Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 182 of 318
Found at i:56926260 original size:12 final size:10
Alignment explanation
Indices: 56926256--56926308 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 10
56926246 TTTTGAAACT
56926256 TTTTTTTGAA
1 TTTTTTTGAA
56926266 TTTTTTTTCGAA
1 -TTTTTTT-GAA
56926278 TTTTTTTCCGAA
1 TTTTTTT--GAA
56926290 TTTTTTTTGAAA
1 -TTTTTTTG-AA
56926302 TTTTTTT
1 TTTTTTT
56926309 ATACTTGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
11 22 0.58
12 9 0.24
13 7 0.18
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.70
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:56926273 original size:24 final size:24
Alignment explanation
Indices: 56926241--56926308 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 24
56926231 TGCACAAATC
*
56926241 ATTTTTTTTGAAACTTTTTTT-TGA
1 ATTTTTTTTGAAA-TTTTTTTCCGA
56926265 ATTTTTTTTCG-AATTTTTTTCCGA
1 ATTTTTTTT-GAAATTTTTTTCCGA
56926289 ATTTTTTTTGAAATTTTTTT
1 ATTTTTTTTGAAATTTTTTT
56926309 ATACTTGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 8 0.20
24 31 0.77
25 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.68
Consensus pattern (24 bp):
ATTTTTTTTGAAATTTTTTTCCGA
Found at i:56928029 original size:30 final size:30
Alignment explanation
Indices: 56927944--56928031 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
56927934 TAAACTAAAA
* *
56927944 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * * *
56927974 TAAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
56928004 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCGTGAGCTGAA
56928032 TATAAGCTAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:56929865 original size:17 final size:17
Alignment explanation
Indices: 56929835--56929889 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
56929825 AATAATTCAT
56929835 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
*
56929853 TTATTAACTAAGATGAAC
1 TTATTAACTAAGATG-AG
*
56929871 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
56929889 T
1 T
56929890 AATTTATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 11 0.34
19 13 0.41
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:56934202 original size:5 final size:5
Alignment explanation
Indices: 56934192--56934256 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
56934182 TAAATGTTGG
56934192 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
56934242 TATAT TATAT TATAT
1 TATAT TATAT TATAT
56934257 ATAATGATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:56935200 original size:30 final size:31
Alignment explanation
Indices: 56935166--56935262 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
56935156 AGCTCACTCC
*
56935166 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
56935196 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
56935226 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
56935256 TAGCTCA
1 TAGCTCA
56935263 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:56937793 original size:5 final size:5
Alignment explanation
Indices: 56937783--56937839 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
56937773 AAGAGAAAAT
*
56937783 AAAGA AAAGA AAAGA AAAGGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAA-G-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
56937830 AAAGA AAAGA
1 AAAGA AAAGA
56937840 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:56937919 original size:11 final size:12
Alignment explanation
Indices: 56937887--56937917 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56937877 TTGAGAGAAC
56937887 TTGAAAAAGCCT
1 TTGAAAAAGCCT
56937899 TTGAAAAAGCCT
1 TTGAAAAAGCCT
56937911 TTGAAAA
1 TTGAAAA
56937918 GCAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:56937983 original size:30 final size:31
Alignment explanation
Indices: 56937930--56937990 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
56937920 AAAAATAAAA
*
56937930 TGAGATTGAAAAAGAGAACG-AAAAGAAATT
1 TGAGAGTGAAAAAGAGAACGAAAAAGAAATT
*
56937960 TGAGAGTGAAAAAGA-AGATGAAAAAGAAATT
1 TGAGAGTGAAAAAGAGA-ACGAAAAAGAAATT
56937991 GAAATAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 16 0.59
31 10 0.37
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (31 bp):
TGAGAGTGAAAAAGAGAACGAAAAAGAAATT
