Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 157 of 770
Found at i:46090191 original size:19 final size:19
Alignment explanation
Indices: 46090169--46090211 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
46090159 GGGACACGAG
46090169 CGTGTCCATAGCACACGGT
1 CGTGTCCATAGCACACGGT
46090188 CGTGTCCATAGCACACGGT
1 CGTGTCCATAGCACACGGT
46090207 CGTGT
1 CGTGT
46090212 GCTCTATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (19 bp):
CGTGTCCATAGCACACGGT
Found at i:46096516 original size:47 final size:45
Alignment explanation
Indices: 46096446--46096754 Score: 214
Period size: 47 Copynumber: 6.7 Consensus size: 45
46096436 GATTTGTGCT
* * *
46096446 CCAGTGTAAGACATGTCTAGGACATGCTTCGGCCACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGAGAG
**
46096492 CCAGTGTAAGATCATGTCTGGGACATGGCATCGG-CATCCAGACAATG-G
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA--CAGATGA-GAG
* * * * *
46096540 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGAGAG
* * * *
46096586 CCAGTGTAAGACCATGTCTGGGACATGGCAACGACACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACAGATGAGAG
* * *
46096634 CCAGTGTAAGACATGTTTGGGACATGCATCAGCCTCGACAGA-GATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GGC-C-ACAGATGAGAG
* * ** * * * * *
46096681 CTAGTATAAGATGTGTTTGGGACACGCATCGGCTA-AGA-GTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATG-AGAG
*
46096725 CTAGTGTAAGACATGTCTGGGACATGCATC
1 CCAGTGTAAGACATGTCTGGGACATGCATC
46096755 AACACGCGTA
Statistics
Matches: 207, Mismatches: 42, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
43 4 0.02
44 27 0.13
45 1 0.00
46 36 0.17
47 89 0.43
48 44 0.21
49 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (45 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGAGAG
Found at i:46096609 original size:94 final size:93
Alignment explanation
Indices: 46096448--46096808 Score: 335
Period size: 94 Copynumber: 3.9 Consensus size: 93
46096438 TTTGTGCTCC
* * * * * *
46096448 AGTGTAAGACATGTCTAGGACATGCTTCGGCCACATTATGAGAGCCAGTGTAAGATCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGG
*
46096513 GACATGGCATCGGCATCCAGACAATG-GCT
66 GACATGGCATCGGCAT-CAGA-GATGTGCT
*
46096542 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGG
* * *
46096607 GACATGGCAACGACA-CAGAGATGAGTGCC
66 GACATGGCATCGGCATCAGAGAT--GTGCT
* * * **
46096636 AGTGTAAGACATGTTTGGGACATGCATCAGCC-TCGAC-A-GAGATAGCTAGTATAAGA-TGTGT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTATGAG--AGCCAGTGTAAGACCATGT
* * * *
46096697 TTGGGACA-CGCATCGGC-TAAGAGTTGTGCT
62 CTGGGACATGGCATCGGCATCAGAGATGTGCT
* * * * *
46096727 AGTGTAAGACATGTCTGGGACATGCATCAACACGCGTA-TATGAGAGCTAGTGTAAGACCATATA
1 AGTGTAAGACATGTCTGGGACATGCATC-A-GC-CATACTATGAGAGCCAGTGTAAGACCATGTC
46096791 TGGGACATGGCATCGGCA
63 TGGGACATGGCATCGGCA
46096809 CTATATCCCA
Statistics
Matches: 218, Mismatches: 32, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
91 33 0.15
92 17 0.08
93 27 0.12
94 127 0.58
95 14 0.06
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGGCATCAGAGATGTGCT
Found at i:46097679 original size:13 final size:13
Alignment explanation
Indices: 46097661--46097685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46097651 GGGCAAGAGA
46097661 CTCGGCCATGTGT
1 CTCGGCCATGTGT
46097674 CTCGGCCATGTG
1 CTCGGCCATGTG
46097686 AATGACACGA
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:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (13 bp):
CTCGGCCATGTGT
Found at i:46101618 original size:12 final size:11
Alignment explanation
Indices: 46101586--46101619 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
46101576 AGCCCACTAG
46101586 TATTAATTTTTA
1 TATT-ATTTTTA
*
46101598 TGTTATTTTTA
1 TATTATTTTTA
46101609 TATTATTTTTA
1 TATTATTTTTA
46101620 AATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:46113155 original size:22 final size:22
Alignment explanation
Indices: 46113129--46113174 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
46113119 ACACTTTATC
46113129 TTAA-TTAAAAACAAATATTCAA
1 TTAATTTAAAAACAAATA-TCAA
* *
46113151 TTAATTTATAAACATATATCAA
1 TTAATTTAAAAACAAATATCAA
46113173 TT
1 TT
46113175 CATAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATTTAAAAACAAATATCAA
Found at i:46115200 original size:15 final size:16
Alignment explanation
Indices: 46115170--46115203 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46115160 TTTGTCATCT
46115170 TTTACACTAATTACTA
1 TTTACACTAATTACTA
*
46115186 TTTAC-CTATTTACTA
1 TTTACACTAATTACTA
46115201 TTT
1 TTT
46115204 TAACCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTACACTAATTACTA
Found at i:46118798 original size:40 final size:41
Alignment explanation
Indices: 46118711--46118811 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 41
46118701 ACTACTAAAG
* * * *
46118711 TAAAAAAAAAGAAAAAAAATAAAATTGAACCAATTTACAAGA
1 TAAAATAAAAGAAAATAAA-AAAATTGAACAAATTTACAAAA
* *
46118753 T--AATAAAAGAAAATAAAAAAATTTAATAAATTTA-AAAA
1 TAAAATAAAAGAAAATAAAAAAATTGAACAAATTTACAAAA
*
46118791 TAAAATAAAATAAAATAAAAA
1 TAAAATAAAAGAAAATAAAAA
46118812 CAAATTGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.08
39 14 0.28
40 31 0.62
42 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (41 bp):
TAAAATAAAAGAAAATAAAAAAATTGAACAAATTTACAAAA
Found at i:46119065 original size:15 final size:16
Alignment explanation
Indices: 46119045--46119078 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46119035 GTTAGTAATT
*
46119045 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
46119060 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
46119076 AAT
1 AAT
46119079 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:46131593 original size:9 final size:9
Alignment explanation
Indices: 46131579--46131609 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
46131569 AATTTGTGAA
46131579 AAATAAAAT
1 AAATAAAAT
46131588 AAATAAAAT
1 AAATAAAAT
46131597 AAATAAAAAT
1 AAAT-AAAAT
46131607 AAA
1 AAA
46131610 GAACACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:46132357 original size:21 final size:21
Alignment explanation
Indices: 46132333--46132379 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
46132323 CTCGGTGTTG
46132333 TGACATAGGATTCCTATGTCA
1 TGACATAGGATTCCTATGTCA
* *
46132354 TGACATAGGATTCCTGTGTCG
1 TGACATAGGATTCCTATGTCA
46132375 TGACA
1 TGACA
46132380 CAGGCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (21 bp):
TGACATAGGATTCCTATGTCA
Found at i:46134375 original size:48 final size:48
Alignment explanation
Indices: 46134319--46134498 Score: 261
Period size: 48 Copynumber: 3.8 Consensus size: 48
46134309 ATATGAGAGT
*
46134319 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGTTACGTGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGC
*
46134367 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTACGTGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGC
* * * * * * *
46134415 TACTGTAAGACCATGTCTGGTACATGGCATCGGTATCGTTATGTAAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGC
* *
46134463 CAGTGTAAGACCATGTCTGAGACATGGCATCAGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
46134499 GAGGTGTCGT
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGTTACGTGAGC
Found at i:46134577 original size:43 final size:42
Alignment explanation
Indices: 46134317--46134578 Score: 123
Period size: 48 Copynumber: 5.7 Consensus size: 42
46134307 CGATATGAGA
** *
46134317 GTCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGTTACGTGA
1 GTCA-TGTAAGACCATGTCTGGGACATGGCATCAGCA-TG--A-G-GT
* * * *
46134365 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTACGT
1 GTCA-TGTAAGACCATGTCTGGGACATGGCATCAGCA-TG--AGGT
* * * * *
46134411 GAGCTACTGTAAGACCATGTCTGGTACATGGCATCGGTATCGTTATGT
1 G-TC-A-TGTAAGACCATGTCTGGGACATGGCATCAGCAT-G--AGGT
* *
46134459 AAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATGAGGT
1 --GTCA-TGTAAGACCATGTCTGGGACATGGCATCAGCATGAGGT
* * * *
46134504 GTCGTGTAAGACCATAG-CTGGGCCATTGGCATC-GATATGAGATT
1 GTCATGTAAGACCAT-GTCTGGGACA-TGGCATCAG-CATGAG-GT
* *
46134548 TTCATGTAAGACCATGTATGGGACATGGCAT
1 GTCATGTAAGACCATGTCTGGGACATGGCAT
46134579 TAGTACAATA
Statistics
Matches: 176, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
42 18 0.10
43 22 0.12
44 20 0.11
45 3 0.02
46 2 0.01
47 3 0.02
48 106 0.60
49 1 0.01
50 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (42 bp):
GTCATGTAAGACCATGTCTGGGACATGGCATCAGCATGAGGT
Found at i:46140985 original size:46 final size:46
Alignment explanation
Indices: 46140930--46141302 Score: 390
Period size: 48 Copynumber: 7.9 Consensus size: 46
46140920 GGCGATATGA
* * *
46140930 GAGCCAGTGTAAGACCATGTCTGGGCCATGGCATCGGCCTAGATAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
* * *
46140976 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
* **
46141022 GTA-TCAGTGTAAGACCATG-CTTGGGACATGGCATCGGCACCAGTATAT
1 G-AGCCAGTGTAAGACCATGTC-TGGGACATGGCATCGGCA-TTG-ATAT
* * *
46141070 GCGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGACATTGTTAGT
1 --GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA-T
* * *
46141119 GAGCCAGTGTAAGACCATGTCTGGGATATGGCATCGACATTGTTACGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA--T
* * * * *
46141167 GAGCCAGTGTAACAACATGTTTGGGACATGGCATTGGCATTGTTACAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG--ATAT
* * * * *
46141215 GAGCCAGTGTAAGACCATGTCTGGGACATGGTATCAGTATCGTTAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
