Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 114 of 210
Found at i:38386626 original size:28 final size:28
Alignment explanation
Indices: 38386571--38386626 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
38386561 ATGCATATGA
* *
38386571 CCCTTAACTTTTCATTAATTACACATTT
1 CCCTAAACTTTTCATTAATCACACATTT
*
38386599 CCCTAAACTTTTACATTTATCACA-ATTT
1 CCCTAAACTTTT-CATTAATCACACATTT
38386627 AGTCCCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (28 bp):
CCCTAAACTTTTCATTAATCACACATTT
Found at i:38398883 original size:249 final size:248
Alignment explanation
Indices: 38398429--38398922 Score: 841
Period size: 249 Copynumber: 2.0 Consensus size: 248
38398419 TCCTAGGGCT
*
38398429 TCCATGATACTTTTTCGTCTCACACCTTATTTCCCGAAAAACTTCCATCAGCTATCTAAAATTCT
1 TCCATGATACTTTTTCGTCTCACACCTTATTTCCCGAAAAACTTCAATCAGCTATCTAAAATTCT
38398494 TACCGGGACAAAATACACAATGAAGAACCAAAAACAAGATTTTATGTATTTATGAATCAAGTAGG
66 TACCGGGACAAAATACACAATGAAGAACCAAAAACAAGATTTTATGTATTTATGAATCAAGTAGG
* *
38398559 CAGAAACATCTACTAAAGAGCGGTTTAGAATTAGGAAAATGATATCGCATACCACGGTTGAATAC
131 CAAAAACATCTACTAAAGAGCGGTTTAAAATTAGGAAAATGATATCGCATACCACGGTTGAATAC
38398624 CGAATCAAACAAAGTTCATATGCTGCAATCCATGTCAATGAAATGCTTACACC
196 CGAATCAAACAAAGTTCATATGCTGCAATCCATGTCAATGAAATGCTTACACC
* *
38398677 TCCATGATACTTTTTTTGTCTCACACCTTATTTCCC-AGAAAACTTCAATCGGCTATCTAAAATT
1 TCCATGATAC-TTTTTCGTCTCACACCTTATTTCCCGA-AAAACTTCAATCAGCTATCTAAAATT
* * * *
38398741 CTTTCTGGGACAAAATACTCAATGAAGAACCAAGAACAAGATTTTATGTATTTATGAATCAAGTA
64 CTTACCGGGACAAAATACACAATGAAGAACCAAAAACAAGATTTTATGTATTTATGAATCAAGTA
*
38398806 GGCAAAAACATCTACTAAAGA-CAGGTTTAAAATTAGGAAAATGATATCGCATACTACGAG-TGA
129 GGCAAAAACATCTACTAAAGAGC-GGTTTAAAATTAGGAAAATGATATCGCATACCACG-GTTGA
38398869 ATACCGAATCAAACAAAGTTCATATGCTGCAATCCATGTCAATGAAATGCTTAC
192 ATACCGAATCAAACAAAGTTCATATGCTGCAATCCATGTCAATGAAATGCTTAC
38398923 CATGAGAAGA
Statistics
Matches: 232, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
248 12 0.05
249 219 0.94
250 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (248 bp):
TCCATGATACTTTTTCGTCTCACACCTTATTTCCCGAAAAACTTCAATCAGCTATCTAAAATTCT
TACCGGGACAAAATACACAATGAAGAACCAAAAACAAGATTTTATGTATTTATGAATCAAGTAGG
CAAAAACATCTACTAAAGAGCGGTTTAAAATTAGGAAAATGATATCGCATACCACGGTTGAATAC
CGAATCAAACAAAGTTCATATGCTGCAATCCATGTCAATGAAATGCTTACACC
Found at i:38410283 original size:70 final size:70
Alignment explanation
Indices: 38410169--38410312 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
38410159 TACGGTACGG
*
38410169 TTGTTTTTATCAGCCAAACCCTAATTATATATTTAACATCGTTTAATTTACGAGAAGAAATTGTA
1 TTGTTTTTATCAGCCAAACCCTAATTATATATTTAACATAGTTTAATTTACGAGAAGAAATTGTA
*
38410234 TGAAA
66 TAAAA
38410239 TTGTTTTTATCAGCCAAACCCTAATTATATATTTAACATAGTTTAATTTACGAGAAGAAATTGTA
1 TTGTTTTTATCAGCCAAACCCTAATTATATATTTAACATAGTTTAATTTACGAGAAGAAATTGTA
38410304 TAAAA
66 TAAAA
38410309 TTGT
1 TTGT
38410313 GATTTAATAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (70 bp):
TTGTTTTTATCAGCCAAACCCTAATTATATATTTAACATAGTTTAATTTACGAGAAGAAATTGTA
TAAAA
Found at i:38413970 original size:18 final size:18
Alignment explanation
Indices: 38413926--38413970 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
38413916 GCAATAAGAA
38413926 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
38413944 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
38413962 AATGTTTTG
1 AACGTTTTG
38413971 GAAACGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:38417349 original size:48 final size:48
Alignment explanation
Indices: 38417297--38417398 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
38417287 GTACCTTAGA
** * * *
38417297 CCGAATGCAGGTTAGTTTCTTGGGCCTGCTAGTGGATAGAATAGTGGG
1 CCGAATGCAGGCCAGTCTCTTGGGCCTGCTAGTGGACAGAATAATGGG
*
38417345 CCGAATGCAGGCCAGTCTCTTGGGCCTGTTAGTGGACAGAATAATGGG
1 CCGAATGCAGGCCAGTCTCTTGGGCCTGCTAGTGGACAGAATAATGGG
38417393 CCGAAT
1 CCGAAT
38417399 AGTAGGTAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (48 bp):
CCGAATGCAGGCCAGTCTCTTGGGCCTGCTAGTGGACAGAATAATGGG
Found at i:38425150 original size:16 final size:16
Alignment explanation
Indices: 38425098--38425154 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
38425088 GTTTGGTTCA
*
38425098 CTGTAATGAAATAGAG
1 CTGTAATTAAATAGAG
*
38425114 CTGCAATTAAATAGAG
1 CTGTAATTAAATAGAG
*
38425130 CTGTAATTGAATAGAG
1 CTGTAATTAAATAGAG
*
38425146 TTGTAATTA
1 CTGTAATTA
38425155 GTAATTCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (16 bp):
CTGTAATTAAATAGAG
Found at i:38425410 original size:58 final size:57
Alignment explanation
Indices: 38425320--38425462 Score: 189
Period size: 58 Copynumber: 2.5 Consensus size: 57
38425310 TTGTTATTAA
*
38425320 ATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCAT
1 ATTTTAATATA-ATTATTATTAAATATAATTTAAT-AAAATAATAAATAATTTAACCAT
* *
38425378 ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAACCAT
* * *
38425435 ATTTCAATCTATTTATTTATATAAATAT
1 ATTTTAATATAATTA-TTAT-TAAATAT
38425463 TTATTTTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
57 33 0.43
58 35 0.46
59 8 0.11
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAACCAT
Found at i:38425451 original size:57 final size:58
Alignment explanation
Indices: 38425331--38425462 Score: 185
Period size: 57 Copynumber: 2.3 Consensus size: 58
38425321 TTTTAATAAG
* *
38425331 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAACCATATTTCAATATA
* * *
38425389 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATCATATTTCAATCTA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAACCATATTTCAATATA
*
38425446 TTTATTTATATAAATAT
1 ATTA-TTAT-TAAATAT
38425463 TTATTTTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 33 0.50
58 26 0.39
59 7 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAACCATATTTCAATATA
Found at i:38438830 original size:43 final size:43
Alignment explanation
Indices: 38438769--38438972 Score: 299
Period size: 43 Copynumber: 4.7 Consensus size: 43
38438759 CTGATAAGTT
*
38438769 TTTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTTTTA
1 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
38438812 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
1 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
38438855 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
1 TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
* *
38438898 TTTTCGTGTAAGACC-CTGTCTGGGATAG-TGACATCGA-TTTGTGA
1 TTTTCGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGACTTT-T-A
* *
38438942 -TTACATGTAAGACCACGTCTGGGACGTTGGC
1 TTTTCGTGTAAGACCACGTCTGGGACGTTGGC
38438973 GTTGTACGAG
Statistics
Matches: 148, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
42 5 0.03
43 140 0.95
44 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTTTA
Found at i:38440841 original size:2 final size:2
Alignment explanation
Indices: 38440834--38440864 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38440824 TTAATGCCGC
*
38440834 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38440865 AAAGAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38441789 original size:17 final size:18
Alignment explanation
Indices: 38441767--38441802 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
38441757 GCTTTAAATG
38441767 AAACATATC-AAAAATAA
1 AAACATATCGAAAAATAA
*
38441784 AAACATATCGAAAACTAA
1 AAACATATCGAAAAATAA
38441802 A
1 A
38441803 TATAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.14, G:0.03, T:0.17
Consensus pattern (18 bp):
AAACATATCGAAAAATAA
Found at i:38452977 original size:25 final size:25
Alignment explanation
Indices: 38452924--38452978 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
38452914 TAATGAGAAA
** *
38452924 CTCATGTGAGTCATGTAACGGGAAT
1 CTCATGTGAACCATGTAACGGGAAG
* *
38452949 CTCATGTGAACCATGTAATGGTAAG
1 CTCATGTGAACCATGTAACGGGAAG
38452974 CTCAT
1 CTCAT
38452979 AAGAGCCGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (25 bp):
CTCATGTGAACCATGTAACGGGAAG
Found at i:38453009 original size:24 final size:24
Alignment explanation
Indices: 38452971--38453036 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
38452961 ATGTAATGGT
**
38452971 AAGCTCAT-AAGAGCCGTAATCGGA
1 AAGCTCATGAA-AGCCAAAATCGGA
* * *
38452995 AAGCTCATGCAAGCCAAAATTGGG
1 AAGCTCATGAAAGCCAAAATCGGA
38453019 AAGCTCATGAAAGCCAAA
1 AAGCTCATGAAAGCCAAA
38453037 TAATGGGAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (24 bp):
AAGCTCATGAAAGCCAAAATCGGA
Found at i:38453043 original size:25 final size:25
Alignment explanation
Indices: 38452995--38453099 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
38452985 CGTAATCGGA
* *
38452995 AAGCTCATGCAAGCCAAA-ATTGGG
1 AAGCTCATGAAAGCCAAATAATGGG
38453019 AAGCTCATGAAAGCCAAATAATGGG
1 AAGCTCATGAAAGCCAAATAATGGG
* * ** *
38453044 AAGCTCAAGAGAGCCATTTAATAGG
1 AAGCTCATGAAAGCCAAATAATGGG
* * * *
38453069 ATGCTCATGAGAGCTAAATAACGGG
1 AAGCTCATGAAAGCCAAATAATGGG
*
38453094 ACGCTC
1 AAGCTC
38453100 TTGCGAGCTG
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
24 17 0.26
25 48 0.74
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (25 bp):
AAGCTCATGAAAGCCAAATAATGGG
Found at i:38455322 original size:22 final size:22
Alignment explanation
Indices: 38455297--38455365 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
38455287 GTTTAATATG
* *
38455297 AAATATATGAATCAATTTATTA
1 AAATATATGAATAAAATTATTA
* *
38455319 AAATCTATGTATAAAATTATT-
1 AAATATATGAATAAAATTATTA
* *
38455340 -AATATGTCAA-AAAATTATT-
1 AAATATATGAATAAAATTATTA
38455359 AAATATA
1 AAATATA
38455366 ATATATATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 9 0.24
20 11 0.30
22 17 0.46
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATATATGAATAAAATTATTA
Found at i:38460833 original size:22 final size:22
Alignment explanation
Indices: 38460808--38460877 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