Found at i:56939629 original size:30 final size:31
Alignment explanation
Indices: 56939595--56939691 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
56939585 AGCTCACTCC
*
56939595 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
56939625 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
56939655 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
56939685 TAGCTCA
1 TAGCTCA
56939692 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:56941209 original size:30 final size:31
Alignment explanation
Indices: 56941175--56941271 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
56941165 AGCTCACTCC
*
56941175 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
56941205 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
56941235 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
56941265 TAGCTCA
1 TAGCTCA
56941272 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:56942875 original size:46 final size:46
Alignment explanation
Indices: 56942825--56943000 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
56942815 TGGTTGAGCA
*
56942825 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
56942871 TCCGAACTCGTTGAGTTGAGTCCGAGCTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
56942916 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
56942964 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56943001 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 59 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:56950132 original size:40 final size:40
Alignment explanation
Indices: 56950048--56950272 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
56950038 TTGAATGATG
* * * *
56950048 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
56950088 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
56950128 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
56950167 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
56950208 T-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
56950248 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56950273 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 35 0.21
40 119 0.72
41 11 0.07
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:56950294 original size:119 final size:119
Alignment explanation
Indices: 56950048--56950305 Score: 294
Period size: 119 Copynumber: 2.2 Consensus size: 119
56950038 TTGAATGATG
*
56950048 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
* * **
56950113 GTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGTCACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * *
56950167 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAAT-CGGGCTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-ATCCGGACTAAGAT-CCGAAGGCA
* * *
56950229 TTTGTGCGAGTCACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
63 TTTGTGCGAGTCACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
56950287 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
56950306 TACGTGATTT
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
118 3 0.03
119 83 0.70
120 33 0.28
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTCACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:56958933 original size:56 final size:55
Alignment explanation
Indices: 56958817--56958934 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
56958807 TGCATGCTTT
* * * *
56958817 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
56958871 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
56958927 CATTAAAT
1 CATTAAAT
56958935 CAGCAAGCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:56959582 original size:20 final size:20
Alignment explanation
Indices: 56959557--56959611 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
56959547 ACGAGTTAAA
* *
56959557 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
56959577 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
56959597 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
56959612 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:56965639 original size:46 final size:45
Alignment explanation
Indices: 56965589--56965764 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
56965579 TGGTTGAGCA
56965589 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-CGAATG