46141261 GTAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 G--AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
46141303 GAGGCATCGT
Statistics
Matches: 276, Mismatches: 37, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.00
46 79 0.29
47 44 0.16
48 115 0.42
49 3 0.01
50 33 0.12
51 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (46 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
Found at i:46145937 original size:27 final size:28
Alignment explanation
Indices: 46145876--46145948 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
46145866 TAAAAACTTG
46145876 TACAGCACTAAGTGTGCGAGTTTGATCA
1 TACAGCACTAAGTGTGCGAGTTTGATCA
* *
46145904 TGCAGCACTAAGTGTGCGAG-TTGATTA
1 TACAGCACTAAGTGTGCGAGTTTGATCA
*
46145931 TATAGCACTAAGTGTGCG
1 TACAGCACTAAGTGTGCG
46145949 GACTCACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
TACAGCACTAAGTGTGCGAGTTTGATCA
Found at i:46145959 original size:27 final size:27
Alignment explanation
Indices: 46145907--46145960 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
46145897 TTGATCATGC
* * *
46145907 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
46145934 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
46145961 GCTTTTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:46167198 original size:46 final size:46
Alignment explanation
Indices: 46167131--46167305 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
46167121 TGTAACCCGC
* *
46167131 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* **
46167177 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTT-ATAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG--GAC--GTTCGCAT
* * *
46167226 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
46167269 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
46167306 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 3 0.03
45 2 0.02
46 90 0.83
47 2 0.02
48 3 0.03
49 2 0.02
50 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:46167250 original size:92 final size:93
Alignment explanation
Indices: 46167139--46167309 Score: 308
Period size: 92 Copynumber: 1.8 Consensus size: 93
46167129 GCCCATAAGT
* *
46167139 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46167204 CGAGTTC-GATGCCTAGTTATATCTCAC
66 CGAGTTCGGATGCCTAGTTATATCTCAC
*
46167231 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
46167296 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
46167310 CAAATATCCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 69 0.92
93 6 0.08
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTATATCTCAC
Found at i:46167324 original size:46 final size:45
Alignment explanation
Indices: 46167182--46167324 Score: 139
Period size: 46 Copynumber: 3.1 Consensus size: 45
46167172 CGCATCCATA
* *
46167182 AGTGAACTCGGACTCAACTCAACGAGTTC-GATGCCTAGTTATATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ATATCCC
* * * ** *
46167229 A-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTC-GCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCC--C
46167274 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AATATCCC
46167320 AGTGA
1 AGTGA
46167325 CATGTCACTT
Statistics
Matches: 76, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
43 3 0.04
45 1 0.01
46 63 0.83
47 5 0.07
48 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCCC
Found at i:46169577 original size:53 final size:53
Alignment explanation
Indices: 46169516--46169622 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
46169506 ATTAAGCAAG
46169516 TTAGTCACATATTTCACATGTACATCAAATAAACATGGATGAGCTCATCATGC
1 TTAGTCACATATTTCACATGTACATCAAATAAACATGGATGAGCTCATCATGC
46169569 TTAGTCACATATTTCACATGTACATCAAATAAACATGGATGAGCTCATCATGC
1 TTAGTCACATATTTCACATGTACATCAAATAAACATGGATGAGCTCATCATGC
46169622 T
1 T
46169623 ACAAAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (53 bp):
TTAGTCACATATTTCACATGTACATCAAATAAACATGGATGAGCTCATCATGC
Found at i:46170236 original size:11 final size:11
Alignment explanation
Indices: 46170213--46170247 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
46170203 CGGCCCGCCC
46170213 ATATTATTTTTT
1 ATATTA-TTTTT
46170225 ATATTATTTTT
1 ATATTATTTTT
46170236 ATATTATTTTT
1 ATATTATTTTT
46170247 A
1 A
46170248 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:46170406 original size:31 final size:30
Alignment explanation
Indices: 46170369--46170429 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
46170359 ACTTAACAAG
46170369 CAAATG-CTTCTAAAATAATAATAAAAATTAA
1 CAAATGCCTT-TAAAATAATAA-AAAAATTAA
*
46170400 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
46170430 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.29
31 17 0.61
32 3 0.11
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:46200143 original size:50 final size:51
Alignment explanation
Indices: 46200027--46200264 Score: 228
Period size: 51 Copynumber: 4.7 Consensus size: 51
46200017 ATTGTGAGAA
* * * * *
46200027 CACATGTGTAGTACTATGTGCAGGCCACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGTTCAAGATAG-CTTAGGT
* * * * *
46200079 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATAG-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGTTCAAGATAGCTTAGGT
* * * * *
46200129 CACATGTGTAGTACTAAGTGCAGGCTATTATGTGTATC-CGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGT-TCAAGATAGCTTAGGT
* ** *
46200180 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
1 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGTTCAAGATAGCTTAGGT
* * * * *
46200231 CACAAGTGTGGTACTATGTGAAGGCCACTTTGTG
1 CACATGTGTAGTACTAAGTGCAGGCCACTATGTG
46200265 AAGAAGGTAG
Statistics
Matches: 155, Mismatches: 28, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
50 43 0.28
51 77 0.50
52 35 0.23
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGGCCACTATGTGTTCAAGATAGCTTAGGT
Found at i:46200276 original size:51 final size:51
Alignment explanation
Indices: 46200027--46200309 Score: 205
Period size: 51 Copynumber: 5.5 Consensus size: 51
46200017 ATTGTGAGAA
* * * * *
46200027 CACATGTGTAGTACTATGTGCAGGCCACTATGTGTTTAAA-ATGGTTTTAGGT
1 CACAAGTGTGGTACTATGTGCAGGCCACTATGTG-TAAAAGATAGCTTT-GGT
** * * * * *** *
46200079 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATAG-TTAGGT
1 CACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
* * * * * *** * *
46200129 CACATGTGTAGTACTAAGTGCAGGCTATTATGTGTATCCGATAGCTTCGAT
1 CACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
* *
46200180 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
1 CACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
* * * *
46200231 CACAAGTGTGGTACTATGTGAAGGCCACTTTGTG-AAGAAGGTAGCTTT-GA
1 CACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAA-AAGATAGCTTTGGT
* *
46200281 CTATAAGGGTGGTACTATGTGCAGGCCAC
1 C-ACAAGTGTGGTACTATGTGCAGGCCAC
46200310 CGAGCATCTA
Statistics
Matches: 193, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
50 45 0.23
51 115 0.60
52 33 0.17
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (51 bp):
CACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
Found at i:46203988 original size:42 final size:42
Alignment explanation
Indices: 46203941--46204032 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
46203931 AGACACGGGT
* * *
46203941 ATGTGTCTCAGCCGTGTGAAACACAAGGCCCAACAGATGGGC
1 ATGTGTCTCAGCCATGTGAAACACAAGACCCAACACATGGGC
* * *
46203983 ATGTGTCTCAGTCATGTGAAACACACGACCCAACACATGGGT
1 ATGTGTCTCAGCCATGTGAAACACAAGACCCAACACATGGGC
*
46204025 GTGTGTCT
1 ATGTGTCT
46204033 TGACCGTGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (42 bp):
ATGTGTCTCAGCCATGTGAAACACAAGACCCAACACATGGGC
Found at i:46206629 original size:14 final size:13
Alignment explanation
Indices: 46206601--46206633 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
46206591 TAAGTTTGTG
46206601 ATGG-AATGAATT
1 ATGGTAATGAATT
46206613 ATGGTAATGAGATT
1 ATGGTAATGA-ATT
46206627 ATGGTAA
1 ATGGTAA
46206634 ATTACGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 5 0.26
14 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (13 bp):
ATGGTAATGAATT
Found at i:46218069 original size:27 final size:27
Alignment explanation
Indices: 46218038--46218129 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
46218028 AATTATCACG
*
46218038 TGTTTCATGTCTCGTCAAACTATCCTA
1 TGTTTAATGTCTCGTCAAACTATCCTA
46218065 TGTTTAATGTCTCGTCAAACTAT-CT-
1 TGTTTAATGTCTCGTCAAACTATCCTA
* * *
46218090 TGTATTCAATATCTCGTCAAAATATCTTA
1 TGT-TT-AATGTCTCGTCAAACTATCCTA
46218119 TGTTTAATGTC
1 TGTTTAATGTC
46218130 CCATAGGACT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.05
26 4 0.07
27 43 0.77
28 3 0.05
29 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (27 bp):
TGTTTAATGTCTCGTCAAACTATCCTA
Found at i:46218267 original size:45 final size:45
Alignment explanation
Indices: 46218213--46218321 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
46218203 TTTTTCAGGC
*
46218213 ATGGCCTTACTCATTTTTGTCATGATGCCATAACATCTTTCAAAT
1 ATGGTCTTACTCATTTTTGTCATGATGCCATAACATCTTTCAAAT
* * ** * * **
46218258 ATGGTCTTACTCACTTTTATTTTGATGCCATAACATTTTTTAGCT
1 ATGGTCTTACTCATTTTTGTCATGATGCCATAACATCTTTCAAAT
* *
46218303 ATGGTCATACTCTTTTTTG
1 ATGGTCTTACTCATTTTTG
46218322 GCGTATAGCC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (45 bp):
ATGGTCTTACTCATTTTTGTCATGATGCCATAACATCTTTCAAAT
Found at i:46224100 original size:15 final size:15
Alignment explanation
Indices: 46224030--46224103 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
46224020 CATAGTATCG
*
46224030 TATCTTGGGTTTCTT
