Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 65 of 253
Found at i:18553991 original size:33 final size:34
Alignment explanation
Indices: 18553920--18553998 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 34
18553910 TTATTGAAAG
*
18553920 TGTTGAAGACACCAACGAAGTAATAAGAGTACTG
1 TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
* *
18553954 TGTTGAAGACACCAATGAAGT-ATTAGAGTACTC
1 TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
18553987 TGTTGAAGACAC
1 TGTTGAAGACAC
18553999 TTTCAACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 22 0.52
34 20 0.48
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (34 bp):
TGTTGAAGACACCAACGAAGTAATAAGAGTACTC
Found at i:18554747 original size:18 final size:18
Alignment explanation
Indices: 18554724--18554758 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18554714 AGGCGCTCTC
* *
18554724 CACCAAGTTATTCTCGAT
1 CACCAAGATATGCTCGAT
18554742 CACCAAGATATGCTCGA
1 CACCAAGATATGCTCGA
18554759 AGTTACTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
CACCAAGATATGCTCGAT
Found at i:18559277 original size:47 final size:46
Alignment explanation
Indices: 18559163--18559285 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 46
18559153 TGTGGACTAG
* * ** * *
18559163 TGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAG
1 TGTAAAACATGTCTGGGACATGCATCGGCAACAAGATAAGAGCCAA
* * * * *
18559209 TGTAAGACCATGCCTAGGACATGGCATCGGCAATAAGATAAGAGCTAA
1 TGTAA-AACATGTCTGGGACAT-GCATCGGCAACAAGATAAGAGCCAA
18559257 TGTAAAACATGTCTGGGACATGCATCGGC
1 TGTAAAACATGTCTGGGACATGCATCGGC
18559286 CTCGAGACGT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
46 13 0.21
47 25 0.41
48 23 0.38
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (46 bp):
TGTAAAACATGTCTGGGACATGCATCGGCAACAAGATAAGAGCCAA
Found at i:18559307 original size:46 final size:47
Alignment explanation
Indices: 18559161--18559379 Score: 137
Period size: 46 Copynumber: 4.7 Consensus size: 47
18559151 TTTGTGGACT
* * **
18559161 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCAC-A-TTATGAGAGCC
1 AGTGTAAAACATGTCTGGGACATGGCATCGGCCTCGAGACAT-A-AGCC
* * * * * * *
18559207 AGTGTAAGACCATGCCTAGGACATGGCATCGGCAAT-AAGATA-AGAGCT
1 AGTGTAA-AACATGTCTGGGACATGGCATCGGC-CTCGAGACATA-AGCC
* *
18559255 AATGTAAAACATGTCTGGGACAT-GCATCGGCCTCGAGACGTAAGCC
1 AGTGTAAAACATGTCTGGGACATGGCATCGGCCTCGAGACATAAGCC
* * ** * * *
18559301 AGTGTAAGACATGTTTGGGACATGGCATC-AACTTGAGATATGAGCC
1 AGTGTAAAACATGTCTGGGACATGGCATCGGCCTCGAGACATAAGCC
* *
18559347 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAA-AACATGTCTGGGACATGGCATCGGC
18559380 ACCTTACCCA
Statistics
Matches: 131, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
45 1 0.01
46 59 0.45
47 49 0.37
48 19 0.15
49 1 0.01
50 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
AGTGTAAAACATGTCTGGGACATGGCATCGGCCTCGAGACATAAGCC
Found at i:18559369 original size:47 final size:47
Alignment explanation
Indices: 18559202--18559377 Score: 160
Period size: 46 Copynumber: 3.8 Consensus size: 47
18559192 CACATTATGA
* * * * *
18559202 GAGCCAGTGTAAGACCATGCCTAGGACATGGCATCGGCAATAAGATAA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC-TTGAGATAT
* * * * * * **
18559250 GAGCTAATGTAA-AACATGTCTGGGACAT-GCATCGGCCTCGAGACGT
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACTTGAGATAT
* * * *
18559296 AAGCCAGTGTAAGA-CATGTTTGGGACATGGCATCAACTTGAGATAT
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGATAT
18559342 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
18559378 GCACCTTACC
Statistics
Matches: 99, Mismatches: 25, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
46 50 0.51
47 39 0.39
48 10 0.10
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGATAT
Found at i:18559376 original size:94 final size:94
Alignment explanation
Indices: 18559161--18559379 Score: 239
Period size: 94 Copynumber: 2.3 Consensus size: 94
18559151 TTTGTGGACT
* *
18559161 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGCCTAG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGCCTAG
** *
18559226 GACATGGCATCGGCAATAAGATAAGAGCT
66 GACATGGCATCAACAATAAGATAAGAGCC
* * * **
18559255 AATGTAAAACATGTCTGGGACATGCATCGGCCTCGA-GACGTA-AGCCAGTGTAAGA-CATGTTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGACG-AGAGCCAGTGTAAGACCATGCCT
* * * *
18559317 GGGACATGGCATCAAC-TTGAGATATGAGCC
64 AGGACATGGCATCAACAATAAGATAAGAGCC
*
18559347 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
18559380 ACCTTACCCA
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
92 17 0.16
93 31 0.30
94 54 0.52
95 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGCCTAG
GACATGGCATCAACAATAAGATAAGAGCC
Found at i:18562346 original size:16 final size:18
Alignment explanation
Indices: 18562325--18562365 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
18562315 AATTAATCAT
18562325 AAATTAATTA-AT-TAAA
1 AAATTAATTAGATATAAA
*
18562341 AAATTAATTAGATATGAA
1 AAATTAATTAGATATAAA
18562359 AAATTAA
1 AAATTAA
18562366 ATAAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
18 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAATTAATTAGATATAAA
Found at i:18569409 original size:29 final size:29
Alignment explanation
Indices: 18569375--18569433 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
18569365 GTTTTTATCG
18569375 TAACTTGGTTTTATTTACTCATTTTGTGC
1 TAACTTGGTTTTATTTACTCATTTTGTGC
18569404 TAACTTGGTTTTATTTACTCATTTTGTGC
1 TAACTTGGTTTTATTTACTCATTTTGTGC
18569433 T
1 T
18569434 TCAAACCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (29 bp):
TAACTTGGTTTTATTTACTCATTTTGTGC
Found at i:18572183 original size:14 final size:14
Alignment explanation
Indices: 18572164--18572194 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18572154 CATGGTCAAT
18572164 GTGATTGTTTGGAG
1 GTGATTGTTTGGAG
18572178 GTGATTGTTTGGAG
1 GTGATTGTTTGGAG
18572192 GTG
1 GTG
18572195 TTCAATGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.45, T:0.42
Consensus pattern (14 bp):
GTGATTGTTTGGAG
Found at i:18572651 original size:29 final size:29
Alignment explanation
Indices: 18572610--18572726 Score: 137
Period size: 29 Copynumber: 4.1 Consensus size: 29
18572600 GAAACATAAA
* *
18572610 TATGCAAATTAATTATGGTGAATTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* * *
18572639 CATTTAAACTAATTATGGTGACTTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
*
18572668 TATGTAAACTAATTATGGT-AAATTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* * * *
18572696 TATGTAAATTAATTATGATAAATATATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
18572725 TA
1 TA
18572727 ACTAATTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 24 0.32
29 50 0.68
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (29 bp):
TATGTAAACTAATTATGGTGAATTTATAT
Found at i:18572702 original size:14 final size:14
Alignment explanation
Indices: 18572662--18572726 Score: 80
Period size: 14 Copynumber: 4.6 Consensus size: 14
18572652 TATGGTGACT
18572662 TTATATTATGTAAA
1 TTATATTATGTAAA
*
18572676 CTA-ATTATGGTAAA
1 TTATATTAT-GTAAA
18572690 TTATATTATGTAAA
1 TTATATTATGTAAA
18572704 TTA-ATTATGATAAA
1 TTATATTATG-TAAA
18572718 TATATATTA
1 T-TATATTA
18572727 ACTAATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.25
14 22 0.50
15 7 0.16
16 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (14 bp):
TTATATTATGTAAA
Found at i:18572724 original size:57 final size:58
Alignment explanation
Indices: 18572610--18572726 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 58
18572600 GAAACATAAA
* * * * * * *
18572610 TATGCAAATTAATTATGGTGAATTTATATCATTTAAACTAATTATGGTGACTTTATAT
1 TATGCAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
* * *
18572668 TATGTAAACTAATTATGGT-AAATTATATTATGTAAATTAATTATGATAAATATATAT
1 TATGCAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
18572725 TA
1 TA
18572727 ACTAATTATA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
57 32 0.65
58 17 0.35
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.44
Consensus pattern (58 bp):
TATGCAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
Found at i:18576885 original size:30 final size:30
Alignment explanation
Indices: 18576849--18576911 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
18576839 ATTTATTTTA
18576849 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
18576879 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
18576909 TTG
1 TTG
18576912 ATTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:18580284 original size:56 final size:56
Alignment explanation
Indices: 18580213--18580349 Score: 202
Period size: 56 Copynumber: 2.4 Consensus size: 56
18580203 TCCCGGACAG
* * *
18580213 GGTCTTACTCACACACATATATCGGAGTCATAGATCAATGCCAACGTATAAAACGT
1 GGTCTTACTCGCACACATATATCGAAGTCACAGATCAATGCCAACGTATAAAACGT
* * * *
18580269 GGTCTTACTTGCACACATATATCAAAGTCACATATCGATGCCAACGTATAAAACGT
1 GGTCTTACTCGCACACATATATCGAAGTCACAGATCAATGCCAACGTATAAAACGT
*
18580325 GGTCTTACTCGCATACATATATCGA
1 GGTCTTACTCGCACACATATATCGA
18580350 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGAAGTCACAGATCAATGCCAACGTATAAAACGT
Found at i:18597017 original size:30 final size:30
Alignment explanation
Indices: 18596982--18597041 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18596972 ATTTAATACG
*
18596982 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