* * **
56965635 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATTTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAA-T--G
*
56965680 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-CGAATG
* * **
56965728 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56965765 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATCGAATG
Found at i:56965745 original size:93 final size:93
Alignment explanation
Indices: 56965586--56965755 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
56965576 GGATGGTTGA
* * *
56965586 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
56965651 TGAGTCCGAGTTCGTGAGATTTAACTAG
66 TGAGTCCGAGTTCGTGAGATTTAACTAG
*
56965679 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
56965744 TGAGTCCGAGTT
66 TGAGTCCGAGTT
56965756 TGCTTATGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATTTAACTAG
Found at i:56982926 original size:20 final size:20
Alignment explanation
Indices: 56982879--56982926 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
56982869 AGTAAGCTCG
56982879 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
56982899 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
56982919 GTTGAGCT
1 GTTGAGCT
56982927 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:56984846 original size:21 final size:21
Alignment explanation
Indices: 56984801--56984863 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
56984791 TTTGAACCAT
* *
56984801 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
56984823 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
56984844 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
56984864 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:56985837 original size:29 final size:29
Alignment explanation
Indices: 56985771--56985827 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
56985761 GATTCAAAGA
*
56985771 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
56985800 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
56985828 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:56986620 original size:30 final size:30
Alignment explanation
Indices: 56986564--56986620 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
56986554 TGGGCTCAAA
* **
56986564 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
56986594 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
56986621 GCCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:56994327 original size:30 final size:30
Alignment explanation
Indices: 56994271--56994327 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
56994261 TGGGCTCAAA
* **
56994271 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
56994301 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
56994328 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:56995856 original size:14 final size:14
Alignment explanation
Indices: 56995814--56995858 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56995804 TTAAAGAAGC
56995814 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
56995828 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
56995841 AACTCATTTAATTA
1 AACTCATTAAATTA
56995855 AACT
1 AACT
56995859 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:56996437 original size:12 final size:12
Alignment explanation
Indices: 56996422--56996451 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
56996412 TTTTCTTTTC
56996422 TTTTTTTCAATT
1 TTTTTTTCAATT
*
56996434 TTTTTTTGAATT
1 TTTTTTTCAATT
56996446 TTTTTT
1 TTTTTT
56996452 AAACTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:57003366 original size:27 final size:27
Alignment explanation
Indices: 57003336--57003513 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
57003326 TTATTGAGCC
* *
57003336 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
57003363 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
57003390 CGCACACTTAGTGCCACATAGTCCAACT
1 CGCACACTTAGTGCTACATAAT-CAACT
** ** *
57003418 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
57003445 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
57003472 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
*
57003499 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
