAAGACATATGT
54268579 ATTGAGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 14 0.47
21 3 0.10
22 11 0.37
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (22 bp):
TCTCAAGACATATGTTGCATTG
Found at i:54270862 original size:67 final size:67
Alignment explanation
Indices: 54270789--54271001 Score: 295
Period size: 67 Copynumber: 3.2 Consensus size: 67
54270779 CACAGCTAAC
* * * *
54270789 CTATGGTCTTACTCGTTAGGTTCCATGTTTAATGTCCTGACGGACTCCATTGGTTACCACAGTCG
1 CTATGGTCTTACTCATTAGGTTCCATGTTTAATGTCCTGGCGGACTCCATTGGTTACCATAGTCA
54270854 AA
66 AA
* * *
54270856 CTATGGTCTTAC-CATTCAGGTTCCATGTTTAATGTCTTGGCGAACTCCATTGGTTGCCATAGTC
1 CTATGGTCTTACTCATT-AGGTTCCATGTTTAATGTCCTGGCGGACTCCATTGGTTACCATAGTC
54270920 AAA
65 AAA
* * *
54270923 CTATGGTCTTACTCATTAGGTTCCATGTTTAATGTCCTGGTGGATTCCATTAGTTGA-CATAGTC
1 CTATGGTCTTACTCATTAGGTTCCATGTTTAATGTCCTGGCGGACTCCATTGGTT-ACCATAGTC
*
54270987 TAA
65 AAA
54270990 CTATGGTCTTAC
1 CTATGGTCTTAC
54271002 CCCCATAATC
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
66 3 0.02
67 122 0.95
68 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (67 bp):
CTATGGTCTTACTCATTAGGTTCCATGTTTAATGTCCTGGCGGACTCCATTGGTTACCATAGTCA
AA
Found at i:54272107 original size:24 final size:24
Alignment explanation
Indices: 54272072--54272127 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
54272062 GTGTACGTAC
54272072 ATACATACTTTAATATATAAAAAT
1 ATACATACTTTAATATATAAAAAT
* *
54272096 ATACATATTTTAATATATAAATAT
1 ATACATACTTTAATATATAAAAAT
*
54272120 ATATATAC
1 ATACATAC
54272128 GAATAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (24 bp):
ATACATACTTTAATATATAAAAAT
Found at i:54272360 original size:3 final size:3
Alignment explanation
Indices: 54272334--54272404 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
54272324 ATATAAGGGA
* * * *
54272334 AAT AAC AAT AAT ATT AAT ACT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
54272382 AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
54272405 AATTACTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54272820 original size:12 final size:12
Alignment explanation
Indices: 54272803--54272827 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54272793 TTTTGCTGAA
54272803 AAAGAGAGAGAG
1 AAAGAGAGAGAG
54272815 AAAGAGAGAGAG
1 AAAGAGAGAGAG
54272827 A
1 A
54272828 TCCTCTCTTT
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:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:54273719 original size:45 final size:45
Alignment explanation
Indices: 54273655--54273785 Score: 156
Period size: 45 Copynumber: 2.9 Consensus size: 45
54273645 CAAGTTTTCA
*
54273655 CATGATGTCCTAACATCTTTCAGCTATGGTCTTACTCATTTCTAT
1 CATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTCTAT
* * * *
54273700 CATGATGTCATAACATCTTTTAGTTATTGTCTTACT-AGTTTTTAT
1 CATGATGTCATAACATCTTTCAGCTATGGTCTTACTCA-TTTCTAT
**** *
54273745 CATGATGTCATAGTGCCTTTCAGGTATGGTCTTACTCATTT
1 CATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTT
54273786 TAAGCGTATA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
44 1 0.01
45 70 0.97
46 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (45 bp):
CATGATGTCATAACATCTTTCAGCTATGGTCTTACTCATTTCTAT
Found at i:54275101 original size:3 final size:3
Alignment explanation
Indices: 54275093--54275137 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
54275083 AGACCAATTG
54275093 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54275138 GTAAGTCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54280033 original size:109 final size:108
Alignment explanation
Indices: 54279839--54280129 Score: 415
Period size: 109 Copynumber: 2.7 Consensus size: 108
54279829 GATTCATCGT
* * ** * *
54279839 AAAAATCGAAACCCAGTA-AGTTAGGGTACGACCTTCTCGAA-TTTCTAAACGCAAGACATTGCC
1 AAAAATCGAAACCCAGCACA-TTAGGGCACG-TTTTCTCGAATTTTC-AAACGCAAAATATTGCC
* *
54279902 TTACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAG
63 TTATTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAG
54279948 AAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAACGCAAAATATTGCCTTA
1 AAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAACGCAAAATATTGCCTTA
54280013 TTTTGAAATTTTTAAAAGGATATTTGGCTATTTGGTCAAACGAG
66 TTTTGAAA-TTTTAAAAGGATATTTGGCTATTTGGTCAAACGAG
* * * *
54280057 AAAAGTCGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACGCAAAATATTACCTTA
1 AAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAACGCAAAATATTGCCTTA
*
54280122 TTTAGAAA
66 TTTTGAAA
54280130 AATTTTCCTT
Statistics
Matches: 166, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
108 33 0.20
109 132 0.80
110 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (108 bp):
AAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAACGCAAAATATTGCCTTA
TTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCAAACGAG
Found at i:54280349 original size:18 final size:18
Alignment explanation
Indices: 54280308--54280354 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
54280298 ATAAATATAT
54280308 AAATAAATAACAAGTAAAA
1 AAAT-AATAACAAGTAAAA
*
54280327 CAATAATAACAA-TAAAGA
1 AAATAATAACAAGTAAA-A
54280345 AAATAGATAA
1 AAATA-ATAA
54280355 AAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATAATAACAAGTAAAA
Found at i:54280521 original size:15 final size:16
Alignment explanation
Indices: 54280480--54280521 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
54280470 TATAAAAGTT
54280480 TATACAAG--TATGTA
1 TATACAAGTTTATGTA
*
54280494 TATACACGTTTATGTA
1 TATACAAGTTTATGTA
54280510 TATA-AAGTTTAT
1 TATACAAGTTTAT
54280522 AAAAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 7 0.29
16 10 0.42
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (16 bp):
TATACAAGTTTATGTA
Found at i:54280895 original size:29 final size:29
Alignment explanation
Indices: 54280838--54280919 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 29
54280828 CAAATAATGT
* *
54280838 TAATAATAATAATAATAGCAATAATAATAGTAG
1 TAATGATAA-AATAATAGTAATAAT-AT-G-AG
54280871 TAAT-AGTAAAAATAA-AGTAATAATATGAG
1 TAATGA-T-AAAATAATAGTAATAATATGAG
54280900 TAATGATAAAATAATAGTAA
1 TAATGATAAAATAATAGTAA
54280920 GAGAAGTGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
28 7 0.16
29 12 0.27
30 2 0.05
31 2 0.05
32 9 0.20
33 10 0.23