38460798 GTTTAATATG
* *
38460808 AAATATATGAATCAATTTATTA
1 AAATATATGAATAAAATTATTA
* *
38460830 AAATCTATGTATAAAATTATT-
1 AAATATATGAATAAAATTATTA
* * *
38460851 -AATATGTCAAAAAAATTATT-
1 AAATATATGAATAAAATTATTA
38460871 AAATATA
1 AAATATA
38460878 ATATATATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 15 0.41
21 5 0.14
22 17 0.46
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATATATGAATAAAATTATTA
Found at i:38465220 original size:21 final size:21
Alignment explanation
Indices: 38465194--38465234 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38465184 TGGGTGGATC
38465194 AGCTCTCACGAGCTTCTGTTT
1 AGCTCTCACGAGCTTCTGTTT
* * *
38465215 AGCTCTTATGAGCTTTTGTT
1 AGCTCTCACGAGCTTCTGTT
38465235 GGCGTGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.44
Consensus pattern (21 bp):
AGCTCTCACGAGCTTCTGTTT
Found at i:38467301 original size:54 final size:54
Alignment explanation
Indices: 38467237--38467346 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
38467227 CTGGGTTTAT
* *
38467237 GAGTGGTGGATGTATAGTGGGAAGTGAA-GAAGCGATTTTAGGAGTGAGTTAGGG
1 GAGTGGTGGATGTATAGTGGGAAGT-AAGGAAGCGATTTTAGGAGTGAATTAAGG
* *
38467291 GAGTGGTGGATGTGTAGTGGGAAGTAAGGGAGCGATTTTAGGAGTGAATTAAGG
1 GAGTGGTGGATGTATAGTGGGAAGTAAGGAAGCGATTTTAGGAGTGAATTAAGG
38467345 GA
1 GA
38467347 TTATGGGGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.28, C:0.02, G:0.45, T:0.25
Consensus pattern (54 bp):
GAGTGGTGGATGTATAGTGGGAAGTAAGGAAGCGATTTTAGGAGTGAATTAAGG
Found at i:38470616 original size:23 final size:22
Alignment explanation
Indices: 38470582--38470624 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
38470572 TTTAGATACC
38470582 TCATTTACTTTTTCTAAAAATCA
1 TCATTTACTTTTT-TAAAAATCA
38470605 TCATATTA-TTTTTTAAAAAT
1 TCAT-TTACTTTTTTAAAAAT
38470625 ATTTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TCATTTACTTTTTTAAAAATCA
Found at i:38474811 original size:42 final size:43
Alignment explanation
Indices: 38474637--38474832 Score: 256
Period size: 43 Copynumber: 4.6 Consensus size: 43
38474627 GTGCCGGAAA
* **
38474637 AAACGCCGCTAAA-AACATAATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTTATCAC
*
38474679 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATA-ACCTTTAGCGGCGCTTTTATCAC
* * *
38474722 AAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTTATCAC
* * *
38474765 AAACGCCGCTAAAGAACA-AACCTTTAGCGGCGCTTCTAGCAA
1 AAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTTATCAC
*
38474807 AAACGCCGCTAAA-AACATAATCTTTA
1 AAACGCCGCTAAAGAACATAACCTTTA
38474833 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.03
42 54 0.39
43 79 0.58
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATAACCTTTAGCGGCGCTTTTATCAC
Found at i:38474811 original size:85 final size:85
Alignment explanation
Indices: 38474635--38474832 Score: 281
Period size: 85 Copynumber: 2.3 Consensus size: 85
38474625 AAGTGCCGGA
* * *
38474635 AAAAACGCCGCTAAAAACATAATCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGA
1 AAAAACGCCGCTAAAAACATAACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACAAGA
* *
38474700 CCTTTAGCGGCGCTTTTATC
66 CCTTTAGCGGCGCTTCTAGC
* * * * *
38474720 ACAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACAA-
1 AAAAACGCCGCTA-AAAACATAACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACAAG
38474784 ACCTTTAGCGGCGCTTCTAGC
65 ACCTTTAGCGGCGCTTCTAGC
*
38474805 AAAAACGCCGCTAAAAACATAATCTTTA
1 AAAAACGCCGCTAAAAACATAACCTTTA
38474833 NNNNNNNNNN
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 11 0.11
85 43 0.44
86 43 0.44
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (85 bp):
AAAAACGCCGCTAAAAACATAACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAACAAGA
CCTTTAGCGGCGCTTCTAGC
Found at i:38480124 original size:82 final size:82
Alignment explanation
Indices: 38479965--38480137 Score: 233
Period size: 82 Copynumber: 2.1 Consensus size: 82
38479955 CCCAAACTCC
* *
38479965 AAACCCTAAACCTTATTTAATATATAAATTAGAAAACACTAATTAGTCTAAATCATAAACCCTAA
1 AAACCCTAAACATTATTTAATATATAAATTAGAAAACACTAATTAGTCTAAACCATAAACCCTAA
* * *
38480030 TCCGACCCCGAATCCCT
66 TCCAACACCGAATCCAT
* * *
38480047 AACCCCTAAACATTATTTAATATATAAATTA-AAATACACTAATTAGTCTAAACCCTAAAGCCTA
1 AAACCCTAAACATTATTTAATATATAAATTAGAAA-ACACTAATTAGTCTAAACCATAAACCCTA
*
38480111 A-CCTAACATCGAATCCAT
65 ATCC-AACACCGAATCCAT
38480129 AAACCCTAA
1 AAACCCTAA
38480138 TCCCTAACTC
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 5 0.06
82 74 0.94
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.27
Consensus pattern (82 bp):
AAACCCTAAACATTATTTAATATATAAATTAGAAAACACTAATTAGTCTAAACCATAAACCCTAA
TCCAACACCGAATCCAT
Found at i:38480235 original size:15 final size:14
Alignment explanation
Indices: 38480206--38480239 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
38480196 CTTAAATCAG
*
38480206 AATCCCTAATCCAT
1 AATCTCTAATCCAT
38480220 AATCTCTAATTCCAT
1 AATCTCTAA-TCCAT
38480235 AATCT
1 AATCT
38480240 ATAAACCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCTCTAATCCAT
Found at i:38480523 original size:41 final size:40
Alignment explanation
Indices: 38480432--38480646 Score: 261
Period size: 41 Copynumber: 5.3 Consensus size: 40
38480422 TCAGTTATGG
* *** *
38480432 GCGGCGCTTTTTAGAAAACGCCGCTAAATCCCCGAGCATTA
1 GCGGCGCTTTTCA-AAAACGCCGCTAAAGATCTGAGCATTA
* * *
38480473 ACGGTGCTTTTCCAAAAACGCCGCTAAAGATCTGAGAATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGATCTGAGCATTA
*
38480514 GCGGCGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
38480555 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATATGAG-AGTTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGATCTGAGCA-TTA
**
38480596 GCGGCGCTTTTCAAAAACGCCGCTTTAGATCTGAGCATTA
1 GCGGCGCTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
38480636 GCGGCGATTTT
1 GCGGCGCTTTT
38480647 TTTTAAATGC
Statistics
Matches: 151, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
40 39 0.26
41 107 0.71
42 5 0.03
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:38480569 original size:82 final size:82
Alignment explanation
Indices: 38480432--38480646 Score: 299
Period size: 82 Copynumber: 2.6 Consensus size: 82
38480422 TCAGTTATGG
*** * * *
38480432 GCGGCGCTTTTT-AGAAAACGCCGCTAAATCCCCGAGCATTAACGGTGCTTTTCCAAAAACGCCG
1 GCGGCGCTTTTTCA-AAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCG
*
38480496 CTAAAGATCTGAGAATTA
65 CTAAAGATATGAGAATTA
*
38480514 GCGGCGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGC
*
38480579 TAAAGATATGAGAGTTA
66 TAAAGATATGAGAATTA
** *
38480596 GCGGCGC-TTTTCAAAAACGCCGCTTTAGATCTGAGCATTAGCGGCGATTTT
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTT
38480647 TTTTAAATGC
Statistics
Matches: 119, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
81 40 0.34
82 78 0.66
83 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (82 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGC
TAAAGATATGAGAATTA
Found at i:38484152 original size:48 final size:48
Alignment explanation
Indices: 38484081--38484177 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
38484071 ACTTAAATAG
38484081 GGTCATCAAAACGGTGTCGTTTCATCCAGGCCCTAAACGTCCCAAAAC
1 GGTCATCAAAACGGTGTCGTTTCATCCAGGCCCTAAACGTCCCAAAAC
38484129 GGTCATCAAAACGGTGTCGTTTCATCCAGGCCCTAAACGTCCCAAAAC
1 GGTCATCAAAACGGTGTCGTTTCATCCAGGCCCTAAACGTCCCAAAAC
38484177 G
1 G
38484178 ATATCGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (48 bp):
GGTCATCAAAACGGTGTCGTTTCATCCAGGCCCTAAACGTCCCAAAAC
Found at i:38485258 original size:5 final size:5
Alignment explanation
Indices: 38485248--38485287 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
38485238 GGCATTTTCC
* *
38485248 ATTTA ATTTA ATTTA ATTTA TTTTA TTTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
38485288 GTCAAGTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
ATTTA
Found at i:38485277 original size:20 final size:20
Alignment explanation
Indices: 38485249--38485287 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38485239 GCATTTTCCA
38485249 TTTAATTTAATTTAATTTAT
1 TTTAATTTAATTTAATTTAT
*
38485269 TTTATTTTAATTTAATTTA
1 TTTAATTTAATTTAATTTA
38485288 GTCAAGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTTAATTTAT
Found at i:38492629 original size:29 final size:29
Alignment explanation
Indices: 38492590--38492665 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
38492580 TTTGTCTCAA
38492590 GTTACATTTTAGTCACTTTTGTTTGAAAT
1 GTTACATTTTAGTCACTTTTGTTTGAAAT
38492619 GTTACATTTTAGTCACTTTTGTTTGAAAT
1 GTTACATTTTAGTCACTTTTGTTTGAAAT
38492648 GTTACATTTTAGTCACTT
1 GTTACATTTTAGTCACTT
38492666 ACGTTATCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.51
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTTTGTTTGAAAT
Found at i:38493432 original size:412 final size:413
Alignment explanation
Indices: 38492657--38493481 Score: 1643
Period size: 412 Copynumber: 2.0 Consensus size: 413
38492647 TGTTACATTT
38492657 TAGTCACTTACGTTATCGTGTTGTAGCATTTTAGGTACTGAGCCATTAATTGCTGTTAACGGTGT
1 TAGTCACTTACGTTATCGTGTTGTAGCATTTTAGGTACTGAGCCATTAATTGCTGTTAACGGTGT
38492722 AACGATAAGCTGATGTGACATATTAAATTATCATTTCAAATGAAAATTTTAGCTTAAATTCTACA
66 AACGATAAGCTGATGTGACATATTAAATTATCATTTCAAATGAAAATTTTAGCTTAAATTCTACA
38492787 ATTGGTCCCTATAATTTTTTTTATTTTGAGCAATTTAATTTTTTTATTTTATGTTCTTTTAACTT
131 ATTGGTCCCTATAATTTTTTTTATTTTGAGCAATTTAATTTTTTTATTTTATGTTCTTTTAACTT
38492852 TCCTTTTTATTTTTATTTATTTTCATTCTCTTCTGCTTCTCCCTTTGTTTTCCTCCCTTTTTCAT
196 TCCTTTTTATTTTTATTTATTTTCATTCTCTTCTGCTTCTCCCTTTGTTTTCCTCCCTTTTTCAT
38492917 TTCTTTTAACGTAGTTTTTCTATGTTTTTCATTTGTTAAAATTAAAATGTAACCTGAGGTAAACA
261 TTCTTTTAACGTAGTTTTTCTATGTTTTTCATTTGTTAAAATTAAAATGTAACCTGAGGTAAACA
38492982 AAAGTGACTATTTTAATAGTTTACCCAAAATTAAAATCATTTTCCCTCAAAAGAAATTTAATCAA
326 AAAGTGACTATTTTAATAGTTTACCCAAAATTAAAATCATTTTCCCTCAAAAGAAATTTAATCAA
38493047 ATTATTAATAAATTTACGTTTTG
