Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 136 of 213
Found at i:40309836 original size:138 final size:138
Alignment explanation
Indices: 40309628--40309911 Score: 489
Period size: 138 Copynumber: 2.1 Consensus size: 138
40309618 TTAGGAAAAG
* * *
40309628 AATTATATTCTTTTCAAAAGAATATTAATTTTTATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
40309693 TATAACTGTTTATATTAATAAATTTGG-AAAACTATATACAATTAATATTTTGTATGAATAAAAT
66 TATAACTGTTTATATTAATAAATTTGGTAAAA-TATATACAATTAATATTTTGTATGAATAAAAT
40309757 TCATATATT
130 TCATATATT
* * *
40309766 AATTATATTCTTTCCAAAATAATATTAATTTTCATGTCTTTTCTATATTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
*
40309831 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATAAAATT
40309896 CATATATT
131 CATATATT
40309904 AATTATAT
1 AATTATAT
40309912 CTATTTTATA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
138 134 0.97
139 4 0.03
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATAAAATT
CATATATT
Found at i:40316412 original size:22 final size:22
Alignment explanation
Indices: 40316384--40316427 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40316374 ATTTGAGTTA
40316384 TCGTCAATAGGTATAGTACGCC
1 TCGTCAATAGGTATAGTACGCC
40316406 TCGTCAATAGGTATAGTACGCC
1 TCGTCAATAGGTATAGTACGCC
40316428 GAGTTTACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TCGTCAATAGGTATAGTACGCC
Found at i:40317903 original size:13 final size:13
Alignment explanation
Indices: 40317885--40317923 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
40317875 CAGCTAAATA
40317885 AGCTTATTGGGTC
1 AGCTTATTGGGTC
40317898 AGCTTATTGGGTC
1 AGCTTATTGGGTC
40317911 AGCTTATTGGGTC
1 AGCTTATTGGGTC
40317924 GGTTTTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
AGCTTATTGGGTC
Found at i:40323395 original size:16 final size:16
Alignment explanation
Indices: 40323374--40323405 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40323364 TAAATAATTT
40323374 ATCAAATAACATATAC
1 ATCAAATAACATATAC
40323390 ATCAAATAACATATAC
1 ATCAAATAACATATAC
40323406 TAACATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (16 bp):
ATCAAATAACATATAC
Found at i:40324625 original size:41 final size:41
Alignment explanation
Indices: 40324530--40324678 Score: 167
Period size: 41 Copynumber: 3.6 Consensus size: 41
40324520 GCAACCCCTC
* * * *
40324530 GGGAAATCTTCACTCAGCAACCTCTTTTTTTATCAGAGTTTC
1 GGGAAATCTGCACTTAGCAACC-CCTTTTTTATCAGAGTTTA
* * * *
40324572 GGGGAATTTGCACTTAGCAACCCCTTTTTGATCAGAGTTTT
1 GGGAAATCTGCACTTAGCAACCCCTTTTTTATCAGAGTTTA
* *
40324613 GGGAAATCTGCACTTAGCAA-CCCTTTTTTATCAGTGATTCA
1 GGGAAATCTGCACTTAGCAACCCCTTTTTTATCAGAG-TTTA
*
40324654 GGG-AATTTGCACTTAGCAACCCCTT
1 GGGAAATCTGCACTTAGCAACCCCTT
40324679 ACATTCAATG
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
40 29 0.32
41 44 0.48
42 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (41 bp):
GGGAAATCTGCACTTAGCAACCCCTTTTTTATCAGAGTTTA
Found at i:40331907 original size:43 final size:42
Alignment explanation
Indices: 40331791--40331936 Score: 145
Period size: 43 Copynumber: 3.5 Consensus size: 42
40331781 GTTACTTGGT
* * *
40331791 GGAATCAGCACTTAGCAACCACC-TTATATTC-AGTGATACGG
1 GGAATCAGCACTTAACAACCACCTTTACAATCAAG-GATACGG
*
40331832 GGAATCAGCACATAACAACC-CCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAACAACCACCTTT-ACAATCAAGGATACGG
* * * ** *
40331874 TGGAATCAACACTTAAAAACCACCTTTAGAATCAATAATTCGG
1 -GGAATCAGCACTTAACAACCACCTTTACAATCAAGGATACGG
*
40331917 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAACAACC
40331937 CCTCGTGGAG
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.02
41 20 0.23
42 28 0.33
43 31 0.36
44 5 0.06
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAACAACCACCTTTACAATCAAGGATACGG
Found at i:40332086 original size:41 final size:41
Alignment explanation
Indices: 40331947--40332089 Score: 187
Period size: 41 Copynumber: 3.5 Consensus size: 41
40331937 CCTCGTGGAG
*
40331947 TCTACACTTAGCAACCACTTTTTTATTAGAGTTTCGGGGAA
1 TCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGGGGAA
* * * *
40331988 TTTACACTTAGCAACCTCTTTTTTATCACAGTTTCGGGGAA
1 TCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGGGGAA
* * * * * *
40332029 TCTGCAGTTAGCAACCCCTTTTTGATTAGTGATTCAGGGAA
1 TCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGGGGAA
40332070 TCTACACTTAGCAACCCCTT
1 TCTACACTTAGCAACCCCTT
40332090 ACATTCAATG
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (41 bp):
TCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGGGGAA
Found at i:40332937 original size:12 final size:12
Alignment explanation
Indices: 40332920--40332950 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40332910 AAAAATTGGC
40332920 TTTTAATTTTGT
1 TTTTAATTTTGT
40332932 TTTTAATTTTGT
1 TTTTAATTTTGT
40332944 TTTTAAT
1 TTTTAAT
40332951 GAAAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTAATTTTGT
Found at i:40334333 original size:19 final size:19
Alignment explanation
Indices: 40334309--40334349 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40334299 AATACTAAAA
40334309 AAATATCAAACAAAACCAT
1 AAATATCAAACAAAACCAT
40334328 AAATATCAAACAAAACCAT
1 AAATATCAAACAAAACCAT
40334347 AAA
1 AAA
40334350 ATGCTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATATCAAACAAAACCAT
Found at i:40350696 original size:31 final size:29
Alignment explanation
Indices: 40350661--40350727 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
40350651 GTAGATGAAG
*
40350661 CTATCCCATTCCATTATTTTGATGGTCGTCA
1 CTATCCCATTCCA-T-TGTTGATGGTCGTCA
* *
40350692 CTATCCCTTTTCATTGTTGATGGTCGTCA
1 CTATCCCATTCCATTGTTGATGGTCGTCA
*
40350721 CCATCCC
1 CTATCCC
40350728 TTTTCATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.62
30 1 0.03
31 11 0.34
ACGTcount: A:0.16, C:0.30, G:0.13, T:0.40
Consensus pattern (29 bp):
CTATCCCATTCCATTGTTGATGGTCGTCA
Found at i:40350714 original size:29 final size:29
Alignment explanation
Indices: 40350679--40350734 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
40350669 TTCCATTATT
*
40350679 TTGATGGTCGTCACTATCCCTTTTCATTG
1 TTGATGGTCGTCACCATCCCTTTTCATTG
40350708 TTGATGGTCGTCACCATCCCTTTTCAT
1 TTGATGGTCGTCACCATCCCTTTTCAT
40350735 AATTTGATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (29 bp):
TTGATGGTCGTCACCATCCCTTTTCATTG
Found at i:40350757 original size:30 final size:30
Alignment explanation
Indices: 40350723--40350799 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
40350713 GGTCGTCACC
* *
40350723 ATCCCTTTTCATAATTTGATAGCCGAGGCT
1 ATCCCTTTTCATAATTTAATAGCCGAAGCT
* * * *
40350753 ATCCCTTTTAATGATTCAATAGCTGAAGCT
1 ATCCCTTTTCATAATTTAATAGCCGAAGCT
*
40350783 ATCCATTTTCATAATTT
1 ATCCCTTTTCATAATTT
40350800 TGATGCTCAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTAATAGCCGAAGCT
Found at i:40350818 original size:120 final size:119
Alignment explanation
Indices: 40350602--40350880 Score: 364
Period size: 120 Copynumber: 2.3 Consensus size: 119
40350592 ATGGTTGGCA
* * * * * **
40350602 CATCCCTTTCCATAATTCGATAGCCAAAGCTATCCTTTTTCATGATTCGGTAGATGAAGCTATCC
1 CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGATGAAGCTATCC
* * * *
40350667 CATTCCATTATTTTGATGGTCGTCACTATCCCTTTTCATTGTTGATGGTCGTCAC
66 CATTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGT-AC
* *
40350722 CATCCCTTTTCATAATTTGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGCTGAAGCTAT-C
1 CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGATGAAGCTATCC
*
40350786 CATTTTCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
66 CA-TTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
** *
40350841 CATCCCTTTTCATAGCTCGATAGTCG-GAGCTATCCCTTTT
1 CATCCCTTTTCATAATTCGATAGCCGAG-GCTATCCCTTTT
40350881 CATTAGTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
118 1 0.01
119 39 0.28
120 99 0.71
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (119 bp):
CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGATGAAGCTATCC
CATTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
Found at i:40350823 original size:31 final size:29
Alignment explanation
Indices: 40350783--40350854 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
40350773 AGCTGAAGCT
* *
40350783 ATCCATTTTCATAATTTTGATGCTCATCACC
1 ATCCCTTTTCAT-ATGTTGATGCTCAT-ACC
* *
40350814 ATCCCTTTTCAT-TGTTGATGGTCGTACC
1 ATCCCTTTTCATATGTTGATGCTCATACC
40350842 ATCCCTTTTCATA
1 ATCCCTTTTCATA
40350855 GCTCGATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.42
29 10 0.28
31 11 0.31
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATATGTTGATGCTCATACC
Found at i:40353007 original size:37 final size:37
Alignment explanation
Indices: 40352957--40353035 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40352947 TTATTACGAA
* *
40352957 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
40352994 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
40353031 GTCTT
1 GTCTT
40353036 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:40353232 original size:47 final size:47
Alignment explanation
Indices: 40353154--40353650 Score: 421
Period size: 47 Copynumber: 10.5 Consensus size: 47
40353144 CCCTTCGGGA
* * * * * *
40353154 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* *
40353201 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
*
40353248 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* ** **
40353295 CTTATTACATATATACACTTTCACATTCATCACATC-GATA-TATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* * * * **
40353340 ACTT-TCACAT-TCAT-CAC-ATCGGCTATT-AGGC-CTTATC--ACACATATAC
1 -CTTATCACATAT-ATACACTTTC-AC-ATTCA-TCAC--ATCGGCCAC-TAGGC
* * *
40353387 ACTT-TCACAT-TCATCACATCGGCTATT-AGGCCTT-ATCACA-CGGCTATTAGGC
1 -CTTATCACATAT-AT-ACA----CT-TTCA--CATTCATCACATCGGCCACTAGGC
* * *
40353439 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* *
40353486 CTTATCACATATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* *
40353535 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
* *