34 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.11, T:0.29
Consensus pattern (29 bp):
TAATGATAAAATAATAGTAATAATATGAG
Found at i:54286594 original size:18 final size:17
Alignment explanation
Indices: 54286573--54286615 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
54286563 ACCTGAAGCT
54286573 GCGAGCTCATCCAAAGAC
1 GCGAGCTCAT-CAAAGAC
**
54286591 GCGAGCTCATCAAAGTT
1 GCGAGCTCATCAAAGAC
54286608 GCGAGCTC
1 GCGAGCTC
54286616 GACCTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (17 bp):
GCGAGCTCATCAAAGAC
Found at i:54286611 original size:17 final size:17
Alignment explanation
Indices: 54286572--54286638 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
54286562 TACCTGAAGC
*
54286572 TGCGAGCTCATCCAAAGA
1 TGCGAGCTCAT-CAAAGT
*
54286590 CGCGAGCTCATCAAAGT
1 TGCGAGCTCATCAAAGT
* *
54286607 TGCGAGCTCGACCTAAGT
1 TGCGAGCTC-ATCAAAGT
* *
54286625 TGTGAGCACATCAA
1 TGCGAGCTCATCAA
54286639 GTGTGAGCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 16 0.41
18 23 0.59
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (17 bp):
TGCGAGCTCATCAAAGT
Found at i:54292404 original size:34 final size:34
Alignment explanation
Indices: 54292364--54292431 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
54292354 AATCAATATT
54292364 TACAGAAATCTCATGTAATATTTGAAATATTTTC
1 TACAGAAATCTCATGTAATATTTGAAATATTTTC
54292398 TACAGAAATCTCATGTAATATTTGAAATATTTTC
1 TACAGAAATCTCATGTAATATTTGAAATATTTTC
54292432 ATTTTAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (34 bp):
TACAGAAATCTCATGTAATATTTGAAATATTTTC
Found at i:54295536 original size:36 final size:36
Alignment explanation
Indices: 54295446--54295538 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
54295436 TTGGAGCCAT
** * *
54295446 TAGTGTGTTTCAAATGTATTAGCTCTTATGAACATC
1 TAGTGTGTTTCGGATGGATTAGCTCTTACGAACATC
* *
54295482 TAGTTTGTTTCGGATGGATTAGCTCTTACGAGCATC
1 TAGTGTGTTTCGGATGGATTAGCTCTTACGAACATC
* * *
54295518 TTGTGTGTTTTGGTTGGATTA
1 TAGTGTGTTTCGGATGGATTA
54295539 TCGATGTACT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (36 bp):
TAGTGTGTTTCGGATGGATTAGCTCTTACGAACATC
Found at i:54307757 original size:21 final size:20
Alignment explanation
Indices: 54307724--54307763 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
54307714 TTTATGGAAC
54307724 TTTTATACATTTTAATATTAA
1 TTTTATACATTTTAA-ATTAA
54307745 TTTTATA-ATTTTTAAATTA
1 TTTTATACA-TTTTAAATTA
54307764 TTTGTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATACATTTTAAATTAA
Found at i:54310325 original size:4 final size:4
Alignment explanation
Indices: 54310308--54310350 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
54310298 TCTTGCTTTT
** * *
54310308 TTTA TTTA AATA TTTA TTTG TTTA TTTA TTTA TCTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
54310351 TTATTATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:54311079 original size:3 final size:3
Alignment explanation
Indices: 54311071--54311136 Score: 87
Period size: 3 Copynumber: 21.0 Consensus size: 3
54311061 AACTAATCAG
*
54311071 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT GCATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT --A-TT
*
54311119 ATT ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
54311137 TACCCATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
3 52 0.93
4 1 0.02
5 1 0.02
6 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:54311206 original size:16 final size:16
Alignment explanation
Indices: 54311185--54311224 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
54311175 CTAGATTTTG
*
54311185 TTATATATATACATAC
1 TTATATATATACACAC
54311201 TTATATATATACACAC
1 TTATATATATACACAC
*
54311217 TTACATAT
1 TTATATAT
54311225 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATATATATACACAC
Found at i:54311755 original size:19 final size:18
Alignment explanation
Indices: 54311723--54311760 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54311713 TTTTAGGAAA
54311723 TATTTTAGTTTTTATTAT
1 TATTTTAGTTTTTATTAT
*
54311741 TATTTTATTTATTTATTAT
1 TATTTTAGTT-TTTATTAT
54311760 T
1 T
54311761 TCATATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTTTAGTTTTTATTAT
Found at i:54311758 original size:16 final size:18
Alignment explanation
Indices: 54311723--54311761 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
54311713 TTTTAGGAAA
*
54311723 TATTTTAGTTTTTATTAT
1 TATTTTAGTTTATATTAT
54311741 TATTTTA-TTTAT-TTAT
1 TATTTTAGTTTATATTAT
54311757 TATTT
1 TATTT
54311762 CATATACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 4 0.20
18 7 0.35
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTTTAGTTTATATTAT
Found at i:54314048 original size:17 final size:17
Alignment explanation
Indices: 54314020--54314079 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
54314010 TCATAAATTT
54314020 AATAATTATATATTTAAA
1 AATAA-TATATATTTAAA
*
54314038 AATAATATATA-ATAAA
1 AATAATATATATTTAAA
*
54314054 TAAAAATATATAGTTTAAA
1 -AATAATATATA-TTTAAA
*
54314073 ACTAATA
1 AATAATA
54314080 ACAACAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.12
17 16 0.47
18 10 0.29
19 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAATATATATTTAAA
Found at i:54326910 original size:16 final size:16
Alignment explanation
Indices: 54326889--54326927 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
54326879 CGAGTGAAAG
*
54326889 AAATAAACAAAA-TATA
1 AAATAAA-AAAAGTAAA
54326905 AAATAAAAAAAGTAAA
1 AAATAAAAAAAGTAAA
54326921 AAATAAA
1 AAATAAA
54326928 GAATATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
AAATAAAAAAAGTAAA
Found at i:54327240 original size:18 final size:16
Alignment explanation
Indices: 54327217--54327258 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
54327207 ATTTTTTAAA
54327217 AAATAATTACATATATAT
1 AAATAATTACAT-TAT-T
54327235 AAATAATTACATTATT
1 AAATAATTACATTATT
*
54327251 AATTAATT
1 AAATAATT
54327259 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
18 12 0.52
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAATTACATTATT
Found at i:54333973 original size:22 final size:23
Alignment explanation
Indices: 54333948--54333993 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
54333938 ATAATTGCTT
54333948 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
54333970 TTATATATTTCTACATATACTTA