18597012 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
18597042 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:18598688 original size:56 final size:57
Alignment explanation
Indices: 18598627--18598760 Score: 200
Period size: 56 Copynumber: 2.4 Consensus size: 57
18598617 TCCCAGATAG
* *
18598627 GGTCTTACTCGCACACATATATTGGA-GTCACATATTGATGCCAATGTATAAAACAT
1 GGTCTTACTCGCACACATATATTCGATGTCACATATCGATGCCAATGTATAAAACAT
* **
18598683 GGTCTTACTCTCACACATATA-TCGATGTCACATATCGATGCCAATGTATAAAAGGT
1 GGTCTTACTCGCACACATATATTCGATGTCACATATCGATGCCAATGTATAAAACAT
*
18598739 GGTCTTACTCGCACAAATATAT
1 GGTCTTACTCGCACACATATAT
18598761 CAATGCCATG
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.04
56 66 0.96
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (57 bp):
GGTCTTACTCGCACACATATATTCGATGTCACATATCGATGCCAATGTATAAAACAT
Found at i:18605880 original size:40 final size:40
Alignment explanation
Indices: 18605825--18606009 Score: 327
Period size: 40 Copynumber: 4.6 Consensus size: 40
18605815 CGGATGATAA
* *
18605825 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
18605865 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18605905 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
18605945 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18605985 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18606010 AGCAAGTAGT
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
40 140 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18606024 original size:80 final size:79
Alignment explanation
Indices: 18605821--18606041 Score: 320
Period size: 80 Copynumber: 2.8 Consensus size: 79
18605811 TATTCGGATG
* *
18605821 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCCGGGCTAAGTCCCGAAGGC
18605885 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* * *
18605901 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGGCTAAGTCCCGAAGGCA
18605966 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
* * *
18605981 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-GGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGGCTAAGTCCCGAAG
18606042 ATGCTTGGGT
Statistics
Matches: 130, Mismatches: 8, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
79 16 0.12
80 112 0.86
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:18606309 original size:22 final size:21
Alignment explanation
Indices: 18606268--18606311 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
18606258 GAATGTGCAT
18606268 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
18606290 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
18606312 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:18613940 original size:40 final size:40
Alignment explanation
Indices: 18613839--18614020 Score: 282
Period size: 40 Copynumber: 4.6 Consensus size: 40
18613829 CGGATGATAA
* *
18613839 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
18613878 TC-GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18613916 CCGGGCTAAGTCCCGAAGGCATTTGTTGC-AGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATAT
* *
18613956 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18613996 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18614021 AGCAAGTAGT
Statistics
Matches: 131, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
37 23 0.18
38 11 0.08
39 12 0.09
40 82 0.63
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18614035 original size:80 final size:77
Alignment explanation
Indices: 18613835--18614052 Score: 298
Period size: 80 Copynumber: 2.8 Consensus size: 77
18613825 TATTCGGATG
18613835 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATTCGGCTAAGTCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTAG-CTATATTCGGCTAAGTCCGAAGGCAT
18613898 TTGTGCGAGTTACT
64 TTGTGCGAGTTACT
* *
18613912 ATATCCGGGCTAAGTCCCGAAGGCATTTGTTGCAGTTA-CTATATCCGGGCTAAGTCTCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG-TGCAG-TAGCTATATTC-GGCTAAGTC-CGAAGGC
18613976 ATTTGTGCGAGTTACT
62 ATTTGTGCGAGTTACT
* * *
18613992 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTCGGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTAGCTATATTCGGCTAAGT-CCGAAG
18614053 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
77 33 0.26
78 7 0.06
79 25 0.20
80 60 0.48
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (77 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAGTAGCTATATTCGGCTAAGTCCGAAGGCATTT
GTGCGAGTTACT
Found at i:18623323 original size:35 final size:36
Alignment explanation
Indices: 18623053--18623340 Score: 201
Period size: 35 Copynumber: 8.0 Consensus size: 36
18623043 CCGCAAAAGA
*
18623053 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACAAAT
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * * **
18623089 AATTACTGAGCCCAGCTCTAGTTGGATAAACTAAC-AAT
1 -ATT--TGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * * *
18623127 ATTTGCACCCAGTGTTAGTCAGATAAACCGAC-AA-
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * * * **
18623161 ATGTGTGCCCAGCACTAGTCAGATAAATTGACGAA-
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * *
18623196 AGTTGCGCCTAGCGCTAGTCGGATAAACTGACGAA-
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * * *
18623231 AGTTGCACCCAGCACTAGTTGGATAAACCGACGAAT
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * * * *
18623267 AATTAGTGAGCCTAGCTCTAGTTGGATAAACCAAC-AAT
1 -ATT--TGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
* * *
18623305 ATTTGCGCCTAGCGCTAGTCAGATAAACCAACGAAT
1 ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
18623341 GTGTGCCCAA
Statistics
Matches: 199, Mismatches: 44, Indels: 17
0.77 0.17 0.07
Matches are distributed among these distances:
34 24 0.12
35 107 0.54
36 3 0.02
37 11 0.06
38 6 0.03
39 48 0.24
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (36 bp):
ATTTGCGCCCAGCGCTAGTCGGATAAACCGACGAAT
Found at i:18623376 original size:178 final size:178
Alignment explanation
Indices: 18623055--18623393 Score: 507
Period size: 178 Copynumber: 1.9 Consensus size: 178
18623045 GCAAAAGAAT
* *
18623055 TTGCGCCCAGCGCTAGTCGGATAAACCGACAAATAATTACTGAGCCCAGCTCTAGTTGGATAAAC
1 TTGCACCCAGCACTAGTCGGATAAACCGACAAATAATTACTGAGCCCAGCTCTAGTTGGATAAAC
* * * * *
18623120 TAACAATATTTGCACCCAGTGTTAGTCAGATAAACCGACAAATGTGTGCCCAGCACTAGTCAGAT
66 CAACAATATTTGCACCCAGCGCTAGTCAGATAAACCAACAAATGTGTGCCCAACACTAGTCAGAT
* *
18623185 AAATTGACGAAAGTTGCGCCTAGCGCTAGTCGGATAAACTGACGAAAG
131 AAACTGACGAAAGTTGCGCCCAGCGCTAGTCGGATAAACTGACGAAAG
* * * *
18623233 TTGCACCCAGCACTAGTTGGATAAACCGACGAATAATTAGTGAGCCTAGCTCTAGTTGGATAAAC
1 TTGCACCCAGCACTAGTCGGATAAACCGACAAATAATTACTGAGCCCAGCTCTAGTTGGATAAAC
* * *
18623298 CAACAATATTTGCGCCTAGCGCTAGTCAGATAAACCAACGAATGTGTGCCCAACACTAGTCAGAT
66 CAACAATATTTGCACCCAGCGCTAGTCAGATAAACCAACAAATGTGTGCCCAACACTAGTCAGAT
* * *
18623363 AAACTGGCGAAAGTTGCTCCCAGTGCTAGTC
131 AAACTGACGAAAGTTGCGCCCAGCGCTAGTC
18623394 AAATGAATCG
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
178 142 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (178 bp):
TTGCACCCAGCACTAGTCGGATAAACCGACAAATAATTACTGAGCCCAGCTCTAGTTGGATAAAC
CAACAATATTTGCACCCAGCGCTAGTCAGATAAACCAACAAATGTGTGCCCAACACTAGTCAGAT
AAACTGACGAAAGTTGCGCCCAGCGCTAGTCGGATAAACTGACGAAAG
Found at i:18625532 original size:15 final size:15
Alignment explanation
Indices: 18625509--18625542 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
18625499 TTCTACCCAC
18625509 TCTTCTATTTCTTTT
1 TCTTCTATTTCTTTT
*
18625524 TCTTTTATTTCTTTT
1 TCTTCTATTTCTTTT
18625539 TCTT
1 TCTT
18625543 ACATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTCTATTTCTTTT
Found at i:18641344 original size:47 final size:47
Alignment explanation
Indices: 18641281--18641385 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
18641271 CCCTTCGGGA
* *
18641281 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
18641328 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
18641375 CTTATCACATA
1 CTTATCACATA
18641386 ATTAATACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:18645201 original size:17 final size:16
Alignment explanation
Indices: 18645181--18645221 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
18645171 AATTAAAATA
18645181 AAAATAAAAACAAAAGG
1 AAAATAAAAAC-AAAGG
* *
18645198 AAAAGAAAAACAAAGT
1 AAAATAAAAACAAAGG
18645214 AAAATAAA
1 AAAATAAA
18645222 TAGACTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (16 bp):
AAAATAAAAACAAAGG
Found at i:18646790 original size:3 final size:3
Alignment explanation
Indices: 18646782--18646814 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
18646772 GATAGAACAG
*
18646782 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18646815 AACAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18663647 original size:13 final size:13
Alignment explanation
Indices: 18663629--18663653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18663619 GCTCTACAGG
18663629 GACACGCCCGTGT
1 GACACGCCCGTGT
18663642 GACACGCCCGTG
1 GACACGCCCGTG
18663654 GTCAAGGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.32, T:0.12
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:18665666 original size:6 final size:6
Alignment explanation
Indices: 18665638--18665677 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
18665628 CTTAATTAAG
* * *