1 TATCTTGGATTTCTT
* *
46224045 TATCCT-GATCTCTT
1 TATCTTGGATTTCTT
46224059 TAT-TTGGATTTCTT
1 TATCTTGGATTTCTT
* *
46224073 TAT-TCTGGGTTTCTC
1 TATCT-TGGATTTCTT
46224088 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
46224103 T
1 T
46224104 GTTCGGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
13 1 0.02
14 20 0.43
15 25 0.53
16 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.58
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:46226658 original size:45 final size:45
Alignment explanation
Indices: 46226501--46226674 Score: 208
Period size: 45 Copynumber: 3.8 Consensus size: 45
46226491 GTTTGGGCAT
*
46226501 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAG
*** * * *
46226546 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-G-CAT
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAAG
*
46226594 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAG
*
46226639 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46226675 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 38 0.35
46 32 0.30
47 31 0.29
48 1 0.01
49 2 0.02
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAAG
Found at i:46234873 original size:40 final size:40
Alignment explanation
Indices: 46234828--46234994 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
46234818 CGGAATATAA
46234828 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
46234868 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
46234908 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
46234948 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
46234987 CCGGATAT
1 CCGGATAT
46234995 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:46240806 original size:29 final size:29
Alignment explanation
Indices: 46240774--46240851 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
46240764 ATACCCTCCG
** *
46240774 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
46240803 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
46240832 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
46240852 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:46251005 original size:27 final size:26
Alignment explanation
Indices: 46250958--46251033 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
46250948 ATCAGTCAAT
* * *
46250958 AGATATTGTGACAAAGTCACCTGATAC
1 AGATATTGTGGCAAAGCCACCAGA-AC
* *
46250985 AGATATTGTGGCAGAGCCACCAGAAT
1 AGATATTGTGGCAAAGCCACCAGAAC
*
46251011 AGATATTTGTGGCATAGCCACCA
1 AGATA-TTGTGGCAAAGCCACCA
46251034 AAACGCTTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.14
27 36 0.86
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (26 bp):
AGATATTGTGGCAAAGCCACCAGAAC
Found at i:46251385 original size:81 final size:81
Alignment explanation
Indices: 46251260--46251533 Score: 367
Period size: 81 Copynumber: 3.4 Consensus size: 81
46251250 GGGGTAAAAT
* * * * *
46251260 GGTAATTTTACCCCACAAGGGTATCTTGA-TAATTCTACCTTACAGAGGTATTTCAGTAATTCTA
1 GGTAATTCTACCCTACAAGGGTAT-TTCAGTAATTCTACCCTACAGAGGTATTTTAGTAATTCTA
*
46251324 CCCTACAGGGGTATTTC
65 CCCTATAGGGGTATTTC
* * *
46251341 GGTAATTCTACCTTAC-AGGAGTATTTTAGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTA
1 GGTAATTCTACCCTACAAGG-GTATTTCAGTAATTCTACCCTACAGAGGTATTTTAGTAATTCTA
46251405 CCCTATAGGGGTATTTC
65 CCCTATAGGGGTATTTC
* *
46251422 GGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACA-AGGGTATTTTAGTAATTCTA
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGA-GGTATTTTAGTAATTCTA
* *
46251486 CCCTATAGTGGTATTTT
65 CCCTATAGGGGTATTTC
*
46251503 AGTAATTCTACCC-ACAAGGGTATTTCAGTAA
1 GGTAATTCTACCCTACAAGGGTATTTCAGTAA
46251534 ATTTACAAAT
Statistics
Matches: 171, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
80 23 0.13
81 145 0.85
82 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (81 bp):
GGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGAGGTATTTTAGTAATTCTAC
CCTATAGGGGTATTTC
Found at i:46251536 original size:27 final size:27
Alignment explanation
Indices: 46251261--46251533 Score: 313
Period size: 27 Copynumber: 10.1 Consensus size: 27
46251251 GGGTAAAATG
* * *
46251261 GTAATTTTACCCCACAAGGGTATCTTGA
1 GTAATTCTACCCTACAAGGGTAT-TTCA
*
46251289 -TAATTCTACCTTAC-AGAGGTATTTCA
1 GTAATTCTACCCTACAAG-GGTATTTCA
* *
46251315 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
46251342 GTAATTCTACCTTAC-AGGAGTATTTTA
1 GTAATTCTACCCTACAAGG-GTATTTCA
* *
46251369 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * *
46251396 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
46251423 GTATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
46251450 GTAATTCTACCCTACAAGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
46251477 GTAATTCTACCCTA-TAGTGGTATTTTA
1 GTAATTCTACCCTACAAG-GGTATTTCA
46251504 GTAATTCTACCC-ACAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
46251530 GTAA
1 GTAA
46251534 ATTTACAAAT
Statistics
Matches: 213, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.10
27 188 0.88
28 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:46251549 original size:27 final size:27
Alignment explanation
Indices: 46251519--46252092 Score: 585
Period size: 27 Copynumber: 21.7 Consensus size: 27
46251509 TCTACCCACA
*
46251519 AGGGTATTTCAGTAAATTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
46251546 AGGGTATTTCAGTAATTTTGCAAA-CTA
1 AGGGTATTTCAGTAATTTTACAAATC-G
*
46251573 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
46251600 AGGGTATTTCAGTAATTTTAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * *
46251626 ATGGTATTTC-GATAACTTTATAAACCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
* * *
46251653 GGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
* *
46251680 AGGGTGTTTCAGTAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAATCG
*
46251707 AGGGTATTTCAGTAATTTTA-TAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
** * * *
46251733 ATAGTATTTCGGTAATTTTATAAA-CT
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
46251759 A-GGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
46251785 AGGGTATTTCAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
46251812 AGGGTATTTCAGTAATTTTACAAA-CTG
1 AGGGTATTTCAGTAATTTTACAAATC-G
* *
46251839 AGGGTATTTCGGTAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAATCG
46251866 AGGGTATTTCAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
46251893 AGGGTATTTCAGTAATTTTGCAAATTG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
46251920 AGGG----T-AGTAATTTTATAAACCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * *
46251942 GGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
* *
46251969 AGGGTATTTTAATAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*
46251996 AGGGTATTTCAGTAATTTTA-TAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * *
46252022 ACGGTATTT-AGTAATTTTATAAACCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * *
46252048 GGGGTACTTT-GGTAA-TTTACAATTGG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
46252074 A-GGTATTTCAGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
46252093 GTAAACTAAA
Statistics
Matches: 453, Mismatches: 70, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
22 16 0.04
23 1 0.00
24 3 0.01
25 34 0.08
26 92 0.20
27 302 0.67
28 5 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:46256207 original size:65 final size:65
Alignment explanation
Indices: 46256121--46256259 Score: 251
Period size: 65 Copynumber: 2.1 Consensus size: 65
46256111 GAAATGGCCA
* * *
46256121 CACACGCCCGTGTGTCAGGCCATGCCAAAACTGTAGGGTACACTGACTTATCAACACGGCCAAGT
1 CACATGCCCATGTGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGT
46256186 CACATGCCCATGTGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGT
1 CACATGCCCATGTGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGT
46256251 CACATGCCC
1 CACATGCCC
46256260 GTATGCTAGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (65 bp):
CACATGCCCATGTGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGT
Found at i:46256271 original size:65 final size:65
Alignment explanation
Indices: 46256133--46256274 Score: 241
Period size: 65 Copynumber: 2.2 Consensus size: 65
46256123 CACGCCCGTG
* *
46256133 TGTCAGGCCATGCCAAAACTGTAGGGTACACTGACTTATCAACACGGCCAAGTCACATGCCCATG
1 TGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGTCACATGCCCATA
*
46256198 TGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGTCACATGCCCGTA
1 TGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGTCACATGCCCATA
46256263 TG-CTAGGCCATG
1 TGTC-AGGCCATG
46256275 TGTGACATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 1 0.01
65 72 0.99
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (65 bp):
TGTCAGGCCATGCCAAAACTATAGGGTACACTGACTTATCAACACGGCCAAGTCACATGCCCATA
Found at i:46257830 original size:42 final size:42
Alignment explanation
Indices: 46257783--46257889 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
46257773 TATTGGTCTC
46257783 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
46257825 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
46257867 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
46257890 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:46257954 original size:27 final size:28
Alignment explanation
Indices: 46257897--46257966 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
46257887 AAAATTGTAC
**
46257897 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
46257925 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