1 TTATAGATATATACATATACTTA
54333993 T
1 T
54333994 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:54334001 original size:22 final size:22
Alignment explanation
Indices: 54333959--54334001 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
54333949 TATAGATATA
* *
54333959 TACATATATTATTATATATTTC
1 TACATATATTATTACACATTTC
54333981 TACATATACTTA-TACACATTT
1 TACATATA-TTATTACACATTT
54334002 TTTTTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (22 bp):
TACATATATTATTACACATTTC
Found at i:54334450 original size:5 final size:5
Alignment explanation
Indices: 54334436--54334469 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
54334426 ACATAAGTGC
54334436 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
54334470 ATTGTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:54334510 original size:13 final size:13
Alignment explanation
Indices: 54334436--54334515 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 13
54334426 ACATAAGTGC
54334436 TTTATTTATTTTAT
1 TTTATTTA-TTTAT
54334450 TTTATTTTATTTTAT
1 TTTA-TTTA-TTTAT
*
54334465 TTTATATTGTTTCACAT
1 TTTAT-TTATTT---AT
* * *
54334482 ATTATTGATTTGT
1 TTTATTTATTTAT
*
54334495 TTTTTTTATTTAT
1 TTTATTTATTTAT
54334508 TTTATTTA
1 TTTATTTA
54334516 GTTGTTATGG
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 17 0.33
14 8 0.16
15 16 0.31
16 4 0.08
17 6 0.12
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:54336336 original size:19 final size:20
Alignment explanation
Indices: 54336296--54336339 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
54336286 GTCTCTTTAG
* *
54336296 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
54336315 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
54336334 GCATTA
1 GCATTA
54336340 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:54340730 original size:43 final size:43
Alignment explanation
Indices: 54340682--54340812 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 43
54340672 ACAAAGCCTC
54340682 GCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTT
1 GCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTT
* ** * * * * *
54340725 GCCTTCCA--GCGTTAACAACGAAGCAGATCAAA-AA-CA-AGCCTT
1 GCCTT-CATTG-GTT-GCAGTGGAGCTGGTTAAAGAAGCAGA-TCTT
54340767 GCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTT
1 GCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTT
54340810 GCC
1 GCC
54340813 CTCCTGCATT
Statistics
Matches: 63, Mismatches: 16, Indels: 18
0.65 0.16 0.19
Matches are distributed among these distances:
41 14 0.22
42 16 0.25
43 19 0.30
44 14 0.22
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
GCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTT
Found at i:54340832 original size:85 final size:88
Alignment explanation
Indices: 54340691--54341197 Score: 546
Period size: 88 Copynumber: 5.8 Consensus size: 88
54340681 CGCCTTCATT
* * *
54340691 GGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCTTCCAGCGTTAACAACGAAGCAGATC-
1 GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
* *
54340754 AA-AAACAAGCCTTGCCT-TCATT
66 AAGAAACAAACCTTGCCTCTC-TC
* *
54340776 GGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATCTTGCCCTCCTGCATTAATAGCGAAGCAGATCG
1 GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
*
54340840 AA-AATA-AAACCTTGCCTC-CATT
66 AAGAA-ACAAACCTTGCCTCTC-TC
* ** * * *
54340862 GGTTGCAATGGAGCTATTTAAAGATAGCAGATCCTGCATTCCTGCATTAACAGCGAAGCAGATCG
1 GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
*
54340927 AAGACACAAACCTTGCCTCTCTC
66 AAGAAACAAACCTTGCCTCTCTC
* * ** * *
54340950 GGGTGTAGCAGAGCTGGTTGAAA-ACAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGACC
1 GGTTGCAGTGGAGCTGGTT-AAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC
*
54341014 GAAGACACAAACCTTGCCTCTCTC
65 GAAGAAACAAACCTTGCCTCTCTC
** * * * * *
54341038 GGTTGTGGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCG
1 GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
*
54341103 AAGACACAAACCTTGCCTCTCTC
66 AAGAAACAAACCTTGCCTCTCTC
* * * * ** * * * * *
54341126 GGTTGTAGTGGAGCTAGTTGAAGATAGTGGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCG
1 GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
54341191 AAGAAAC
66 AAGAAAC
54341198 TAGATCTTAT
Statistics
Matches: 364, Mismatches: 49, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
85 58 0.16
86 39 0.11
87 42 0.12
88 221 0.61
89 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
GGTTGCAGTGGAGCTGGTTAAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
AAGAAACAAACCTTGCCTCTCTC
Found at i:54341074 original size:44 final size:43
Alignment explanation
Indices: 54341014--54341149 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 43
54341004 GAAGCAGACC
54341014 GAAGACACAAACCTTGCCTCTCTCGGTTGTGGTGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGGTGGAGCTGGTT
* * * * * * *
54341057 GAAGACAACAGATCTTGCCT-TC-CTGTAT-TGACAGCGAAGCAGGTC
1 GAAGAC-ACAAACCTTGCCTCTCTCGGT-TGTG---GTGGAGCTGGTT
* *
54341102 GAAGACACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTAGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTGTGGTGGAGCTGGTT
54341145 GAAGA
1 GAAGA
54341150 TAGTGGATCT
Statistics
Matches: 69, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
42 5 0.07
43 21 0.30
44 22 0.32
45 17 0.25
46 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTCTCGGTTGTGGTGGAGCTGGTT
Found at i:54342753 original size:22 final size:23
Alignment explanation
Indices: 54342728--54342773 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
54342718 ATAATTGCTT
54342728 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
54342750 TTATATATTTCTACATATACTTA
1 TTATAGATATATACATATACTTA
54342773 T
1 T
54342774 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:54342781 original size:22 final size:22
Alignment explanation
Indices: 54342739--54342781 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
54342729 TATAGATATA
* *
54342739 TACATATATTATTATATATTTC
1 TACATATATTATTACACATTTC
54342761 TACATATACTTA-TACACATTT
1 TACATATA-TTATTACACATTT
54342782 TTTTTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (22 bp):
TACATATATTATTACACATTTC
Found at i:54343230 original size:5 final size:5
Alignment explanation