18665638 AAAAAT AAAGAT AAAAGT GAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
18665678 TGTTTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:18667337 original size:72 final size:71
Alignment explanation
Indices: 18667221--18667363 Score: 277
Period size: 72 Copynumber: 2.0 Consensus size: 71
18667211 CCAGAGAAAA
18667221 CATGAAATAGGAAAATATTTAAAGAAAATAGAGAGAAAAGAGTAAACAAACGCAAAAGGGAGAAG
1 CATGAAATAGGAAAATATTTAAAGAAAATAGAGAGAAAAGAGTAAACAAACGCAAAAGGGAGAAG
18667286 CTTGAG
66 CTTGAG
18667292 CATGAAATAGGCAAAATATTTAAAGAAAATAGAGAGAAAAGAGTAAACAAACGCAAAAGGGAGAA
1 CATGAAATAGG-AAAATATTTAAAGAAAATAGAGAGAAAAGAGTAAACAAACGCAAAAGGGAGAA
18667357 GCTTGAG
65 GCTTGAG
18667364 TCGTTGGAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 11 0.15
72 60 0.85
ACGTcount: A:0.55, C:0.08, G:0.24, T:0.14
Consensus pattern (71 bp):
CATGAAATAGGAAAATATTTAAAGAAAATAGAGAGAAAAGAGTAAACAAACGCAAAAGGGAGAAG
CTTGAG
Found at i:18675755 original size:39 final size:40
Alignment explanation
Indices: 18675596--18675849 Score: 349
Period size: 40 Copynumber: 6.4 Consensus size: 40
18675586 GATGATAACG
* * *
18675596 GGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
** * *
18675636 ACGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
18675676 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
18675716 GGGCTAAGTCCCGAAGGCATTTGT-CGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
18675755 GGGCTAAGTCCC-AAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
18675794 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
18675834 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
18675850 TACTTGGTTT
Statistics
Matches: 200, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
38 11 0.05
39 70 0.35
40 118 0.59
41 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:18675806 original size:118 final size:120
Alignment explanation
Indices: 18675596--18675849 Score: 349
Period size: 118 Copynumber: 2.1 Consensus size: 120
18675586 GATGATAACG
* *
18675596 GGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTAATTCCACGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCACGCTAAGTCCCGAAGGCATTTGTG
* *
18675661 CTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
66 CGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
* **
18675716 GGGCTAAGTCCCGAAGGCATTTGT-CGAGTTACT-ATATCCGGGCTAAGTCCC-AAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCACGCTAAGTCCCGAAGGCATTTGT
*
18675778 GCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
65 GCGAGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
* *
18675834 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
18675850 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
117 18 0.15
118 60 0.50
119 20 0.17
120 23 0.19
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (120 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCACGCTAAGTCCCGAAGGCATTTGTG
CGAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
Found at i:18683722 original size:40 final size:40
Alignment explanation
Indices: 18683666--18683907 Score: 330
Period size: 40 Copynumber: 6.0 Consensus size: 40
18683656 GATGATAACG
*
18683666 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCC
* * * *
18683706 GGGCTAAGTCCTGAAGGCATTAGTGCTAGTGACTA-ATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCC
*
18683746 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCC
* *
18683786 GGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCC
*
18683826 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTATATCC
*
18683866 GGGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATATCC
18683906 GG
1 GG
18683908 TTAAATCCCA
Statistics
Matches: 186, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 3 0.02
40 180 0.97
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCC
Found at i:18688439 original size:36 final size:37
Alignment explanation
Indices: 18688394--18688469 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
18688384 CACACCCACC
* * *
18688394 AAATGATAAGATATTTCATTTAT-TTTTTTAAATAAT
1 AAATGATAAGATATTTAATTTATAATTTTTAAAAAAT
* * *
18688430 AAATTATAAGTTCTTTAATTTATAATTTTTAAAAAAT
1 AAATGATAAGATATTTAATTTATAATTTTTAAAAAAT
18688467 AAA
1 AAA
18688470 CAATTCTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
AAATGATAAGATATTTAATTTATAATTTTTAAAAAAT
Found at i:18690209 original size:35 final size:38
Alignment explanation
Indices: 18690139--18690215 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 38
18690129 AATATACGGG
*
18690139 ATATATTAAGATTCAGTTAATATTTTAAACTATTTTTA
1 ATATATTAAGATTCAGTTAATATTTTAAACTATTTTAA
18690177 ATAT-TTAA-ATT-AGTT-ATATTTTAATA-TAATTTTAA
1 ATATATTAAGATTCAGTTAATATTTTAA-ACT-ATTTTAA
18690212 ATAT
1 ATAT
18690216 GAATTTATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
34 10 0.28
35 15 0.42
36 3 0.08
37 4 0.11
38 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (38 bp):
ATATATTAAGATTCAGTTAATATTTTAAACTATTTTAA
Found at i:18690210 original size:34 final size:38
Alignment explanation
Indices: 18690139--18690215 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 38
18690129 AATATACGGG
*
18690139 ATATATTAAGATTCAGTTAATATTTTAAACTATTTTTA
1 ATATATTAAGATTCAGTTAATATTTTAAACTAATTTTA
18690177 ATAT-TTAA-ATT-AGTT-ATATTTTAATA-TAATTTTA
1 ATATATTAAGATTCAGTTAATATTTTAA-ACTAATTTTA
18690211 A-ATAT
1 ATATAT
18690216 GAATTTATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
33 2 0.06
34 18 0.50
35 5 0.14
36 3 0.08
37 4 0.11
38 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (38 bp):
ATATATTAAGATTCAGTTAATATTTTAAACTAATTTTA
Found at i:18690248 original size:12 final size:13
Alignment explanation
Indices: 18690198--18690248 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
18690188 AGTTATATTT
18690198 TAATATAATTTTA
1 TAATATAATTTTA
18690211 -AATATGAA-TTTA
1 TAATAT-AATTTTA
*
18690223 TAGATACAATTTTA
1 TA-ATATAATTTTA
18690237 TAATAT-ATTTTA
1 TAATATAATTTTA
18690249 ATTAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 15 0.47
13 8 0.25
14 9 0.28
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (13 bp):
TAATATAATTTTA
Found at i:18690555 original size:22 final size:22
Alignment explanation
Indices: 18690512--18690557 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18690502 TATATTTTAC
* *
18690512 TATTTATTATATTATTAATTTG
1 TATTTATTATATAATAAATTTG
18690534 TATTT-TTATATAATAAAGTTTG
1 TATTTATTATATAATAAA-TTTG
18690556 TA
1 TA
18690558 ATAATTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (22 bp):
TATTTATTATATAATAAATTTG
Found at i:18690806 original size:19 final size:19
Alignment explanation
Indices: 18690762--18690810 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
18690752 ATTATTATAG
18690762 CATTAAATCAATTAAAATTAA
1 CATTAAA-C-ATTAAAATTAA
*
18690783 GATTAAACATTATAAA-TAA
1 CATTAAACATTA-AAATTAA
18690802 CATTAAACA
1 CATTAAACA
18690811 AAAATGAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 15 0.60
20 4 0.16
21 6 0.24
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
CATTAAACATTAAAATTAA
Found at i:18696710 original size:20 final size:20
Alignment explanation
Indices: 18696687--18696765 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 20
18696677 CTTCTAAGTC
18696687 ATTACCAAAATTTCTAATAA
1 ATTACCAAAATTTCTAATAA
***
18696707 ATTATTGAAATTTCT-A-AA
1 ATTACCAAAATTTCTAATAA
* ** *
18696725 GTTACTCAAAAATTTCTAGGAC
1 ATTAC-C-AAAATTTCTAATAA
*
18696747 TTTACCAAAATTTCTAATA
1 ATTACCAAAATTTCTAATA
18696766 TGCCATATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
18 5 0.12
19 1 0.02
20 31 0.72
21 1 0.02
22 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTACCAAAATTTCTAATAA
Found at i:18697414 original size:22 final size:22
Alignment explanation
Indices: 18697372--18697414 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
18697362 ATCATTTGTA
*
18697372 ATTTATAATCATTCAAGTTCAT
1 ATTTATAATCATTCAACTTCAT
*
18697394 ATTTGATAATCA-TGAACTTCA
1 ATTT-ATAATCATTCAACTTCA
18697415 AAACATTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (22 bp):
ATTTATAATCATTCAACTTCAT
Found at i:18698533 original size:21 final size:21
Alignment explanation
Indices: 18698494--18698533 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18698484 TATCATATAA
*
18698494 CTCAATTCACATTCTATTTTT
1 CTCAATTCACATTCAATTTTT
18698515 CTCAATTCA-ATATCAATTT
1 CTCAATTCACAT-TCAATTT
18698534 CACTATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (21 bp):
CTCAATTCACATTCAATTTTT
Found at i:18702441 original size:47 final size:46
Alignment explanation
Indices: 18702373--18702548 Score: 216
Period size: 47 Copynumber: 3.8 Consensus size: 46
18702363 TGTAACCCGC
*
18702373 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
18702419 CCATAAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
18702470 -C-TTA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
18702513 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
18702549 ATGCTCAACC
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 32 0.29
47 59 0.53
48 1 0.01
49 2 0.02
50 2 0.02
51 3 0.03
52 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:18702552 original size:93 final size:94
Alignment explanation
Indices: 18702381--18702552 Score: 310
Period size: 94 Copynumber: 1.8 Consensus size: 94
18702371 GCCCATAAGT
* *
18702381 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAAGTGAACTCGGACTCAACTCA
18702446 ACGAGTTCGGATGCCTAGTTACATCTTAC
66 ACGAGTTCGGATGCCTAGTTACATCTTAC
*
18702475 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAAGTGAACTCGGACTCAACTCA
18702539 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
18702553 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 36 0.48
94 39 0.52
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (94 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTTAC
Found at i:18704952 original size:14 final size:14
Alignment explanation
Indices: 18704933--18704980 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18704923 CAAAGATAAC
18704933 AAGAAAACCGAATA
1 AAGAAAACCGAATA
* *
18704947 AAGAAATCCAAGATA
1 AAGAAAACCGA-ATA
* *
18704962 GAGAAACCCGAATA
1 AAGAAAACCGAATA
18704976 AAGAA
1 AAGAA
18704981 TCCAGGATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (14 bp):
AAGAAAACCGAATA
Found at i:18704982 original size:28 final size:29
Alignment explanation
Indices: 18704933--18704998 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
18704923 CAAAGATAAC
*
18704933 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
* *
18704962 GAGAAACCCGAATAAAG-AATCCAGGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
18704990 AAGAAACCC
1 AAGAAACCC
18704999 AAGATACGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.56, C:0.18, G:0.17, T:0.09
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:18712036 original size:24 final size:24
Alignment explanation
Indices: 18712001--18712061 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
18711991 TTTGAATCCA
*
18712001 CACACATAGTGCTATACAAGTCCG
1 CACACATAGTGCCATACAAGTCCG
* * *
18712025 CAGACATAGTGCCATACAATTTCG
1 CACACATAGTGCCATACAAGTCCG
18712049 CACACATAGTGCC
1 CACACATAGTGCC
18712062 GAAGTCAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (24 bp):
CACACATAGTGCCATACAAGTCCG
Found at i:18720057 original size:24 final size:24
Alignment explanation
Indices: 18720027--18720115 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
18720017 ATTGACATTT
18720027 AAATCCGCACACATAGTGCTATAC
1 AAATCCGCACACATAGTGCTATAC
* *
18720051 AAGTCCGCACACATAGTGCCATAC
1 AAATCCGCACACATAGTGCTATAC
* * *
18720075 AATTTCGCACACATAGTGCTATTC
1 AAATCCGCACACATAGTGCTATAC
*
18720099 AAATTCGCACACATAGT
1 AAATCCGCACACATAGT
18720116 ACCGAAGTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCTATAC
Found at i:18720065 original size:48 final size:48
Alignment explanation
Indices: 18720013--18720115 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
18720003 TAATTCACAT
* ** *
18720013 ACATATTGACATTTAAATCCGCACACATAGTGCTATACAAGTCCGCAC
1 ACATAGTGACATACAAATCCGCACACATAGTGCTATACAAATCCGCAC
* * * * *
18720061 ACATAGTGCCATACAATTTCGCACACATAGTGCTATTCAAATTCGCAC
1 ACATAGTGACATACAAATCCGCACACATAGTGCTATACAAATCCGCAC
18720109 ACATAGT
1 ACATAGT
18720116 ACCGAAGTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (48 bp):
ACATAGTGACATACAAATCCGCACACATAGTGCTATACAAATCCGCAC
Found at i:18724916 original size:76 final size:76
Alignment explanation
Indices: 18724824--18724977 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
18724814 TTAGGCAGCG
* * *
18724824 GCGATGGATTGAACTACTTAAAGATTATGACTGCACCATTTAGTATCATCCTAGTAAGGATAATA
1 GCGATGAATTGAACTACTTAAAGATTATGACTACACCATTGAGTATCATCCTAGTAAGGATAATA
*
18724889 TAGTAGTCGAT
66 TAGTAGCCGAT
*
18724900 GCGATGAATTGAACTACTTAAAGATTATGACTACACCATTGAGTATCATCCTAGTAAGGCTAATA
1 GCGATGAATTGAACTACTTAAAGATTATGACTACACCATTGAGTATCATCCTAGTAAGGATAATA
18724965 TAGTAGCCGAT
66 TAGTAGCCGAT
18724976 GC
1 GC
18724978 TCTAAGTCGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (76 bp):
GCGATGAATTGAACTACTTAAAGATTATGACTACACCATTGAGTATCATCCTAGTAAGGATAATA
TAGTAGCCGAT
Found at i:18728620 original size:21 final size:20
Alignment explanation
Indices: 18728586--18728624 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
18728576 ATATAAAATT
18728586 ATATTTAATAAATAATTTTAA
1 ATATTTAATAAAT-ATTTTAA
* *
18728607 ATATTTTATTAATATTTT
1 ATATTTAATAAATATTTT
18728625 GGGTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTAATAAATATTTTAA
Found at i:18739270 original size:40 final size:39
Alignment explanation
Indices: 18739214--18739398 Score: 223
Period size: 40 Copynumber: 4.7 Consensus size: 39
18739204 TCGGATGATA
** * *
18739214 ACCGGGCTAAGTCCCG-AGAGCATTTAAGCTAGTGGCTAAT
1 ACCGGGCTAAGTCCCGAAG-GCATTTGTGCAAGT-ACTAAT
* *
18739254 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTAAT
* *
18739294 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-TTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTAAT
18739333 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-AT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTAAT
18739372 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -ACCGGGCTAAGTCCCGAAGGCATTTG
18739399 AGCTAGTGGC
Statistics
Matches: 132, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 39 0.30
40 90 0.68
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTAAT
Found at i:18739349 original size:39 final size:39
Alignment explanation
Indices: 18739255--18739398 Score: 225
Period size: 40 Copynumber: 3.6 Consensus size: 39
18739245 GTGGCTAATT
* * * *
18739255 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-TTATA
18739295 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATA
*
18739334 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTAT-A
18739374 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18739399 AGCTAGTGGC
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 40 0.41
40 58 0.59
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATTATA
Found at i:18739412 original size:40 final size:40
Alignment explanation
Indices: 18739211--18739417 Score: 210
Period size: 40 Copynumber: 5.2 Consensus size: 40
18739201 TGTTCGGATG
** *
18739211 ATAACCGGGCTAAGTCCCG-AGAGCATTTAAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTGGCT
* *
18739251 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGCT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGGCT
***
18739288 ACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTATT
1 A-TAA--CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGGCT
**
18739331 AT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGGCT
* *
18739370 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGGCT
*
18739410 ATATCCGG
1 ATAACCGG
18739418 CTTGTGACAG
Statistics
Matches: 143, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 39 0.27
40 92 0.64
41 3 0.02
42 2 0.01
43 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGGCT
Found at i:18741102 original size:82 final size:81
Alignment explanation
Indices: 18740986--18741141 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
18740976 AAATTGTACA
* * * *
18740986 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
18741050 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
18741067 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
18741132 TGCGAGTTGA
65 TGCGAATTGA
18741142 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:18741109 original size:55 final size:52
Alignment explanation
Indices: 18740985--18741138 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
18740975 TAAATTGTAC
* *
18740985 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
18741038 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
18741093 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
18741139 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:18741143 original size:27 final size:27
Alignment explanation
Indices: 18740986--18741141 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
18740976 AAATTGTACA
*
18740986 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
18741013 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
18741040 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
18741067 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
18741095 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
18741122 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
18741142 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:18741152 original size:27 final size:27
Alignment explanation
Indices: 18740978--18741162 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
18740968 GCGGGATTAA
*
18740978 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
18741005 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
18741032 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
18741059 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
18741087 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
18741114 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
18741141 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
18741163 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:18741153 original size:82 final size:81
Alignment explanation
Indices: 18740978--18741162 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
18740968 GCGGGATTAA
* * * *
18740978 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
18741043 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
18741059 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
18741123 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
18741141 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
18741163 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:18746116 original size:34 final size:34