40353582 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
40353629 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
40353651 TTGGCTGAAT
Statistics
Matches: 381, Mismatches: 40, Indels: 58
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.01
44 7 0.02
45 19 0.05
46 16 0.04
47 263 0.69
49 46 0.12
51 7 0.02
52 11 0.03
53 4 0.01
54 4 0.01
55 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
Found at i:40353344 original size:76 final size:76
Alignment explanation
Indices: 40353256--40353475 Score: 314
Period size: 76 Copynumber: 3.0 Consensus size: 76
40353246 GCCTTATCAC
* * *
40353256 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
40353321 TCATCACATCG
66 TCATCACATCG
40353332 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
40353397 TCATCACATCGG
66 TCATCACATC-G
* **
40353409 CTAT-T--A--GGC-C-TT-ATCACA-CGGCTATTAGGCCTTATCACACATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
40353465 TCATCACATCG
66 TCATCACATCG
40353476 GCTATTAGGC
Statistics
Matches: 137, Mismatches: 6, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
67 1 0.01
68 48 0.35
69 6 0.04
70 2 0.01
71 1 0.01
72 1 0.01
74 1 0.01
76 73 0.53
77 4 0.03
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (76 bp):
ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
TCATCACATCG
Found at i:40353345 original size:29 final size:29
Alignment explanation
Indices: 40353303--40353360 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40353293 GCCTTATTAC
40353303 ATATATACACTTTCACATTCATCACATCG
1 ATATATACACTTTCACATTCATCACATCG
40353332 ATATATACACTTTCACATTCATCACATCG
1 ATATATACACTTTCACATTCATCACATCG
40353361 GCTATTAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
ATATATACACTTTCACATTCATCACATCG
Found at i:40353372 original size:123 final size:123
Alignment explanation
Indices: 40353209--40353571 Score: 526
Period size: 123 Copynumber: 3.0 Consensus size: 123
40353199 GCCCTGTCAC
* *
40353209 ATATATACACTTTCACATTCATCACATCGGCCACTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
*
40353274 TCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCG
66 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
*
40353332 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
* **** *** *
40353397 TCATCACATCGGCTATTAGGCCTTATCACACGGCT--A-TTAGGCCTT-ATCACA-C-
66 TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
40353449 --ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC--ATATATACACTTTCAC
*
40353512 ATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
64 ATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
40353572 GCTATTAGGC
Statistics
Matches: 208, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
115 45 0.22
117 46 0.22
118 1 0.00
119 7 0.03
120 10 0.05
121 7 0.03
122 1 0.00
123 91 0.44
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.33
Consensus pattern (123 bp):
ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
Found at i:40353432 original size:21 final size:21
Alignment explanation
Indices: 40353399--40353448 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
40353389 TTTCACATTC
40353399 ATCACATCGGCTATTAGGCCTT
1 ATCACA-CGGCTATTAGGCCTT
40353421 ATCACACGGCTATTAGGCCTT
1 ATCACACGGCTATTAGGCCTT
40353442 ATCACAC
1 ATCACAC
40353449 ATATACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
ATCACACGGCTATTAGGCCTT
Found at i:40353432 original size:68 final size:69
Alignment explanation
Indices: 40353352--40353495 Score: 281
Period size: 68 Copynumber: 2.1 Consensus size: 69
40353342 TTTCACATTC
40353352 ATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGG
1 ATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGG
40353417 CCTT
66 CCTT
40353421 ATCACA-CGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGG
1 ATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGG
40353485 CCTT
66 CCTT
40353489 ATCACAT
1 ATCACAT
40353496 ATATATACAC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 68 0.92
69 6 0.08
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.31
Consensus pattern (69 bp):
ATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGG
CCTT
Found at i:40364118 original size:22 final size:21
Alignment explanation
Indices: 40364092--40364133 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40364082 TAACACATCA
40364092 TGGATAAACCACCACATAATTG
1 TGGAT-AACCACCACATAATTG
* *
40364114 TGGATAACGATCACATAATT
1 TGGATAACCACCACATAATT
40364134 ATAGTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (21 bp):
TGGATAACCACCACATAATTG
Found at i:40381785 original size:38 final size:38
Alignment explanation
Indices: 40381734--40381809 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
40381724 AGAATTCTTC
40381734 CTCTATTTCTTATCTTGTTTCTTCGCGAGCTTAATTGA
1 CTCTATTTCTTATCTTGTTTCTTCGCGAGCTTAATTGA
* * *
40381772 CTCTATTTCTTATCTTGTTTCTTTGTGAGCTTATTTGA
1 CTCTATTTCTTATCTTGTTTCTTCGCGAGCTTAATTGA
40381810 TAAAGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.14, C:0.18, G:0.13, T:0.54
Consensus pattern (38 bp):
CTCTATTTCTTATCTTGTTTCTTCGCGAGCTTAATTGA
Found at i:40386768 original size:27 final size:27
Alignment explanation
Indices: 40386737--40387094 Score: 354
Period size: 27 Copynumber: 13.3 Consensus size: 27
40386727 CCCTAAAATA
* * *
40386737 GGTAAAATGACTAAAATACCCTTACAG
1 GGTAAAATGACTGAAATACCCTCATAG
* **
40386764 GGTAAAATAACCAAAATACCCTCATAG
1 GGTAAAATGACTGAAATACCCTCATAG
* ** *
40386791 GGTAGAATGACCAAAATACTCTCATAG
1 GGTAAAATGACTGAAATACCCTCATAG
* *
40386818 GGTAAAATGACCGAAATACCCTTATAG
1 GGTAAAATGACTGAAATACCCTCATAG
*
40386845 GGTAGAATGACTGAAATATCCCT-ATAG
1 GGTAAAATGACTGAAATA-CCCTCATAG
*
40386872 GGTAAAATGACTGAAATACTCC-C-TAA
1 GGTAAAATGACTGAAATAC-CCTCATAG
* * *
40386898 GGTAGAATGATTGAAATAACCTCATAG
1 GGTAAAATGACTGAAATACCCTCATAG
40386925 GGTAAAATGA-TAGAAATACTCC-CATAG
1 GGTAAAATGACT-GAAATAC-CCTCATAG
* * *
40386952 GGTAAAATGACTAAAATACCCCCATAT
1 GGTAAAATGACTGAAATACCCTCATAG
*
40386979 GGTAGAATGA-TCGAAATACCC-CAATAG
1 GGTAAAATGACT-GAAATACCCTC-ATAG
*
40387006 GGTAAAATGACCGAAATACCC-CTATAG
1 GGTAAAATGACTGAAATACCCTC-ATAG
*
40387033 GGTAAAATGACTGAAATACCCTCTTAG
1 GGTAAAATGACTGAAATACCCTCATAG
* ** *
40387060 AGTAGTATGACTAAAATACCCTCATAG
1 GGTAAAATGACTGAAATACCCTCATAG
40387087 GGTAAAAT
1 GGTAAAAT
40387095 AAAAGTTATA
Statistics
Matches: 279, Mismatches: 39, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.01
26 25 0.09
27 244 0.87
28 8 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCTCATAG
Found at i:40387631 original size:33 final size:32
Alignment explanation
Indices: 40387567--40387636 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
40387557 ATGACAGATT
** *
40387567 TATATTACTGTTATGGGCCAACGCCCCACTGA
1 TATATTACTGAAATGGGCAAACGCCCCACTGA
* *
40387599 TATATTACTGAAATTGGGCAAAGGCCCTACTGA
1 TATATTACTGAAA-TGGGCAAACGCCCCACTGA
40387632 T-TATT
1 TATATT
40387637 TGCATCGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (32 bp):
TATATTACTGAAATGGGCAAACGCCCCACTGA
Found at i:40392981 original size:21 final size:22
Alignment explanation
Indices: 40392952--40392998 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
40392942 CAGAAGGAGT
*
40392952 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
40392974 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
40392995 GAGT
1 GAGT
40392999 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:40412818 original size:14 final size:15
Alignment explanation
Indices: 40412799--40412827 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40412789 TCATGCTATG
40412799 TCATATCAAA-CATA
1 TCATATCAAATCATA
40412813 TCATATCAAATCATA
1 TCATATCAAATCATA
40412828 ACATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TCATATCAAATCATA
Found at i:40416849 original size:22 final size:23
Alignment explanation
Indices: 40416824--40416867 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40416814 GAACTGGCGT
*
40416824 AGTCAAAACAAGGA-ATAGGAAA
1 AGTCAAAACAAGAACATAGGAAA
*
40416846 AGTCAATACAAGAACATAGGAA
1 AGTCAAAACAAGAACATAGGAA
40416868 TAGATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (23 bp):
AGTCAAAACAAGAACATAGGAAA
Found at i:40419426 original size:13 final size:13
Alignment explanation
Indices: 40419408--40419432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40419398 GAGGAGAGAA
40419408 AAAATGAAAAGTG
1 AAAATGAAAAGTG
40419421 AAAATGAAAAGT
1 AAAATGAAAAGT
40419433 CTAGGTGCAT
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:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
AAAATGAAAAGTG
Found at i:40431707 original size:25 final size:25
Alignment explanation
Indices: 40431679--40431732 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40431669 AAGTATTATA
*
40431679 CAGAGAACATAAATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
** **
40431704 CAGAGTGCACCGATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
40431729 CAGA
1 CAGA
40431733 CAGCACGCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
CAGAGAACACAAATGTGCTAATAAT
Found at i:40431738 original size:25 final size:25
Alignment explanation
Indices: 40431691--40431738 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40431681 GAGAACATAA
**
40431691 ATGTGCTAATAATCAGAGTGCACCG
1 ATGTGCTAATAATCAGACAGCACCG
40431716 ATGTGCTAATAATCAGACAGCAC
1 ATGTGCTAATAATCAGACAGCAC
40431739 GCTAAACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (25 bp):
ATGTGCTAATAATCAGACAGCACCG
Found at i:40432765 original size:50 final size:50
Alignment explanation
Indices: 40432687--40432916 Score: 275
Period size: 50 Copynumber: 4.6 Consensus size: 50
40432677 TTTCCTATAC
* * * * * *
40432687 TGCCAATGACATATCCCAGATAAGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * * *
40432737 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACTTCTCATCTCGG
*
40432787 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA-TCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATCTCGG
* * *
40432837 TGCCAACGACATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