57003514 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 102 0.80
28 26 0.20
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:57003475 original size:82 final size:81
Alignment explanation
Indices: 57003357--57003512 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
57003347 TGCTATATAA
* *
57003357 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCCAA-TCGCA
57003422 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
57003439 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCA
*
57003503 CCCTTAGTGC
65 CACTTAGTGC
57003513 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCAC
ACTTAGTGCCGCATGG
Found at i:57004997 original size:30 final size:30
Alignment explanation
Indices: 57004963--57005059 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
57004953 AGCTCACTCC
57004963 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
57004993 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
57005023 CAGCTCAACTTTAGATCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
57005053 TAGCTCA
1 TAGCTCA
57005060 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:57013189 original size:27 final size:27
Alignment explanation
Indices: 57013159--57013336 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
57013149 TTATTGAGCC
* *
57013159 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
57013186 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
57013213 CGCACACTTAGTGCCACATAGTCCAACT
1 CGCACACTTAGTGCTACATAAT-CAACT
** ** *
57013241 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
57013268 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
57013295 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
*
57013322 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
57013337 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 102 0.80
28 26 0.20
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:57013298 original size:82 final size:81
Alignment explanation
Indices: 57013180--57013335 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
57013170 TGCTATATAA
* *
57013180 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCCAA-TCGCA
57013245 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
57013262 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCA
*
57013326 CCCTTAGTGC
65 CACTTAGTGC
57013336 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCCAATCGCAC
ACTTAGTGCCGCATGG
Found at i:57024609 original size:20 final size:22
Alignment explanation
Indices: 57024584--57024637 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
57024574 ATGAAAAAAT
*
57024584 GAAAGAAAAA-GAGTATGA-AA
1 GAAAGAAAAATGAGAATGAGAA
57024604 GAAAGAAAAATGAGAATGAGAA
1 GAAAGAAAAATGAGAATGAGAA
57024626 -AAAGAAAAATGA
1 GAAAGAAAAATGA
57024638 AATTGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 10 0.32
21 19 0.61
22 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (22 bp):
GAAAGAAAAATGAGAATGAGAA
Found at i:57024622 original size:21 final size:21
Alignment explanation
Indices: 57024584--57024645 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
57024574 ATGAAAAAAT
*
57024584 GAAAGAAAAA-GAGTATGAAA
1 GAAAGAAAAATGAGAATGAAA
57024604 GAAAGAAAAATGAGAATGAGAA
1 GAAAGAAAAATGAGAATGA-AA
57024626 -AAAGAAAAATGA-AATTGAAA
1 GAAAGAAAAATGAGAA-TGAAA
57024646 AATAAAGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 14 0.37
21 22 0.58
22 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (21 bp):
GAAAGAAAAATGAGAATGAAA
Found at i:57030602 original size:16 final size:16
Alignment explanation
Indices: 57030583--57030630 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
57030573 ATTGAACCAG
*
57030583 CCCGTGCATGAATCTT
1 CCCGTTCATGAATCTT
57030599 CCCGTTCATTGAA-CTTT
1 CCCGTTCA-TGAATC-TT
*
57030616 CCCGTTCATGCATCT
1 CCCGTTCATGAATCT
57030631 CTTCATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (16 bp):
CCCGTTCATGAATCTT
Found at i:57050323 original size:34 final size:34
Alignment explanation
Indices: 57050252--57050324 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
57050242 CATACTATAT
* *
57050252 TGAAATGGGCTAAGGCCCAGACTGCCTCTGGTAC
1 TGAAATGGGCTAAGGCCCAGACTGCATCTGATAC
* *
57050286 TGAAATGGGCTTAGGCCCAGACTG-ATACTGATTC
1 TGAAATGGGCTAAGGCCCAGACTGCAT-CTGATAC
57050320 TGAAA
1 TGAAA