Indices: 54343216--54343244 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
54343206 ACATAAGTGC
54343216 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
54343245 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:54343240 original size:15 final size:14
Alignment explanation
Indices: 54343216--54343289 Score: 53
Period size: 13 Copynumber: 5.1 Consensus size: 14
54343206 ACATAAGTGC
54343216 TTTATTTATTTTAT
1 TTTATTTATTTTAT
54343230 TTTATTTTATTTTAT
1 TTTA-TTTATTTTAT
* * *
54343245 ATTGTTTCACATATTA-
1 TTTATTT---ATTTTAT
* *
54343261 TTGATTTGTTTT-T
1 TTTATTTATTTTAT
54343274 TTTATTTATTTTAT
1 TTTATTTATTTTAT
54343288 TT
1 TT
54343290 AGTTGTTATG
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
13 13 0.30
14 10 0.23
15 12 0.27
16 4 0.09
17 5 0.11
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:54345054 original size:21 final size:21
Alignment explanation
Indices: 54345029--54345095 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
54345019 AGTTTATGTG
54345029 ATTATATTATTATCATATATT
1 ATTATATTATTATCATATATT
* **
54345050 TTTATATTATT-TCA-CCATT
1 ATTATATTATTATCATATATT
*
54345069 ATTATCATTATTATCATATAGT
1 ATTAT-ATTATTATCATATATT
54345091 ATTAT
1 ATTAT
54345096 TAATTGAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 7 0.19
20 9 0.25
21 13 0.36
22 7 0.19
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.55
Consensus pattern (21 bp):
ATTATATTATTATCATATATT
Found at i:54351486 original size:15 final size:18
Alignment explanation
Indices: 54351452--54351490 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
54351442 GTAATTAAAA
54351452 TGTATTTCATACTATTTT
1 TGTATTTCATACTATTTT
54351470 TGTATTT-A-ACT-TTTT
1 TGTATTTCATACTATTTT
54351485 TGTATT
1 TGTATT
54351491 ATTTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 3 0.14
17 1 0.05
18 7 0.33
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (18 bp):
TGTATTTCATACTATTTT
Found at i:54353556 original size:26 final size:27
Alignment explanation
Indices: 54353512--54353563 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
54353502 ATGGAGTTGC
* *
54353512 ATTTTATAAAAAAATATTTTTTATTTA
1 ATTTTATAAAAAAAGATTTTATATTTA
*
54353539 ATTTTA-AAAAATAGATTTTATATTT
1 ATTTTATAAAAAAAGATTTTATATTT
54353564 TTGATGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTTATAAAAAAAGATTTTATATTTA
Found at i:54358640 original size:18 final size:18
Alignment explanation
Indices: 54358617--54358688 Score: 117
Period size: 18 Copynumber: 4.0 Consensus size: 18
54358607 CCCAACTACT
*
54358617 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
54358635 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
54358653 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
54358671 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
54358689 ATAAACGGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:54358669 original size:36 final size:36
Alignment explanation
Indices: 54358618--54358691 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
54358608 CCAACTACTG
*
54358618 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAACAGTACCGTATACGTGAATAGTACCA
*
54358654 TATACGTGAATAGTACCGTATACGTGAATAGTACCA
1 TATACGTGAACAGTACCGTATACGTGAATAGTACCA
54358690 TA
1 TA
54358692 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (36 bp):
TATACGTGAACAGTACCGTATACGTGAATAGTACCA
Found at i:54361916 original size:20 final size:18
Alignment explanation
Indices: 54361888--54361931 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
54361878 ATTGAGGTAA
*
54361888 TAAAGTGTACATAATAAGAT
1 TAAAATGTACA-AA-AAGAT
*
54361908 TAAAATGTACAAAAATAT
1 TAAAATGTACAAAAAGAT
54361926 TAAAAT
1 TAAAAT
54361932 AAATCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (18 bp):
TAAAATGTACAAAAAGAT
Found at i:54362536 original size:9 final size:9
Alignment explanation
Indices: 54362524--54362572 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
54362514 TCAATTCGAT
*
54362524 TAATTTGGG
1 TAATTCGGG
*
54362533 TAATTCAGG
1 TAATTCGGG
54362542 TAATTCGGG
1 TAATTCGGG
**
54362551 TAATTCGAT
1 TAATTCGGG
*
54362560 TAATTCGGT
1 TAATTCGGG
54362569 TAAT
1 TAAT
54362573 ATTTAACAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:54362563 original size:18 final size:18
Alignment explanation
Indices: 54362516--54362572 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
54362506 GTAGTGATTC
*
54362516 AATTCGATTAATTTGGGT
1 AATTCGATTAATTCGGGT
*
54362534 AATTC-AGGTAATTCGGGT
1 AATTCGA-TTAATTCGGGT
*
54362552 AATTCGATTAATTCGGTT
1 AATTCGATTAATTCGGGT
54362570 AAT
1 AAT
54362573 ATTTAACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (18 bp):
AATTCGATTAATTCGGGT
Found at i:54368343 original size:20 final size:20
Alignment explanation
Indices: 54368276--54368346 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
54368266 ACCCAAATCT
54368276 CCAATACCCAACTAGCCTAAC
1 CCAA-ACCCAACTAGCCTAAC
* * *
54368297 CCAAACCC-TC-AGCCCAAAA
1 CCAAACCCAACTAG-CCTAAC
*
54368316 CAATAACCCAACTAGCCTAAC
1 CCA-AACCCAACTAGCCTAAC
54368337 CCAAACCCAA
1 CCAAACCCAA
54368347 GGCCCAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 16 0.42
21 11 0.29
22 2 0.05
ACGTcount: A:0.42, C:0.44, G:0.04, T:0.10
Consensus pattern (20 bp):
CCAAACCCAACTAGCCTAAC
Found at i:54368352 original size:40 final size:39
Alignment explanation
Indices: 54368277--54368354 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
54368267 CCCAAATCTC
*
54368277 CAATACCCAACTAGCCTAACCCAAACCCTCAGCCCAAAA
1 CAATACCCAACTAGCCTAACCCAAACCCTAAGCCCAAAA
54368316 CAATAACCCAACTAGCCTAACCCAAACCC-AAGGCCCAAA
1 CAAT-ACCCAACTAGCCTAACCCAAACCCTAA-GCCCAAA
54368355 TTCGGAGCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 5 0.14
40 31 0.86
ACGTcount: A:0.42, C:0.42, G:0.06, T:0.09
Consensus pattern (39 bp):
CAATACCCAACTAGCCTAACCCAAACCCTAAGCCCAAAA
Found at i:54370032 original size:24 final size:24
Alignment explanation
Indices: 54369957--54370057 Score: 82
Period size: 24 Copynumber: 4.2 Consensus size: 24
54369947 ATAAGATAAC
* * * *
54369957 TTAAAATAATAATACCTAATAGCT
1 TTAAAACAATCATACATAATAGAT
* *
54369981 TTAAAACAA-CAATACATAATAAAA
1 TTAAAACAATC-ATACATAATAGAT
*
54370005 TTAAAACAATCATACATAACAGAT
1 TTAAAACAATCATACATAATAGAT
* *
54370029 TTAAAAGAAT-GTACATAAT-GATT
1 TTAAAACAATCATACATAATAGA-T
54370052 TTAAAA
1 TTAAAA