* * *
40432887 CGCCAACGCCATGTCCCAAACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
40432917 TCGAGATCGC
Statistics
Matches: 154, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 152 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
Found at i:40432815 original size:100 final size:100
Alignment explanation
Indices: 40432687--40432916 Score: 311
Period size: 100 Copynumber: 2.3 Consensus size: 100
40432677 TTTCCTATAC
* * * * * * * *
40432687 TGCCAATGACATATCCCAGATAAGGTCTTACATGGGAGT-TCTCATATCGGTGCCCATGCCATGT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA-TCTCTCATATCGGTGCCAACGACATGT
*
40432751 CCCAGACATGGTCTTAC-GGAGGACCTCTCATCTTGG
65 CCCAGACATGGTCTTACAGG-GGACCTCTCATCTCGG
*
40432787 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAACGACATGTC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCTCATATCGGTGCCAACGACATGTC
*
40432852 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
66 CCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
40432887 CGCCAACGCCATGTCCCAAACATGGTCTTA
1 TGCCAATGCCATGTCCCAAACATGGTCTTA
40432917 TCGAGATCGC
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 1 0.01
100 113 0.98
101 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (100 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCTCATATCGGTGCCAACGACATGTC
CCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:40440682 original size:91 final size:91
Alignment explanation
Indices: 40440526--40440707 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
40440516 GTGACTTGTA
* * *
40440526 GGTTCGTGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTGGTCATTGTCTTGTCCACACGGCCTA
1 GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
40440591 ACACATGGGCATTTATCTCAGCCGTG
66 ACACATGGGCATTTATCTCAGCCGTG
* * * * *
40440617 GGTTCGCGTTTTAAATGGTGAGGAAAATGGCTTGATTTTCGTCATTTTCTTGTCTACATGACCTA
1 GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
* * *
40440682 AGACATGGGCGTTTGTCTCAGCCGTG
66 ACACATGGGCATTTATCTCAGCCGTG
40440708 TGTAACACGC
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (91 bp):
GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
ACACATGGGCATTTATCTCAGCCGTG
Found at i:40455856 original size:19 final size:18
Alignment explanation
Indices: 40455828--40455871 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
40455818 CTCATTCTCA
*
40455828 TCTCTTCTCTCACAACTTT
1 TCTCTCCTCTCACAA-TTT
*
40455847 TCTCTCCTCTCTCAATTT
1 TCTCTCCTCTCACAATTT
*
40455865 TTTCTCC
1 TCTCTCC
40455872 CATTTTCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.11, C:0.39, G:0.00, T:0.50
Consensus pattern (18 bp):
TCTCTCCTCTCACAATTT
Found at i:40470980 original size:12 final size:12
Alignment explanation
Indices: 40470963--40470987 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40470953 TTTCACTCTT
40470963 CTCTTTTTCAAA
1 CTCTTTTTCAAA
40470975 CTCTTTTTCAAA
1 CTCTTTTTCAAA
40470987 C
1 C
40470988 CCTCTCTCTT
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:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:40472004 original size:30 final size:30
Alignment explanation
Indices: 40471955--40472016 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
40471945 TTTAACTTGA
**
40471955 TTTTTTTTGCTCACCTTTTTTTTTCTTTTT
1 TTTTTTTTGCTCACCTTTTTTTCACTTTTT
*
40471985 TTTTTTTTGCTCGA-TTTTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACCTTTTTTTCACTTTTT
40472015 TT
1 TT
40472017 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (30 bp):
TTTTTTTTGCTCACCTTTTTTTCACTTTTT
Found at i:40475398 original size:20 final size:20
Alignment explanation
Indices: 40475375--40475421 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40475365 GGGTTAAGAT
*
40475375 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40475395 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40475415 TGAGCTG
1 TGAGCTG
40475422 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40475898 original size:10 final size:10
Alignment explanation
Indices: 40475883--40475944 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
40475873 TTTGAACCAT
*
40475883 TACCAATTCG
1 TACCAATTCA
*
40475893 TACCAAATACCA
1 TACC-AAT-TCA
*
40475905 TACCATTTCA
1 TACCAATTCA
40475915 TACCAATTCCA
1 TACCAATT-CA
* *
40475926 TACCATTTCG
1 TACCAATTCA
40475936 TACCAATTC
1 TACCAATTC
40475945 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:40475928 original size:21 final size:21
Alignment explanation
Indices: 40475883--40475945 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40475873 TTTGAACCAT
* *
40475883 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
40475905 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
40475926 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
40475946 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:40476665 original size:10 final size:10
Alignment explanation
Indices: 40476650--40476687 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40476640 TTGGGTTAAG
40476650 ATTGAGCTGA
1 ATTGAGCTGA
40476660 ATTGAGCTCGA
1 ATTGAGCT-GA
40476671 A-TGAGCTGA
1 ATTGAGCTGA
*
40476680 CTTGAGCT
1 ATTGAGCT
40476688 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:40476675 original size:20 final size:20
Alignment explanation
Indices: 40476652--40476698 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40476642 GGGTTAAGAT
40476652 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40476672 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
40476692 TGAGCTG
1 TGAGCTG
40476699 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40478066 original size:13 final size:13
Alignment explanation
Indices: 40478048--40478093 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
40478038 TAGTTTCTTC
40478048 AAAAAAAAATTCA
1 AAAAAAAAATTCA
40478061 AAAAAAAAA-TCA
1 AAAAAAAAATTCA
*
40478073 AAAAAAAAATTTTA
1 AAAAAAAAA-TTCA
40478087 AAAAAAA
1 AAAAAAA
40478094 TTGGTTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 12 0.40
13 9 0.30
14 9 0.30
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:40478156 original size:16 final size:16
Alignment explanation
Indices: 40478135--40478173 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40478125 ATCGAGTTGA
40478135 AAAAAAAAATTTCGTG
1 AAAAAAAAATTTCGTG
40478151 AAAAAAAAATTTCGTG
1 AAAAAAAAATTTCGTG
40478167 AAAAAAA
1 AAAAAAA
40478174 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (16 bp):
AAAAAAAAATTTCGTG
Found at i:40480669 original size:11 final size:11
Alignment explanation
Indices: 40480653--40480695 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
40480643 GTTCGTAACG
40480653 AAAAAAAATCAA
1 AAAAAAAATC-A
40480665 AAAAAAGAAGTCA
1 AAAAAA-AA-TCA
*
40480678 AAAAAAAGTCA
1 AAAAAAAATCA
40480689 AAAAAAA
1 AAAAAAA
40480696 TTTTTTGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 7 0.25
13 9 0.32
14 2 0.07
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:40480678 original size:14 final size:13
Alignment explanation
Indices: 40480653--40480695 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
40480643 GTTCGTAACG
40480653 AAAAAA-AATCAA
1 AAAAAAGAATCAA
40480665 AAAAAAGAAGTCAA
1 AAAAAAGAA-TCAA
40480679 AAAAAAG--TCAA
1 AAAAAAGAATCAA
40480690 AAAAAA
1 AAAAAA
40480696 TTTTTTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.34
12 6 0.21
13 2 0.07
14 11 0.38
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAAGAATCAA
Found at i:40480802 original size:12 final size:13
Alignment explanation
Indices: 40480778--40480804 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40480768 AAAGGAGAAG
40480778 AAATTCAAAAAAA
1 AAATTCAAAAAAA
40480791 AAATTCAAAAAAA
1 AAATTCAAAAAAA
40480804 A
1 A
40480805 TCGAAAAAAA
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATTCAAAAAAA
Found at i:40481779 original size:21 final size:21
Alignment explanation
Indices: 40481745--40481816 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
40481735 ACATTCTTGT
40481745 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAAGAAAAGA
*
40481766 AAAGAAAAAGCAAA-AGCAAGA
1 AAAGAAAAAGCAAAGA-AAAGA
* *
40481787 GAAGAAAAAGAAAATGAAATA-A
1 AAAGAAAAAGCAAA-GAAA-AGA
40481809 AAAGAAAA
1 AAAGAAAA
40481817 GAGAGGCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.12
21 25 0.61
22 9 0.22
23 2 0.05
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGCAAAGAAAAGA
Found at i:40481797 original size:37 final size:36
Alignment explanation
Indices: 40481746--40481817 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
40481736 CATTCTTGTA
40481746 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGCAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAG-AAAAGC
*
40481783 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAAG
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAAG
40481818 AGAGGCAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 5 0.16
37 24 0.75
38 3 0.09
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.03
Consensus pattern (36 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAGC
Found at i:40484099 original size:30 final size:30
Alignment explanation
Indices: 40484065--40484161 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40484055 AGCTCACTCC
40484065 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40484095 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40484125 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40484155 TAGCTCA
1 TAGCTCA
40484162 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40488608 original size:19 final size:19
Alignment explanation
Indices: 40488586--40488623 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40488576 AACTAGCCAA
40488586 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
40488605 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
40488624 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:40490450 original size:12 final size:12
Alignment explanation