46257952 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
46257967 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:46265062 original size:42 final size:42
Alignment explanation
Indices: 46265015--46265121 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
46265005 TATTGGTCTC
46265015 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
46265057 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
46265099 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
46265122 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:46265186 original size:27 final size:28
Alignment explanation
Indices: 46265129--46265198 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
46265119 AAAATTGTAC
**
46265129 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
46265157 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
46265184 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
46265199 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:46267657 original size:23 final size:23
Alignment explanation
Indices: 46267628--46267736 Score: 89
Period size: 23 Copynumber: 4.7 Consensus size: 23
46267618 TTGATGAACA
46267628 GTAAGCTCTATTGAGCTAAAATG
1 GTAAGCTCTATTGAGCTAAAATG
* * *
46267651 GTAAGCTCTATCGAGCTGAACT-
1 GTAAGCTCTATTGAGCTAAAATG
* *
46267673 GTAAGCT-TATACGAGCTGAAATG
1 GTAAGCTCTAT-TGAGCTAAAATG
* * * *
46267696 ATAAGCTCCAATGAGCTGAAAATA
1 GTAAGCTCTATTGAGCT-AAAATG
46267720 GTAAGCTCT-TATGAGCT
1 GTAAGCTCTAT-TGAGCT
46267737 GATATATCGA
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.04
22 17 0.25
23 30 0.44
24 18 0.26
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTAAAATG
Found at i:46267712 original size:45 final size:45
Alignment explanation
Indices: 46267622--46267715 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
46267612 CCTAGGTTGA
* * *
46267622 TGAACAGTAAGCTCTATTGAGCTAAAATGGTAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTATCGAGCTAAAATGATAAGCTCAATCGAGC
* *
46267667 TGAACTGTAAGCT-TATACGAGCTGAAATGATAAGCTCCAAT-GAGC
1 TGAACAGTAAGCTCTAT-CGAGCTAAAATGATAAGCT-CAATCGAGC
46267712 TGAA
1 TGAA
46267716 AATAGTAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 3 0.07
45 36 0.86
46 3 0.07
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (45 bp):
TGAACAGTAAGCTCTATCGAGCTAAAATGATAAGCTCAATCGAGC
Found at i:46268382 original size:25 final size:25
Alignment explanation
Indices: 46268348--46268399 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
46268338 TTTGTCAAAA
46268348 ATAACTTTACAAAACATGATAAACT
1 ATAACTTTACAAAACATGATAAACT
46268373 ATAACTTTACAAAACATGATAAACT
1 ATAACTTTACAAAACATGATAAACT
46268398 AT
1 AT
46268400 CATCAAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (25 bp):
ATAACTTTACAAAACATGATAAACT
Found at i:46270151 original size:15 final size:15
Alignment explanation
Indices: 46270131--46270164 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
46270121 GGAAATAGCT
46270131 TAAAGGACCACTTTG
1 TAAAGGACCACTTTG
*
46270146 TAAAGGACCATTTTG
1 TAAAGGACCACTTTG
46270161 TAAA
1 TAAA
46270165 AGTTGTGAAA
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:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (15 bp):
TAAAGGACCACTTTG
Found at i:46272141 original size:16 final size:16
Alignment explanation
Indices: 46272122--46272152 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46272112 CTTCTTCACT
46272122 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
46272138 TACTTACTTACTTAA
1 TACTCACTTACTTAA
46272153 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:46272158 original size:20 final size:20
Alignment explanation
Indices: 46272119--46272158 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46272109 AAACTTCTTC
* *
46272119 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
46272139 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
46272159 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:46272531 original size:107 final size:110
Alignment explanation
Indices: 46272390--46272586 Score: 294
Period size: 107 Copynumber: 1.8 Consensus size: 110
46272380 ATCCTTTTGA
* *
46272390 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTT-CCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
* *
46272452 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATACCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
46272497 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
46272562 TGCCATACCTTAGCATGGTCTTACA
66 TGCCATACCTTAGCATGGTCTTACA
46272587 GGTATCCTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 42 0.53
108 7 0.09
109 7 0.09
110 23 0.29
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATACCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:46272544 original size:55 final size:52
Alignment explanation
Indices: 46272343--46272595 Score: 209
Period size: 55 Copynumber: 4.8 Consensus size: 52
46272333 TACACGGTAC
* * * *
46272343 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTTGCCTTATG-AA
*
46272392 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTT-CCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCCTTGCCTTATGAA
* * * *
46272444 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GTATCC-TTGCCTTAT-G-AA
* *
46272499 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATG-TATCCTTGCCTTATG-AA
** *
46272552 CCTTACCAATTGCCATACCTT-AGCATGGTCTTACAGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGA-CATGGTCTTACATGTATCCTT
46272596 AAACCCTAAT
Statistics
Matches: 171, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
49 38 0.22
50 1 0.01
51 2 0.01
52 39 0.23
53 11 0.06
54 16 0.09
55 62 0.36
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (52 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGTATCCTTGCCTTATGAA
Found at i:46279671 original size:16 final size:16
Alignment explanation
Indices: 46279652--46279682 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46279642 CTTCTTCACT
46279652 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
46279668 TACTTACTTACTTAA
1 TACTCACTTACTTAA
46279683 TCAATTTATT
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:46280061 original size:55 final size:53
Alignment explanation
Indices: 46279871--46280124 Score: 254
Period size: 55 Copynumber: 4.8 Consensus size: 53
46279861 ACACGGGTAC
* * * *
46279871 CTTACCATTGCCATGACTTGTCATGGTCTTACATGGTA---T-CCTT-TTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAG-AA
* *
46279920 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAA
* * *
46279973 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AA
* * * * *
46280028 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAA
46280081 CCTTACCAATTGCCATGCCTTG-CATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
46280125 AACCCTAATG
Statistics
Matches: 173, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
49 36 0.21
52 2 0.01
53 48 0.28
54 31 0.18
55 54 0.31
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAA
Found at i:46280062 original size:108 final size:109
Alignment explanation
Indices: 46279918--46280117 Score: 316
Period size: 108 Copynumber: 1.8 Consensus size: 109
46279908 ATCCTTTTGA
* *
46279918 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
46279981 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTT-GCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
46280026 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
46280091 TGCCATGCCTTGCATGGTCTTACATGG
66 TGCCATGCCTTGCATGGTCTTACATGG
46280118 TATCCTTAAC
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 23 0.27
110 11 0.13
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (109 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:46288584 original size:44 final size:44
Alignment explanation
Indices: 46288535--46288623 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
46288525 CCAAAACACG
* *
46288535 TGTCACATA-ATTATGAACTTAGACCACAACTCAATGAGCTCAGA
1 TGTCACATATATCATGAA-TCAGACCACAACTCAATGAGCTCAGA
*
46288579 TGTCACATATATCATGAATCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATATATCATGAATCAGACCACAACTCAATGAGCTCAGA
46288623 T
1 T
46288624 CACATAGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 34 0.83
45 7 0.17
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (44 bp):
TGTCACATATATCATGAATCAGACCACAACTCAATGAGCTCAGA
Found at i:46298126 original size:43 final size:43
Alignment explanation
Indices: 46298077--46298181 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
46298067 GATTACCGAG
*
46298077 ATGTGATTACATGTAAGACAATGTCTAGGACATTGGAATT-TT
1 ATGTGATTACGTGTAAGACAATGTCTAGGACATTGGAATTGTT
** * * *
46298119 ATTGTGATTGTGTGTAAGACCATGTCTGGGACATTGGCATTGTT
1 A-TGTGATTACGTGTAAGACAATGTCTAGGACATTGGAATTGTT
* *
46298163 ATATGATTTCGTGTAAGAC
1 ATGTGATTACGTGTAAGAC
46298182 CCTATCTGGG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 48 0.92
44 3 0.06
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACAATGTCTAGGACATTGGAATTGTT
Found at i:46298182 original size:43 final size:43
Alignment explanation
Indices: 46298088--46298192 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 43
46298078 TGTGATTACA
* * *
46298088 TGTAAGACAATGTCTAGGACATTGGAATTTTATTGTGATTGTG
1 TGTAAGACCATGTCTGGGACATTGGAATTTTATTATGATTGTG
*
46298131 TGTAAGACCATGTCTGGGACATTGGCATTGTTA-TATGATT-TCG
1 TGTAAGACCATGTCTGGGACATTGGAATT-TTATTATGATTGT-G
* *
46298174 TGTAAGACCCTATCTGGGA
1 TGTAAGACCATGTCTGGGA
46298193 TAGTGGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