391 ATTATTAATAAATTTACGTTTTG
38493070 TAGTCACTTA-GTTATCGTGTTGTAGCATTTTAGGTACTGAGCCATTAATTGCTGTTAACGGTGT
1 TAGTCACTTACGTTATCGTGTTGTAGCATTTTAGGTACTGAGCCATTAATTGCTGTTAACGGTGT
38493134 AACGATAAGCTGATGTGACATATTAAATTATCATTTCAAATGAAAATTTTAGCTTAAATTCTACA
66 AACGATAAGCTGATGTGACATATTAAATTATCATTTCAAATGAAAATTTTAGCTTAAATTCTACA
38493199 ATTGGTCCCTATAATTTTTTTTATTTTGAGCAATTTAATTTTTTTATTTTATGTTCTTTTAACTT
131 ATTGGTCCCTATAATTTTTTTTATTTTGAGCAATTTAATTTTTTTATTTTATGTTCTTTTAACTT
38493264 TCCTTTTTATTTTTATTTATTTTCATTCTCTTCTGCTTCTCCCTTTGTTTTCCTCCCTTTTTCAT
196 TCCTTTTTATTTTTATTTATTTTCATTCTCTTCTGCTTCTCCCTTTGTTTTCCTCCCTTTTTCAT
38493329 TTCTTTTAACGTAGTTTTTCTATGTTTTTCATTTGTTAAAATTAAAATGTAACCTGAGGTAAACA
261 TTCTTTTAACGTAGTTTTTCTATGTTTTTCATTTGTTAAAATTAAAATGTAACCTGAGGTAAACA
38493394 AAAGTGACTATTTTAATAGTTTACCCAAAATTAAAATCATTTTCCCTCAAAAGAAATTTAATCAA
326 AAAGTGACTATTTTAATAGTTTACCCAAAATTAAAATCATTTTCCCTCAAAAGAAATTTAATCAA
38493459 ATTATTAATAAATTTACGTTTTG
391 ATTATTAATAAATTTACGTTTTG
38493482 ATAACTTAAT
Statistics
Matches: 412, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
412 402 0.98
413 10 0.02
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (413 bp):
TAGTCACTTACGTTATCGTGTTGTAGCATTTTAGGTACTGAGCCATTAATTGCTGTTAACGGTGT
AACGATAAGCTGATGTGACATATTAAATTATCATTTCAAATGAAAATTTTAGCTTAAATTCTACA
ATTGGTCCCTATAATTTTTTTTATTTTGAGCAATTTAATTTTTTTATTTTATGTTCTTTTAACTT
TCCTTTTTATTTTTATTTATTTTCATTCTCTTCTGCTTCTCCCTTTGTTTTCCTCCCTTTTTCAT
TTCTTTTAACGTAGTTTTTCTATGTTTTTCATTTGTTAAAATTAAAATGTAACCTGAGGTAAACA
AAAGTGACTATTTTAATAGTTTACCCAAAATTAAAATCATTTTCCCTCAAAAGAAATTTAATCAA
ATTATTAATAAATTTACGTTTTG
Found at i:38502707 original size:11 final size:11
Alignment explanation
Indices: 38502689--38502735 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
38502679 TACACCAATG
38502689 AATAACAAACA
1 AATAACAAACA
*
38502700 ATTAACAAACA
1 AATAACAAACA
38502711 AAT-ACAAACA
1 AATAACAAACA
*
38502721 AGCATAACAACCA
1 A--ATAACAAACA
38502734 AA
1 AA
38502736 ATTTCAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 2 0.07
13 7 0.23
ACGTcount: A:0.66, C:0.21, G:0.02, T:0.11
Consensus pattern (11 bp):
AATAACAAACA
Found at i:38503108 original size:22 final size:23
Alignment explanation
Indices: 38503077--38503119 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
38503067 TAATAAAGCA
* *
38503077 ATAAATTTAAA-TGATATTAATC
1 ATAAAGTTAAAGTAATATTAATC
38503099 ATAAAGTTAAAGTAATATTAA
1 ATAAAGTTAAAGTAATATTAA
38503120 GTATGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
ATAAAGTTAAAGTAATATTAATC
Found at i:38503165 original size:19 final size:20
Alignment explanation
Indices: 38503143--38503188 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38503133 ATGATATATG
38503143 ATTTAAAAAAGAATTA-AA-T
1 ATTTAAAAAA-AATTATAAGT
* *
38503162 ATTTTAAGAAAATTATAAGT
1 ATTTAAAAAAAATTATAAGT
38503182 ATTTAAA
1 ATTTAAA
38503189 TGAAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTTAAAAAAAATTATAAGT
Found at i:38505051 original size:217 final size:217
Alignment explanation
Indices: 38504676--38505514 Score: 1110
Period size: 217 Copynumber: 3.8 Consensus size: 217
38504666 TAAGATTCGT
* *
38504676 AATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTAATGCGATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* *
38504741 ACTTT-AGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTA
66 A-TTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTA
38504805 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTATTTTCGATTAGCTCCACTA
130 CTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTATTTTCGATTAGCTCCACTA
38504870 CTGCTTAGGGAGATAAGATCTGA
195 CTGCTTAGGGAGATAAGATCTGA
*
38504893 AATTCTTCGGTTTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* * * * *
38504958 ATTTCAGAGAGATAATATCCTTTATTTTAATCTGCCCCACTGTAATCTCAGGGAGATATGATTAC
66 ATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* * *
38505023 TAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAAATAAGATTCCATTTTCGATTAGCTCCACTAC
131 TAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTATTTTCGATTAGCTCCACTAC
*
38505088 TGCTTAGGGAGATAAGATTTGA
196 TGCTTAGGGAGATAAGATCTGA
38505110 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
* * *
38505175 ATTTCAAAGAGATAAGATCATTTATTTTACTCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
66 ATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* *** *
38505240 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTA-CTCCACT
131 TAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-TTCTATTTTCGAT-TAGCTCCAC-
38505304 GTAAC--CTTAGGGAGATAAGATTCACCATTTTCGATTA
193 -T-ACTGCTTAGGGAGATAAGA-T---C----T-G---A
* * * * * * * * *
38505341 GGAATTCTTTGTTCTATTCCACTGTAACCTCAGAGAGATAATACCTGGTACAATCTACTCTACTA
1 --AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTG
* **
38505406 TAATTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTTGGGGAAATAGGATT
64 TAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATT
* ** * * *
38505471 ACTGGCTTTGATCTACTCTGCTGTAACCTCAGGGAGATAAGATT
129 ACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
38505515 TCTGGCTTCA
Statistics
Matches: 552, Mismatches: 50, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
216 3 0.01
217 359 0.65
218 14 0.03
219 17 0.03
220 2 0.00
221 2 0.00
227 1 0.00
228 1 0.00
231 1 0.00
232 2 0.00
233 150 0.27
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (217 bp):
AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
ATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
TAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTCTATTTTCGATTAGCTCCACTAC
TGCTTAGGGAGATAAGATCTGA
Found at i:38505256 original size:44 final size:44
Alignment explanation
Indices: 38505208--38505325 Score: 173
Period size: 44 Copynumber: 2.7 Consensus size: 44
38505198 ATTTTACTCC
* *
38505208 GCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCT
* *
38505252 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCT
* * *
38505296 ACTCCACTGTAACCTTAGGGAGATAAGATT
1 GCTCCACTGTAATCTCAGGGAGATAAGATT
38505326 CACCATTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCT
Found at i:38505517 original size:233 final size:233
Alignment explanation
Indices: 38505110--38505574 Score: 723
Period size: 233 Copynumber: 2.0 Consensus size: 233
38505100 TAAGATTTGA
* * * * *
38505110 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAACCTCAGAGAGATAAGACCTGATACAATCTACTCTACTATA
*
38505175 ATTTCAAAGAGATAAGATCATTTATTTTACTCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
66 ATTTCAAAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
* *
38505240 TGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCACTG
131 TGGCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCACTG
*
38505305 TAACCTTAGGGAGATAAGATTCACCATTTTCGATTAGG
196 TAACCTCAGGGAGATAAGATTCACCATTTTCGATTAGG
* * * *
38505343 AATTCTTTGTTCTATTCCACTGTAACCTCAGAGAGATAATACCTGGTACAATCTACTCTACTATA
1 AATTCTTCGGTCTATTCCACTGTAACCTCAGAGAGATAAGACCTGATACAATCTACTCTACTATA
* * * **
38505408 ATTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTTGGGGAAATAGGATTAC
66 ATTTCAAAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
** * * *
38505473 TGGCTTTGATCTACTCTGCTGTAACCTCAGGGAGATAAGATTTCTGGCTTCAATTTGCTCCACTG
131 TGGCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCACTG
38505538 TAACCTCAGGGAGATAAGATTCACCATTTTCGATTAG
196 TAACCTCAGGGAGATAAGATTCACCATTTTCGATTAG
38505575 CTTTACTACT
Statistics
Matches: 209, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
233 209 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (233 bp):
AATTCTTCGGTCTATTCCACTGTAACCTCAGAGAGATAAGACCTGATACAATCTACTCTACTATA
ATTTCAAAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTAC
TGGCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAGATTTCTGGCTTCAATCTACTCCACTG
TAACCTCAGGGAGATAAGATTCACCATTTTCGATTAGG
Found at i:38505521 original size:44 final size:44
Alignment explanation
Indices: 38505442--38505558 Score: 126
Period size: 44 Copynumber: 2.7 Consensus size: 44
38505432 TTTTAATCCG
* ** * * **
38505442 CTCCACTGTAATCTTGGGGAAATAGGATTACTGGCTTTGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATTACTGGCTTCAATCTA
** * * *
38505486 CTCTGCTGTAACCTCAGGGAGATAAGATTTCTGGCTTCAATTTG
1 CTCCACTGTAACCTCAGGGAGATAAGATTACTGGCTTCAATCTA
38505530 CTCCACTGTAACCTCAGGGAGATAAGATT
1 CTCCACTGTAACCTCAGGGAGATAAGATT
38505559 CACCATTTTC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAACCTCAGGGAGATAAGATTACTGGCTTCAATCTA
Found at i:38505998 original size:120 final size:120
Alignment explanation
Indices: 38505785--38506023 Score: 397
Period size: 120 Copynumber: 2.0 Consensus size: 120
38505775 CGCCGTCTTC
** * * * *
38505785 GATCTGCTCCGTTATTGCTTAGGGAGGCAAGATCTGTAATTTCCCAACCTATTCCACTGTTGATC
1 GATCTGCTCCACTATTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACC
*
38505850 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTT
66 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACATGAAGATAAGATTT
38505905 GATCTGCTCCACTATTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACC
1 GATCTGCTCCACTATTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACC
* *
38505970 AGGGATATAGGATTTGTGGCTTAAATCTGCTTCCTTACTCATGAAGATAAGATT
66 AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACATGAAGATAAGATT
38506024 CACCGTCTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (120 bp):
GATCTGCTCCACTATTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACC
AGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACATGAAGATAAGATTT
Found at i:38507310 original size:8 final size:7
Alignment explanation
Indices: 38507299--38507339 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
38507289 CTATTTTTAC
38507299 TTTTTCA
1 TTTTTCA
38507306 TTTTTTCA
1 -TTTTTCA
38507314 TTTTTCA
1 TTTTTCA
38507321 -TTTTCA
1 TTTTTCA
38507327 TTTTTCA
1 TTTTTCA