Indices: 40490433--40490457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40490423 TTTCACTCTT
40490433 CTCTTTTTCAAA
1 CTCTTTTTCAAA
40490445 CTCTTTTTCAAA
1 CTCTTTTTCAAA
40490457 C
1 C
40490458 CCTCTCTCTT
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:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:40492946 original size:13 final size:13
Alignment explanation
Indices: 40492921--40492977 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 13
40492911 TTGGAGTAAC
*
40492921 AAAAAA-TCAAAA
1 AAAAAATTCGAAA
40492933 AAAAAATTCGAAA
1 AAAAAATTCGAAA
40492946 AAAAAATT-GATTGAA
1 AAAAAATTCGA---AA
40492961 AAAAAATTC-AAA
1 AAAAAATTCGAAA
40492973 AAAAA
1 AAAAA
40492978 GTGAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 15 0.38
13 13 0.33
15 11 0.28
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAATTCGAAA
Found at i:40492974 original size:12 final size:13
Alignment explanation
Indices: 40492921--40492977 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
40492911 TTGGAGTAAC
40492921 AAAAAA-TCAAAA
1 AAAAAATTCAAAA
*
40492933 AAAAAATTCGAAA
1 AAAAAATTCAAAA
* *
40492946 AAAAAATTGATTGAA
1 AAAAAATTCA--AAA
40492961 AAAAAATTCAAAA
1 AAAAAATTCAAAA
40492974 AAAA
1 AAAA
40492978 GTGAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 6 0.17
13 19 0.53
15 11 0.31
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAATTCAAAA
Found at i:40497821 original size:30 final size:28
Alignment explanation
Indices: 40497743--40497825 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 28
40497733 GCAAGACTTT
*
40497743 TCACTTTTTTTTAACTTGATTTTTTTTTGC
1 TCACTTTTTTTT-ACTT-TTTTTTTTTTGC
*
40497773 TCACCTTTTTTTTTCTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTACTTTT-TTTTTTTTGC
40497803 TCGA-TTTTTTTTCACTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTT
40497826 GAATTTTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 13 0.28
30 23 0.50
31 10 0.22
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:40497822 original size:12 final size:12
Alignment explanation
Indices: 40497807--40497873 Score: 57
Period size: 13 Copynumber: 5.6 Consensus size: 12
40497797 TTTTGCTCGA
*
40497807 TTTTTTTTC-AC
1 TTTTTTTTCAAT
*
40497818 TTTTTTTTGAAT
1 TTTTTTTTCAAT
**
40497830 TTTTTCAATCAAT
1 TTTTT-TTTCAAT
40497843 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
*
40497856 TTTTTTTT-GAT
1 TTTTTTTTCAAT
40497867 TTTTTTT
1 TTTTTTT
40497874 GTTACTCCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 17 0.38
12 8 0.18
13 20 0.44
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:40497834 original size:13 final size:13
Alignment explanation
Indices: 40497818--40497873 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
40497808 TTTTTTTCAC
40497818 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*** *
40497831 TTTTCAATCAATT
1 TTTTTTTTGAATT
*
40497844 TTTTTTTCGAA-T
1 TTTTTTTTGAATT
40497856 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
40497868 TTTTTT
1 TTTTTT
40497874 GTTACTCCAA
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
11 1 0.03
12 16 0.50
13 15 0.47
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:40499354 original size:10 final size:10
Alignment explanation
Indices: 40499339--40499376 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40499329 TTGGGTTAAG
40499339 ATTGAGCTGA
1 ATTGAGCTGA
40499349 ATTGAGCTCGA
1 ATTGAGCT-GA
40499360 A-TGAGCTGA
1 ATTGAGCTGA
*
40499369 CTTGAGCT
1 ATTGAGCT
40499377 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:40499364 original size:20 final size:20
Alignment explanation
Indices: 40499341--40499387 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40499331 GGGTTAAGAT
40499341 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40499361 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
40499381 TGAGCTG
1 TGAGCTG
40499388 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40507059 original size:960 final size:956
Alignment explanation
Indices: 40505677--40507578 Score: 3411
Period size: 960 Copynumber: 2.0 Consensus size: 956
40505667 GGGCCCAATT
* * * *
40505677 GTAAACATTTTAGTTGTTTAAGTTAATTTTTTAAGTTTTAGGAATATCACATGTTAAATTAGGCC
1 GTAAACATCTTACTTGTTTAAGTTAATTTTTTAAGTTTTAGGAACATCACATGTAAAATTAGGCC
* * *
40505742 CAAAACAGTCCAATAGGATGCATGGCCGAATTTTCCTTTGTTTTTTTTAATTAAGTTTAAATTTT
66 CAAAACAGCCCAATAAGATGCATGGCCGAATTTACCTTTGTTTTTTTTAATTAAGTTTAAATTTT
* *
40505807 TTAAGTTTTCTAATTAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTG
131 TTAAGTTTACTAATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTG
*
40505872 TAAACATCTTATTATTATTTTTTCTATCAAATTTTAGATCGTTGAGTGCAGAATTTTCTTTGGGG
196 TAAACATCTTATTATTATTTTTTCTATCAAATTTTAGATCGTTGAGTGCAGAATTTTCTTTCGGG
*
40505937 TTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTTGATTGTGGG
261 TTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGTGGG
* *
40506002 AGCCATCTTCAACCTTCTTCTTGCCATCGATATTCTTTGGAGGGGAGATTAGAGCCGTTTGAAGA
326 AACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGAAGA
40506067 GATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCAT
391 GATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCAT
*
40506132 TCTTTTCTTTTAAATTCTGTTTATGCCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAAT
456 TCTTTTCTTTTAAATTCTGTTTATACCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAAT
40506197 TTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACTA
521 TTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACTA
*
40506262 AACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGTTG
586 AACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGCTG
40506327 GAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACAG
651 GAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACAG
40506392 ATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTAT
716 ATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTAT
40506457 TCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTCTTGGGGATCTTAATTTCCAGATCTGATT
781 TCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTCTTGGGGATCTTAATTTCCAGATCTGATT
* *
40506522 TGTTTTTAATCTTATTCTTTGTTTTAATTTTTAGATCTGTTCAATTAGAGCTTTTGTAGGAGTTT
846 TGTTTTTAATCTTATTCTTTGTTTTAA-TTTCAGATCTGTTCAATTAGAGCTTTCGTAGGAGTTT
40506587 CTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
910 CTCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
* * * *
40506634 GTAAACATCTTACTTGTTTAATTTAATTTTTTAA-TCTTTAGGAGCATTACATGTAAAATTCGGC
1 GTAAACATCTTACTTGTTTAAGTTAATTTTTTAAGT-TTTAGGAACATCACATGTAAAATTAGGC
*
40506698 CCAAAACAGCCCATATAAG-TGCATGGCCGAATTTACC-TTGTTATTTTATTAATTAGGTTT-AA
65 CCAAAACAGCCCA-ATAAGATGCATGGCCGAATTTACCTTTGTT-TTTT-TTAATTAAGTTTAAA
**
40506760 TTTTTTATTAG-TTACTTGTGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCAC
127 TTTTTTA--AGTTTACTAATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCAC
*
40506824 CCTTTGTAAACACATCTTATTATTA-TTTTTCTATCAAATTTTAGATTTGTTGAGTGCAGAATTT
190 CCTTTGT-AA-ACATCTTATTATTATTTTTTCTATCAAATTTTAGA-TCGTTGAGTGCAGAATTT
40506888 TCTTTCGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTG
252 TCTTTCGGGTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTG
40506953 GATTGTGGGAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCC
317 GATTGTGGGAACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCC
40507018 GTTTGAAGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTT
382 GTTTGAAGAGATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTT
*
40507083 GCTGTTCATTCTTTTCTTTTAAATTTTGTTTATACCGATTCTTTTGATCTAACTTGTTTATTCTT
447 GCTGTTCATTCTTTTCTTTTAAATTCTGTTTATACCGATTCTTTTGATCTAACTTGTTTATTCTT
40507148 CTTGTGAATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAA
512 CTTGTGAATTTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAA
40507213 ATTCGACTAAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTT
577 ATTCGACTAAACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTT
40507278 AGGTTGCTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTT
642 AGGTTGCTGGAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTT
40507343 CTTGGACAGATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAA
707 CTTGGACAGATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAA
*
40507408 AACATCTATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTTTTGGGGATCTTAATTTCCA
772 AACATCTATTCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTCTTGGGGATCTTAATTTCCA
* *
40507473 GATCTGATTTGTTTTTAATCTTATTCTTTGTTTTGATTTCAGATCTGTTCGATTAGAGCTTTCGT
837 GATCTGATTTGTTTTTAATCTTATTCTTTGTTTTAATTTCAGATCTGTTCAATTAGAGCTTTCGT
40507538 AGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGC
902 AGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGC
40507579 ACAACCCCCA
Statistics
Matches: 907, Mismatches: 29, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
956 6 0.01
957 96 0.11
958 71 0.08
959 91 0.10
960 643 0.71
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (956 bp):
GTAAACATCTTACTTGTTTAAGTTAATTTTTTAAGTTTTAGGAACATCACATGTAAAATTAGGCC
CAAAACAGCCCAATAAGATGCATGGCCGAATTTACCTTTGTTTTTTTTAATTAAGTTTAAATTTT
TTAAGTTTACTAATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCAGCCACCCTTTG
TAAACATCTTATTATTATTTTTTCTATCAAATTTTAGATCGTTGAGTGCAGAATTTTCTTTCGGG
TTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAGTTGTTTTAACAATCTTTGGATTGTGGG
AACCATCTTCAACCTTCTTCTTGCCATCGATATTCGTTGGAGGGGAGATTAGAGCCGTTTGAAGA
GATTTGTGAAATCTTTCGGGATTTCAAGGATCTTTAGGACTTCAATTTACTTTCTTGCTGTTCAT
TCTTTTCTTTTAAATTCTGTTTATACCGATTCTTTTGATCTAACTTGTTTATTCTTCTTGTGAAT
TTCCAGCCATCTTTATTACTCAAAAAGATCGATCGGTACTCATTCTTGGTAGCCAAATTCGACTA
AACTTATCTTTTCCAATTAATCTTGTCGAATTCTTCTTGTCAAAACTGACTGTTTTAGGTTGCTG
GAATTTTGGGAAAAATCAAGTTGCTGGAATTTGGGGCTTTATTCATCGGTTTAGTTCTTGGACAG
ATTCGGCTTGTTGAAAATCAATCTTGGAGATCGATTTCGTGTTTTTGCATTCCGAAAACATCTAT
TCATAAGATCTTTGATTCTTGGCTGTTCTTGATTGTCTTGGGGATCTTAATTTCCAGATCTGATT
TGTTTTTAATCTTATTCTTTGTTTTAATTTCAGATCTGTTCAATTAGAGCTTTCGTAGGAGTTTC