Alignment explanation
Indices: 18746077--18746141 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
18746067 GCTGAGAGTC
18746077 TATTTTTTAGTTGAAAATTGTAGTCCTTTTATTT
1 TATTTTTTAGTTGAAAATTGTAGTCCTTTTATTT
*
18746111 TATTTTTTAGTTGAAAATTGTAGTTCTTTTA
1 TATTTTTTAGTTGAAAATTGTAGTCCTTTTA
18746142 CTTCGACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (34 bp):
TATTTTTTAGTTGAAAATTGTAGTCCTTTTATTT
Found at i:18758009 original size:49 final size:49
Alignment explanation
Indices: 18757941--18758221 Score: 341
Period size: 49 Copynumber: 5.7 Consensus size: 49
18757931 TCTATTGTGA
* *
18757941 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATTATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
* * * * *
18757990 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCG-ATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGAATAA-TT
* * **
18758040 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGA-ATAATT
*
18758090 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
**
18758140 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTGAATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
* * * *
18758189 GGTCGCATGTGTAGAACTAAGTTCAGGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
18758222 TGCGTACGGA
Statistics
Matches: 199, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
49 113 0.57
50 51 0.26
51 35 0.18
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
Found at i:18758176 original size:99 final size:101
Alignment explanation
Indices: 18757941--18758228 Score: 379
Period size: 99 Copynumber: 2.9 Consensus size: 101
18757931 TCTATTGTGA
* * * *
18757941 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTA-CCGAATTATTGGTCGCATGTGTAGT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAATGATTGGTCACATGTGTAGT
* *
18758005 ACTAAGTGTAGGCTACTATGCGTACCCGATAACTTC
66 ACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* * *
18758041 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAG-ATGGTTAGGTCACGTGTGTAG
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAATGATT-GGTCACATGTGTAG
* *
18758105 TACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-
65 TACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* * * *
18758140 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAT-TGAATAATTGGTCGCATGTGTAGA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAATGATTGGTCACATGTGTAGT
* *
18758204 ACTAAGTTCAGGCTACTATGCGTAC
66 ACTAAGTGCAGGCTACTACGCGTAC
18758229 GGATAGCTTT
Statistics
Matches: 164, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
98 35 0.21
99 43 0.26
100 43 0.26
101 43 0.26
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAATGATTGGTCACATGTGTAGT
ACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
Found at i:18758251 original size:150 final size:150
Alignment explanation
Indices: 18757940--18758227 Score: 366
Period size: 150 Copynumber: 1.9 Consensus size: 150
18757930 ATCTATTGTG
* * * *
18757940 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATTATTGGTCGCATGTGTAGT
1 AGGTCAAGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGT
* * * *
18758005 ACTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCT
66 ACTAAGTGCAGGCTACTACGCGTACCCGATAACTTCGATCACATGTGTAGAACTAAGTGCAGGCT
* *
18758070 ACTACGTGTATCAGATGGTT
131 ACTACGCGTATCAGATGCTT
* * *
18758090 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACGTGTGTAGT
1 AGGTCAAGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGT
* ** * * *
18758155 ACTAAGTGCAGGCTACTACGTGTA-TTGAATAA-TT-GGTCGCATGTGTAGAACTAAGTTCAGGC
66 ACTAAGTGCAGGCTACTACGCGTACCCG-ATAACTTCGATCACATGTGTAGAACTAAGTGCAGGC
*
18758217 TACTATGCGTA
130 TACTACGCGTA
18758228 CGGATAGCTT
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
148 32 0.27
149 3 0.03
150 85 0.71
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (150 bp):
AGGTCAAGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCACATGTGTAGT
ACTAAGTGCAGGCTACTACGCGTACCCGATAACTTCGATCACATGTGTAGAACTAAGTGCAGGCT
ACTACGCGTATCAGATGCTT
Found at i:18768978 original size:17 final size:18
Alignment explanation
Indices: 18768952--18768988 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18768942 CGGCCAAATT
18768952 AAAAATTTTTAAGAATCA
1 AAAAATTTTTAAGAATCA
18768970 AAAAATTTTTAAGAATCA
1 AAAAATTTTTAAGAATCA
18768988 A
1 A
18768989 TCACATCGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAAATTTTTAAGAATCA
Found at i:18775352 original size:24 final size:25
Alignment explanation
Indices: 18775305--18775367 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
18775295 CTATATAATA
* *
18775305 GGAAGCTCA-TAAGAGCCATAATTG
1 GGAAGCTCACAAAGAACCATAATTG
*
18775329 GGAAGTTCACAAAGAACCAT-ATTG
1 GGAAGCTCACAAAGAACCATAATTG
*
18775353 GGAAGCTCACGAAGA
1 GGAAGCTCACAAAGA
18775368 GCTTATCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 25 0.76
25 8 0.24
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (25 bp):
GGAAGCTCACAAAGAACCATAATTG
Found at i:18787176 original size:37 final size:38
Alignment explanation
Indices: 18787135--18787222 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 38
18787125 AAAAAATAGT
18787135 ATTATTTTAATAGT-TTATTATTAAATTTAAT-TTAAAA-
1 ATTATTTTAATAGTATT-TTATT-AATTTAATATTAAAAG
18787172 ATTATTTTAATAGTATTTTATTAATTTAATATTAAAATG
1 ATTATTTTAATAGTATTTTATTAATTTAATATTAAAA-G
*
18787211 ATTATCTTAATA
1 ATTATTTTAATA
18787223 TTGAAACGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
36 8 0.17
37 25 0.54
38 2 0.04
39 11 0.24
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (38 bp):
ATTATTTTAATAGTATTTTATTAATTTAATATTAAAAG
Found at i:18788328 original size:36 final size:36
Alignment explanation
Indices: 18788274--18788344 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
18788264 CATTGTTGAT
18788274 ATTCAGTTCAGCAAGCTTTTGGATCTATTCTGACTA
1 ATTCAGTTCAGCAAGCTTTTGGATCTATTCTGACTA
* * *
18788310 ATTCAGTTCAGTAGGCTTTTGGATCTATTTTGACT
1 ATTCAGTTCAGCAAGCTTTTGGATCTATTCTGACT
18788345 GATGCGTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (36 bp):
ATTCAGTTCAGCAAGCTTTTGGATCTATTCTGACTA
Found at i:18791099 original size:27 final size:27
Alignment explanation
Indices: 18791045--18791101 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
18791035 CATCTCATAA
* *
18791045 GGGCATATCGGTCATTTTACCATGTAG
1 GGGCATATCAGTCATTTTACAATGTAG
*
18791072 GGGCATTTCAGTCATTTTATCAAT-TAG
1 GGGCATATCAGTCATTTTA-CAATGTAG
18791099 GGG
1 GGG
18791102 GTCTAGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (27 bp):
GGGCATATCAGTCATTTTACAATGTAG
Found at i:18792945 original size:39 final size:40
Alignment explanation
Indices: 18792845--18793029 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
18792835 TTGAATGATG
* * * *
18792845 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
18792885 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18792925 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
18792964 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
18793005 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18793030 AACGAGTAGC
Statistics
Matches: 132, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 40 0.30
40 82 0.62
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18792982 original size:79 final size:82
Alignment explanation
Indices: 18792845--18793029 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 82
18792835 TTGAATGATG
*
18792845 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
18792909 TGTGCGAGTTACTA-AA
66 TGTGCGAGTTACTATAA
* * * * **
18792925 TCCGGGTTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
18792987 TTGTGCGAGTTACTATAA
65 TTGTGCGAGTTACTATAA
*
18793005 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
18793030 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATAA
Found at i:18793051 original size:79 final size:79
Alignment explanation
Indices: 18792898--18793062 Score: 219
Period size: 79 Copynumber: 2.1 Consensus size: 79
18792888 GGACTAAGAT
* **
18792898 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAA
*
18792963 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
18792977 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATTTGAACGAGTTA-C
* *
18793040 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
18793056 CCGAAGG
1 CCGAAGG
18793063 TACGTGATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
79 50 0.66
80 26 0.34
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:18793059 original size:119 final size:119
Alignment explanation
Indices: 18792845--18793062 Score: 273
Period size: 119 Copynumber: 1.8 Consensus size: 119
18792835 TTGAATGATG
*
18792845 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
18792910 GTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
66 GAACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* * * * * *
18792964 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
* *
18793027 TTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
64 TTGAACGAGTTA-CTAAATCCGGGTT-AAGTCCGAAGG
18793063 TACGTGATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
118 7 0.08
119 70 0.83
120 7 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18806679 original size:12 final size:12
Alignment explanation
Indices: 18806656--18806699 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