54370058 TAACAAAACC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
22 2 0.03
23 14 0.23
24 45 0.73
25 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (24 bp):
TTAAAACAATCATACATAATAGAT
Found at i:54374772 original size:13 final size:12
Alignment explanation
Indices: 54374748--54374799 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
54374738 GTTCAGATTG
54374748 AAAA-AAGAAAA
1 AAAAGAAGAAAA
54374759 AAAAGAAGGAAAA
1 AAAAGAA-GAAAA
*
54374772 AGAAGAAGAAAA
1 AAAAGAAGAAAA
*
54374784 AAGAAAAAGAAAA
1 AA-AAGAAGAAAA
54374797 AAA
1 AAA
54374800 GGAGAGGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 4 0.11
12 9 0.26
13 22 0.63
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:54374773 original size:19 final size:17
Alignment explanation
Indices: 54374749--54374799 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 17
54374739 TTCAGATTGA
54374749 AAAAAGAAAAAAAAGAAGG
1 AAAAAGAAAAAAAA-AA-G
54374768 AAAAAGAAGAAGAAAAAAG
1 AAAAAGAA-AA-AAAAAAG
54374787 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
54374800 GGAGAGGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.10
18 2 0.07
19 17 0.57
20 4 0.13
21 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:54374790 original size:6 final size:6
Alignment explanation
Indices: 54374749--54374797 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
54374739 TTCAGATTGA
*
54374749 AAAAAG AAAAA- AAAGAAGG AAAAAG AAGAAG AAAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAA-AA-G AAAAAG AAAAAG -AAAAAG AAAAAG AAAAA
54374798 AAGGAGAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 24 0.65
7 7 0.19
8 3 0.08
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:54374940 original size:42 final size:42
Alignment explanation
Indices: 54374880--54374987 Score: 153
Period size: 42 Copynumber: 2.5 Consensus size: 42
54374870 GGGCGACTCC
* *
54374880 AATTTTGGATCAAATTGGGGCATGAGGCGATCAGAACAGCTTA
1 AATTTT-GATCAAATTGGGGCATGAGGCAATCAGAACAGCTCA
* * * *
54374923 AATTTTGATCAGATTGGGGTATGAGGTAATCAGAGCAGCTCA
1 AATTTTGATCAAATTGGGGCATGAGGCAATCAGAACAGCTCA
54374965 AATTTTGATCAAATTGGGGCATG
1 AATTTTGATCAAATTGGGGCATG
54374988 TGGTGATCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 51 0.89
43 6 0.11
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (42 bp):
AATTTTGATCAAATTGGGGCATGAGGCAATCAGAACAGCTCA
Found at i:54376010 original size:43 final size:43
Alignment explanation
Indices: 54375962--54376099 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
54375952 GAAGCAGGTC
54375962 GAAGACACAAACTTTGCCTCTCTCGGTTGTAGTGGAGCTGGTT
1 GAAGACACAAACTTTGCCTCTCTCGGTTGTAGTGGAGCTGGTT
* * * * * * *
54376005 GAAGACAACAGA-TCTTGCCT-TC-CTGTCTTGACAGCGAAGCAGATT
1 GAAGAC-ACAAACT-TTGCCTCTCTC-G-GTTG-TAGTGGAGCTGGTT
* *
54376050 GAAGACACAAACCTTGCCTCTCTTGGTTGTAGTGGAGCTGGTT
1 GAAGACACAAACTTTGCCTCTCTCGGTTGTAGTGGAGCTGGTT
54376093 GAAGACA
1 GAAGACA
54376100 ACAGATCTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
42 1 0.01
43 26 0.37
44 26 0.37
45 18 0.25
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (43 bp):
GAAGACACAAACTTTGCCTCTCTCGGTTGTAGTGGAGCTGGTT
Found at i:54376023 original size:44 final size:44
Alignment explanation
Indices: 54375975--54376112 Score: 147
Period size: 44 Copynumber: 3.1 Consensus size: 44
54375965 GACACAAACT
54375975 TTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGATC
1 TTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGATC
* * * * * * * *
54376019 TTGCCT-TC-CTGTCTTGACAGCGAAGCAGATTGAAGAC-ACAAACC
1 TTGCCTCTCTC-G-GTTG-TAGTGGAGCTGGTTGAAGACAACAGATC
*
54376063 TTGCCTCTCTTGGTTGTAGTGGAGCTGGTTGAAGACAACAGATC
1 TTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGATC
54376107 TTGCCT
1 TTGCCT
54376113 TCCTGCATTG
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
42 1 0.01
43 18 0.25
44 34 0.48
45 18 0.25
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (44 bp):
TTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGATC
Found at i:54376078 original size:88 final size:88
Alignment explanation
Indices: 54375925--54376156 Score: 358
Period size: 88 Copynumber: 2.6 Consensus size: 88
54375915 GTGAATATAG
* * * *
54375925 CAGATCTTGCCTTCCTGTATTGACGGCGAAGCAGGTCGAAGACACAAACTTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGTCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTT
54375990 GTAGTGGAGCTGGTTGAAGACAA
66 GTAGTGGAGCTGGTTGAAGACAA
* *
54376013 CAGATCTTGCCTTCCTGTCTTGACAGCGAAGCAGATTGAAGACACAAACCTTGCCTCTCTTGGTT
1 CAGATCTTGCCTTCCTGTCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTT
54376078 GTAGTGGAGCTGGTTGAAGACAA
66 GTAGTGGAGCTGGTTGAAGACAA
* * **
54376101 CAGATCTTGCCTTCCTG-CATTGACAGTGAAGCAGATCGAAAACACAAGTCTTGCCT
1 CAGATCTTGCCTTCCTGTC-TTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
54376157 TCCTGTACTG
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
87 1 0.01
88 131 0.99
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGTCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTT
GTAGTGGAGCTGGTTGAAGACAA
Found at i:54376679 original size:20 final size:20
Alignment explanation
Indices: 54376654--54376703 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
54376644 GGGGCAGCTG
54376654 TAGGGCCCAATTTTTTTACC
1 TAGGGCCCAATTTTTTTACC
54376674 TAGGGCCCAATTTTTTTACC
1 TAGGGCCCAATTTTTTTACC
54376694 TAGGGCCCAA
1 TAGGGCCCAA
54376704 GTACAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (20 bp):
TAGGGCCCAATTTTTTTACC
Found at i:54376795 original size:20 final size:20
Alignment explanation
Indices: 54376728--54376796 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
54376718 ACCCAAATCT
54376728 CCAATACCCAACTAGCCTAAC
1 CCAA-ACCCAACTAGCCTAAC
* * *
54376749 CCAAACCC-TC-AGCCCAAAA
1 CCAAACCCAACTAG-CCTAAC
*
54376768 CAATAACCCAACTAGCCTAAC
1 CCA-AACCCAACTAGCCTAAC
54376789 CCAAACCC
1 CCAAACCC
54376797 GAGGCCCAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.19
20 14 0.39
21 11 0.31
22 2 0.06
ACGTcount: A:0.41, C:0.45, G:0.04, T:0.10
Consensus pattern (20 bp):
CCAAACCCAACTAGCCTAAC
Found at i:54377913 original size:3 final size:3
Alignment explanation
Indices: 54377898--54377956 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
54377888 AAATTTCATT
*
54377898 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54377946 TTA TTA TTA TT