TCGTGACTTGGCAACTCGATCTTGGTCCGCGCGCGCCTCCGTACCA
Found at i:40507630 original size:6 final size:6
Alignment explanation
Indices: 40507621--40507719 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
40507611 CATTTTCATA
* * * **
40507621 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * **
40507672 GTTTTC TTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
40507720 AAATTCATTA
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:40508686 original size:10 final size:9
Alignment explanation
Indices: 40508670--40508716 Score: 60
Period size: 10 Copynumber: 5.1 Consensus size: 9
40508660 CCATCCACGA
40508670 ATTTTTTTT
1 ATTTTTTTT
40508679 ACTTTTTTTT
1 A-TTTTTTTT
40508689 A-TTTTTTT
1 ATTTTTTTT
40508697 ATTTTTTTT
1 ATTTTTTTT
*
40508706 AAATTTTTTT
1 -ATTTTTTTT
40508716 A
1 A
40508717 ATCACTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
8 8 0.24
9 9 0.26
10 17 0.50
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:40508694 original size:19 final size:18
Alignment explanation
Indices: 40508672--40508716 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
40508662 ATCCACGAAT
40508672 TTTTTTTACTTTTTTTT-A
1 TTTTTTTA-TTTTTTTTAA
40508690 TTTTTTTATTTTTTTTAAA
1 TTTTTTTATTTTTTTT-AA
40508709 TTTTTTTA
1 TTTTTTTA
40508717 ATCACTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.32
18 8 0.32
19 9 0.36
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTATTTTTTTTAA
Found at i:40508717 original size:10 final size:9
Alignment explanation
Indices: 40508672--40508718 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
40508662 ATCCACGAAT
*
40508672 TTTTTTTAC
1 TTTTTTTAA
*
40508681 TTTTTTTTA
1 TTTTTTTAA
*
40508690 TTTTTTTAT
1 TTTTTTTAA
40508699 TTTTTTTAAA
1 TTTTTTT-AA
40508709 TTTTTTTAA
1 TTTTTTTAA
40508718 T
1 T
40508719 CACTTTCTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:40509842 original size:13 final size:13
Alignment explanation
Indices: 40509824--40509849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40509814 ACCTGAAAGC
40509824 AATTTAATTCATA
1 AATTTAATTCATA
40509837 AATTTAATTCATA
1 AATTTAATTCATA
40509850 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:40514325 original size:12 final size:13
Alignment explanation
Indices: 40514303--40514331 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40514293 AAGTTTTATT
40514303 TTTATTTTATTTA
1 TTTATTTTATTTA
40514316 TTTA-TTTATTTA
1 TTTATTTTATTTA
40514328 TTTA
1 TTTA
40514332 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:40516078 original size:18 final size:18
Alignment explanation
Indices: 40516055--40516089 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40516045 CTTTTCTTTT
40516055 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
40516073 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
40516090 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:40519425 original size:22 final size:22
Alignment explanation
Indices: 40519395--40519438 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40519385 TTTGGTATTT
*
40519395 GGGAATTGGTATGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
40519417 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
40519439 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:40524424 original size:22 final size:22
Alignment explanation
Indices: 40524394--40524437 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40524384 TTTAGTATTT
40524394 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
40524416 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
40524438 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:40525879 original size:13 final size:13
Alignment explanation
Indices: 40525861--40525895 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
40525851 AGTTTCTTCA
40525861 AAAAAAAAATTCG
1 AAAAAAAAATTCG
40525874 AAAAAAAAATTCG
1 AAAAAAAAATTCG
40525887 AAAAAAAAA
1 AAAAAAAAA
40525896 CTAGTTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:40525954 original size:13 final size:13
Alignment explanation
Indices: 40525936--40525987 Score: 77
Period size: 14 Copynumber: 3.8 Consensus size: 13
40525926 TATCAAGTTG
40525936 TGAAAAAAAAATT
1 TGAAAAAAAAATT
40525949 TGAAAAAAAAATT
1 TGAAAAAAAAATT
*
40525962 GTGAAAAAAAAAAT
1 -TGAAAAAAAAATT
40525976 TGTAAAAAAAAA
1 TG-AAAAAAAAA
40525988 GAGAGCTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
13 15 0.42
14 21 0.58
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:40525958 original size:15 final size:14
Alignment explanation
Indices: 40525938--40525987 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
40525928 TCAAGTTGTG
40525938 AAAAAAAAATTTG-
1 AAAAAAAAATTTGA
40525951 AAAAAAAAATTGTGA
1 AAAAAAAAATT-TGA
40525966 AAAAAAAAA-TTGTA
1 AAAAAAAAATTTG-A
40525980 AAAAAAAA
1 AAAAAAAA
40525988 GAGAGCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.38
14 12 0.35
15 9 0.26
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (14 bp):
AAAAAAAAATTTGA
Found at i:40525963 original size:27 final size:28
Alignment explanation
Indices: 40525933--40525987 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
40525923 GGATATCAAG
*
40525933 TTGTGAAAAAAAAATTTG-AAAAAAAAA
1 TTGTGAAAAAAAAAATTGTAAAAAAAAA
40525960 TTGTGAAAAAAAAAATTGTAAAAAAAAA
1 TTGTGAAAAAAAAAATTGTAAAAAAAAA
40525988 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (28 bp):
TTGTGAAAAAAAAAATTGTAAAAAAAAA
Found at i:40536891 original size:27 final size:27
Alignment explanation
Indices: 40536861--40536912 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40536851 ACAAGTGAGG
40536861 AAAAAGAAATAGAGAATGAAAAAGAGC
1 AAAAAGAAATAGAGAATGAAAAAGAGC
* * *
40536888 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAATAGAGAATGAAAAAGA
40536913 AATTGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.25, T:0.10
Consensus pattern (27 bp):
AAAAAGAAATAGAGAATGAAAAAGAGC
Found at i:40550421 original size:37 final size:37
Alignment explanation
Indices: 40550360--40550438 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40550350 TTATTACGAA
* * * *
40550360 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
*
40550397 GTCTTACCCGAACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
40550434 GTCTT
1 GTCTT
40550439 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGAACAAAATCCCCACACGAAGTCATCGG
Found at i:40550633 original size:49 final size:48
Alignment explanation
Indices: 40550556--40550713 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
40550546 GCCCTTCGGG
40550556 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATACAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATA-AC
40550606 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATA-AC
*
40550655 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT-AC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAAC
40550702 ACTTTCACATTC
1 ACTTTCACATTC
40550714 TCAAAGTAAG
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
47 14 0.13
49 88 0.83
50 4 0.04
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (48 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAAC
Found at i:40555289 original size:21 final size:21
Alignment explanation
Indices: 40555244--40555306 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
40555234 TTTGAACCAT
* *
40555244 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
40555266 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
40555287 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
40555307 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:40561774 original size:22 final size:20
Alignment explanation
Indices: 40561724--40561775 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
40561714 ACCGTATGCA
*
40561724 TTTTTTTCTTTTCAATTTTT
1 TTTTTTTTTTTTCAATTTTT
40561744 TTTGATTTTTTTTTCAATTTTGAT
1 TTT--TTTTTTTTTCAATTTT--T
40561768 TTTTTTTT
1 TTTTTTTT
40561776 CGAACTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
22 20 0.74
24 4 0.15
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTTTCAATTTTT
Found at i:40571747 original size:30 final size:30
Alignment explanation
Indices: 40571691--40571747 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
40571681 TGGGCTCAAA
* **
40571691 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
40571721 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
40571748 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:40577240 original size:18 final size:18
Alignment explanation
Indices: 40577219--40577257 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40577209 GATTGAGAGT
* *
40577219 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
40577237 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
40577255 GAA
1 GAA
40577258 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:40579807 original size:18 final size:18
Alignment explanation
Indices: 40579786--40579820 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40579776 TTTTTCTTTT
40579786 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
40579804 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
40579821 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:40580711 original size:8 final size:8
Alignment explanation
Indices: 40580700--40580727 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
40580690 CTTTTCACTT
40580700 TTTTTTTC
1 TTTTTTTC
40580708 TTTTTTTC
1 TTTTTTTC
40580716 TTTTTTTC
1 TTTTTTTC
40580724 TTTT
1 TTTT
40580728 AACTCGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:40586946 original size:23 final size:22
Alignment explanation
Indices: 40586895--40586946 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
40586885 CCTCGTCTTT
*
40586895 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
40586917 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
40586940 TTCTTTT
1 TTCTTTT
40586947 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:40599254 original size:18 final size:17
Alignment explanation