18806646 AAGACAAAGA
*
18806656 TAAAAATGAAAAT
1 TAAAAAT-AAAAC
18806669 TAAAAATAAAAC
1 TAAAAATAAAAC
*
18806681 TAAAACTAAAAC
1 TAAAAATAAAAC
18806693 TAAAAAT
1 TAAAAAT
18806700 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 21 0.75
13 7 0.25
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (12 bp):
TAAAAATAAAAC
Found at i:18806710 original size:6 final size:6
Alignment explanation
Indices: 18806664--18806697 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
18806654 GATAAAAATG
* *
18806664 AAAATT AAAAAT AAAACT AAAACT AAAACT AAAA
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAA
18806698 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAACT
Found at i:18811726 original size:30 final size:30
Alignment explanation
Indices: 18811692--18811751 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
18811682 CTTTAATATG
* * *
18811692 AACTTTGGCAAAATTACATTTTTTCCCCTA
1 AACTTTGACAAAATTACACTTTTACCCCTA
* *
18811722 AACTTTTACATAATTACACTTTTACCCCTA
1 AACTTTGACAAAATTACACTTTTACCCCTA
18811752 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTACCCCTA
Found at i:18812893 original size:42 final size:42
Alignment explanation
Indices: 18812832--18812945 Score: 174
Period size: 43 Copynumber: 2.7 Consensus size: 42
18812822 GTTGAAATTA
* **
18812832 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATGGCATCGATATAAGATCC
*
18812874 CGTGTAAGACCATAGCTGGGATATTGGCATCGATATAAGATCC
1 CGTGTAAGACCATATCTGGGATA-TGGCATCGATATAAGATCC
*
18812917 CATGTAAGACCATATCTGGGATATGGCAT
1 CGTGTAAGACCATATCTGGGATATGGCAT
18812946 TGGTACTATG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 28 0.43
43 37 0.57
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCATCGATATAAGATCC
Found at i:18814886 original size:92 final size:92
Alignment explanation
Indices: 18814727--18814912 Score: 309
Period size: 92 Copynumber: 2.0 Consensus size: 92
18814717 GTAGTCAATA
** * *
18814727 TAGATTCTCCAACCTGTGGCAGTTCTCATTGGGATTAACTCGTTACGTTCATTCTTGACAATCGT
1 TAGATTCTCCAACCCATGACAGTTCTCATTGGGATTAACTCATTACGTTCATTCTTGACAATCGT
18814792 GATTCCTCCTTTCTTTGGTACACATTG
66 GATTCCTCCTTTCTTTGGTACACATTG
* *
18814819 TAGATTCTCCAACCCATGACAGTTCTCGTTGGGATTAACTCATTACGTTCATTCTTGACAATTGT
1 TAGATTCTCCAACCCATGACAGTTCTCATTGGGATTAACTCATTACGTTCATTCTTGACAATCGT
*
18814884 GATTCCTCCTTTCTTTGGTACGCATTG
66 GATTCCTCCTTTCTTTGGTACACATTG
18814911 TA
1 TA
18814913 CTGGACTTAC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (92 bp):
TAGATTCTCCAACCCATGACAGTTCTCATTGGGATTAACTCATTACGTTCATTCTTGACAATCGT
GATTCCTCCTTTCTTTGGTACACATTG
Found at i:18820376 original size:15 final size:15
Alignment explanation
Indices: 18820356--18820385 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18820346 CCAGAGTAAG
*
18820356 TATGTGGGTGCTCGT
1 TATGTGGATGCTCGT
18820371 TATGTGGATGCTCGT
1 TATGTGGATGCTCGT
18820386 AGATGTGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.37, T:0.40
Consensus pattern (15 bp):
TATGTGGATGCTCGT
Found at i:18824796 original size:10 final size:10
Alignment explanation
Indices: 18824783--18824817 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
18824773 TAAGAAGTCA
*
18824783 TAAGTTATGG
1 TAAGTTGTGG
18824793 TAAGTTGTGG
1 TAAGTTGTGG
18824803 TAAGTTGTGG
1 TAAGTTGTGG
18824813 TAAGT
1 TAAGT
18824818 GGTCTCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (10 bp):
TAAGTTGTGG
Found at i:18831964 original size:19 final size:19
Alignment explanation
Indices: 18831940--18832000 Score: 113
Period size: 19 Copynumber: 3.2 Consensus size: 19
18831930 GACAATGTGG
*
18831940 AAGTAGACTCGATACGGTT
1 AAGTAGACTCGATACAGTT
18831959 AAGTAGACTCGATACAGTT
1 AAGTAGACTCGATACAGTT
18831978 AAGTAGACTCGATACAGTT
1 AAGTAGACTCGATACAGTT
18831997 AAGT
1 AAGT
18832001 CTATCCACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (19 bp):
AAGTAGACTCGATACAGTT
Found at i:18849830 original size:33 final size:33
Alignment explanation
Indices: 18849793--18849888 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
18849783 TGCAAAGGTT
18849793 AGGTATACTTTGTGTATACCA-TATGAAAAGGAA
1 AGGTATACTTTGTGTATACCACT-TGAAAAGGAA
*
18849826 AGGTATGCTTTGTGTATACCACTTGAAAAGGAA
1 AGGTATACTTTGTGTATACCACTTGAAAAGGAA
* * * *
18849859 AGGTACACTATATGTGTA-CACTTGAAAAGG
1 AGGTATACTTTGTGTATACCACTTGAAAAGG
18849889 CTATGTGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 12 0.21
33 43 0.77
34 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCACTTGAAAAGGAA
Found at i:18849902 original size:65 final size:66
Alignment explanation
Indices: 18849833--18849993 Score: 173
Period size: 66 Copynumber: 2.5 Consensus size: 66
18849823 GAAAGGTATG
* * *
18849833 CTTTGTGTATACCACTTGAAAAGGAAAGGTACACTAT-ATGTGTA-CACTTGAAAAGGCTATGTG
1 CTTTGTGTGTACAACTTGAAAAGGAAAGGTACACT-TCATGTGTACCACTTGAAAAGGCAATGTG
18849896 CA
65 CA
* ** * * * *
18849898 CTTTGTGTGTACAAATTGAAAAGGGTATGTACACTTCGTGTGTACCATTTGAAAAGGGAATGTGC
1 CTTTGTGTGTACAACTTGAAAAGGAAAGGTACACTTCATGTGTACCACTTGAAAAGGCAATGTGC
18849963 A
66 A
* * * *
18849964 CCTCGGGTGTACAACTAGAAAAGGAAAGGT
1 CTTTGTGTGTACAACTTGAAAAGGAAAGGT
18849994 CCATCGAAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
64 1 0.01
65 35 0.46
66 40 0.53
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (66 bp):
CTTTGTGTGTACAACTTGAAAAGGAAAGGTACACTTCATGTGTACCACTTGAAAAGGCAATGTGC
A
Found at i:18849920 original size:33 final size:33
Alignment explanation
Indices: 18849871--18849987 Score: 137
Period size: 33 Copynumber: 3.6 Consensus size: 33
18849861 GTACACTATA
* *
18849871 TGTGTAC-ACTTGAAAAGGCTATGTGCACTTTG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* *
18849903 TGTGTACAAATTGAAAAGGGTATGTACACTTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* * * *
18849936 TGTGTACCATTTGAAAAGGGAATGTGCACCTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* *
18849969 GGTGTACAACTAGAAAAGG
1 TGTGTACAACTTGAAAAGG
18849988 AAAGGTCCAT
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 7 0.10
33 64 0.90
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (33 bp):
TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
Found at i:18859345 original size:36 final size:36
Alignment explanation
Indices: 18859298--18859369 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
18859288 TACATAATAA
*
18859298 GTTTTCATATTATCATCTTTTAAATTTTTACCCTAT
1 GTTTTCATATTATCATCTTGTAAATTTTTACCCTAT
18859334 GTTTTCATATTATCATCTTGTAAATTTTTACCCTAT
1 GTTTTCATATTATCATCTTGTAAATTTTTACCCTAT
18859370 CTTGCACCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (36 bp):
GTTTTCATATTATCATCTTGTAAATTTTTACCCTAT
Found at i:18863977 original size:26 final size:26
Alignment explanation
Indices: 18863939--18863998 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
18863929 TGCAACTAAT
* *
18863939 GCCTGCTACATATACAAC-GGCACAAA
1 GCCTGCTAAATATAC-ACTGACACAAA
*
18863965 GCCTTCTAAATATACACTGACACAAA
1 GCCTGCTAAATATACACTGACACAAA
18863991 GCCTGCTA
1 GCCTGCTA
18863999 CACATTAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (26 bp):
GCCTGCTAAATATACACTGACACAAA
Found at i:18870894 original size:18 final size:17
Alignment explanation
Indices: 18870871--18870910 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
18870861 TTATGTAAAG
18870871 TATATAATATGTTATTA
1 TATATAATATGTTATTA
18870888 TTATATAATATGTTATTA
1 -TATATAATATGTTATTA
18870906 TATAT
1 TATAT
18870911 CATAAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TATATAATATGTTATTA
Found at i:18871874 original size:41 final size:41
Alignment explanation
Indices: 18871817--18871929 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
18871807 GCGATATTTG
*
18871817 GGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGAATTAAATCA
1 GGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGAATAAAATCA
* * **
18871858 GGCTTT-ATGCCTAGCAAG-CTTATTGCCGGTTTATAAAATCA
1 GGCTTTGA-GCCTAGCAAGCCTT-GTGCTGGTGAATAAAATCA
* * *
18871899 GTCTTTGAGTCTAGCAGGCCTTGTGCTGGTG
1 GGCTTTGAGCCTAGCAAGCCTTGTGCTGGTG
18871930 TGTGATACAG
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
40 4 0.07
41 49 0.86
42 4 0.07
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (41 bp):
GGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGAATAAAATCA
Found at i:18878729 original size:28 final size:28
Alignment explanation
Indices: 18878689--18878815 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
18878679 CTAGTAAGTC
18878689 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGTTATATAATCAAACT
*
18878717 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTG-TTATATAATCAAACT
18878746 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGTTATATAATCAAACT
* * ** * *
18878774 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGTTATATAA-TCAAACT
18878803 CGCACACTTAGTG
1 CGCACACTTAGTG
18878816 CCAATCTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.50
29 44 0.50
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGTTATATAATCAAACT
Found at i:18878747 original size:29 final size:29
Alignment explanation
Indices: 18878689--18878816 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
18878679 CTAGTAAGTC
*
18878689 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
18878717 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
*
18878746 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
18878774 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