42 1 0.02
43 50 0.93
44 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGAATTTTATTATGATTGTG
Found at i:46301176 original size:46 final size:46
Alignment explanation
Indices: 46301123--46301292 Score: 211
Period size: 46 Copynumber: 3.7 Consensus size: 46
46301113 GGCATCCGTA
46301123 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAG
* * * * * * *
46301169 CTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATATAACTAGGCATCCAAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATG-GAT-GCGA-ACGTCCAAG
*
46301216 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CAAG
46301262 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46301293 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
44 1 0.01
45 5 0.05
46 60 0.58
47 32 0.31
48 4 0.04
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAG
Found at i:46304304 original size:15 final size:15
Alignment explanation
Indices: 46304270--46304327 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
46304260 GTATCTTGGG
46304270 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
46304285 CTTCTTTATTCTAGG-
1 TTTCTTTATTCT-GGA
* *
46304300 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
46304315 TTTCTTTATTCTG
1 TTTCTTTATTCTG
46304328 TTTTCTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 6 0.18
15 21 0.64
16 6 0.18
ACGTcount: A:0.14, C:0.17, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:46304304 original size:30 final size:30
Alignment explanation
Indices: 46304268--46304334 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
46304258 TCGTATCTTG
* *
46304268 GGTTTCTTTATTC-TGGACTTCTTTATTCT
1 GGTTTCTTCAATCTTGGACTTCTTTATTCT
*
46304297 AGGTTTC-TCAATCTTGGATTTCTTTATTCT
1 -GGTTTCTTCAATCTTGGACTTCTTTATTCT
*
46304327 GTTTTCTT
1 GGTTTCTT
46304335 ATTATCTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.12, C:0.16, G:0.13, T:0.58
Consensus pattern (30 bp):
GGTTTCTTCAATCTTGGACTTCTTTATTCT
Found at i:46307107 original size:46 final size:44
Alignment explanation
Indices: 46307051--46307183 Score: 160
Period size: 46 Copynumber: 2.9 Consensus size: 44
46307041 ATATTTGGGC
46307051 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGA
* * *
46307095 ACGTCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGAGATGTAACTAGGA
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-TACGA
* *
46307144 ATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT
46307184 GCAAATGCCC
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 33 0.44
47 31 0.41
48 2 0.03
49 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGA
Found at i:46310105 original size:22 final size:22
Alignment explanation
Indices: 46310075--46310137 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
46310065 ATGGGTTAAA
46310075 GGTTAGGGTTTAAGTTTTAAGG
1 GGTTAGGGTTTAAGTTTTAAGG
* *
46310097 GGTTGGGGTTTAAGGTTT-AGG
1 GGTTAGGGTTTAAGTTTTAAGG
*
46310118 GGTTAAGGGTTTATGTTTTA
1 GGTT-AGGGTTTAAGTTTTA
46310138 TGGTTTAAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 7 0.21
22 27 0.79
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (22 bp):
GGTTAGGGTTTAAGTTTTAAGG
Found at i:46310145 original size:22 final size:22
Alignment explanation
Indices: 46310075--46310183 Score: 82
Period size: 22 Copynumber: 5.0 Consensus size: 22
46310065 ATGGGTTAAA
*
46310075 GGTT-AGGGTTTAAGTTTTAAGG
1 GGTTAAGGGTTTAAGGTTT-AGG
*
46310097 GGTT-GGGGTTTAAGGTTTAGG
1 GGTTAAGGGTTTAAGGTTTAGG
* * *
46310118 GGTTAAGGGTTTATGTTTTATG
1 GGTTAAGGGTTTAAGGTTTAGG
* * *
46310140 GTTTAA-GGTTTAGGGGTTAGG
1 GGTTAAGGGTTTAAGGTTTAGG
*
46310161 GGTT-AGGGATTTAGGGATTTAGG
1 GGTTAAGGG-TTTAAGG-TTTAGG
46310184 ATTTAGATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.01
21 23 0.33
22 41 0.59
23 5 0.07
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
GGTTAAGGGTTTAAGGTTTAGG
Found at i:46311242 original size:52 final size:52
Alignment explanation
Indices: 46311164--46311267 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
46311154 TCCAGTTAGA
*
46311164 CTCTGAGATAGAAGAGATGGCAGTGAACCAGACGGCGGCGTTGAAGGTGGGG
1 CTCTGAGATAGAAGAGATGACAGTGAACCAGACGGCGGCGTTGAAGGTGGGG
*
46311216 CTCTGAGATAGAAGAGATGACAGTGAACCAGACGGCGGCGTTGATGGTGGGG
1 CTCTGAGATAGAAGAGATGACAGTGAACCAGACGGCGGCGTTGAAGGTGGGG
46311268 TTGTGTCTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.41, T:0.16
Consensus pattern (52 bp):
CTCTGAGATAGAAGAGATGACAGTGAACCAGACGGCGGCGTTGAAGGTGGGG
Found at i:46318113 original size:40 final size:40
Alignment explanation
Indices: 46318068--46318235 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
46318058 CGGAATATAA
46318068 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
46318108 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
46318148 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
46318188 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
46318228 CCGGATAT
1 CCGGATAT
46318236 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 105 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:46330147 original size:20 final size:20
Alignment explanation
Indices: 46330122--46330180 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
46330112 TAAATATGGT
46330122 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
46330142 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
46330162 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
46330181 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:46330162 original size:11 final size:11
Alignment explanation
Indices: 46330126--46330180 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
46330116 TATGGTATGT
46330126 ATGATATGCAC
1 ATGATATGCAC
* *
46330137 ATGAAATG--T
1 ATGATATGCAC
46330146 ATGATATGCAC
1 ATGATATGCAC
*
46330157 ATGATATG--T
1 ATGATATGCAC
46330166 ATGATATGCAC
1 ATGATATGCAC
46330177 ATGA
1 ATGA
46330181 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:46330258 original size:24 final size:24
Alignment explanation
Indices: 46330231--46330373 Score: 184
Period size: 24 Copynumber: 6.0 Consensus size: 24
46330221 GAGGAAGTGA
46330231 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
46330255 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
46330279 AAAAGGGCTTATACCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* *
46330302 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
46330326 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATC
*
46330350 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
46330374 ATAATAAAGC
Statistics
Matches: 107, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
23 22 0.21
24 74 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:46330324 original size:47 final size:47
Alignment explanation
Indices: 46330231--46330373 Score: 182
Period size: 47 Copynumber: 3.0 Consensus size: 47
46330221 GAGGAAGTGA
46330231 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
* * *
46330279 AAAAGGGCTTATACCCCAGTTATAAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* *
46330326 GAAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTAT-GCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
46330374 ATAATAAAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
46 1 0.01
47 40 0.48
48 33 0.39
49 10 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:46330600 original size:31 final size:31
Alignment explanation
Indices: 46330565--46330628 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
46330555 CGTTTACAGT
46330565 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
46330596 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
46330627 AA
1 AA
46330629 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:46332442 original size:40 final size:40
Alignment explanation
Indices: 46332398--46332510 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 40
46332388 TGCTGAAAAT
* * *
46332398 TATATCTGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCCAGTAGC
* *
46332438 TATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCCAGTTGT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCCAGTAGC
* *
46332478 TAAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
46332511 AAATCGTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
39 3 0.05
40 59 0.92
41 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCCAGTAGC
Found at i:46332525 original size:40 final size:38
Alignment explanation
Indices: 46332355--46332542 Score: 146
Period size: 40 Copynumber: 4.8 Consensus size: 38
46332345 TGAGAAATTG
* * *
46332355 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGAA
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * * *
46332395 AAT-TATATCTGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
46332432 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTG-CA
** *
46332473 GTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 AATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* * *
46332512 AATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 AAT-GT-ATATCCGGGCTAAGACCCGAAGGC
46332543 CTTGGTGCGG
Statistics
Matches: 117, Mismatches: 24, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
37 4 0.03
38 2 0.02
39 6 0.05
40 103 0.88
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:46337072 original size:43 final size:42
Alignment explanation
Indices: 46336910--46337072 Score: 136
Period size: 44 Copynumber: 3.9 Consensus size: 42
46336900 CAACGCCAAT
* * * *