38507334 TCTTTT
1 T-TTTT
38507340 TTTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 14 0.45
8 11 0.35
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:38507324 original size:13 final size:13
Alignment explanation
Indices: 38507308--38507334 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38507298 CTTTTTCATT
38507308 TTTTCATTTTTCA
1 TTTTCATTTTTCA
38507321 TTTTCATTTTTCA
1 TTTTCATTTTTCA
38507334 T
1 T
38507335 CTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:38508222 original size:14 final size:14
Alignment explanation
Indices: 38508201--38508281 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 14
38508191 TCTTTTCCTA
38508201 TTTC-TTTTTT-AT
1 TTTCATTTTTTGAT
38508213 TTTCATTTTTTGAT
1 TTTCATTTTTTGAT
*
38508227 TTTGA--TTTTGAT
1 TTTCATTTTTTGAT
*
38508239 TTTGA--TTTTGAT
1 TTTCATTTTTTGAT
*
38508251 TTTGA--TTTTGAT
1 TTTCATTTTTTGAT
*
38508263 TTTGATTTTGATTGAT
1 TTTCATTTT--TTGAT
38508279 TTT
1 TTT
38508282 TTTCATTTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
12 40 0.65
13 6 0.10
14 8 0.13
16 8 0.13
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.70
Consensus pattern (14 bp):
TTTCATTTTTTGAT
Found at i:38508229 original size:6 final size:6
Alignment explanation
Indices: 38508220--38508322 Score: 118
Period size: 6 Copynumber: 16.7 Consensus size: 6
38508210 TATTTTCATT
38508220 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * * * *
38508268 TTTTGA TTGATT-T TTTTCA TTTTCA TTTTTTTA CTTTGA TTTTGA TTTTGA
1 TTTTGA TT--TTGA TTTTGA TTTTGA --TTTTGA TTTTGA TTTTGA TTTTGA
38508319 TTTT
1 TTTT
38508323 TTTCTTTTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
5 2 0.02
6 75 0.87
7 2 0.02
8 7 0.08
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:38512862 original size:22 final size:23
Alignment explanation
Indices: 38512831--38512873 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
38512821 TAATAAAGCA
* *
38512831 ATAAATTTAAA-TGATATTAATC
1 ATAAAGTTAAAGTAATATTAATC
38512853 ATAAAGTTAAAGTAATATTAA
1 ATAAAGTTAAAGTAATATTAA
38512874 GTATGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
ATAAAGTTAAAGTAATATTAATC
Found at i:38512919 original size:19 final size:20
Alignment explanation
Indices: 38512897--38512942 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38512887 ATGATATATG
38512897 ATTTAAAAAAGAATTA-AA-T
1 ATTTAAAAAA-AATTATAAGT
* *
38512916 ATTTTAAGAAAATTATAAGT
1 ATTTAAAAAAAATTATAAGT
38512936 ATTTAAA
1 ATTTAAA
38512943 TGAAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTTAAAAAAAATTATAAGT
Found at i:38516951 original size:28 final size:28
Alignment explanation
Indices: 38516914--38516972 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
38516904 ACAGTGTAAG
38516914 TAATGGAATTGTAAATCTTGAGGTATAA
1 TAATGGAATTGTAAATCTTGAGGTATAA
38516942 TAATGGAATTGTAAATCTTGAGGTATAA
1 TAATGGAATTGTAAATCTTGAGGTATAA
38516970 TAA
1 TAA
38516973 ACTTTGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (28 bp):
TAATGGAATTGTAAATCTTGAGGTATAA
Found at i:38526163 original size:16 final size:16
Alignment explanation
Indices: 38526142--38526174 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38526132 TTTATAGTAT
38526142 TTTAAATGGGTTAGAC
1 TTTAAATGGGTTAGAC
38526158 TTTAAATGGGTTAGAC
1 TTTAAATGGGTTAGAC
38526174 T
1 T
38526175 GAAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
TTTAAATGGGTTAGAC
Found at i:38526180 original size:16 final size:16
Alignment explanation
Indices: 38526145--38526180 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38526135 ATAGTATTTT
**
38526145 AAATGGGTTAGACTTT
1 AAATGGGTTAGACTGA
38526161 AAATGGGTTAGACTGA
1 AAATGGGTTAGACTGA
38526177 AAAT
1 AAAT
38526181 TTTTCATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
AAATGGGTTAGACTGA
Found at i:38527127 original size:60 final size:60
Alignment explanation
Indices: 38526995--38527135 Score: 144
Period size: 60 Copynumber: 2.4 Consensus size: 60
38526985 TTAATCTTTT
* *
38526995 AACTTCACAATTGTTCCCACACTAAGGTCTAAACTTTTTCTTTGTCCAAGTTAGTTCCTG
1 AACTTAACAATTGTTCCCACACTAAGGTCTAAACTTTTTCTTTGTCCAAGTTAGTTCCTA
* ** * *
38527055 AATTTAACAATTGTTCCCACGTTAGGGTCTGAAA-TTTTT-TTTGTTTCAAGTTAG-TCCTTA
1 AACTTAACAATTGTTCCCACACTAAGGTCT-AAACTTTTTCTTTG-TCCAAGTTAGTTCC-TA
* * *
38527115 AACTTGATAATTGTTCTCACA
1 AACTTAACAATTGTTCCCACA
38527136 TTGGGGCATG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 7 0.11
60 56 0.85
61 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (60 bp):
AACTTAACAATTGTTCCCACACTAAGGTCTAAACTTTTTCTTTGTCCAAGTTAGTTCCTA
Found at i:38531218 original size:28 final size:28
Alignment explanation
Indices: 38531125--38531221 Score: 77
Period size: 28 Copynumber: 3.2 Consensus size: 28
38531115 CAACTTCATG
38531125 TTTAAAAAATTTACTTTCATTTTAACTC
1 TTTAAAAAATTTACTTTCATTTTAACTC
* ** ** *
38531153 TTTGAAAGCTAAACTTATCATTTTGCATTCTTC
1 TTTAAAAAATTTACTT-TCATTTT--A-AC-TC
*
38531186 ATTTAAAAATTTTACTTTCATTTTAACTC
1 -TTTAAAAAATTTACTTTCATTTTAACTC
38531215 TTTAAAA
1 TTTAAAA
38531222 GCTAAATTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 18 0.35
29 9 0.18
30 1 0.02
31 2 0.04
32 1 0.02
33 9 0.18
34 11 0.22
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTAAAAAATTTACTTTCATTTTAACTC
Found at i:38531223 original size:62 final size:62
Alignment explanation
Indices: 38531125--38531248 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
38531115 CAACTTCATG
*
38531125 TTTAAAAAATTTACTTTCATTTTAACTCTTTGAAAGCTAAACTTATCATTTTGCATTCTTCA
1 TTTAAAAAATTTACTTTCATTTTAACTCTTTAAAAGCTAAACTTATCATTTTGCATTCTTCA
* *
38531187 TTTAAAAATTTTACTTTCATTTTAACTCTTTAAAAGCTAAATTTATCATTTTGCATTCTTCA
1 TTTAAAAAATTTACTTTCATTTTAACTCTTTAAAAGCTAAACTTATCATTTTGCATTCTTCA
38531249 AGTCTTGTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.48
Consensus pattern (62 bp):
TTTAAAAAATTTACTTTCATTTTAACTCTTTAAAAGCTAAACTTATCATTTTGCATTCTTCA
Found at i:38531238 original size:29 final size:29
Alignment explanation
Indices: 38531137--38531238 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
38531127 TAAAAAATTT
*
38531137 ACTT-TCATTTTAACTCTTTGAAAGCTAA
1 ACTTATCATTTTAACTCTTTAAAAGCTAA
* ** **
38531165 ACTTATCATTTTGCATTCTTCATTTAAAAATTTT
1 ACTTATCATTTT--A-AC-TC-TTTAAAAGCTAA
38531199 ACTT-TCATTTTAACTCTTTAAAAGCTAA
1 ACTTATCATTTTAACTCTTTAAAAGCTAA
*
38531227 ATTTATCATTTT
1 ACTTATCATTTT
38531239 GCATTCTTCA
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
28 15 0.27
29 16 0.29
30 1 0.02
31 2 0.04
32 1 0.02
33 9 0.16
34 11 0.20
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (29 bp):
ACTTATCATTTTAACTCTTTAAAAGCTAA
Found at i:38533543 original size:22 final size:22
Alignment explanation
Indices: 38533515--38533565 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
38533505 CTCTCTAATC
38533515 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
38533537 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
38533559 CTCTCAA
1 CTCTCAA
38533566 ACCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:38533593 original size:51 final size:51
Alignment explanation
Indices: 38533537--38533649 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
38533527 TTCCAAAATT
38533537 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
38533588 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
38533639 CCCTCAATTTC
1 CTCTCAATTTC
38533650 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:38533679 original size:10 final size:10
Alignment explanation
Indices: 38533664--38533715 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
38533654 TTTAAAATAA
38533664 TTTTATATTT
1 TTTTATATTT
38533674 TTTTATATTT
1 TTTTATATTT
* **
38533684 TTTTAAAATAA
1 TTTT-ATATTT
*
38533695 TTTTAAATTT
1 TTTTATATTT
38533705 TTTTATATTT
1 TTTTATATTT
38533715 T
1 T
38533716 CATCAATGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 28 0.80
11 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATATTT
Found at i:38533689 original size:31 final size:31
Alignment explanation
Indices: 38533651--38533715 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
38533641 CTCAATTTCA
*
38533651 TTTTTTAAAATAATTTTATATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
38533682 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
38533713 TTT
1 TTT
38533716 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATAT
Found at i:38534493 original size:7 final size:7
Alignment explanation
Indices: 38534481--38534505 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38534471 AGTCGATTGA
38534481 TATTTAG
1 TATTTAG
38534488 TATTTAG
1 TATTTAG
38534495 TATTTAG
1 TATTTAG
38534502 TATT
1 TATT
38534506 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:38535185 original size:18 final size:18
Alignment explanation
Indices: 38535159--38535193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38535149 AGGTGTGTTT
* *
38535159 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
38535177 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
38535194 TCATTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:38535625 original size:25 final size:25
Alignment explanation
Indices: 38535597--38535665 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
38535587 TTTAAATTTA
*
38535597 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
38535622 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
38535647 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
38535666 ACCCTAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:38539892 original size:29 final size:29
Alignment explanation
Indices: 38539827--38539892 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
38539817 GATTTCCCGG
*
38539827 AAAATGGCCCATTCCGGTAAATAATCAAA
1 AAAACGGCCCATTCCGGTAAATAATCAAA
* * ** *
38539856 AAATCGGCCCATTTCGGTAAATTTTGAAA
1 AAAACGGCCCATTCCGGTAAATAATCAAA
38539885 AAAACGGC
1 AAAACGGC