1 TTA TTA TTA TT
54377957 TCTTTTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54378049 original size:27 final size:25
Alignment explanation
Indices: 54377985--54378049 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 25
54377975 GTATGTTTTT
*
54377985 TATATAT-TTTTATATATACACTTA
1 TATATATATTTTATATACACACTTA
* *
54378009 TATACATACTTTTTATATACATATCTATA
1 TATATATA--TTTTATATACACA-CT-TA
54378038 TATATATATTTT
1 TATATATATTTT
54378050 TTTTTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 6 0.19
27 15 0.47
28 2 0.06
29 9 0.28
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATATTTTATATACACACTTA
Found at i:54378165 original size:13 final size:13
Alignment explanation
Indices: 54378147--54378171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54378137 ATATATTTTT
54378147 TTATTTTTTTATC
1 TTATTTTTTTATC
54378160 TTATTTTTTTAT
1 TTATTTTTTTAT
54378172 TTTTTATAAT
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTATC
Found at i:54378408 original size:39 final size:40
Alignment explanation
Indices: 54378345--54378435 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
54378335 ATATATGTTC
* * *
54378345 TTTATATTTTATGATTTATATATACCTATATATATAC-TT
1 TTTATATTTTATGATGTATATATACCTACATATATACATA
* *
54378384 TTTATATTTTATGATAGT-TATATACGTACATATGTACATA
1 TTTATATTTTATGAT-GTATATATACCTACATATATACATA
*
54378424 TATATATTTTAT
1 TTTATATTTTAT
54378436 ATAATAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (40 bp):
TTTATATTTTATGATGTATATATACCTACATATATACATA
Found at i:54378512 original size:32 final size:32
Alignment explanation
Indices: 54378452--54378512 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
54378442 ATTTTAGAAT
* *
54378452 ACATATATACATATATTTTTCATGTTTTTATA
1 ACATACATACATATATTTTTCATATTTTTATA
*
54378484 ACATACATACTTATATTTTAT-ATATTTTT
1 ACATACATACATATATTTT-TCATATTTTT
54378513 GCATTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (32 bp):
ACATACATACATATATTTTTCATATTTTTATA
Found at i:54378603 original size:30 final size:29
Alignment explanation
Indices: 54378565--54378621 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
54378555 TTTATATCTT
* *
54378565 ATAATTTATATATATATATTCATATATTC
1 ATAATTTATATATATACATACATATATTC
*
54378594 ATAATTTTATGTATATACATACATATAT
1 ATAA-TTTATATATATACATACATATAT
54378622 ATTTCCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (29 bp):
ATAATTTATATATATACATACATATATTC
Found at i:54379137 original size:109 final size:109
Alignment explanation
Indices: 54378865--54379150 Score: 475
Period size: 109 Copynumber: 2.6 Consensus size: 109
54378855 TTCAAAAAGA
* *
54378865 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
54378930 GGTGTCGATTTTTATCGTTCAACCAAATGGCTTAATATCCTTTT
66 GGTGTCGATTTTTATCGTTCAACCAAATGGCTAAATATCCTTTT
54378974 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
54379039 GGTGTCGATTTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
66 GGTGTCGA-TTTTTATCGTTCAACCAAATGGCTAAATATCCTTTT
* * * * *
54379084 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTTGA-AGAACGTGCCCTAATGTGTTG
1 AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
54379148 GGT
66 GGT
54379151 TTCAATTTCT
Statistics
Matches: 167, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
109 91 0.54
110 76 0.46
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTATCGTTCAACCAAATGGCTAAATATCCTTTT
Found at i:54390852 original size:12 final size:12
Alignment explanation
Indices: 54390806--54390854 Score: 64
Period size: 12 Copynumber: 3.9 Consensus size: 12
54390796 ATCGGCTTCT
54390806 TTTTATTTATTTTC
1 TTTTATTTA--TTC
54390820 TTTTATTGT-TTC
1 TTTTATT-TATTC
54390832 TTTTATTTATTC
1 TTTTATTTATTC
54390844 TTTTATTTATT
1 TTTTATTTATT
54390855 TGCTACTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.03
12 24 0.73
14 7 0.21
15 1 0.03
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTATTTATTC
Found at i:54390906 original size:18 final size:18
Alignment explanation
Indices: 54390883--54390929 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
54390873 AAAATTTAGA
54390883 TATTATTATTAAAAGTAT
1 TATTATTATTAAAAGTAT
* * *
54390901 TATTATTATCACAATTAT
1 TATTATTATTAAAAGTAT
*
54390919 TATTTTTATTA
1 TATTATTATTA
54390930 TACATATTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTATTATTAAAAGTAT
Found at i:54394154 original size:18 final size:18
Alignment explanation
Indices: 54394133--54394177 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
54394123 CATTCGTTTC
54394133 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
54394150 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
54394169 CAAAACATT
1 CAAAACATT
54394178 TTCTTATTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:54398746 original size:17 final size:18
Alignment explanation
Indices: 54398724--54398774 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
54398714 ACTTTTTTTA
*
54398724 AAAAAAGAGAGAAAAA-G
1 AAAAAAGAAAGAAAAAGG
*
54398741 AAAAAAGAAACAAAAAGG
1 AAAAAAGAAAGAAAAAGG
*
54398759 AAAAAGGAAAGAAAAA
1 AAAAAAGAAAGAAAAA
54398775 AAGAAACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAGG
Found at i:54399832 original size:45 final size:45
Alignment explanation
Indices: 54399669--54400430 Score: 236
Period size: 45 Copynumber: 16.4 Consensus size: 45
54399659 CATCATGGCA
* *
54399669 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * ** * * * * *
54399714 AATCTTATTTCCCTGAAATTATAGTGGACCAGATTAAAGCTATAAATTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--AT--AGT-G
* *
54399764 ACATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTGAAGATAGTG
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * * ** **
54399810 AATCTTATCTCCCTGAATTTGCAGTGAAGTAGATTGAAGCCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * ** * * ***
54399854 AACCTTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * * **
54399899 AATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGTTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
** *
54399943 AATCCCATAC-CCCTGAAGTTGCAGTGG-G-ATGGATTGAAGATCA-TAG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCA--GACTGAAGAT-AGT-G
* ** *
54399989 CAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-AT--TAC
1 -AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGT-G