Indices: 40599231--40599266 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40599221 TTTTCACTTC
*
40599231 TTTTTTTTATACTTCAAA
1 TTTTTTTT-CACTTCAAA
40599249 TTTTTTTTCACTTCAAA
1 TTTTTTTTCACTTCAAA
40599266 T
1 T
40599267 ACAATTGAAT
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:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTTTTCACTTCAAA
Found at i:40599333 original size:11 final size:11
Alignment explanation
Indices: 40599317--40599402 Score: 61
Period size: 11 Copynumber: 7.7 Consensus size: 11
40599307 TCCTCTTCTC
40599317 TTTTTTTTCAA
1 TTTTTTTTCAA
40599328 TTTTTTTTCAA
1 TTTTTTTTCAA
40599339 -TTTTTTT--A
1 TTTTTTTTCAA
* * **
40599347 TTTCTCTCTCTT
1 TTT-TTTTTCAA
40599359 TTTTTTTGCTCAA
1 TTTTTTT--TCAA
*
40599372 TTTTTTTTGAA
1 TTTTTTTTCAA
*
40599383 TTTTTTTTCGA
1 TTTTTTTTCAA
40599394 TTTTATTTT
1 TTTT-TTTT
40599403 TTTAATCCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
8 1 0.02
9 2 0.03
10 10 0.17
11 29 0.50
12 7 0.12
13 9 0.16
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:40599374 original size:44 final size:41
Alignment explanation
Indices: 40599309--40599389 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 41
40599299 TCACGAAATC
40599309 CTCTTCTCTTTTTTTTCAATTTTTTTTCAATTTTTTTATTT
1 CTCTTCTCTTTTTTTTCAATTTTTTTTCAATTTTTTTATTT
* *
40599350 CTCTCTCTTTTTTTTTGCTCAATTTTTTTTGAATTTTTTT
1 CTCT-TCTCTTTTTTT--TCAATTTTTTTTCAATTTTTTT
40599390 TCGATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 4 0.11
42 10 0.29
44 21 0.60
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (41 bp):
CTCTTCTCTTTTTTTTCAATTTTTTTTCAATTTTTTTATTT
Found at i:40600916 original size:20 final size:20
Alignment explanation
Indices: 40600893--40600939 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40600883 GGGTTAAGAT
*
40600893 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40600913 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
40600933 TGAGCTG
1 TGAGCTG
40600940 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40601481 original size:19 final size:21
Alignment explanation
Indices: 40601434--40601487 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
40601424 GAAGGCAAAG
*
40601434 AAACAAAAAGAAAAGATGGGA
1 AAACAAAAAGAAAAGATGAGA
* *
40601455 AAAGAAAAA-AAGAG-TGAGA
1 AAACAAAAAGAAAAGATGAGA
40601474 AAACAAAAAGAAAA
1 AAACAAAAAGAAAA
40601488 AGTGAGTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.44
20 7 0.26
21 8 0.30
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (21 bp):
AAACAAAAAGAAAAGATGAGA
Found at i:40604916 original size:15 final size:16
Alignment explanation
Indices: 40604877--40604917 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
40604867 AACAACACTC
40604877 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
40604893 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
40604907 CTTTCTTTTTC
1 CTTTCTTTTTC
40604918 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:40606049 original size:26 final size:28
Alignment explanation
Indices: 40606010--40606073 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 28
40606000 CAATCACTCT
40606010 TTTTTTTTTCAATT-TCG-ATTTTTTTTC
1 TTTTTTTTTCAATTCT-GAATTTTTTTTC
40606037 TTTTTTTTT-AATTCTGAATTTTTTTTC
1 TTTTTTTTTCAATTCTGAATTTTTTTTC
40606064 TTCTTTTTTT
1 TT-TTTTTTT
40606074 TCTTCAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 5 0.15
27 22 0.65
28 7 0.21
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (28 bp):
TTTTTTTTTCAATTCTGAATTTTTTTTC
Found at i:40606136 original size:12 final size:12
Alignment explanation
Indices: 40606119--40606177 Score: 91
Period size: 12 Copynumber: 4.7 Consensus size: 12
40606109 GAATACAAAC
40606119 TTTTTTTTTGAA
1 TTTTTTTTTGAA
40606131 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
40606144 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
40606157 TTTTTTTTTTGAA
1 -TTTTTTTTTGAA
40606170 TTTTTTTT
1 TTTTTTTT
40606178 ACAATACCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.41
13 16 0.36
14 10 0.23
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:40606137 original size:13 final size:13
Alignment explanation
Indices: 40606119--40606177 Score: 93
Period size: 13 Copynumber: 4.5 Consensus size: 13
40606109 GAATACAAAC
40606119 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
40606131 TTTTTTTTTGAAAT
1 TTTTTTTTTG-AAT
*
40606145 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
40606158 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
40606171 TTTTTTT
1 TTTTTTT
40606178 ACAATACCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
12 10 0.23
13 24 0.56
14 9 0.21
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:40610413 original size:40 final size:40
Alignment explanation
Indices: 40610066--40610413 Score: 527
Period size: 40 Copynumber: 8.7 Consensus size: 40
40610056 GCAAACACAC
* * * * *
40610066 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
***
40610106 TTGCCTTCGGGTCTTAGCCCGGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* * * *
40610146 TTGCCTTCGGGTCATAGCCCGGACATATTAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
***
40610186 TTGCCTTC-GGTCTTAGCCCGGATATATCGTCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
* *
40610225 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
*
40610265 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
40610305 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
40610345 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
40610385 TTGCCTTCGGGTCTTAGCCCGGATATATT
1 TTGCCTTCGGGTCTTAGCCCGGATATATT
40610414 CCAATGCTCA
Statistics
Matches: 278, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 32 0.12
40 246 0.88
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
Found at i:40617074 original size:23 final size:22
Alignment explanation
Indices: 40617022--40617074 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40617012 TCCACGTCTT
*
40617022 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40617044 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40617067 TTTCTTTT
1 TTTCTTTT
40617075 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40619997 original size:18 final size:18
Alignment explanation
Indices: 40619976--40620014 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40619966 GATTGAGAGT
* *
40619976 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
40619994 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
40620012 GAA
1 GAA
40620015 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:40630231 original size:14 final size:14
Alignment explanation
Indices: 40630212--40630245 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40630202 CAAGATGAAA
*
40630212 GTGGAAGATCTTAT
1 GTGGAAGACCTTAT
40630226 GTGGAAGACCTTAT
1 GTGGAAGACCTTAT
*
40630240 CTGGAA
1 GTGGAA
40630246 TAACATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (14 bp):
GTGGAAGACCTTAT
Found at i:40632242 original size:88 final size:88
Alignment explanation
Indices: 40632046--40633203 Score: 1327
Period size: 88 Copynumber: 13.2 Consensus size: 88
40632036 AACAGATCAG
* * * *
40632046 TGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40632110 CCCTCGGTTGTAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * ** * * *
40632133 T-AAAGATAACAAATATTGCCTTTTTGCATTC-ACAGCGAAGCAGATCGAAGATACTAGCCTAGC
1 TGAAA-ATAGCAGATCTTGCCTTCCTGCA-TCGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * * *
40632196 CACCGTGGGTTACAGCGGAACAGGT
64 CTCCCTGGGTTGCAGCGGAGCAGGT
* * *
40632221 TGAAAATAGTAGATCTTGCCTTCCGGCA-CTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* * * * *
40632285 TCCCTAGATTGTAGTGGAGTAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
* ** * *
40632309 T-AAAGATAGCAGATCTTGCCTTCCTGTA-CTGACAGTTAAGAAGATCGAAGACACCAGACTTGC
1 TGAAA-ATAGCAGATCTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGC
*
40632372 CTCCCT-GGTTACAGCGGAGCAGGT
64 CTCCCTGGGTTGCAGCGGAGCAGGT
* *
40632396 TGAAAATAGCAGATCTTGCCTTCCTGCACCGAC-GACGAAGCAGATCGAAGACACCAACCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAG-CGAAGCAGATCGAAGACACCAGCCTTGCC
* *
40632460 TCCCTGGATTGCAGTGGAGCAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
* * ** * *
40632484 TGAAGATAGCAGATCTTGCCTTCCTGTA-CTGACAGTTAAGTAGATCGAAGACACCAGACTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* **
40632548 TCCCTAGGTTGCAGTAGAGCAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
*
40632572 TGAAAATAGCAGATCTTGCCTTCCTGTAAT-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTG-CATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* *
40632636 TCCCTGGGTTGTAGCAGAGCAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
* * *
40632660 TGAAAATAGCAGATCTTGCCTTCCTGCATCGATAGCGAAGCTGATCAAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40632725 TCCTGGGCTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
40632748 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACAAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40632813 CCCTGGATTACAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * *
40632836 TGAAAATAGTAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACA-CAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
40632900 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
40632923 TGAAAATAGTATATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTAT-CC
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCT-TGCC
*
40632987 TCCTTGGGTTGCAGCGGAGCAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
* * * * * * *
40633011 TTAAAATAGTAGATTTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACGCTAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
40633076 CCCTGGATTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * * ** * * *
40633099 TGAAGATAGCAGATCTTTCCTTCCTGTAGT-GATAGTTAAGTAGATTGAAGACCCCAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGCA-TCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* *