38539893 TTTTTTTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAACGGCCCATTCCGGTAAATAATCAAA
Found at i:38542170 original size:22 final size:22
Alignment explanation
Indices: 38542120--38542184 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
38542110 ACATAATTAT
*
38542120 TATTAAATATAA-TTTAATAAC
1 TATTTAATATAATTTTAATAAC
*
38542141 TTTCTTAATATAATTCTTAATAA-
1 TAT-TTAATATAATT-TTAATAAC
38542164 TATTTAATAATAATTTTAATA
1 TATTTAAT-ATAATTTTAATA
38542185 TAATATTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.05
22 19 0.51
23 9 0.24
24 7 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAATATAATTTTAATAAC
Found at i:38542176 original size:13 final size:13
Alignment explanation
Indices: 38542158--38542191 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
38542148 ATATAATTCT
38542158 TAATAATATTTAA
1 TAATAATATTTAA
38542171 TAATAAT-TTTAA
1 TAATAATATTTAA
38542183 T-ATAATATT
1 TAATAATATT
38542192 AGTATTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:38547329 original size:25 final size:25
Alignment explanation
Indices: 38547301--38547484 Score: 107
Period size: 25 Copynumber: 7.4 Consensus size: 25
38547291 GGAAGTTTCA
*
38547301 GAGAGCCATTAATCGAGAAGCTCGT
1 GAGAGCCATTAATCGAGAAGCTCAT
* **
38547326 GAGAGCCAATT-ATCGAAAAGCTCCG
1 GAGAGCC-ATTAATCGAGAAGCTCAT
38547351 GAGAGCCAAATT-ATC-AGGAAGCTCAT
1 GAGAGCC--ATTAATCGA-GAAGCTCAT
* * *
38547377 -ACGAGCCA-TAAACGAGAAGCTTAA
1 GA-GAGCCATTAATCGAGAAGCTCAT
38547401 GAGAGCCAAATT-ATC-AGGAAGCTCAT
1 GAGAGCC--ATTAATCGA-GAAGCTCAT
* * * *
38547427 -ACGAGCCA-TAAACAAGAAGCTTAA
1 GA-GAGCCATTAATCGAGAAGCTCAT
* *
38547451 GAGAGCCATTAATCTAGAAGCTCGT
1 GAGAGCCATTAATCGAGAAGCTCAT
38547476 GAGAGCCAT
1 GAGAGCCAT
38547485 ATAACGGGAT
Statistics
Matches: 123, Mismatches: 20, Indels: 32
0.70 0.11 0.18
Matches are distributed among these distances:
23 2 0.02
24 31 0.25
25 53 0.43
26 36 0.29
27 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (25 bp):
GAGAGCCATTAATCGAGAAGCTCAT
Found at i:38547382 original size:26 final size:26
Alignment explanation
Indices: 38547353--38547434 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
38547343 AAGCTCCGGA
38547353 GAGCCAAATTATCAGGAAGCTCATAC
1 GAGCCAAATTATCAGGAAGCTCATAC
* *
38547379 GAGCCATAA--A-C-GAGAAGCTTA-AGA
1 GAGCCA-AATTATCAG-GAAGCTCATA-C
38547403 GAGCCAAATTATCAGGAAGCTCATAC
1 GAGCCAAATTATCAGGAAGCTCATAC
38547429 GAGCCA
1 GAGCCA
38547435 TAAACAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
23 4 0.09
24 14 0.32
25 2 0.05
26 20 0.45
27 4 0.09
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (26 bp):
GAGCCAAATTATCAGGAAGCTCATAC
Found at i:38547397 original size:50 final size:50
Alignment explanation
Indices: 38547351--38547458 Score: 189
Period size: 50 Copynumber: 2.2 Consensus size: 50
38547341 AAAAGCTCCG
* *
38547351 GAGAGCCAAATTATCAGGAAGCTCATACGAGCCATAAACGAGAAGCTTAA
1 GAGAGCCAAATTATCAGGAAGCTCATACGAGCCATAAACAAGAAGCTCAA
*
38547401 GAGAGCCAAATTATCAGGAAGCTCATACGAGCCATAAACAAGAAGCTTAA
1 GAGAGCCAAATTATCAGGAAGCTCATACGAGCCATAAACAAGAAGCTCAA
38547451 GAGAGCCA
1 GAGAGCCA
38547459 TTAATCTAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (50 bp):
GAGAGCCAAATTATCAGGAAGCTCATACGAGCCATAAACAAGAAGCTCAA
Found at i:38547406 original size:24 final size:23
Alignment explanation
Indices: 38547379--38547459 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
38547369 AAGCTCATAC
38547379 GAGCCATAAACGAGAAGCTTAAGA
1 GAGCCATAAAC-AGAAGCTTAAGA
* *
38547403 GAGCCA-AATTATCAGGAAGCTCATA-C
1 GAGCCATAA--A-CA-GAAGCTTA-AGA
38547429 GAGCCATAAACAAGAAGCTTAAGA
1 GAGCCATAAAC-AGAAGCTTAAGA
38547453 GAGCCAT
1 GAGCCAT
38547460 TAATCTAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
23 3 0.07
24 21 0.47
25 4 0.09
26 14 0.31
27 3 0.07
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (23 bp):
GAGCCATAAACAGAAGCTTAAGA
Found at i:38550719 original size:21 final size:21
Alignment explanation
Indices: 38550684--38550725 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38550674 TGAATTTAGC
*
38550684 TCAATTTAATACAATTCACAT
1 TCAATTTAATACAATACACAT
* *
38550705 TCAATTTAGTCCAATACACAT
1 TCAATTTAATACAATACACAT
38550726 CTTTAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.36
Consensus pattern (21 bp):
TCAATTTAATACAATACACAT
Found at i:38559999 original size:18 final size:18
Alignment explanation
Indices: 38559964--38560015 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
38559954 TAGGGGTGTG
*
38559964 AAAAATTCGGGTAAAACCGA
1 AAAAATTC-GGT-TAACCGA
38559984 AAAAATTCGGTTAACCGA
1 AAAAATTCGGTTAACCGA
***
38560002 CCGAATTCGGTTAA
1 AAAAATTCGGTTAA
38560016 TCGGTCGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 17 0.61
19 3 0.11
20 8 0.29
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (18 bp):
AAAAATTCGGTTAACCGA
Found at i:38560334 original size:9 final size:8
Alignment explanation
Indices: 38560322--38560380 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 8
38560312 TCAATTTGGT
38560322 TAATTCAGG
1 TAATTC-GG
38560331 TAATTCGG
1 TAATTCGG
38560339 TTAATTCGGG
1 -TAATTC-GG
38560349 TAATTCGGG
1 TAATTC-GG
38560358 TAATTCGG
1 TAATTCGG
38560366 TTAATTCGG
1 -TAATTCGG
38560375 TTAATT
1 -TAATT
38560381 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
8 4 0.09
9 41 0.87
10 2 0.04
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (8 bp):
TAATTCGG
Found at i:38560389 original size:18 final size:18
Alignment explanation
Indices: 38560314--38560380 Score: 91
Period size: 18 Copynumber: 3.7 Consensus size: 18
38560304 GTAGTGATTC
*
38560314 AATTTGGTTAATTCAGG-T
1 AATTCGGTTAATTC-GGTT
*
38560332 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTT
*
38560350 AATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGTT
38560368 AATTCGGTTAATT
1 AATTCGGTTAATT
38560381 TTGTTAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 2 0.05
18 42 0.95
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGTT
Found at i:38560389 original size:27 final size:27
Alignment explanation
Indices: 38560322--38560380 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
38560312 TCAATTTGGT
*
38560322 TAATTCAGGTAATTCGGTTAATTCGGG
1 TAATTCGGGTAATTCGGTTAATTCGGG
*
38560349 TAATTCGGGTAATTCGGTTAATTCGGT
1 TAATTCGGGTAATTCGGTTAATTCGGG
38560376 TAATT
1 TAATT
38560381 TTGTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGTTAATTCGGG
Found at i:38562969 original size:25 final size:25
Alignment explanation
Indices: 38562929--38562982 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
38562919 TACACCACAA
**
38562929 CTCTTATGAGTTTCCC-ATTATTTAG
1 CTCTTATGAGCATCCCGA-TATTTAG
*
38562954 CTCTTATGAGCATCCCGATATTTGG
1 CTCTTATGAGCATCCCGATATTTAG
38562979 CTCT
1 CTCT
38562983 CACAAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.43
Consensus pattern (25 bp):
CTCTTATGAGCATCCCGATATTTAG
Found at i:38563015 original size:25 final size:25
Alignment explanation
Indices: 38562947--38563016 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
38562937 AGTTTCCCAT
* *
38562947 TATTTAGCTCT-TATGAGCATCCCGA
1 TATTTGGCTCTCT-TGAGCTTCCCGA
*** *
38562972 TATTTGGCTCTCACAAGCTTCCTGA
1 TATTTGGCTCTCTTGAGCTTCCCGA
38562997 TATTTGGCTCTCTTGAGCTT
1 TATTTGGCTCTCTTGAGCTT
38563017 TCCAATAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (25 bp):
TATTTGGCTCTCTTGAGCTTCCCGA
Found at i:38563081 original size:25 final size:25
Alignment explanation
Indices: 38563025--38563081 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
38563015 TTTCCAATAA
*
38563025 ATGGCTCGCAAGAGCTTCCCGTTAT
1 ATGGCTCACAAGAGCTTCCCGTTAT
** * *
38563050 ACAGCTCACATGAGTTTCCCGTTAT
1 ATGGCTCACAAGAGCTTCCCGTTAT
38563075 ATGGCTC
1 ATGGCTC
38563082 GATAGAGCTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (25 bp):
ATGGCTCACAAGAGCTTCCCGTTAT
Found at i:38565448 original size:71 final size:71
Alignment explanation
Indices: 38565329--38565467 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 71
38565319 AGAGGATTGA
*
38565329 ATTAAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTTAAAATAAAACTACGAGGACAAAT
1 ATTAAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAAAATAAAACTACGAGGACAAAT
38565394 CTTCGG
66 CTTCGG
* * * *
38565400 ATTAAAGCTACAATTCCTATACCCCTGAAGTTGTAGTGGGTCAGAATAAAACTACGAGGGCGAAT
1 ATTAAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAAAATAAAACTACGAGGACAAAT
38565465 CTT
66 CTT
38565468 ATCTTCCTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (71 bp):
ATTAAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTCAAAATAAAACTACGAGGACAAAT
CTTCGG
Found at i:38565571 original size:94 final size:94
Alignment explanation
Indices: 38565399--38566150 Score: 868
Period size: 94 Copynumber: 8.0 Consensus size: 94
38565389 CAAATCTTCG
* * * * * * **
38565399 GATTAAAGCTACAATTCCTATACCCCTGAAGTTGTAGTGGGTCAGAA-TAAAACTACGAGGGCGA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTC-GAATTGAATCTACCATAGCGA
*
38565463 ATCTTATCTTCCTAAAGTTGCAGTGGAGCA
65 ATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* **
38565493 GGTTGAAGCTACAAATCCTATACCCCTGAAGTCCCAGTGGGTCGAATTGAATCTACCATAGCGAA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGAA
* * *
38565558 TCTTGTCACCCTAAAGTTGCAGTGGAGTA
66 TCTTATCTCCCTAAAGTTGCAGTGGAGCA
* *
38565587 GATTGAAGCTACAAATCTTATACCCCTGAAGTTACAGTGGGTC-AGATTGAATCTACCATAAG-G
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAATCTACCAT-AGCG
* *
38565650 AATCTTATCTCCCTAAAGTTACAGTGGAGTA
64 AATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * *
38565681 GATTGAAGCTACAACTCCTATACCCCTGAAATTGCTGTGGGTCGGATTGAATCTACCATAGCGAA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGAA
* *
38565746 TCTTATCTCCTTGAAA-TTGCAGTGAAGCA
66 TCTTATCTCCCT-AAAGTTGCAGTGGAGCA
* * * * * * *
38565775 GATTGAAACTACAAATCTTATACCCCTGAAGTTGCAATGGGTTGGATTGATTCTACTATAGCGAA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGAA
* *
38565840 TATTATCTCCCTAAAGTTGCAGTAGAGCA
66 TCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * *
38565869 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAATCTACCATGGAGAA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGAA
* * * * *
38565934 TTTTATCTCCTTAAAATTGTAGTGGAGCG
66 TCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * * *
38565963 GAATGAAACTACAAATCCTATACCTCTGAAGTTTCAGTGGGTC-AGATTGAATCTACTATAGCGA
1 GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGA-ATTGAATCTACCATAGCGA
* *
38566027 ATCTTATCTCTCTAAAGTTGCAGTGGAACA
65 ATCTTATCTCCCTAAAGTTGCAGTGGAGCA
* * * * * * *
38566057 GATTGAAGCTACAAA-CCTTATACCCCTGAAGTTGCGGTGGGTTGGATTGAAACTACAATAACAA
1 GATTGAAGCTACAAATCC-TATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGA
* * *
38566121 ATCTTATCTTCTTAAAGTTGCAATGGAGCA
65 ATCTTATCTCCCTAAAGTTGCAGTGGAGCA
38566151 ACATGAAACT
Statistics
Matches: 556, Mismatches: 92, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
93 11 0.02
94 540 0.97
95 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (94 bp):
GATTGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTGAATCTACCATAGCGAA
TCTTATCTCCCTAAAGTTGCAGTGGAGCA
Found at i:38565675 original size:50 final size:48
Alignment explanation
Indices: 38565461--38565692 Score: 173
Period size: 50 Copynumber: 4.9 Consensus size: 48
38565451 CTACGAGGGC
* * * *
38565461 GAATCTTATCTTCCTAAAGTTGCAGTGGAGCAGGTTGAAGCTA-C--A-
1 GAATCTTATC-CCCTAAAGTTACAGTGGAGTAGATTGAAGCTACCATAG
* * ** * *
38565506 -AATCCTATACCCCTGAAGTCCCAGTGG-GTCGAATTGAATCTACCATAG
1 GAATCTTAT-CCCCTAAAGTTACAGTGGAGTAG-ATTGAAGCTACCATAG
* *
38565554 CGAATCTTGTCACCCTAAAGTTGCAGTGGAGTAGATTGAAGCTA-C--A-
1 -GAATCTTATC-CCCTAAAGTTACAGTGGAGTAGATTGAAGCTACCATAG
* *
38565600 -AATCTTATACCCCTGAAGTTACAGTGG-GTCAGATTGAATCTACCATAAG
1 GAATCTTAT-CCCCTAAAGTTACAGTGGAGT-AGATTGAAGCTACCAT-AG
38565649 GAATCTTATCTCCCTAAAGTTACAGTGGAGTAGATTGAAGCTAC
1 GAATCTTATC-CCCTAAAGTTACAGTGGAGTAGATTGAAGCTAC
38565693 AACTCCTATA
Statistics
Matches: 145, Mismatches: 22, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
43 4 0.03
44 61 0.42
45 4 0.03
47 2 0.01
48 1 0.01
49 3 0.02
50 65 0.45
51 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (48 bp):
GAATCTTATCCCCTAAAGTTACAGTGGAGTAGATTGAAGCTACCATAG
Found at i:38567850 original size:7 final size:7
Alignment explanation
Indices: 38567832--38567862 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38567822 TTTTTGTTTG
38567832 TTATTA-
1 TTATTAT
38567838 TTATTAT
1 TTATTAT
38567845 TTATTAT
1 TTATTAT
38567852 TTATTAT
1 TTATTAT
38567859 TTAT
1 TTAT
38567863 ATTAGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:38567857 original size:14 final size:13
Alignment explanation
Indices: 38567832--38567871 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
38567822 TTTTTGTTTG
38567832 TTATTATTATTAT
1 TTATTATTATTAT
38567845 TTATTATTTATTAT
1 TTATTA-TTATTAT
*
38567859 TTA-TATTAGTAT
1 TTATTATTATTAT
38567871 T
1 T
38567872 ATAGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 8 0.32
14 10 0.40
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:38567976 original size:5 final size:5
Alignment explanation
Indices: 38567968--38568033 Score: 74
Period size: 5 Copynumber: 14.6 Consensus size: 5
38567958 AGCATAGCAT
*
38567968 TTTTA TTTTA -TCT- TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
38568015 -TTTA -TTTA -TTTA -TTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTT
38568034 AATATCATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
4 24 0.43
5 32 0.57
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:38567999 original size:28 final size:27
Alignment explanation
Indices: 38567968--38568029 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
38567958 AGCATAGCAT
38567968 TTTTATTTTATCTT-TTTATTTTATTTTA
1 TTTTATTTTATCTTATTTA-TTTA-TTTA
*
38567996 TTTTATTTTATTTTATTTATTTATTTA
1 TTTTATTTTATCTTATTTATTTATTTA
38568023 -TTTATTT
1 TTTTATTT
38568030 ATTTAATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.22
27 4 0.12
28 17 0.53
29 4 0.12
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTATTTTATCTTATTTATTTATTTA
Found at i:38568020 original size:8 final size:8
Alignment explanation
Indices: 38567969--38568034 Score: 62
Period size: 8 Copynumber: 7.5 Consensus size: 8
38567959 GCATAGCATT
38567969 TTTATTTTA
1 TTTA-TTTA
38567978 TCTT-TTTA
1 T-TTATTTA
38567986 TTTTATTTTA
1 -TTTA-TTTA
38567996 TTTTATTTTA
1 -TTTA-TTTA
38568006 TTTTATTTA
1 -TTTATTTA
38568015 TTTATTTA
1 TTTATTTA
38568023 TTTATTTA
1 TTTATTTA
38568031 TTTA
1 TTTA
38568035 ATATCATCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
8 26 0.49
9 6 0.11
10 21 0.40
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTTA
Found at i:38572192 original size:24 final size:24
Alignment explanation
Indices: 38572165--38572211 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38572155 AGCCTATAAC
* *
38572165 GGGTAGCTCCAAAGTGCAATTAAT
1 GGGTAGCTACAAAGAGCAATTAAT
*
38572189 GGGTAGCTACGAAGAGCAATTAA
1 GGGTAGCTACAAAGAGCAATTAA
38572212 CGGGAAGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (24 bp):
GGGTAGCTACAAAGAGCAATTAAT
Found at i:38572323 original size:26 final size:25
Alignment explanation
Indices: 38572257--38572329 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
38572247 AAGCGAGCAC
* *
38572257 TAAC-AGGAAGCTCACAAAGAGCCTT
1 TAACGAGGAAGCTCA-TAAGAGCCTA
*
38572282 TAATGAGGAAGCTCATGAAGAGCCATA
1 TAACGAGGAAGCTCAT-AAGAGCC-TA
38572309 TAACGA-GAAGCTCATAAGAGC
1 TAACGAGGAAGCTCATAAGAGC
38572330 TGCGGTGTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.22
26 26 0.63
27 6 0.15
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.16
Consensus pattern (25 bp):
TAACGAGGAAGCTCATAAGAGCCTA
Found at i:38579239 original size:27 final size:28
Alignment explanation
Indices: 38579184--38579248 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
38579174 ATAAAAAATA
*
38579184 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
38579212 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
38579239 ACCAAAATAT
1 ACCAAAATAT
38579249 ACCAAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:38579340 original size:27 final size:27
Alignment explanation
Indices: 38579310--38579388 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
38579300 GGCCAATCAC
*
38579310 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
38579337 ATTGGCGACACCAATGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
38579364 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
38579389 GACTAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.14
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:38579857 original size:19 final size:19
Alignment explanation
Indices: 38579815--38579887 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 19
38579805 TCTATTTGGG
*
38579815 TAATTTAATAA-ACTATTC
1 TAATTTAATAACTCTATTC
* *
38579833 TCATTTAATAACTCTATTT
1 TAATTTAATAACTCTATTC
*
38579852 TAATTTAATAAAT-TATTC
1 TAATTTAATAACTCTATTC
*
38579870 TCATTTAATAACTCTATT
1 TAATTTAATAACTCTATT
38579888 TTAAATTACG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
18 25 0.56
19 20 0.44
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTTAATAACTCTATTC
Found at i:38579863 original size:37 final size:37
Alignment explanation
Indices: 38579815--38579891 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
38579805 TCTATTTGGG
38579815 TAATTTAATAAACTATTCTCATTTAATAACTCTATTT
1 TAATTTAATAAACTATTCTCATTTAATAACTCTATTT
*
38579852 TAATTTAATAAATTATTCTCATTTAATAACTCTATTT
1 TAATTTAATAAACTATTCTCATTTAATAACTCTATTT
38579889 TAA
1 TAA
38579892 ATTACGAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (37 bp):
TAATTTAATAAACTATTCTCATTTAATAACTCTATTT
Found at i:38580126 original size:19 final size:19
Alignment explanation
Indices: 38580089--38580127 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38580079 GCTTTTTGCA
*
38580089 GTTTTTTTTCTGTTTTTTT
1 GTTTTTTTTCTGTTATTTT
38580108 GTTTTTTTT-TGTATATTTT
1 GTTTTTTTTCTGT-TATTTT
38580127 G
1 G
38580128 GTAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (19 bp):
GTTTTTTTTCTGTTATTTT
Found at i:38580149 original size:26 final size:28
Alignment explanation
Indices: 38580120--38580183 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
38580110 TTTTTTTTGT
38580120 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
38580146 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
38580174 ATATTTTGGT
1 ATATTTTGGT
38580184 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:38581000 original size:2 final size:2
Alignment explanation
Indices: 38580993--38581030 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38580983 TTGTAGAGTA
38580993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38581031 GGTCCAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38595543 original size:13 final size:13
Alignment explanation
Indices: 38595525--38595580 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
38595515 ACAATATATT
38595525 TATTAACTAAAAA
1 TATTAACTAAAAA
* *
38595538 TATTAATTTAAAA
1 TATTAACTAAAAA
* **
38595551 TTTTAA--AAATT
1 TATTAACTAAAAA
38595562 TATTAACTAAAAA
1 TATTAACTAAAAA
38595575 TATTAA
1 TATTAA
38595581 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
11 7 0.22
13 25 0.78
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTAACTAAAAA
Found at i:38595568 original size:37 final size:37
Alignment explanation
Indices: 38595522--38595596 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
38595512 AAAACAATAT
38595522 ATTTATTAACTAAAAATATTAATTTAAAATTTTAAAA
1 ATTTATTAACTAAAAATATTAATTTAAAATTTTAAAA
38595559 ATTTATTAACTAAAAATATTAATTTAAAATTTTAAAA
1 ATTTATTAACTAAAAATATTAATTTAAAATTTTAAAA
38595596 A
1 A
38595597 ACTAAAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (37 bp):