18878803 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18878817 CAATCTCATG
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
28 39 0.44
29 47 0.53
30 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:18878779 original size:57 final size:57
Alignment explanation
Indices: 18878688--18878815 Score: 195
Period size: 57 Copynumber: 2.2 Consensus size: 57
18878678 TCTAGTAAGT
18878688 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
18878745 TCGCACACTTAGTGTTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
18878802 CCGCACACTTAGTG
1 CCGCACACTTAGTG
18878816 CCAATCTCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (57 bp):
CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:18880727 original size:39 final size:40
Alignment explanation
Indices: 18880681--18880791 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
18880671 CGGGGTTTAG
* * *
18880681 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
18880720 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
18880760 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
18880792 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:18880751 original size:40 final size:40
Alignment explanation
Indices: 18880704--18880848 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
18880694 CTCGCACAAG
* * * * *
18880704 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
18880744 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
18880784 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
*
18880825 GCCTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
18880849 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.65
41 26 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:18882077 original size:38 final size:38
Alignment explanation
Indices: 18882035--18882110 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
18882025 CAAGAACTCC
18882035 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
18882073 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
18882111 AAAGGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:18886103 original size:50 final size:49
Alignment explanation
Indices: 18885993--18886166 Score: 242
Period size: 49 Copynumber: 3.5 Consensus size: 49
18885983 CTAGTACGCA
* *
18885993 TAGTAGCCTGCACATAGTACTACATATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
* * ** *
18886042 TAGTAGACTGCACTTAGTACTACACATGTGACCTAACCAT-CTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCAG-TACACG
*
18886092 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
*
18886141 TAGTAGCATGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
18886167 CGTGACCTCA
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
49 65 0.60
50 43 0.40
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
Found at i:18886164 original size:99 final size:99
Alignment explanation
Indices: 18885993--18886174 Score: 312
Period size: 99 Copynumber: 1.8 Consensus size: 99
18885983 CTAGTACGCA
* *
18885993 TAGTAGCCTGCACATAGTACTACATATGCGACCAATTATCCAGTACACGTAGTAGACTGCACTTA
1 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACACATAGTAGACTGCACTTA
*
18886058 GTACTACACATGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
*
18886092 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACATAGTAG-CATGCACTT
1 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACACATAGTAGAC-TGCACTT
18886156 AGTACTACACACGTGACCT
65 AGTACTACACACGTGACCT
18886175 CACAATAGAT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 1 0.01
99 77 0.99
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACACATAGTAGACTGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:18892700 original size:101 final size:100
Alignment explanation
Indices: 18892521--18892778 Score: 322
Period size: 101 Copynumber: 2.6 Consensus size: 100
18892511 AATTGATGGA
* * *
18892521 TAAGACCATGGTTGGACCATGGACATGTTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGG-CATGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTAA
* *
18892586 TGAAAAGATCATAACTAGGTTATGGCACTATGAACG
65 TGAAAAGACCATAACTAGGTTATGGCACTACGAACG
* **
18892622 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGGTGGACTATGGCATTCTGG
1 TAAGACCATGGTTGGACCATGGCA-TGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTAA
* *
18892687 TGATAAGACCATAACTAGGTTATGGCACTACGAATG
65 TGAAAAGACCATAACTAGGTTATGGCACTACGAACG
** * * * **
18892723 TAAGACCATGGCGGGGCCATGGCAATG--CATATGTAAGACTATAATTGGACTATGGC
1 TAAGACCATGGTTGGACCATGGC-ATGTTTATATGTAAGACCATAGCTGGACTATGGC
18892779 CCAAAGAAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
99 25 0.18
100 2 0.01
101 110 0.80
102 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGGCATGTTTATATGTAAGACCATAGCTGGACTATGGCATTCTAAT
GAAAAGACCATAACTAGGTTATGGCACTACGAACG
Found at i:18895489 original size:16 final size:16
Alignment explanation
Indices: 18895470--18895500 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18895460 CTTCTTCACT
18895470 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
18895486 TACTTACTTACTTAA
1 TACTCACTTACTTAA
18895501 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:18895506 original size:20 final size:20
Alignment explanation
Indices: 18895467--18895506 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18895457 AAACTTCTTC
* *
18895467 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
18895487 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
18895507 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:18895827 original size:53 final size:54
Alignment explanation
Indices: 18895719--18895952 Score: 196
Period size: 55 Copynumber: 4.4 Consensus size: 54
18895709 CATGACTTTT
* * * * * *
18895719 CATGGTCTTACGTGGTATCC-T---TT-TGAAACTTACCATTGCCATGTCTCGA
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGTCATGCCTTGG
* * *
18895768 CATGGTCTTACATTGTATCCCTGCCTTATG-AACTCACCAATGTCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGTCATGCCTTGG
* ** * * *
18895821 CATGGTCTTACATGGGA-CCTTTGCCTTATAGAAACTTATTAATGCCATGTCTTGA
1 CATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTTACCAATGTCATGCCTTGG
* ** *
18895876 CATGGTCTTACATGATATCCTTTACTTA-GAAACCTTACCAATTTCCATGCCTTGG
1 CATGGTCTTACATGGTATCCTTGCCTTATGAAA-CTTACCAATGT-CATGCCTTGG
*
18895931 CATGGACTTACATGGTATCCTT
1 CATGGTCTTACATGGTATCCTT
18895953 AAACCTTAAT
Statistics
Matches: 145, Mismatches: 29, Indels: 16
0.76 0.15 0.08
Matches are distributed among these distances:
49 18 0.12
50 1 0.01
52 2 0.01
53 46 0.32
54 10 0.07
55 66 0.46
56 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
CATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGTCATGCCTTGG
Found at i:18895886 original size:55 final size:53
Alignment explanation
Indices: 18895745--18895889 Score: 148
Period size: 53 Copynumber: 2.7 Consensus size: 53
18895735 ATCCTTTTGA
* * * * *
18895745 AACTTACCATTGCCATGTCTCGACATGGTCTTACATTGTATCCCTGCCTTATG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCCTGCCTTATG
* * * *
18895798 AACTCACCAATGTCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-CTGCCTTAT-G
* **
18895852 AAACTTATTAATGCCATGTCTTGACATGGTCTTACATG
1 -AACTCACCAATGCCATGTCTTGACATGGTCTTACATG
18895890 ATATCCTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
52 2 0.03
53 40 0.54
54 1 0.01
55 31 0.42
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCCTGCCTTATG
Found at i:18903055 original size:5 final size:5
Alignment explanation
Indices: 18903045--18903083 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
18903035 AATCAAAGCT
*
18903045 TTTTC TTTTC TTTTC TTTTC TTTTC TTTGCC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC TTT
18903084 GGGTTTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:18911883 original size:43 final size:42
Alignment explanation
Indices: 18911822--18911926 Score: 138
Period size: 43 Copynumber: 2.5 Consensus size: 42
18911812 ACCATACCAG
* * * *
18911822 TGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCGA
1 TGCCATATCCCAGATATGGTCTTACACGAAATATCATATCAA
* * *
18911864 TGCCAATAGCCCAGCTATGGTCTTACACGAAATATCGTATCAA
1 TGCC-ATATCCCAGATATGGTCTTACACGAAATATCATATCAA
18911907 TGCCATATCCCAGATATGGT
1 TGCCATATCCCAGATATGGT
18911927 GTAACACCCC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 18 0.34
43 35 0.66
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
TGCCATATCCCAGATATGGTCTTACACGAAATATCATATCAA
Found at i:18916486 original size:22 final size:21
Alignment explanation
Indices: 18916435--18916489 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
18916425 CCTAGACATA
18916435 TCCATTTCACTTTTTATTTTT
1 TCCATTTCACTTTTTATTTTT
* *
18916456 T-CATTTTTCTCTTTTTTTTTTCT
1 TCCA--TTTCACTTTTTATTTT-T
18916479 TCCATTTCACT
1 TCCATTTCACT
18916490 ACTTAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.07
21 1 0.04
22 20 0.74
23 2 0.07
24 2 0.07
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (21 bp):
TCCATTTCACTTTTTATTTTT
Found at i:18924707 original size:16 final size:16
Alignment explanation
Indices: 18924673--18924707 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18924663 TTGTTATTTT
* *
18924673 TTTATTTTATTGTTTA
1 TTTATTTTATTATTAA
18924689 TTTATTTTATTATTAA
1 TTTATTTTATTATTAA
18924705 TTT
1 TTT
18924708 TTGATGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTATTAA
Found at i:18925839 original size:23 final size:25