40633163 TCCCTCGGTTACAGCGGAGCAGGT
65 TCCCTGGGTTGCAGCGGAGCAGGT
*
40633187 TAAAAATTA-CAGATCTT
1 TGAAAA-TAGCAGATCTT
40633204 ATCTCCCTAA
Statistics
Matches: 919, Mismatches: 131, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
86 4 0.00
87 197 0.21
88 710 0.77
89 8 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (88 bp):
TGAAAATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:40632517 original size:263 final size:265
Alignment explanation
Indices: 40632048--40633203 Score: 1445
Period size: 263 Copynumber: 4.4 Consensus size: 265
40632038 CAGATCAGTG
* * * * *
40632048 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * * * ** *
40632112 CTCGGTTGTAGCGGAGCAGGTT-AAAGATAACAAATATTGCCTTTTTGCATTC-ACAGCGAAGCA
66 CTCGGTTGCAGCGGAGCAGGTTGAAA-ATAGCAGATCTTGCCTTCCTGCA-CCGACAGCGAAGCA
* * * * * * * *
40632175 GATCGAAGATACTAGCCTAGCCACCGTGGGTTACAGCGGAACAGGTTGAAAATAGTAGATCTTGC
129 GATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGC
* * * * *
40632240 CTTCCGGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGTAGTGGAGT
194 CTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGCAGTGGAGC
40632305 AGGTT-A
259 AGGTTGA
* * *
40632311 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGAAGATCGAAGACACCAGACTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
40632376 CT-GGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGAC-GACGAAGCAG
66 CTCGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAG-CGAAGCAG
* * * *
40632439 ATCGAAGACACCAACCTTGCCTCCCTGGATTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCC
130 ATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCC
* * ** * * * *
40632504 TTCCTGTACTGACAGTTAAGTAGATCGAAGACACCAGACTTGCCTCCCTAGGTTGCAGTAGAGCA
195 TTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGCAGTGGAGCA
40632569 GGTTGA
260 GGTTGA
* *
40632575 AA-ATAGCAGATCTTGCCTTCCTGTAATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * * * * *
40632639 CTGGGTTGTAGCAGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCATCGATAGCGAAGCTGA
66 CTCGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGA
* * *
40632704 TCAAAGACACCAGCCTTGCCTTCCTGGGCTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCT
131 TCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCT
* * * * * *
40632769 TCCTGCACCGACAACAAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGATTACAGCGGAGCAG
196 TCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGCAGTGGAGCAG
40632834 GTTGA
261 GTTGA
* * *
40632839 AA-ATAGTAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACA-CAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
40632902 CTGGGTTGCAGCGGAGCAGGTTGAAAATAGTATATCTTGCCTTCCTGCACCGACAGCGAAGCAGA
66 CTCGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGA
* * * * *
40632967 TCGAAGACACTAGCCTAT-CCTCCTTGGGTTGCAGCGGAGCAGGTTTAAAATAGTAGATTTTGCC
131 TCGAAGACACCAGCCT-TGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCC
* * * *
40633031 TTCCTGCACCGATAGCGAAGCAGATCGAAGACGCTAGCCTTGCCTCCCTGGATTGCAGTGGAGCA
195 TTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGCAGTGGAGCA
40633096 GGTTG-
260 GGTTGA
* * * * * * *
40633101 AAGATAGCAGATCTTTCCTTCCTGTAGTGATAGTTAAGTAGATTGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* *
40633166 CTCGGTTACAGCGGAGCAGGTTAAAAATTA-CAGATCTT
66 CTCGGTTGCAGCGGAGCAGGTTGAAAA-TAGCAGATCTT
40633204 ATCTCCCTAA
Statistics
Matches: 771, Mismatches: 111, Indels: 21
0.85 0.12 0.02
Matches are distributed among these distances:
262 4 0.01
263 487 0.63
264 277 0.36
265 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (265 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTCGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGA
TCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCT
TCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGCAGTGGAGCAG
GTTGA
Found at i:40632678 original size:44 final size:43
Alignment explanation
Indices: 40632363--40632948 Score: 170
Period size: 44 Copynumber: 13.4 Consensus size: 43
40632353 TCGAAGACAC
* *
40632363 CAGA-CTTGCCTCCCT-GGTTACAGCGGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAGC-GAGCAGGTTGAAAATAG
**** * * * * *
40632405 CAGATCTTGCCTTCCTGCACCG-ACGACGAAGCAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGGGTTGCA-G-CG-AGCAGGTTGAAAATAG
* * * * *
40632450 CA-ACCTTGCCTCCCTGGATTGCAGTGGAGCAGGTTGAAGATAG
1 CAGATCTTGCCTTCCTGGGTTGCAG-CGAGCAGGTTGAAAATAG
*** ** * * * * * *
40632493 CAGATCTTGCCTTCCTGTACTGACAGTTAAGTAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGGGTTG-CAG-CGAGCAGGTTGAAAATAG
* * *
40632538 CAGA-CTTGCCTCCCTAGGTTGCAGTAGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAG-CGAGCAGGTTGAAAATAG
*** * * * * *
40632581 CAGATCTTGCCTTCCTGTAATGACAGCGAAGCAGATCGAAGACAC
1 CAGATCTTGCCTTCCTGGGTTG-CAGCG-AGCAGGTTGAAAATAG
* * *
40632626 CAG-CCTTGCCTCCCTGGGTTGTAGCAGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAGC-GAGCAGGTTGAAAATAG
** * * * * * * *
40632669 CAGATCTTGCCTTCCTGCATCGATAGCGAAGC-TGATCAAAGACAC
1 CAGATCTTGCCTTCCTGGGTTG-CAGCG-AGCAGGTTGAAA-ATAG
* *
40632714 CAG-CCTTGCCTTCCTGGGCTGCAGCGGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAGC-GAGCAGGTTGAAAATAG
**** * * * * * *
40632757 CAGATCTTGCCTTCCTGCACCGACAACAAAGCA-GATCAAAGACAC
1 CAGATCTTGCCTTCCTGGGTTG-CAGC-GAGCAGGTTGAAA-ATAG
* * * *
40632802 CAG-CCTTGCCTCCCTGGATTACAGCGGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAGC-GAGCAGGTTGAAAATAG
* **** * * * * *
40632845 TAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACA-
1 CAGATCTTGCCTTCCTGGGTTG-CAGCG-AGCAGGTTGAAAATAG
* *
40632889 CAG-CCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAG
1 CAGATCTTGCCTTCCTGGGTTGCAGC-GAGCAGGTTGAAAATAG
* *
40632932 TATATCTTGCCTTCCTG
1 CAGATCTTGCCTTCCTG
40632949 CACCGACAGC
Statistics
Matches: 375, Mismatches: 141, Indels: 54
0.66 0.25 0.09
Matches are distributed among these distances:
42 18 0.05
43 96 0.26
44 172 0.46
45 89 0.24
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (43 bp):
CAGATCTTGCCTTCCTGGGTTGCAGCGAGCAGGTTGAAAATAG
Found at i:40632911 original size:351 final size:349
Alignment explanation
Indices: 40632046--40633203 Score: 1380
Period size: 351 Copynumber: 3.3 Consensus size: 349
40632036 AACAGATCAG
* ** * *
40632046 TGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAA-ACA-AAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATC-AAAGACACCAGCCTTGCC
** * * * ** * *
40632109 TCCCTCGGTTGTAGCGGAGCAGGTT-AAAGATAACAAATATTGCCTTTTTGCATTC-ACAGCGAA
65 TCCCTCGGTTACAGCGGAGCAGGTTGAAA-ATAGCAGATCTTGCCTTCCTGCA-CCGACAGTGAA
* * * * * *
40632172 GCAGATCGAAGATACTAGCCTAGCCACCGTGGGTTACAGCGGAACAGGTTGAAAATAGTAGATCT
128 GCAGATCGAAGACAC-AGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGTAGATCT
* * * * *
40632237 TGCCTTCCGGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGATTGTAGTGG
192 TGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGG
* * * ** * *
40632302 AGTAGGTTAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGAAGATCGAAGACACCAGA
257 AGCAGGTTAAA-ATAGCAGATCTTGCCTTCCTGCAC-GATAGCGAAGCAGATCGAAGACACCAGC
*
40632367 CTTGCCTCCCT-GGTTACAGCGGAGCAGGT
320 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGT
* * *
40632396 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACGACGAAGCAGATCGAAGACACCAACCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
* * * * * * *
40632461 CCCT-GGATTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTTAAGT
66 CCCTCGG-TTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGC
* * ** *
40632525 AGATCGAAGACACCAGACTTGCCTCCCTAGGTTGCAGTAGAGCAGGTTGAAAATAGCAGATCTTG
130 AGATCGAAGACA-CAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGTAGATCTTG
* * *
40632590 CCTTCCTGTAATGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCAGAG
194 CCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGGAG
* *
40632655 CAGGTTGAAAATAGCAGATCTTGCCTTCCTGCATCGATAGCGAAGCTGATCAAAGACACCAGCCT
259 CAGGTT-AAAATAGCAGATCTTGCCTTCCTGCA-CGATAGCGAAGCAGATCGAAGACACCAGCCT
* *
40632720 TGCCTTCCTGGGCTGCAGCGGAGCAGGT
322 TGCCTCCCTGGGTTGCAGCGGAGCAGGT
*
40632748 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACAAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
*
40632813 CCCT-GGATTACAGCGGAGCAGGTTGAAAATAGTAGATCTTGCCTTCCTGCACCGACAGTGAAGC
66 CCCTCGG-TTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGC
*
40632877 AGATCGAAGACACAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGTATATCTTGC
130 AGATCGAAGACACAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGTAGATCTTGC
* * * *
40632942 CTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTAT-CCTCCTTGGGTTGCAGCGGAG
195 CTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCT-TGCCTCCCTGGGTTGTAGCGGAG
* * * *
40633006 CAGGTTTAAAATAGTAGATTTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACGCTAGCCT
259 CAGG-TTAAAATAGCAGATCTTGCCTTCCTGCA-CGATAGCGAAGCAGATCGAAGACACCAGCCT
* *
40633071 TGCCTCCCTGGATTGCAGTGGAGCAGGT
322 TGCCTCCCTGGGTTGCAGCGGAGCAGGT
* * * ** * *** * ** *
40633099 TGAAGATAGCAGATCTTTCCTTCCTGTAGTGATAGTTAAGTAGATTGAAGACCCCAGCCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
*
40633164 CCCTCGGTTACAGCGGAGCAGGTTAAAAATTA-CAGATCTT
66 CCCTCGGTTACAGCGGAGCAGGTTGAAAA-TAGCAGATCTT
40633204 ATCTCCCTAA
Statistics
Matches: 691, Mismatches: 104, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
349 2 0.00
350 46 0.07
351 484 0.70
352 159 0.23
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (349 bp):
TGAAAATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCT
CCCTCGGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCA
GATCGAAGACACAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAAATAGTAGATCTTGCC
TTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGGAGCA
GGTTAAAATAGCAGATCTTGCCTTCCTGCACGATAGCGAAGCAGATCGAAGACACCAGCCTTGCC
TCCCTGGGTTGCAGCGGAGCAGGT
Found at i:40633334 original size:44 final size:44
Alignment explanation
Indices: 40633286--40633501 Score: 326