57050325 AAGGGGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 1 0.03
34 33 0.97
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (34 bp):
TGAAATGGGCTAAGGCCCAGACTGCATCTGATAC
Found at i:57050696 original size:29 final size:29
Alignment explanation
Indices: 57050654--57050713 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
57050644 TATTTTTAAG
57050654 AAAGCACAAACCAATGTTTTTCTAAAATC
1 AAAGCACAAACCAATGTTTTTCTAAAATC
57050683 AAAGCACAAACCAATGTTTTTCTAAAATC
1 AAAGCACAAACCAATGTTTTTCTAAAATC
57050712 AA
1 AA
57050714 CACGCTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAGCACAAACCAATGTTTTTCTAAAATC
Found at i:57055040 original size:75 final size:75
Alignment explanation
Indices: 57054872--57055041 Score: 209
Period size: 75 Copynumber: 2.3 Consensus size: 75
57054862 CAGCAAAAGA
* * **
57054872 GTTTGTGTCCAGCCCTAGTCGGATTACTCGGTGATATTGAATGTGAGCCCAGCTCTAGTTGGATA
1 GTTTGTGCCCAGCACTAGTCGGATTACTCGACGATATTGAATGTGAGCCCAGCTCTAGTTGGATA
57054937 AACCAACAGT
66 AACCAACAGT
* * ** * *
57054947 GTTTGGGCCTAGTGCTAGTCGGCTATACT-GACGATATTGAGTGTGAGCCCAGCTCTAGTTGGAT
1 GTTTGTGCCCAGCACTAGTCGGAT-TACTCGACGATATTGAATGTGAGCCCAGCTCTAGTTGGAT
*
57055011 AAACCAATTA-T
65 AAACCAA-CAGT
57055022 GTTTGTGCCCAGCACTAGTC
1 GTTTGTGCCCAGCACTAGTC
57055042 AGTTATACCG
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
75 74 0.94
76 5 0.06
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (75 bp):
GTTTGTGCCCAGCACTAGTCGGATTACTCGACGATATTGAATGTGAGCCCAGCTCTAGTTGGATA
AACCAACAGT
Found at i:57057519 original size:13 final size:13
Alignment explanation
Indices: 57057497--57057526 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57057487 ACGAAGCGAC
57057497 ACACAACCATGCG
1 ACACAACCATGCG
*
57057510 ACACAGCCATGCG
1 ACACAACCATGCG
57057523 ACAC
1 ACAC
57057527 GGCCGTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.40, G:0.17, T:0.07
Consensus pattern (13 bp):
ACACAACCATGCG
Found at i:57063880 original size:16 final size:16
Alignment explanation
Indices: 57063859--57063894 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
57063849 TGCAACAAAT
57063859 TATGTTGGCTACTAAG
1 TATGTTGGCTACTAAG
57063875 TATGTTGGCTACTAAG
1 TATGTTGGCTACTAAG
57063891 TATG
1 TATG
57063895 GGTAGGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (16 bp):
TATGTTGGCTACTAAG
Found at i:57064266 original size:20 final size:20
Alignment explanation
Indices: 57064229--57064271 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
57064219 ATTGAAATTA
* *
57064229 AAATTACTGATTATATGATT
1 AAATTACTGATTACATGAAT
57064249 AAATTACT-ATTTACATGAAT
1 AAATTACTGA-TTACATGAAT
57064269 AAA
1 AAA
57064272 AGTGAAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
AAATTACTGATTACATGAAT
Found at i:57064622 original size:23 final size:23
Alignment explanation
Indices: 57064579--57064681 Score: 97
Period size: 23 Copynumber: 4.5 Consensus size: 23
57064569 TCAACTCGTA
*
57064579 AGAGCTTACT-ATTTTCAGCTCATT
1 AGAGCTTACTGA--TTCAGCTCAAT
* *
57064603 GGAGCTTACTGATTCAGCTC-GT
1 AGAGCTTACTGATTCAGCTCAAT
57064625 ATGAGCTTACTG-TTCAGCTCAAT
1 A-GAGCTTACTGATTCAGCTCAAT
* *
57064648 AAAGCTTAC-CATTTCAGCTCAAT
1 AGAGCTTACTGA-TTCAGCTCAAT
57064671 AGAGCTTACTG
1 AGAGCTTACTG
57064682 TTTATCAGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
22 16 0.25
23 39 0.60
24 9 0.14
25 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (23 bp):
AGAGCTTACTGATTCAGCTCAAT
Found at i:57064653 original size:22 final size:22
Alignment explanation
Indices: 57064592--57064683 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 22
57064582 GCTTACTATT
* *
57064592 TTCAGCTCATTGGAGCTTACTG
1 TTCAGCTCAATAGAGCTTACTG
*
57064614 ATTCAGCTC-GTATGAGCTTACTG
1 -TTCAGCTCAATA-GAGCTTACTG
*
57064637 TTCAGCTCAATAAAGCTTACCAT-
1 TTCAGCTCAATAGAGCTTA-C-TG
57064660 TTCAGCTCAATAGAGCTTACTG
1 TTCAGCTCAATAGAGCTTACTG
57064682 TT
1 TT
57064684 TATCAGGTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
22 18 0.31
23 39 0.66
24 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (22 bp):
TTCAGCTCAATAGAGCTTACTG
Found at i:57067271 original size:47 final size:44
Alignment explanation
Indices: 57067198--57067320 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 44
57067188 CATTTGTGTA
57067198 AGCTAGTGTAAGACATGTCTGGGACATGCATCGCCCACATT-ATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCG---ACATTGATGAG