46336910 GTCCCAGACGTGGTCTTACATGTAATCACATATCAATGCCAC
1 GTCCCAGACGTGGTCTTACACGAAATCACATATCGATGCAAC
* * * *
46336952 TGTCCCAGAC--AGTCTTACAC-AAA-CTCATAAACGATGCCAAT
1 -GTCCCAGACGTGGTCTTACACGAAATCACAT-ATCGATG-CAAC
* * * *
46336993 GTCCTAGACATGGTCTTATACGTAAATCACAAATCGATGTCAAC
1 GTCCCAGACGTGGTCTTACACG-AAATCACATATCGATG-CAAC
*
46337037 GTCCCAAACGTGGTCTTACACGAAATCACATATCGA
1 GTCCCAGACGTGGTCTTACACGAAATCACATATCGA
46337073 AATCCTATGT
Statistics
Matches: 92, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
39 4 0.04
40 15 0.16
41 10 0.11
42 8 0.09
43 22 0.24
44 30 0.33
45 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (42 bp):
GTCCCAGACGTGGTCTTACACGAAATCACATATCGATGCAAC
Found at i:46341767 original size:22 final size:20
Alignment explanation
Indices: 46341742--46341790 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 20
46341732 GTTATGTAAG
*
46341742 TTTGATGATTTTGGCATATTGA
1 TTTGATG-TTTTGGC-TATGGA
46341764 TTTGGTATGTTTTGGCTATGGA
1 TTT-G-ATGTTTTGGCTATGGA
46341786 TTTGA
1 TTTGA
46341791 GTAGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 11 0.46
23 8 0.33
24 3 0.12
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (20 bp):
TTTGATGTTTTGGCTATGGA
Found at i:46343668 original size:49 final size:48
Alignment explanation
Indices: 46343613--46343844 Score: 239
Period size: 49 Copynumber: 4.7 Consensus size: 48
46343603 CTGGTACGCA
* *
46343613 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACTAT-CAGTACACG
* * * **
46343662 TAGTAGCTTGCACTTAGTACTACACACGTGACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AACTATCAG-TACACG
* * * * * *
46343712 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTGCGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-CTATCA-GTACACG
* * * *
46343763 TAGTAGCCTGCACTTAGTACTACACATGCAACCAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACTATC-AGTACACG
*
46343812 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
46343845 TCACAATAGC
Statistics
Matches: 148, Mismatches: 29, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
49 68 0.46
50 45 0.30
51 34 0.23
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACTATCAGTACACG
Found at i:46343835 original size:100 final size:99
Alignment explanation
Indices: 46343601--46343844 Score: 312
Period size: 100 Copynumber: 2.5 Consensus size: 99
46343591 AGCCGAAGCT
* * * * *
46343601 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGT
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACATAGT
* ** *
46343666 AGCTTGCACTTAGTACTACACACGTGACCTAACC
66 AGCCTGCACTTAGTACTACACACGCAACCTAACA
* * * * *
46343700 ATTTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAT-CAGGTGCGCAT
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCA-GTACACAT
*
46343764 AGTAGCCTGCACTTAGTACTACACATGCAACC-AACA
63 AGTAGCCTGCACTTAGTACTACACACGCAACCTAACA
46343800 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
46343845 TCACAATAGC
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
99 38 0.31
100 49 0.40
101 37 0.30
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (99 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCAGTACACATAGT
AGCCTGCACTTAGTACTACACACGCAACCTAACA
Found at i:46350084 original size:43 final size:43
Alignment explanation
Indices: 46350019--46350185 Score: 182
Period size: 43 Copynumber: 3.9 Consensus size: 43
46350009 AGCTCGTACA
* * *
46350019 ATGCC-ATATCCCAAATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACATATCG
* * * *
46350061 ATGCCACTGTCCCAGACAGGGTCTTACACT-AAATCGA-ATAAT-G
1 ATGCCAATGTCCCAAACATGGTCTTACA-TGTAATC-ACAT-ATCG
* *
46350104 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCACA-ATACA
1 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACATAT-CG
46350147 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACAT
46350186 CTTGGTAATC
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 6 0.06
43 90 0.88
44 4 0.04
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACATATCG
Found at i:46356225 original size:42 final size:42
Alignment explanation
Indices: 46356112--46356231 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
46356102 TACCGTACCA
*
46356112 ATGCCATATCCCAGATATGGTCTTACATGTAATCTGATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTGATATCG
* * * * *
46356154 ATGCTAATAGCCCAGCTATAGTCTTACACG-AAGTCTTATATCG
1 ATGC-CATATCCCAGATATGGTCTTACACGTAA-TCTGATATCG
* *
46356197 ATGCCATATCCTAGATATGGTCTTACACGTGATCT
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCT
46356232 CAGTAACCCT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTGATATCG
Found at i:46359383 original size:20 final size:22
Alignment explanation
Indices: 46359326--46359383 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
46359316 TAAATATTAG
*
46359326 TTATTAATATTTTAATTTGATT
1 TTATTATTATTTTAATTTGATT
46359348 TT-TTATATGATATTTAA-TT-ATT
1 TTATTAT-T-AT-TTTAATTTGATT
46359370 TTATTATTATTTTA
1 TTATTATTATTTTA
46359384 TTAGTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 9 0.29
23 8 0.26
24 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
TTATTATTATTTTAATTTGATT
Found at i:46363295 original size:49 final size:49
Alignment explanation
Indices: 46363004--46363299 Score: 174
Period size: 48 Copynumber: 6.2 Consensus size: 49
46362994 AGATATGTGT
* * * **
46363004 GCTAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTCGAGATATTTAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAA
* * * * * * * * *
46363052 GCCAGTGTAAGACAC-ATCTGAGACAT-GCATCAGCATTG--AGACGAGA
1 GCTAGTGTAAGAC-CTGTCTGGGACATGGCATCGGCCTCGATATATGAAA
* * * *
46363098 GCTAGTGTAAGACATGTCTGGGACAT-ACATTGGCCTCGAGATA-GACAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGA-AA
* * * * *
46363146 GCTAGTGTAAGACCTGTCTGGGACATGGCGTCAG-CTTG-T-TGTG--T
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAA
* * * *
46363190 G-TCAGTGTAAAACCTGTCTAGGACATGGCATCGACAC-CGATAGAT-AAGA
1 GCT-AGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTCGATATATGAA-A
*
46363239 GCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTC-ACTATATGAAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGA-TATATGAAA
46363288 GCTAGTGTAAGA
1 GCTAGTGTAAGA
46363300 TTTTCTAGAA
Statistics
Matches: 181, Mismatches: 48, Indels: 37
0.68 0.18 0.14
Matches are distributed among these distances:
43 1 0.01
44 27 0.15
45 1 0.01
46 34 0.19
47 4 0.02
48 62 0.34
49 50 0.28
50 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAA
Found at i:46364149 original size:17 final size:17
Alignment explanation
Indices: 46364127--46364160 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46364117 AATCTAGGCA
*
46364127 CATGCATCTATGAACCG
1 CATGCATCTACGAACCG
46364144 CATGCATCTACGAACCG
1 CATGCATCTACGAACCG
46364161 TATGTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (17 bp):
CATGCATCTACGAACCG
Found at i:46365827 original size:28 final size:27
Alignment explanation
Indices: 46365769--46365839 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
46365759 ATCCCAACAA
* *
46365769 ACTTACCCCGTGTTTATTATCCTACCAG
1 ACTTA-CCCGTGTTTACTATCCGACCAG
*
46365797 ACTTACCTCGTGTTTACTATCTCGA-CGG
1 ACTTACC-CGTGTTTACTATC-CGACCAG
*
46365825 ACTTACCCGTATTTA
1 ACTTACCCGTGTTTA
46365840 TTGTCCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 9 0.24
28 26 0.70
29 2 0.05
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.37
Consensus pattern (27 bp):
ACTTACCCGTGTTTACTATCCGACCAG
Found at i:46365881 original size:27 final size:27
Alignment explanation
Indices: 46365824--46365881 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
46365814 TATCTCGACG
* *
46365824 GACTTACCCGTATTTATTGTCCCAATG
1 GACTTACCCGTATTTACTGTCCCAATA
** * *
46365851 GACTTACTTGTATTTACTGTCTCAGTA
1 GACTTACCCGTATTTACTGTCCCAATA
46365878 GACT
1 GACT
46365882 ATCTCTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (27 bp):
GACTTACCCGTATTTACTGTCCCAATA
Found at i:46369909 original size:40 final size:39
Alignment explanation
Indices: 46369852--46370013 Score: 218
Period size: 40 Copynumber: 4.1 Consensus size: 39
46369842 GATGATAACG
* *
46369852 GGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ACTATA-TCC
*
46369892 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATATCC
*
46369932 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-AAGTACTATATCC
* *
46369972 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-CTATATCC
46370012 GG
1 GG
46370014 TTAAATCTCG
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
39 3 0.03
40 105 0.95
41 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTATATCC
Found at i:46369985 original size:80 final size:80
Alignment explanation
Indices: 46369852--46370013 Score: 240
Period size: 80 Copynumber: 2.0 Consensus size: 80
46369842 GATGATAACG
* * *
46369852 GGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCAAAGGCATTTGTGCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAG
46369917 CGAGTTA-CTATATCC
66 CGAG-TAGCTATATCC
*
46369932 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCAAAGGCATTTGTGC-AACTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTG
46369995 AGCGAGTAGCTATATCC
64 AGCGAGTAGCTATATCC
46370012 GG
1 GG
46370014 TTAAATCTCG
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
79 4 0.05
80 69 0.92
81 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
GGGCTAAGTCCCAAAGGCATTTGTGCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAG
CGAGTAGCTATATCC
Found at i:46377910 original size:40 final size:40
Alignment explanation