Alignment explanation
Indices: 18925794--18925842 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
18925784 AAAAATCCAT
*
18925794 AAAAAGTCAAAAGAAGAACGAGAAA
1 AAAAAGTCAAAAGAAGAAAGAGAAA
*
18925819 AAAAAGT-AAAA-AATAAAGAGAAA
1 AAAAAGTCAAAAGAAGAAAGAGAAA
18925842 A
1 A
18925843 GCATTGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 4 0.18
25 7 0.32
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (25 bp):
AAAAAGTCAAAAGAAGAAAGAGAAA
Found at i:18927361 original size:29 final size:28
Alignment explanation
Indices: 18927328--18927382 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
18927318 AGTTATACCA
18927328 ATTTGGCTTCGGCCCATGAATATCAGTTG
1 ATTTGGCTTCGGCCCATG-ATATCAGTTG
* *
18927357 ATTTGGCTTTGGGCCATGATATCAGT
1 ATTTGGCTTCGGCCCATGATATCAGT
18927383 ACTTCGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (28 bp):
ATTTGGCTTCGGCCCATGATATCAGTTG
Found at i:18928967 original size:99 final size:92
Alignment explanation
Indices: 18928763--18928983 Score: 237
Period size: 92 Copynumber: 2.3 Consensus size: 92
18928753 TTTGTGTGCT
* * * * *
18928763 AGTGTAAGACCATGTTTGGGACTTGGCATCCGCATTGAGACGAGTGCCAGTGTAAGACATGTCCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGACGAGAGCCAGTGTAAGACATGTCCG
* *
18928828 GGACATGCATCGGCTACGAGACATGTC
66 GGACAGGCATCGGCTACGAGACATGCC
* * *
18928855 AGTGTAAGACCATGTGTGGGACATGACATCAGCATGTAAGTACGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCAT-TAAG-ACGAGAGCCAGTGTAAGA-CATGT
* **
18928920 CTGGGACACGGCATCGGCCT-CGATGAGGGTAGCC
63 CCGGGACA-GGCATCGG-CTACGA-GA-CAT-GCC
*
18928954 AGTGTAAGACCATGTCTAGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
18928984 GACAACTTAA
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
92 31 0.29
93 3 0.03
94 16 0.15
95 12 0.11
96 10 0.09
97 4 0.04
98 1 0.01
99 29 0.27
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGACGAGAGCCAGTGTAAGACATGTCCG
GGACAGGCATCGGCTACGAGACATGCC
Found at i:18929921 original size:13 final size:13
Alignment explanation
Indices: 18929903--18929928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18929893 TGGCCGTGTG
18929903 AAAGGACACGGGC
1 AAAGGACACGGGC
18929916 AAAGGACACGGGC
1 AAAGGACACGGGC
18929929 GTGTGTCCAG
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:0.38, C:0.23, G:0.38, T:0.00
Consensus pattern (13 bp):
AAAGGACACGGGC
Found at i:18933605 original size:48 final size:48
Alignment explanation
Indices: 18933501--18933741 Score: 394
Period size: 48 Copynumber: 5.0 Consensus size: 48
18933491 TACAAGATAA
*
18933501 ATATATATGTGTGGTAAAGCCGAATGGCTAAT-TGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
18933548 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * **
18933596 ATATGTATATGTGGTAAACCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
18933644 ATATATATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
18933692 ATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
18933740 AT
1 AT
18933742 GTGTGTATAT
Statistics
Matches: 180, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
47 31 0.17
48 149 0.83
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:18933932 original size:37 final size:37
Alignment explanation
Indices: 18933882--18933991 Score: 193
Period size: 37 Copynumber: 3.0 Consensus size: 37
18933872 GGAAATATAT
18933882 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
18933919 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
18933956 TCCGGGTAAGACCCGATAACTACGTGTGGGGATTAT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
18933992 TTGAGCTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:18939079 original size:40 final size:40
Alignment explanation
Indices: 18939023--18939244 Score: 286
Period size: 40 Copynumber: 5.5 Consensus size: 40
18939013 CATTTGAATG
* *
18939023 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* * *
18939063 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* * *
18939103 TTATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
*
18939143 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* * *
18939183 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
18939223 ATACCCGGGTTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
18939245 AAACTTGGGT
Statistics
Matches: 169, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 166 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:18961523 original size:9 final size:9
Alignment explanation
Indices: 18961509--18961534 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18961499 TTTGTTTGCC
18961509 AAAATTGTT
1 AAAATTGTT
18961518 AAAATTGTT
1 AAAATTGTT
18961527 AAAATTGT
1 AAAATTGT
18961535 GTTTATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (9 bp):
AAAATTGTT
Found at i:18968590 original size:42 final size:42
Alignment explanation
Indices: 18968543--18968628 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
18968533 CCTCGTGAAT
18968543 CTGACTTTCTCTCAGCTCAGTCCAATATAAGGGCGTTCGACA
1 CTGACTTTCTCTCAGCTCAGTCCAATATAAGGGCGTTCGACA
18968585 CTGACTTTCTCTCAGCTCAGTCCAATATAAGGGCGTTCGACA
1 CTGACTTTCTCTCAGCTCAGTCCAATATAAGGGCGTTCGACA
18968627 CT
1 CT
18968629 TTTGCCTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (42 bp):
CTGACTTTCTCTCAGCTCAGTCCAATATAAGGGCGTTCGACA
Found at i:18974229 original size:47 final size:48
Alignment explanation
Indices: 18974160--18974284 Score: 168
Period size: 47 Copynumber: 2.7 Consensus size: 48
18974150 GGTAAAGTGC
* *
18974160 CGATGCCATGTCCCAGACATGGTCTTACCCTGTCTCA-CATCTC-AAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGAAGT
* * *
18974207 CGATGCCATATCCTAGACATGGTCTTACACTGACTATCATCTCGTAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGAAGT
18974255 CGATG-CATGTCCCAGACAT-GTCTTACACTG
1 CGATGCCATGTCCCAGACATGGTCTTACACTG
18974285 GCTTACGTCT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
46 12 0.17
47 49 0.71
48 8 0.12
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGAAGT
Found at i:18974306 original size:46 final size:46
Alignment explanation
Indices: 18974255--18974380 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 46
18974245 ATCTCGTAGT
* *
18974255 CGATGCATGTCCCAGACATGTCTTACACTGGC-TTACGTCTTGAG-GC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTT-AGTGC
* **
18974301 TGATGCATGTCTAAGACATGTCTTACACTAGCACTCGTCTTAGTGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTTAGTGC
*
18974347 CGATGCCATGTCCCGGACATCGTCTTACACTAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGC
18974381 TCACGCAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.03
46 40 0.60
47 12 0.18
48 13 0.19
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTTAGTGC
Found at i:18978281 original size:46 final size:46
Alignment explanation
Indices: 18978228--18978403 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
18978218 TGGTTGAGCA
18978228 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
18978274 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
18978319 CATCCAAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
18978367 -CTCGAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18978404 GCGGGTTACT
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 58 0.55
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:18978384 original size:93 final size:93
Alignment explanation
Indices: 18978225--18978396 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
18978215 AGATGGTTGA
* * * *
18978225 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGTCCGAACTCATTGAGT
18978290 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
18978318 GCATCCAAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACG-CTCGAGCTCATTGAG
1 GCATCCAAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGTC-CGAACTCATTGAG
*
18978382 TTGAGTCTGAGTTCG
65 TTGAGTCCGAGTTCG
18978397 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGTCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:18985338 original size:30 final size:30
Alignment explanation
Indices: 18985292--18985348 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
18985282 ATCCCGAGCC
18985292 TAGGGGCAAAAATGTAAATATGCAAAAGTT
1 TAGGGGCAAAAATGTAAATATGCAAAAGTT
* * * *
18985322 TAGGGGTAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAAATGTAAATATGCAAAA
18985349 ATTTGAGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATGCAAAAGTT
Found at i:18985821 original size:46 final size:46
Alignment explanation
Indices: 18985771--18985946 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
18985761 TGGTTGAGCA
*
18985771 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
18985817 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
18985862 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
18985910 CCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
18985947 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:18985927 original size:93 final size:93
Alignment explanation
Indices: 18985768--18985938 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
18985758 GTATGGTTGA
* * * *
18985768 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
18985833 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
18985861 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
18985926 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
18985939 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.