*
57067244 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAG
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATT--GATGAG
* *
57067292 TGCTAGTGTAAGGCATGTCTGGGACATGC
1 AGCTAGTGTAAGACATGTCTGGGACATGC
57067321 TTCAGCCTCG
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 28 0.41
48 22 0.32
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (44 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGATGAG
Found at i:57069325 original size:23 final size:23
Alignment explanation
Indices: 57069299--57069413 Score: 69
Period size: 23 Copynumber: 5.0 Consensus size: 23
57069289 GAACCATATC
57069299 GGGAAGCTCACGAAAAGCCTATA
1 GGGAAGCTCACGAAAAGCCTATA
* *
57069322 GGGAAGCTC-CGGATAGCCATATA
1 GGGAAGCTCACGAAAAGCC-TATA
* * *
57069345 TCGGGAAGTTCA--AACGAGCACTATC
1 --GGGAAGCTCACGAA-AAGC-CTATA
* * *
57069370 GGGAAGCTCACAAAAAACCTATC
1 GGGAAGCTCACGAAAAGCCTATA
*
57069393 GGGAAGCTC-CGAATAG-CTATA
1 GGGAAGCTCACGAAAAGCCTATA
57069414 TATCGGGAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 18
0.70 0.13 0.18
Matches are distributed among these distances:
21 4 0.06
22 11 0.15
23 36 0.51
24 3 0.04
25 16 0.23
26 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (23 bp):
GGGAAGCTCACGAAAAGCCTATA
Found at i:57069370 original size:71 final size:71
Alignment explanation
Indices: 57069295--57069426 Score: 219
Period size: 71 Copynumber: 1.9 Consensus size: 71
57069285 CAAAGAACCA
* * *
57069295 TATCGGGAAGCTCACGAAAAGCCTATAGGGAAGCTCCGGATAGCCATATATCGGGAAGTTCAAAC
1 TATCGGGAAGCTCACAAAAAACCTATAGGGAAGCTCCGAATAGCCATATATCGGGAAGTTCAAAC
57069360 GAGCAC
66 GAGCAC
* *
57069366 TATCGGGAAGCTCACAAAAAACCTATCGGGAAGCTCCGAATAGCTATATATCGGGAAGTTC
1 TATCGGGAAGCTCACAAAAAACCTATAGGGAAGCTCCGAATAGCCATATATCGGGAAGTTC
57069427 TTAAGGGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (71 bp):
TATCGGGAAGCTCACAAAAAACCTATAGGGAAGCTCCGAATAGCCATATATCGGGAAGTTCAAAC
GAGCAC
Found at i:57071560 original size:3 final size:3
Alignment explanation
Indices: 57071546--57071624 Score: 73
Period size: 3 Copynumber: 28.3 Consensus size: 3
57071536 TTTTATACTA
*
57071546 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT -AT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
57071588 AAA AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57071625 TCTTATTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 12 0.19
3 47 0.76
4 3 0.05
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:57071566 original size:8 final size:8
Alignment explanation
Indices: 57071545--57071624 Score: 60
Period size: 8 Copynumber: 9.6 Consensus size: 8
57071535 CTTTTATACT
57071545 AAATAATTA
1 AAATAA-TA
57071554 ATAATAA-A
1 A-AATAATA
57071562 ATAATAATGA
1 A-AATAAT-A
57071572 AATATAATA
1 AA-ATAATA
57071581 AAATAAT-
1 AAATAATA
57071588 AAA-AATA
1 AAATAATA
57071595 ATAATGAA-A
1 A-AAT-AATA
*
57071604 TAATAATA
1 AAATAATA
57071612 AAATAATA
1 AAATAATA
57071620 AAATA
1 AAATA
57071625 TCTTATTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 31 0.52
9 6 0.10
10 14 0.23
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (8 bp):
AAATAATA
Found at i:57071568 original size:11 final size:11
Alignment explanation
Indices: 57071552--57071620 Score: 99
Period size: 11 Copynumber: 6.5 Consensus size: 11
57071542 ACTAAATAAT
57071552 TAATAATAAAA
1 TAATAATAAAA
*
57071563 TAATAATGAAA
1 TAATAATAAAA
57071574 T-ATAATAAAA
1 TAATAATAAAA
57071584 TAAT-A-AAAA
1 TAATAATAAAA
*
57071593 TAATAATGAAA
1 TAATAATAAAA
57071604 TAATAATAAAA
1 TAATAATAAAA
57071615 TAATAA
1 TAATAA
57071621 AATATCTTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
9 8 0.16
10 11 0.22
11 32 0.63
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:57071635 original size:52 final size:50
Alignment explanation
Indices: 57071552--57071667 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 50
57071542 ACTAAATAAT
57071552 TAATAATAAAATAATAATGAAATATAATAAAATAATAAAAATAATAATGAAA
1 TAATAATAAAATAATAA-GAAATATAATAAAATAATAAAAAT-ATAATGAAA
* * * * * *
57071604 TAATAATAAAATAATAA-AATATCTTATTAAAATAATATATATCTAATTAAA
1 TAATAATAAAATAATAAGAA-AT-ATAATAAAATAATAAAAATATAATGAAA
*
57071655 TAATCATAAAATA
1 TAATAATAAAATA
57071668 TCATCAACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
50 2 0.04
51 21 0.38