Indices: 46377855--46378071 Score: 332
Period size: 40 Copynumber: 5.5 Consensus size: 40
46377845 CGGATGATAA
* *
46377855 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
46377895 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
46377935 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
**
46377975 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
46378015 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
46378055 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
46378072 TACTTGGTTT
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 16 0.10
40 150 0.90
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:46386300 original size:29 final size:29
Alignment explanation
Indices: 46386267--46386398 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
46386257 GTGACGAGAT
46386267 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
46386296 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * *
46386325 TGGCACTAAATGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
46386354 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
46386383 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
46386399 GGCTTAAATT
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:46394802 original size:5 final size:5
Alignment explanation
Indices: 46394792--46394819 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
46394782 AATGCCTATC
46394792 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
46394820 AGTATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:46395784 original size:18 final size:19
Alignment explanation
Indices: 46395752--46395814 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
46395742 ATTTCTTGCT
46395752 AATTTTTTAAACTTTTATC
1 AATTTTTTAAACTTTTATC
*
46395771 AATTTTTT-ATCTTTTAT-
1 AATTTTTTAAACTTTTATC
* * *
46395788 ACATTTTTGAATATTTTTATA
1 A-ATTTTTTAA-ACTTTTATC
46395809 AATTTT
1 AATTTT
46395815 AAATTATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.39
19 9 0.25
20 11 0.31
21 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTTAAACTTTTATC
Found at i:46395822 original size:20 final size:21
Alignment explanation
Indices: 46395777--46395823 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
46395767 TATCAATTTT
* *
46395777 TTATCTTTTATACATTTTTGAA
1 TTAT-TTTTATACAATTTTAAA
46395799 -TATTTTTATA-AATTTTAAA
1 TTATTTTTATACAATTTTAAA
46395818 TTATTT
1 TTATTT
46395824 GTTGATGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTTTTATACAATTTTAAA
Found at i:46396162 original size:17 final size:17
Alignment explanation
Indices: 46396142--46396175 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46396132 AATAAGAAAA
46396142 ATTTTAAAAATATTTCT
1 ATTTTAAAAATATTTCT
* *
46396159 ATTTTAATATTATTTCT
1 ATTTTAAAAATATTTCT
46396176 TAAAATATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAAAATATTTCT
Found at i:46398611 original size:25 final size:24
Alignment explanation
Indices: 46398556--46398613 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
46398546 ATATATATGT
*
46398556 ATATAATACTAAGTAATAATAATA
1 ATATAATACCAAGTAATAATAATA
*
46398580 ATAATAATACCATGCTAATAAATAA-A
1 AT-ATAATACCAAG-TAAT-AATAATA
46398606 ATATAATA
1 ATATAATA
46398614 ATGATAGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 15 0.52
26 7 0.24
27 5 0.17
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (24 bp):
ATATAATACCAAGTAATAATAATA
Found at i:46399842 original size:39 final size:41
Alignment explanation
Indices: 46399799--46399890 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 41
46399789 GTGTGTATGA
* *
46399799 TATTTCAA-C-TATTTTTATATGTGAAATATTTCAATTAAT
1 TATTTCAATCATATGTTTATATGTGAAATATTTCAAATAAT
46399838 TATTTCAAATATCATTATGTTTATATGTGAAATATTTCAAATAAT
1 TATTTC--A-ATCA-TATGTTTATATGTGAAATATTTCAAATAAT
46399883 TATTTCAA
1 TATTTCAA
46399891 ATATACATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
39 6 0.13
41 1 0.02
42 2 0.04
43 2 0.04
45 34 0.76
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (41 bp):
TATTTCAATCATATGTTTATATGTGAAATATTTCAAATAAT
Found at i:46400052 original size:13 final size:13
Alignment explanation
Indices: 46400034--46400058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46400024 TAAAAGAGTT
46400034 ATTAATTAAAAAG
1 ATTAATTAAAAAG
46400047 ATTAATTAAAAA
1 ATTAATTAAAAA
46400059 CAAAAAAAAA
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:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:46405325 original size:21 final size:19
Alignment explanation
Indices: 46405301--46405339 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
46405291 TTTTTTAATC
*
46405301 TTCATTAAAATTATTATAACT
1 TTCA-TAAAATAATT-TAACT
46405322 TTCATAAAATAATTTAAC
1 TTCATAAAATAATTTAAC
46405340 AATTATGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCATAAAATAATTTAACT
Found at i:46407338 original size:19 final size:19
Alignment explanation
Indices: 46407305--46407341 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46407295 TAATAAATTA
**
46407305 TTTAATAATTCAATTTTAT
1 TTTAATAATAAAATTTTAT
46407324 TTTAATAATAAAATTTTA
1 TTTAATAATAAAATTTTA
46407342 AAATGATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATAATAAAATTTTAT
Found at i:46407622 original size:15 final size:15
Alignment explanation
Indices: 46407602--46407633 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46407592 CTATGTACTT
46407602 TTCACAAATTTGCAA
1 TTCACAAATTTGCAA
46407617 TTCACAAATTTGCAA
1 TTCACAAATTTGCAA
46407632 TT
1 TT
46407634 TAGTCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCACAAATTTGCAA
Found at i:46408032 original size:19 final size:20
Alignment explanation
Indices: 46408008--46408049 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
46407998 TTCAAATACT
*
46408008 AAAAAAT-ATTTATTTTTTA
1 AAAAAATAAATTATTTTTTA
46408027 AAAAAATAAATTATTTTTTA
1 AAAAAATAAATTATTTTTTA
46408047 AAA
1 AAA
46408050 TTATTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAAATAAATTATTTTTTA
Found at i:46410691 original size:79 final size:81
Alignment explanation
Indices: 46410590--46410774 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
46410580 ACGACTCGCT
** *
46410590 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGA-CTCGCACGAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TA-TGATCTCGCACGAATGCCTTC-GGATCCTAACC
* *
46410652 CGGGTTTAGTAACTT-GCA
63 CGGATATAGTAACTTAGCA
* **
46410670 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTATCTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTATGATCTCGCACGAATGCCTTCGGATCCTAACCCGG
*
46410734 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
46410750 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
46410775 CATCATTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 5 0.05
79 52 0.57
80 34 0.37
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTATGATCTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:46410715 original size:39 final size:40
Alignment explanation
Indices: 46410583--46410774 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
46410573 GGATATAACG
* * * *
46410583 ACTCGCTCAAATGCCTTCGGGAC-GAAGCCCGG-TTATAGTG
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGGATT-TAGTA
*
46410623 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
* * * *
46410663 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
* * ** * *
46410702 TCTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAGTA
* * *
46410742 ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
46410775 CATCATTCGA
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.24
40 80 0.65
41 12 0.10
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
Found at i:46418722 original size:79 final size:81
Alignment explanation
Indices: 46418621--46418805 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
46418611 ACGACTCGCT
** *
46418621 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGA-CTCGCACGAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TA-TGATCTCGCACGAATGCCTTC-GGATCCTAACC
* *
46418683 CGGGTTTAGTAACTT-GCA
63 CGGATATAGTAACTTAGCA
* **
46418701 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTATCTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTATGATCTCGCACGAATGCCTTCGGATCCTAACCCGG
*
46418765 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
46418781 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
46418806 CATCATTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 5 0.05
79 52 0.57
80 34 0.37
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTATGATCTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:46418746 original size:39 final size:40
Alignment explanation
Indices: 46418614--46418805 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
46418604 GGATATAACG
* * * *
46418614 ACTCGCTCAAATGCCTTCGGGAC-GAAGCCCGG-TTATAGTG
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGGATT-TAGTA
*
46418654 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
* * * *
46418694 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
* * ** * *
46418733 TCTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAGTA
* * *
46418773 ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
46418806 CATCATTCGA
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.24
40 80 0.65
41 12 0.10
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTA
Found at i:46421101 original size:27 final size:25
Alignment explanation
Indices: 46421041--46421101 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 25