ATTTATTAACTAAAAATATTAATTTAAAATTTTAAAA
Found at i:38598586 original size:3 final size:3
Alignment explanation
Indices: 38598578--38598650 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
38598568 AGTACTAAAT
* * ** * *
38598578 ATA ATA ATA ACA ATA ATA AGA ATA AGT- ATA ATA ACG CTA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* *
38598623 ATA ATA ATA AGA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38598651 GGACTAATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.96
4 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:38600564 original size:13 final size:13
Alignment explanation
Indices: 38600546--38600573 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38600536 ATTCCTCATT
38600546 AATAGTTTAGGAG
1 AATAGTTTAGGAG
38600559 AATAGTTTAGGAG
1 AATAGTTTAGGAG
38600572 AA
1 AA
38600574 ATCATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (13 bp):
AATAGTTTAGGAG
Found at i:38600863 original size:14 final size:14
Alignment explanation
Indices: 38600837--38600872 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38600827 TAGTGTTTAA
*
38600837 GATTTATGGTTTGG
1 GATTCATGGTTTGG
38600851 GATTCATGGTTTGG
1 GATTCATGGTTTGG
*
38600865 GGTTCATG
1 GATTCATG
38600873 TTTAAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.36, T:0.44
Consensus pattern (14 bp):
GATTCATGGTTTGG
Found at i:38600922 original size:27 final size:27
Alignment explanation
Indices: 38600878--38600936 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
38600868 TCATGTTTAA
*
38600878 GGTTTAATGTTCAATGTTTGAT-TTTGG
1 GGTTTAAAGTTCAATGTTT-ATGTTTGG
* *
38600905 GGTTTAAAGTTTAGTGTTTATGGTTTGG
1 GGTTTAAAGTTCAATGTTTAT-GTTTGG
38600933 GGTT
1 GGTT
38600937 CAAGGTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 16 0.59
28 9 0.33
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.51
Consensus pattern (27 bp):
GGTTTAAAGTTCAATGTTTATGTTTGG
Found at i:38632666 original size:23 final size:23
Alignment explanation
Indices: 38632640--38632687 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
38632630 GCAGTTTTAA
38632640 TTGCGGTACTTTTGTACAGCGGT
1 TTGCGGTACTTTTGTACAGCGGT
38632663 TTGCGGTACTTTTGTACAGCGGT
1 TTGCGGTACTTTTGTACAGCGGT
38632686 TT
1 TT
38632688 ACTGCACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (23 bp):
TTGCGGTACTTTTGTACAGCGGT
Found at i:38632947 original size:21 final size:20
Alignment explanation
Indices: 38632910--38632952 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
38632900 TCTGAATATA
38632910 TGTCTGTTTGTCAGAACATTT
1 TGTCTGTTTGTCAGAAC-TTT
**
38632931 TGTCTGTTTGTGTGAACTTT
1 TGTCTGTTTGTCAGAACTTT
38632951 TG
1 TG
38632953 GTTATTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.14, C:0.12, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTCTGTTTGTCAGAACTTT
Found at i:38634503 original size:51 final size:47
Alignment explanation
Indices: 38634444--38634538 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 47
38634434 TGATTAAATT
* *
38634444 TAAGATTAAGATAATCACTTTAATATTAAATTAATAAAATATTATTAAGA
1 TAAGATTAAGATAA--A-TTTAATATTAAACTAATAAAATAATATTAAGA
** *
38634494 TAAGTATTAATTTAAATTTAATATTAAACTATTAAAATAATATTA
1 TAAG-ATTAAGATAAATTTAATATTAAACTAATAAAATAATATTA
38634539 TTTTTGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 26 0.67
49 1 0.03
50 4 0.10
51 8 0.21
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (47 bp):
TAAGATTAAGATAAATTTAATATTAAACTAATAAAATAATATTAAGA
Found at i:38635868 original size:320 final size:320
Alignment explanation
Indices: 38635286--38635925 Score: 1280
Period size: 320 Copynumber: 2.0 Consensus size: 320
38635276 AGTCCACAAG
38635286 AAGTACCGTGATTGAAAACTCCTTATTGTATACTCTTCACGAAAGTAATTCATCCAACTGCTTTA
1 AAGTACCGTGATTGAAAACTCCTTATTGTATACTCTTCACGAAAGTAATTCATCCAACTGCTTTA
38635351 TCCAACAACCTCGTCATTTGTGTGTTACCCTTATATGATATCTTTGATTCCTTTGAGTTAAATTC
66 TCCAACAACCTCGTCATTTGTGTGTTACCCTTATATGATATCTTTGATTCCTTTGAGTTAAATTC
38635416 ACTCACTCAATACAATTTTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATTTGA
131 ACTCACTCAATACAATTTTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATTTGA
38635481 TCACTGTCAACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACACGTGGCCACGTTCC
196 TCACTGTCAACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACACGTGGCCACGTTCC
38635546 ATATTTATCAATTCACACGATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGCTAT
261 ATATTTATCAATTCACACGATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGCTAT
38635606 AAGTACCGTGATTGAAAACTCCTTATTGTATACTCTTCACGAAAGTAATTCATCCAACTGCTTTA
1 AAGTACCGTGATTGAAAACTCCTTATTGTATACTCTTCACGAAAGTAATTCATCCAACTGCTTTA
38635671 TCCAACAACCTCGTCATTTGTGTGTTACCCTTATATGATATCTTTGATTCCTTTGAGTTAAATTC
66 TCCAACAACCTCGTCATTTGTGTGTTACCCTTATATGATATCTTTGATTCCTTTGAGTTAAATTC
38635736 ACTCACTCAATACAATTTTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATTTGA
131 ACTCACTCAATACAATTTTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATTTGA
38635801 TCACTGTCAACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACACGTGGCCACGTTCC
196 TCACTGTCAACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACACGTGGCCACGTTCC
38635866 ATATTTATCAATTCACACGATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGCTAT
261 ATATTTATCAATTCACACGATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGCTAT
38635926 GAATTCCATT
Statistics
Matches: 320, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
320 320 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (320 bp):
AAGTACCGTGATTGAAAACTCCTTATTGTATACTCTTCACGAAAGTAATTCATCCAACTGCTTTA
TCCAACAACCTCGTCATTTGTGTGTTACCCTTATATGATATCTTTGATTCCTTTGAGTTAAATTC
ACTCACTCAATACAATTTTATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATTTGA
TCACTGTCAACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACACGTGGCCACGTTCC
ATATTTATCAATTCACACGATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGCTAT
Found at i:38640684 original size:25 final size:24
Alignment explanation
Indices: 38640653--38640711 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
38640643 ATAATTTAAT
* *
38640653 AAATAAAATAAAATTCTAAAACTA
1 AAATAAAATAAAAGTCTAAAAATA
38640677 AAACTAAAACT-AAAGTCTAAAAATA
1 AAA-TAAAA-TAAAAGTCTAAAAATA
38640702 AAA-AAAATAA
1 AAATAAAATAA
38640712 TTCGGGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 5 0.17
24 3 0.10
25 20 0.67
26 1 0.03
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.20
Consensus pattern (24 bp):
AAATAAAATAAAAGTCTAAAAATA
Found at i:38643667 original size:23 final size:23
Alignment explanation
Indices: 38643641--38643687 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
38643631 AAAATCCCGA
*
38643641 TAACCCCCAAAATTCTTTAATTT
1 TAACCCCCAAAATTCGTTAATTT
*
38643664 TAACCCTCAAAATTCGTTAATTT
1 TAACCCCCAAAATTCGTTAATTT
38643687 T
1 T
38643688 CTCCCCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (23 bp):
TAACCCCCAAAATTCGTTAATTT
Found at i:38652721 original size:24 final size:24
Alignment explanation
Indices: 38652693--38652756 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
38652683 TTTCTAGAAG
* * *
38652693 ATTTAGTATTTATTGGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
38652717 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
38652741 ATTTAACATTGATTAG
1 ATTTAGCATTTATTAG
38652757 AATTAGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:38655168 original size:16 final size:16
Alignment explanation
Indices: 38655147--38655218 Score: 83
Period size: 16 Copynumber: 4.5 Consensus size: 16
38655137 CGTTTGGTTC
38655147 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
38655163 GCTGTAATTGTATAGA
1 GCTGTAATGGAATAGA
* *
38655179 GCTATAATGTAATAGAA
1 GCTGTAATGGAATAG-A
38655196 G-TGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
38655211 ACTGTAAT
1 GCTGTAAT
38655219 AGTAATTCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
15 1 0.02
16 42 0.93
17 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:38655309 original size:50 final size:50
Alignment explanation
Indices: 38655200--38655297 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
38655190 ATAGAAGTGT
38655200 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGATTGAATGGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGATTGAATGGAATGG
* * *
38655250 AATGGAATAGAACTGTAATGGT-ATTC-TTGTGTTTGGTTGAATGGAATG
1 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGATTGAATGGAATG
38655298 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 1 0.02
49 22 0.50
50 21 0.48
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (50 bp):
AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGATTGAATGGAATGG
Found at i:38662681 original size:9 final size:9
Alignment explanation
Indices: 38662667--38662697 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38662657 GTTAAACGAA
38662667 TCGAGTTAT
1 TCGAGTTAT
*
38662676 TCGAGTTAA
1 TCGAGTTAT
38662685 TCGAGTTAT
1 TCGAGTTAT
38662694 TCGA
1 TCGA
38662698 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:38669369 original size:14 final size:13
Alignment explanation
Indices: 38669352--38669381 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
38669342 CAAATTTAAA
38669352 AATTAAAAGAGTAC
1 AATTAAAAGAGT-C
38669366 AATTAAAAGAGTC
1 AATTAAAAGAGTC
38669379 AAT
1 AAT
38669382 ATTTAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (13 bp):
AATTAAAAGAGTC
Found at i:38687110 original size:13 final size:13
Alignment explanation
Indices: 38687092--38687120 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38687082 CACGAGAAGA
38687092 AGAAATCTTCAAC
1 AGAAATCTTCAAC
38687105 AGAAATCTTCAAC
1 AGAAATCTTCAAC
38687118 AGA
1 AGA
38687121 TTTTCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (13 bp):
AGAAATCTTCAAC
Found at i:38692142 original size:23 final size:23
Alignment explanation
Indices: 38692117--38692448 Score: 470
Period size: 23 Copynumber: 14.4 Consensus size: 23