Period size: 44 Copynumber: 4.9 Consensus size: 44
40633276 TTAAGCCACT
* *
40633286 AGTCCTATCTCCCTGGACAGTAGTGGTATAGGTTAAAGATCGTA
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCGTA
* * *
40633330 AGTCCTATCTCCCTGGACAGTAGTGAAATAGGTT-AACAATCTTA
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAA-GATCGTA
*
40633374 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCATA
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCGTA
* * *
40633418 AGTCCTATCTCCCTGGATAGTAGTGGAATAGGTTGATGATTGTA
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCGTA
*
40633462 AGTCCTATCTCCCTGGACAATAGTGGAATAGGTTGAAGAT
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGAT
40633502 TACAGATCAT
Statistics
Matches: 156, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 152 0.97
45 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCGTA
Found at i:40633544 original size:132 final size:131
Alignment explanation
Indices: 40633286--40633544 Score: 308
Period size: 132 Copynumber: 2.0 Consensus size: 131
40633276 TTAAGCCACT
* *
40633286 AGTCCTATCTCCCTGGACAGTAGTGGTATAGGTTAAAGATCGTAAGTCCTATCTCCCTGGACAGT
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATCGTAAGTCCTATCTCCCTGGACAAT
* * ** * *
40633351 AGTGAAATAGGTTAACAATCTTAAGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATCA
66 AGTGAAATAGGTTAACAA-CTTAAGTCATATCTCCCTAGACAGTAGCAGAATAGATCGAAGATCA
40633416 TA
130 TA
* * * *
40633418 AGTCCTATCTCCCTGGATAGTAGTGGAATAGGTTGATGATTGTAAGTCCTATCTCCCTGGACAAT
1 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATCGTAAGTCCTATCTCCCTGGACAAT
* * * *
40633483 AGTGGAATAGGTTGAA-GA-TTACAGATCATGTCTCCCTA-AGCAGTAGCAGAGTAGATCGAAGA
66 AGTGAAATAGGTT-AACAACTTA-AG-TCATATCTCCCTAGA-CAGTAGCAGAATAGATCGAAGA
40633545 CGGCGAATCT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
130 3 0.03
131 3 0.03
132 99 0.93
133 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (131 bp):
AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATCGTAAGTCCTATCTCCCTGGACAAT
AGTGAAATAGGTTAACAACTTAAGTCATATCTCCCTAGACAGTAGCAGAATAGATCGAAGATCAT
A
Found at i:40634210 original size:19 final size:19
Alignment explanation
Indices: 40634170--40634213 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
40634160 CAAAAAAAAC
*
40634170 AAATAAAATTAAAAATTAA
1 AAATAAAATTAAAAATCAA
40634189 AAAT-AAATTAAAAAGTCCAA
1 AAATAAAATTAAAAA-T-CAA
40634209 AAATA
1 AAATA
40634214 CATAAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 5 0.24
20 6 0.29
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAAATTAAAAATCAA
Found at i:40634292 original size:16 final size:16
Alignment explanation
Indices: 40634268--40634307 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
40634258 AACTCGGTTA
40634268 TAACCCAAACCCAAT-
1 TAACCCAAACCCAATC
*
40634283 TAAGCCCAAACCTAATC
1 TAA-CCCAAACCCAATC
40634300 TAACCCAA
1 TAACCCAA
40634308 CACGATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (16 bp):
TAACCCAAACCCAATC
Found at i:40634669 original size:16 final size:17
Alignment explanation
Indices: 40634639--40634672 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40634629 CAAAGATTTT
*
40634639 AAAAAGAAAATACAAAA
1 AAAAACAAAATACAAAA
40634656 AAAAACAAAA-ACAAAA
1 AAAAACAAAATACAAAA
40634672 A
1 A
40634673 GGTGATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAACAAAATACAAAA
Found at i:40635369 original size:12 final size:12
Alignment explanation
Indices: 40635352--40635433 Score: 67
Period size: 12 Copynumber: 6.7 Consensus size: 12
40635342 ATTTTAATGT
*
40635352 TTTTTATTTTTA
1 TTTTTATTATTA
40635364 TTTTTATTATTA
1 TTTTTATTATTA
**
40635376 TTGCTATTATTA
1 TTTTTATTATTA
* *
40635388 TTTTTTATCACTA
1 -TTTTTATTATTA
40635401 TTTATTATTATTA
1 TTT-TTATTATTA
*
40635414 TATTTGATTA-TA
1 T-TTTTATTATTA
*
40635426 TTTATATT
1 TTTTTATT
40635434 TTCCTATATA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
11 5 0.09
12 27 0.49
13 21 0.38
14 2 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:40638732 original size:22 final size:23
Alignment explanation
Indices: 40638698--40638741 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
40638688 CTTGGGCCAA
40638698 GATTTCCAAGATT-TGAAATCTT
1 GATTTCCAAGATTATGAAATCTT
* *
40638720 GATTTTCATGATTCATGAAATC
1 GATTTCCAAGATT-ATGAAATC
40638742 GCTCAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
24 7 0.39
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (23 bp):
GATTTCCAAGATTATGAAATCTT
Found at i:40639420 original size:33 final size:34
Alignment explanation
Indices: 40639369--40639443 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
40639359 AAATTTAAAC
40639369 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
* *
40639403 AAATTAATT-CTAACACTTATTTGAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
40639436 AATTTAAT
1 AAATTAAT
40639444 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:40640315 original size:20 final size:20
Alignment explanation
Indices: 40640290--40640336 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
40640280 GTTAAGATTA
40640290 AGCTGAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCGAATG
* *
40640310 AGCTGACTTGAGCTCGAGTG
1 AGCTGAATTGAGCTCGAATG
40640330 AGCTGAA
1 AGCTGAA
40640337 CTAAGTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (20 bp):
AGCTGAATTGAGCTCGAATG
Found at i:40650278 original size:20 final size:19
Alignment explanation
Indices: 40650235--40650292 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
40650225 AGCTGATTTT
** *
40650235 AGCTCAATTTCAGCTCCCTT
1 AGCTC-ATTTCAGCTCAATC
40650255 AGCTCATTTCAGCTGCAATC
1 AGCTCATTTCAGCT-CAATC
*
40650275 AGCTCATTTGAGCTCAAT
1 AGCTCATTTCAGCTCAAT
40650293 TTTGACCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (19 bp):
AGCTCATTTCAGCTCAATC
Found at i:40658011 original size:19 final size:20
Alignment explanation
Indices: 40657979--40658016 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
40657969 CAAGCTGATT
40657979 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
40657999 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
40658017 AATCAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:40660646 original size:11 final size:12
Alignment explanation
Indices: 40660630--40660671 Score: 70
Period size: 11 Copynumber: 3.7 Consensus size: 12
40660620 ACGAGATTGT
40660630 AAAAAAAA-TCG
1 AAAAAAAATTCG
40660641 AAAAAAAATTCG
1 AAAAAAAATTCG
40660653 AAAAAAAATTC-
1 AAAAAAAATTCG
40660664 AAAAAAAA
1 AAAAAAAA
40660672 AGTTTGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 16 0.53
12 14 0.47
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:40660647 original size:12 final size:12
Alignment explanation
Indices: 40660630--40660672 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
40660620 ACGAGATTGT
40660630 AAAAAAAATCGA
1 AAAAAAAATCGA
*
40660642 AAAAAAATTCGA
1 AAAAAAAATCGA
*
40660654 AAAAAAATTC-A
1 AAAAAAAATCGA
40660665 AAAAAAAA
1 AAAAAAAA
40660673 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:40662792 original size:15 final size:14
Alignment explanation
Indices: 40662756--40662810 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
40662746 TCTATTGAGC
40662756 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
40662770 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
40662784 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
40662799 GAAAGAAAAGAA
1 GAGA-AAAAGAA
40662811 TGAGGAGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:40672653 original size:16 final size:16
Alignment explanation
Indices: 40672641--40672670 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40672631 GAAAAGATGA
40672641 AAAAAGAAAAAGAAAT
1 AAAAAGAAAAAGAAAT
40672657 AAAAAG-AAAAGAAA
1 AAAAAGAAAAAGAAA
40672671 GACAAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAT
Found at i:40673725 original size:33 final size:34
Alignment explanation
Indices: 40673688--40673756 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
40673678 TGATCGAGCC
* *
40673688 AGGTAATACCGAACTTTGTTTCCCTGCT-CTAAA
1 AGGTAAAACCGAACTTTATTTCCCTGCTCCTAAA
* * *
40673721 AGGTAAAACTGAACTTTATTTTCTTGCTCCTAAA
1 AGGTAAAACCGAACTTTATTTCCCTGCTCCTAAA
40673755 AG
1 AG
40673757 TAAGCCTCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (34 bp):
AGGTAAAACCGAACTTTATTTCCCTGCTCCTAAA
Found at i:40675916 original size:22 final size:23
Alignment explanation
Indices: 40675891--40675939 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
40675881 ATCAGCTTCT
40675891 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
40675913 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
40675935 TTAAT
1 TTAAT
40675940 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:40680196 original size:13 final size:12
Alignment explanation
Indices: 40680178--40680235 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
40680168 TTGTAGATTC
40680178 AAAAAAAAATC-
1 AAAAAAAAATCA
40680189 AAAAAAAAATCA
1 AAAAAAAAATCA
* *
40680201 AAAAAAAATTGA
1 AAAAAAAAATCA
*
40680213 AAAAAAAAATTGA
1 AAAAAAAAA-TCA
40680226 AAAAAAAAAT
1 AAAAAAAAAT
40680236 TGCATACGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.26
12 19 0.45
13 12 0.29
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:40680232 original size:11 final size:11
Alignment explanation
Indices: 40680176--40680220 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
40680166 AATTGTAGAT
40680176 TCAAAAAAAAA
1 TCAAAAAAAAA
40680187 TCAAAAAAAAA
1 TCAAAAAAAAA
40680198 TCAAAAAAAAA
1 TCAAAAAAAAA
*
40680209 TTGAAAAAAAAA
1 -TCAAAAAAAAA
40680221 ATTGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:40680236 original size:13 final size:13
Alignment explanation
Indices: 40680200--40680237 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
40680190 AAAAAAAATC
40680200 AAAAAAAAATTGA
1 AAAAAAAAATTGA
40680213 AAAAAAAAATTGA
1 AAAAAAAAATTGA
40680226 AAAAAAAAATTG
1 AAAAAAAAATTG
40680238 CATACGGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Done.