46421031 ATCAAATCCA
* * *
46421041 AAATTAAATCACGAAAATTTAACAG
1 AAATTAATTCACCAAAATATAACAG
* *
46421066 ATATAAATTCACACAAAATATACACAG
1 AAATTAATTCAC-CAAAATATA-ACAG
46421093 AAATTAATT
1 AAATTAATT
46421102 TTTAAATATT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 9 0.33
26 7 0.26
27 11 0.41
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (25 bp):
AAATTAATTCACCAAAATATAACAG
Found at i:46422762 original size:28 final size:29
Alignment explanation
Indices: 46422695--46422795 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
46422685 ATAGTGAATC
*
46422695 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
46422724 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
46422752 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
46422782 CGCACACTTAGTGC
1 CGCACACTTAGTGC
46422796 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:46429241 original size:2 final size:2
Alignment explanation
Indices: 46429234--46429265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46429224 ATAATCCAAA
46429234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46429266 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46430423 original size:39 final size:39
Alignment explanation
Indices: 46430361--46430459 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
46430351 CATGGTCTGT
* * * * *
46430361 AGCCCGAAGTCTAGCCGAAGCACATAAGTGCTAAACGGA
1 AGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACAGA
*
46430400 AGCCCGAAGGCTAACTGATGCACACAAGTGCTAAACAGA
1 AGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACAGA
46430439 AGCCCGAAGGCTAACTGAAGC
1 AGCCCGAAGGCTAACTGAAGC
46430460 TCATCAGAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.36, C:0.26, G:0.25, T:0.12
Consensus pattern (39 bp):
AGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACAGA
Found at i:46430966 original size:40 final size:40
Alignment explanation
Indices: 46430911--46430991 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
46430901 ATCGGGCATG
*
46430911 TGATCAATTTATACACAAGTCATTCATATATATATGTATA
1 TGATCAATTTATACACAAGTCAATCATATATATATGTATA
46430951 TGATCAATTTATACACAAGTCAATCATATATATATGTATA
1 TGATCAATTTATACACAAGTCAATCATATATATATGTATA
46430991 T
1 T
46430992 TTTCCTCATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (40 bp):
TGATCAATTTATACACAAGTCAATCATATATATATGTATA
Found at i:46432905 original size:2 final size:2
Alignment explanation
Indices: 46432871--46432895 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46432861 GAACACACAC
46432871 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
46432896 GGTGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46435346 original size:81 final size:81
Alignment explanation
Indices: 46435208--46435369 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 81
46435198 ATCGTGTAAC
* **
46435208 AGCCCGATTTTGGGCCTAGTTGAAATAGTGGTTTTGAGACCACAAATCTAACAAGGAAAAATTTA
1 AGCCCAATTTTGGGCCTAGTCAAAATAGTGGTTTTGAGACCACAAATCTAACAAGGAAAAATTTA
*
46435273 TTATTATTATTATTAT
66 TTATTACTATTATTAT
* * *
46435289 AGCCCAATTTTGGGCCTAGTCAAAATAGTGGTTTTGGGACCACAAATCTGACGAGGAAAAATTTA
1 AGCCCAATTTTGGGCCTAGTCAAAATAGTGGTTTTGAGACCACAAATCTAACAAGGAAAAATTTA
46435354 TTATTACTATTATTAT
66 TTATTACTATTATTAT
46435370 TATATAATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (81 bp):
AGCCCAATTTTGGGCCTAGTCAAAATAGTGGTTTTGAGACCACAAATCTAACAAGGAAAAATTTA
TTATTACTATTATTAT
Found at i:46435359 original size:3 final size:3
Alignment explanation
Indices: 46435351--46435392 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
46435341 GAGGAAAAAT
* *
46435351 TTA TTA TTA CTA TTA TTA TTA -TA TAA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
46435393 ATTTTTATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:46435400 original size:20 final size:20
Alignment explanation
Indices: 46435356--46435394 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46435346 AAAATTTATT
*
46435356 ATTACTATTATTATTATATA
1 ATTATTATTATTATTATATA
46435376 ATTATTATTATTATTATAT
1 ATTATTATTATTATTATAT
46435395 TTTTATGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTATTATTATATA
Found at i:46438653 original size:40 final size:40
Alignment explanation
Indices: 46438608--46438775 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
46438598 CGGAATATAA
46438608 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
46438648 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
46438688 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
46438728 CCGGATATAATTTCGAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
46438768 CCGGATAT
1 CCGGATAT
46438776 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:46454674 original size:27 final size:26
Alignment explanation
Indices: 46454626--46454677 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
46454616 GCGAGACTGC
*
46454626 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
46454652 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
46454678 TTGCAGTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:46468792 original size:38 final size:39
Alignment explanation
Indices: 46468722--46468836 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 39
46468712 TGAAACTAAT
* * * *
46468722 TACCAGCAC-AAGCCTGCGGGAATTTAAACCTGG-TATAA
1 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCTGGACATAA
*
46468760 TACCAGCTCGAAGCCTGCGGGACTTTAGCCTGGACATAT
1 TACCAGCTCGAAGCCTGCGGGACTTTAGCCTGGACATAA
* * * * *
46468799 TTCTAGCTCGAAGCCTACGGTACTTTAGCCCGGACATA
1 TACCAGCTCGAAGCCTGCGGGACTTTAGCCTGGACATA
46468837 TTTCCAGCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 14 0.22
39 51 0.78
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (39 bp):
TACCAGCTCGAAGCCTGCGGGACTTTAGCCTGGACATAA
Found at i:46468807 original size:39 final size:39
Alignment explanation
Indices: 46468764--46468840 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
46468754 GTATAATACC
* *
46468764 AGCTCGAAGCCTGCGGGACTTTAGCCTGGACATATTTCT
1 AGCTCGAAGCCTACGGGACTTTAGCCCGGACATATTTCT
*
46468803 AGCTCGAAGCCTACGGTACTTTAGCCCGGACATATTTC
1 AGCTCGAAGCCTACGGGACTTTAGCCCGGACATATTTC
46468841 CAGCACGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (39 bp):
AGCTCGAAGCCTACGGGACTTTAGCCCGGACATATTTCT
Found at i:46468899 original size:39 final size:39
Alignment explanation
Indices: 46468828--46468918 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
46468818 GTACTTTAGC
* * * *
46468828 CCGGACATATTTCCAGCACGTACCCTGTGGACCTTAAGT
1 CCGGATATAATTCCAGCACATACCCTGCGGACCTTAAGT
* * *
46468867 CTGGTTATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATACCCTGCGGACCTTAAGT
46468906 CCGGATATAATTC
1 CCGGATATAATTC
46468919 ATCACTGAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATACCCTGCGGACCTTAAGT
Found at i:46473556 original size:30 final size:30
Alignment explanation
Indices: 46473501--46473631 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
46473491 ATAGTGAATC
*
46473501 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
46473530 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
46473560 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
46473588 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
46473618 CGCACACTTAGTGC
1 CGCACACTTAGTGC
46473632 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:46473611 original size:58 final size:58
Alignment explanation
Indices: 46473500--46473631 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
46473490 TATAGTGAAT
* * * * *
46473500 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
46473559 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
46473617 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
46473632 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:46481509 original size:30 final size:30
Alignment explanation
Indices: 46481454--46481584 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
46481444 ATAGTGAATC
*
46481454 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
46481483 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
46481513 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
46481541 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
46481571 CGCACACTTAGTGC
1 CGCACACTTAGTGC
46481585 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:46481564 original size:58 final size:58
Alignment explanation
Indices: 46481453--46481584 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
46481443 TATAGTGAAT
* * * * *
46481453 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
46481512 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
46481570 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
46481585 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:46485202 original size:42 final size:42
Alignment explanation
Indices: 46485095--46485249 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
46485085 TACCATACCA
* * ** **
46485095 ATGCCATATCCCATATATGGTCCTACATGGGATCTTGTATTA-
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATA-TAG
* * *
46485137 ATGCCATTAGCCCAGCTATGGTCTTACATGAAATCTCATATCG
1 ATGCCA-TATCCCAGATATGGTCTTACATGAAATCTCATATAG
* * *
46485180 ATTCCATATCCCAGATATGGTCTTACACGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATAG
46485222 ATGCCATATCCCAGATATGGTCTTACAT
1 ATGCCATATCCCAGATATGGTCTTACAT
46485250 ATAGTCTTAG
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 64 0.68
43 30 0.32
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATAG
Done.