38692107 GTGGCACAGG
*
38692117 GGGTTTTCAACTTAATTAGGTTG
1 GGGTTTTCAACTTAATTAGGTTA
*
38692140 GGGTTTTCAACTTACTTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
38692163 GGGTTTTCAACTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
*
38692186 GGATTTTCAACTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
*
38692209 GGGTTTTCAACTTAATTATGTTA
1 GGGTTTTCAACTTAATTAGGTTA
*
38692232 GGGTTTTCAACTTAAATAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
* *
38692255 GGTTTTTCAATTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
38692278 GGGTTTTCAACTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
* *
38692301 GGGTTTTCAACTTAAATCGGTATA
1 GGGTTTTCAACTTAATTAGGT-TA
** * *
38692325 CTAG-CTGC-ACTTAATTAGGTTA
1 -GGGTTTTCAACTTAATTAGGTTA
*
38692347 GGGTTTTCAACTTAAATAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
* *
38692370 GGGTTTTTAATTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
38692393 GGGTTTTCAACTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
38692416 GGGTTTTCAACTTAATTAGGTTA
1 GGGTTTTCAACTTAATTAGGTTA
**
38692439 AAGTTTTCAA
1 GGGTTTTCAA
38692449 TTTTTATCAC
Statistics
Matches: 272, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
21 1 0.00
22 4 0.01
23 262 0.96
24 4 0.01
25 1 0.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (23 bp):
GGGTTTTCAACTTAATTAGGTTA
Found at i:38692478 original size:25 final size:25
Alignment explanation
Indices: 38692450--38692638 Score: 194
Period size: 25 Copynumber: 7.7 Consensus size: 25
38692440 AGTTTTCAAT
*
38692450 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
* *
38692475 TTTTATTACATTATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
38692500 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
38692525 TTTTATTACATCAGAT-AA----TA
1 TTTTATTACATCAAATAAACTTCTA
** * * * **
38692545 TTAAAATA-ACTCAAAAAAATTTAAA
1 TTTTATTACA-TCAAATAAACTTCTA
38692570 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
*
38692596 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
38692621 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
38692639 TATCAAAATA
Statistics
Matches: 133, Mismatches: 21, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
19 1 0.01
20 11 0.08
21 2 0.02
24 2 0.02
25 101 0.76
26 15 0.11
27 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.43
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:38692592 original size:96 final size:96
Alignment explanation
Indices: 38692475--38692713 Score: 392
Period size: 96 Copynumber: 2.5 Consensus size: 96
38692465 TAAACTTCTA
* *
38692475 TTTTATTACAT-TATATAAACTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAG
1 TTTTATTACATCAATA-AAACTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAA
*
38692539 ATAATATTAAAATAACTCAAAAAAATTTAAAT
65 ATAATATCAAAATAACTCAAAAAAATTTAAAT
*
38692571 TTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTCTATTTTATTACATCAAA
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAA
38692636 TAATATCAAAATAACTCAAAAAAATTTAAAT
66 TAATATCAAAATAACTCAAAAAAATTTAAAT
* * *
38692667 TTTT-TTACATCAATAAAGCTTATATTTTATTACATCAAACAAACTTC
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAAACTTC
38692714 AACTCAAAGA
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
95 39 0.29
96 92 0.69
97 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (96 bp):
TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAA
TAATATCAAAATAACTCAAAAAAATTTAAAT
Found at i:38692679 original size:25 final size:25
Alignment explanation
Indices: 38692651--38692712 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
38692641 TCAAAATAAC
* *
38692651 TCAAAAAAATTTAAATTTTTTTACA
1 TCAAAAAAACTTAAATTTTATTACA
* * *
38692676 TCAATAAAGCTTATATTTTATTACA
1 TCAAAAAAACTTAAATTTTATTACA
*
38692701 TCAAACAAACTT
1 TCAAAAAAACTT
38692713 CAACTCAAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (25 bp):
TCAAAAAAACTTAAATTTTATTACA
Found at i:38692760 original size:137 final size:140
Alignment explanation
Indices: 38692596--38692927 Score: 464
Period size: 137 Copynumber: 2.4 Consensus size: 140
38692586 AAAACTTCTA
38692596 TTTTATTACATC-ATATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
1 TTTTATTACATCAATA-AAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
* *
38692660 TTTAAATTTTT-TTACATCAATAAAGCTTATATTTTATTACATCAAACAA-A-C-TTCAACTCAA
65 TTTAAATTTTTATTACATCAATAAAACTTATATTTTATTACATCAAACAATATCAAT-AACTCAA
** *
38692721 AGAAA-TTCCAAT
129 A-AAATTTAAAAC
38692733 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
* * *
38692798 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAA
66 TTAAATTTTTATTACATCAATAAAACTTATATTTTATTACATCAAACAATATC--AATAACTCAA
38692863 AAAATTTTAAAAC
129 AAAA-TTTAAAAC
*
38692876 TTTT-TTACATCAATAAAACTTCTATTTTATTACATCAAACAA-ACTCAAAATA
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATA-TCAAAATA
38692928 TTCAAAATAT
Statistics
Matches: 176, Mismatches: 9, Indels: 15
0.88 0.05 0.08
Matches are distributed among these distances:
137 70 0.40
138 38 0.22
139 1 0.01
140 1 0.01
141 4 0.02
142 53 0.30
143 9 0.05
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (140 bp):
TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
TTAAATTTTTATTACATCAATAAAACTTATATTTTATTACATCAAACAATATCAATAACTCAAAA
AATTTAAAAC
Found at i:38692816 original size:71 final size:71
Alignment explanation
Indices: 38692596--38692927 Score: 466
Period size: 71 Copynumber: 4.7 Consensus size: 71
38692586 AAAACTTCTA
38692596 TTTTATTACATC-ATATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
1 TTTTATTACATCAATA-AAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAA
38692660 TTTAAAT
65 TTTAAAT
* * * * *
38692667 TTTT-TTACATCAATAAAGCTTATATTTTATTACATCAAACAA-A-C---TTCAACTCAAAGAAA
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAAT-AACTCAAAAAAA
**
38692726 TTCCAAT
65 TTTAAAT
38692733 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
*
38692798 TTCAAT
66 TTAAAT
*
38692804 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
*
38692869 TTAAAAC
66 TT-AAAT
*
38692876 TTTT-TTACATCAATAAAACTTCTATTTTATTACATCAAACAA-ACTCAAAATA
1 TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATA-TCAAAATA
38692928 TTCAAAATAT
Statistics
Matches: 234, Mismatches: 17, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
65 1 0.00
66 20 0.09
67 35 0.15
68 2 0.01
69 2 0.01
70 32 0.14
71 135 0.58
72 7 0.03
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (71 bp):
TTTTATTACATCAATAAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
TTAAAT
Found at i:38692845 original size:26 final size:26
Alignment explanation
Indices: 38692733--38692846 Score: 102
Period size: 25 Copynumber: 4.7 Consensus size: 26
38692723 AAATTCCAAT
38692733 TTTTATTACATC-AATAAAACTTCTA
1 TTTTATTACATCAAATAAAACTTCTA
*
38692758 TTTTATTACATCAAATAATA--TC-A
1 TTTTATTACATCAAATAAAACTTCTA
** * * *
38692781 --AAATAAC-TCAAA-AAAATTTCAA
1 TTTTATTACATCAAATAAAACTTCTA
38692803 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAATAAAACTTCTA
38692829 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
38692847 TATCAAAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 19
0.70 0.10 0.19
Matches are distributed among these distances:
19 3 0.04
20 5 0.07
21 6 0.09
22 1 0.01
23 1 0.01
24 2 0.03
25 30 0.43
26 21 0.30
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTTATTACATCAAATAAAACTTCTA
Found at i:38693369 original size:18 final size:18
Alignment explanation
Indices: 38693346--38693385 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
38693336 GACTCGGAAA
*
38693346 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGAT
38693364 AGGATACATATAAGGGAT
1 AGGATACATATAAGGGAT
38693382 AGGA
1 AGGA
38693386 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGAT
Found at i:38694047 original size:7 final size:7
Alignment explanation
Indices: 38694037--38694103 Score: 125
Period size: 7 Copynumber: 9.6 Consensus size: 7
38694027 TTATATACAT
38694037 AATACTA
1 AATACTA
38694044 AATACTA
1 AATACTA
38694051 AATACTA
1 AATACTA
38694058 AATACTA
1 AATACTA
38694065 AATACTA
1 AATACTA
38694072 AATACTA
1 AATACTA
38694079 AATACTA
1 AATACTA
38694086 AATACTA
1 AATACTA
*
38694093 AATACAA
1 AATACTA
38694100 AATA
1 AATA
38694104 TCTATTTACA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:38695228 original size:51 final size:51
Alignment explanation
Indices: 38695169--38695291 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
38695159 TATTTTAAAA
* * *
38695169 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGCTTTGA-GAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGG
* * *
38695220 AATGAAATTGAGAGGAAATTGAAATTGAATATGGATTTATGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGG
38695271 AAGGAAATTGAGAGAAAATTG
1 AAGGAAATTGAGAGAAAATTG
38695292 GGAGGAAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 63 0.98
ACGTcount: A:0.42, C:0.02, G:0.26, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGG
Found at i:38695286 original size:22 final size:22
Alignment explanation
Indices: 38695267--38695311 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
38695257 TATGAGAATT
38695267 TTGGAAGGAAATTGAGAGAAAA
1 TTGGAAGGAAATTGAGAGAAAA
* *
38695289 TTGGGAGGAAATTGAGAGGAAA
1 TTGGAAGGAAATTGAGAGAAAA
38695311 T
1 T
38695312 ATGAGGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (22 bp):
TTGGAAGGAAATTGAGAGAAAA
Found at i:38695291 original size:11 final size:11
Alignment explanation
Indices: 38695272--38695316 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
38695262 GAATTTTGGA
38695272 AGGAAATTGAG
1 AGGAAATTGAG
* *
38695283 AGAAAATTGGG
1 AGGAAATTGAG
38695294 AGGAAATTGAG
1 AGGAAATTGAG
38695305 AGGAAATATGAG
1 AGGAAAT-TGAG
38695317 GGAGGATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
AGGAAATTGAG
Done.