* * * * **
54400034 AAGTCTTATCTCCCTGAAGGTGTAGTGGAACAGCCTGAAGATAGCA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * * * * * *
54400080 AATCTTATTTCCCTGAAGTTGTAGTGGAACATATTAAAACTATAAATTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAA-GAT--AGTG
* * * * *
54400129 CAGGTCTTATCTCCCTGAAATTGTAGTGGAACAGACTGAAGATAGCG
1 -A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * * * *
54400176 AATCCTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTATAGATAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--ATAG-T-G
* ** * ** * * *
54400225 CAAATTTTATAC-CTTTGAAGCTAAAGTGG-GTCGGA-TCAAAGTTATCATGGCG
1 --AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGACT-GAAG--AT-A--GTG
* * * * ** *
54400277 AATCTTATCTCCCTAAAGTTGCAGTGAAGTAGATTGAAGCCACT-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
* * * *
54400321 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAAATAAGCTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AG-T-G
* * * * *
54400369 AAGTCTTATCTCCCTAAAGTTGCGGTAGAGCAAACTAAAGATAGTG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
54400415 AATCTTATCTCCCTGA
1 AATCTTATCTCCCTGA
54400431 GGTTACAGCA
Statistics
Matches: 530, Mismatches: 140, Indels: 94
0.69 0.18 0.12
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 132 0.25
45 178 0.34
46 9 0.02
47 20 0.04
48 29 0.05
49 42 0.08
50 28 0.05
51 87 0.16
52 2 0.00
54 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTG
Found at i:54399944 original size:89 final size:89
Alignment explanation
Indices: 54399768--54400107 Score: 285
Period size: 89 Copynumber: 3.8 Consensus size: 89
54399758 AATTATACAT
* * ** * * ** *
54399768 CTTATCTCTCTGAAGTTGCAGTAGAGCAGACTGAAGATAGTGAATCTTATCTCCCTGAATTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAGCAAATCTTATCTCCCTGAAGTTGCA
* **
54399833 GTGAAGTAGATTGAAGCCACAAAC
66 GTGGAGTAGATTGAAGTTACAAAC
* * * *
54399857 CTTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCCCTGAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAGCAAATCTTATCTCCCTGAAGTTGCA
54399922 GTGGAGTAGATTGAAGTTACAAATC
66 GTGGAGTAGATTGAAGTTACAAA-C
* *
54399947 C-CATAC-CCCTGAAGTTGCAGTGG-G-ATGGATTGAAGATCATAGCAAA-CATTATCTCCCTGA
1 CTTAT-CTCCCTGAAGTTGCAGTGGAGCA-GG-TT-AA-A-AATAGCAAATC-TTATCTCCCTGA
* * * **
54400007 AGTTGCAGTGGAGCAGGTTGAAATTACAAGT
59 AGTTGCAGTGGAGTAGATTGAAGTTACAAAC
* * * ** * * * *
54400038 CTTATCTCCCTGAAGGTGTAGTGGAACAGCCTGAAGATAGCAAATCTTATTTCCCTGAAGTTGTA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAGCAAATCTTATCTCCCTGAAGTTGCA
54400103 GTGGA
66 GTGGA
54400108 ACATATTAAA
Statistics
Matches: 201, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
87 1 0.00
88 3 0.01
89 121 0.60
90 7 0.03
91 5 0.02
92 62 0.31
93 1 0.00
94 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (89 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAAATAGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGTAGATTGAAGTTACAAAC
Found at i:54400061 original size:44 final size:44
Alignment explanation
Indices: 54399757--54400107 Score: 237
Period size: 45 Copynumber: 7.8 Consensus size: 44
54399747 TTAAAGCTAT
* * * * **
54399757 AAATTATACATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACTG
1 AAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
** * * * *
54399801 AAGA-TAGTGAATCTTATCTCCCTGAATTTGCAGTGAAGTAGATTG
1 AA-ATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
*** * * * *
54399846 AAGCCACAAACCTTATCTCCCTAAAATTGCAGTGGAGCAGGTTAA
1 AAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-G
* * * *
54399891 AAATAACAAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTG
1 AAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
* **
54399935 AAGTTACAAATCCCATAC-CCCTGAAGTTGCAGTGG-G-ATGGATTG
1 AAATTACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCA-GG-TTG
54399979 AAGATCATAGCAAA-CATTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
1 AA-AT--TA-CAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
* * * * **
54400027 AAATTACAAGTCTTATCTCCCTGAAGGTGTAGTGGAACAGCCTG
1 AAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
* *
54400071 AAGA-TAGCAAATCTTATTTCCCTGAAGTTGTAGTGGA
1 AA-ATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGA
54400108 ACATATTAAA
Statistics
Matches: 242, Mismatches: 47, Indels: 35
0.75 0.15 0.11
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 100 0.41
45 101 0.42
47 6 0.02
48 28 0.12
49 3 0.01
50 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
Found at i:54400082 original size:137 final size:137
Alignment explanation
Indices: 54399852--54400106 Score: 341
Period size: 137 Copynumber: 1.9 Consensus size: 137
54399842 ATTGAAGCCA
*
54399852 CAAACCTTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCCCTGAAG
1 CAAACATTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCCCTGAAG
* ** * *
54399917 TTGTAGTGGAGTAGATTGAAGTTACAAATCCCATACCCCTGAAGTTGCAGTGGGATGGATTGAAG
66 GTGTAGTGGAACAGACTGAAGATACAAATCCCATACCCCTGAAGTTGCAGTGGGATGGATTGAAG
54399982 ATCATAG
131 ATCATAG
* * * * *
54399989 CAAACATTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-GAAATTACAAGTCTTATCTCCCTGAAG
1 CAAACATTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCCCTGAAG
* ** ** *
54400053 GTGTAGTGGAACAGCCTGAAGATAGCAAATCTTATTTCCCTGAAGTTGTAGTGG
66 GTGTAGTGGAACAGACTGAAGATA-CAAATCCCATACCCCTGAAGTTGCAGTGG
54400107 AACATATTAA
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
136 42 0.42
137 58 0.58
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (137 bp):
CAAACATTATCTCCCTAAAATTGCAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCCCTGAAG
GTGTAGTGGAACAGACTGAAGATACAAATCCCATACCCCTGAAGTTGCAGTGGGATGGATTGAAG
ATCATAG
Found at i:54400154 original size:96 final size:96
Alignment explanation
Indices: 54400027--54400219 Score: 287
Period size: 96 Copynumber: 2.0 Consensus size: 96
54400017 GAGCAGGTTG
* * *
54400027 AAATTACAAGTCTTATCTCCCTGAAGGTGTAGTGGAACAGCCTGAAGATAGCAAATCTTATTTCC
1 AAATTACAAGTCTTATCTCCCTGAAAGTGTAGTGGAACAGACTGAAGATAGCAAATCCTATTTCC
* * *
54400092 CTGAAGTTGTAGTGGAACATATTAAAACTAT
66 CTAAAGTTGCAGTGGAACAGATTAAAACTAT
* * * *
54400123 AAATTGCAGGTCTTATCTCCCTGAAATTGTAGTGGAACAGACTGAAGATAGCGAATCCTATTTCC
1 AAATTACAAGTCTTATCTCCCTGAAAGTGTAGTGGAACAGACTGAAGATAGCAAATCCTATTTCC
*
54400188 CTAAAGTTGCAGTGGAACAGATTAAAGCTAT
66 CTAAAGTTGCAGTGGAACAGATTAAAACTAT
54400219 A
1 A
54400220 GATAGCAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (96 bp):
AAATTACAAGTCTTATCTCCCTGAAAGTGTAGTGGAACAGACTGAAGATAGCAAATCCTATTTCC
CTAAAGTTGCAGTGGAACAGATTAAAACTAT
Found at i:54401853 original size:12 final size:12
Alignment explanation
Indices: 54401811--54401854 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
54401801 TTCATATTTA
*
54401811 TTTTTTTTCTTT
1 TTTTTTTTCTAT
*
54401823 TTTGTTTTGTCTGT
1 TTT-TTTT-TCTAT
54401837 TTTTTTTTCTAT
1 TTTTTTTTCTAT
54401849 TTTTTT
1 TTTTTT
54401855 GTTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 13 0.46
13 8 0.29
14 7 0.25
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTTTTTCTAT
Found at i:54407600 original size:21 final size:21
Alignment explanation
Indices: 54407575--54407630 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
54407565 AACACGAAAA
54407575 TTTTGAAACACGAGATTTT-TT
1 TTTTGAAACACGA-ATTTTCTT
54407596 TTTTGAAACACGAATTTTCTT
1 TTTTGAAACACGAATTTTCTT
*
54407617 TTTTTAAACACGAA
1 TTTTGAAACACGAA
54407631 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (21 bp):
TTTTGAAACACGAATTTTCTT
Found at i:54407642 original size:17 final size:16
Alignment explanation
Indices: 54407616--54407651 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
54407606 CGAATTTTCT
*
54407616 TTTTTTAAACACGAAAA
1 TTTTTAAAACAC-AAAA
54407633 TTTTTAAAACACAAAA
1 TTTTTAAAACACAAAA
54407649 TTT
1 TTT
54407652 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTTAAAACACAAAA
Found at i:54407664 original size:38 final size:38
Alignment explanation
Indices: 54407595--54407674 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
54407585 CGAGATTTTT
* * * ** *
54407595 TTTTTGAAACACGAATTTTCTTTTTTTAAACACGAAAA
1 TTTTTAAAACACAAAATTTCTTTTTGAAAACACAAAAA
* *
54407633 TTTTTAAAACACAAAATTTGTTTTTGAAAACATAAAAA
1 TTTTTAAAACACAAAATTTCTTTTTGAAAACACAAAAA
54407671 TTTT
1 TTTT
54407675 GATAAAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.42
Consensus pattern (38 bp):
TTTTTAAAACACAAAATTTCTTTTTGAAAACACAAAAA
Found at i:54407673 original size:22 final size:20
Alignment explanation
Indices: 54407633--54407673 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
54407623 AACACGAAAA
*
54407633 TTTTTAAAACACAAAATTTG
1 TTTTTAAAACAAAAAATTTG
54407653 TTTTTGAAAACATAAAAATTT
1 TTTTT-AAAACA-AAAAATTT
54407674 TGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTTTAAAACAAAAAATTTG
Found at i:54407728 original size:37 final size:38
Alignment explanation
Indices: 54407683--54407794 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 38
54407673 TTGATAAAAA
*
54407683 ATGAAACACGAGGATTTTTTTTTAAAACACGAAAATTT
1 ATGAAACACGAGAATTTTTTTTTAAAACACGAAAATTT
*
54407721 ATG-AACACG-GTCAA--TTTTTTGAAAACACGAAAATTT
1 ATGAAACACGAG--AATTTTTTTTTAAAACACGAAAATTT
* * * * *
54407757 TTGAAAGACGAGAATTTTTTTGTAAAACATGGAAATTT
1 ATGAAACACGAGAATTTTTTTTTAAAACACGAAAATTT
54407795 TTTTTTTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
36 26 0.43
37 11 0.18
38 23 0.38
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (38 bp):
ATGAAACACGAGAATTTTTTTTTAAAACACGAAAATTT
Found at i:54407767 original size:17 final size:18
Alignment explanation
Indices: 54407700--54408006 Score: 106
Period size: 18 Copynumber: 16.8 Consensus size: 18
54407690 ACGAGGATTT
*
54407700 TTTTTTAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
54407718 TTTATG--AACACGGTCAAT
1 TTTTTGAAAACAC-G-AAAA
54407736 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
54407754 TTTTTGAAAGACGA-GAATT
1 TTTTTGAAA-AC-ACGAAAA
* *
54407773 TTTTTGTAAAACATGGAAATTTTTT
1 TTTTTG-AAAACA-CGAAA-----A
*
54407798 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * **
54407816 -TTTTCAAAATACGGGAA
1 TTTTTGAAAACACGAAAA
*
54407833 TTTTTGAAAACAC----T
1 TTTTTGAAAACACGAAAA
*
54407847 TTTTTTAAAACA-GAAAAA
1 TTTTTGAAAACACG-AAAA
* *
54407865 TTTTTG-AAACATTG-GAA
1 TTTTTGAAAACA-CGAAAA
54407882 -TTTTGAAAACAC-AAAGA
1 TTTTTGAAAACACGAAA-A
** *
54407899 TTTTTG-AAACGTGAGAA
1 TTTTTGAAAACACGAAAA
54407916 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
54407934 TTTTTTAAAAAACACGGAAA
1 -TTTTT-GAAAACACGAAAA
*
54407954 TTTTTG-AAACACGAGAATTT
1 TTTTTGAAAACACGA-AA--A
*
54407974 TTTTTAAAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
54407993 TTTTTG-AAACACGA
1 TTTTTGAAAACACGA
54408007 TTTTTTTTAA
Statistics
Matches: 214, Mismatches: 40, Indels: 71
0.66 0.12 0.22
Matches are distributed among these distances:
14 11 0.05
16 11 0.05
17 52 0.24
18 55 0.26
19 30 0.14
20 28 0.13
21 2 0.01
22 8 0.04
23 4 0.02
24 6 0.03
25 7 0.03
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:54407807 original size:24 final size:25
Alignment explanation
Indices: 54407771--54407819 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
54407761 AAGACGAGAA
* *
54407771 TTTTTTTGTAAAACATGGAAATTTT
1 TTTTTTTGTAAAACAAGAAAATTTT
54407796 TTTTTTTG-AAAACAAGAAAATTTT
1 TTTTTTTGTAAAACAAGAAAATTTT
54407820 CAAAATACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TTTTTTTGTAAAACAAGAAAATTTT
Found at i:54407814 original size:23 final size:25
Alignment explanation
Indices: 54407771--54407819 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
54407761 AAGACGAGAA
* *
54407771 TTTTTTTGTAAAACATGGAAATTTT
1 TTTTTTTGTAAAACATAGAAAATTT
54407796 TTTTTTTG-AAAACA-AGAAAATTT
1 TTTTTTTGTAAAACATAGAAAATTT
54407819 T
1 T
54407820 CAAAATACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 6 0.27
25 8 0.36
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (25 bp):
TTTTTTTGTAAAACATAGAAAATTT
Found at i:54407902 original size:34 final size:34
Alignment explanation
Indices: 54407847--54407938 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 34
54407837 TGAAAACACT
* * *
54407847 TTTTTTAAAACAGAAAAATTTTTGAAACATTG-GAA
1 TTTTTGAAAACA-CAAAATTTTTGAAAC-GTGAGAA
54407882 -TTTTGAAAACACAAAGATTTTTGAAACGTGAGAA
1 TTTTTGAAAACACAAA-ATTTTTGAAACGTGAGAA
54407916 TTTTTGAAAACACGAAAATTTTT
1 TTTTTGAAAACAC-AAAATTTTT
54407939 TAAAAAACAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
33 5 0.10
34 24 0.48
35 18 0.36
36 3 0.06
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (34 bp):
TTTTTGAAAACACAAAATTTTTGAAACGTGAGAA
Done.