52 32 0.58
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (50 bp):
TAATAATAAAATAATAAGAAATATAATAAAATAATAAAAATATAATGAAA
Found at i:57071647 original size:20 final size:21
Alignment explanation
Indices: 57071553--57071669 Score: 75
Period size: 20 Copynumber: 5.7 Consensus size: 21
57071543 CTAAATAATT
* *
57071553 AATAATAAAATA-ATAATGAA
1 AATAATAAAATATCTAATTAA
* *
57071573 ATATAATAAAATA-ATAA-AAA
1 A-ATAATAAAATATCTAATTAA
* *
57071593 TAATAATGAAATA-ATAA-TAA
1 -AATAATAAAATATCTAATTAA
*
57071613 AATAATAAAATATCTTATTAA
1 AATAATAAAATATCTAATTAA
*
57071634 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
57071655 TAATCATAAAATATC
1 -AATAATAAAATATC
57071670 ATCAACATCA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
19 11 0.14
20 31 0.39
21 27 0.34
22 5 0.06
23 6 0.08
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:57072292 original size:41 final size:41
Alignment explanation
Indices: 57072247--57072326 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
57072237 ACACGGGTTA
* *
57072247 GGACACGGGTGTGTCATGGCCATGTGAAGGACACGGGCCAG
1 GGACACGAGCGTGTCATGGCCATGTGAAGGACACGGGCCAG
57072288 GGACACGAGCGTGTCATGGCCATGTGAAGGACACGGGCC
1 GGACACGAGCGTGTCATGGCCATGTGAAGGACACGGGCC
57072327 GAAAACCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.23, C:0.24, G:0.40, T:0.14
Consensus pattern (41 bp):
GGACACGAGCGTGTCATGGCCATGTGAAGGACACGGGCCAG
Found at i:57073151 original size:31 final size:31
Alignment explanation
Indices: 57073113--57073176 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
57073103 CCTTTTCATA
57073113 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
57073144 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
57073175 TT
1 TT
57073177 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:57073421 original size:24 final size:24
Alignment explanation
Indices: 57073370--57073537 Score: 243
Period size: 25 Copynumber: 7.0 Consensus size: 24
57073360 ACTTTATCAT
*
57073370 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
57073395 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
57073419 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
* *
57073444 ATAACTGGGGAATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
57073469 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
57073492 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
57073515 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
57073538 GCACTTCCTC
Statistics
Matches: 135, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
23 43 0.32
24 37 0.27
25 55 0.41
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:57073499 original size:23 final size:23
Alignment explanation
Indices: 57073391--57073536 Score: 238
Period size: 23 Copynumber: 6.1 Consensus size: 23
57073381 CCTAGCCTCT
57073391 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
57073414 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
57073438 TTTATCATAACTGGGGAATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
57073463 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
57073488 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
57073511 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
57073534 TTT
1 TTT
57073537 TGCACTTCCT
Statistics
Matches: 118, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
23 49 0.42
24 23 0.19
25 46 0.39
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:57073651 original size:20 final size:20
Alignment explanation
Indices: 57073583--57073653 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
57073573 GCATTTATGA
*
57073583 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
57073603 ACATATCAGGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
57073623 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
57073643 ATATATCATGT
1 ACATATCATGT
57073654 TTATCAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:57073733 original size:25 final size:25
Alignment explanation
Indices: 57073690--57073737 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57073680 ATATATAAAC
* *
57073690 CCTAGGGGTATAATAGTCATTTTTA
1 CCTAGGGGTAAAACAGTCATTTTTA
*
57073715 CCTAGGGGTAAAACGGTCATTTT
1 CCTAGGGGTAAAACAGTCATTTT
57073738 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGTAAAACAGTCATTTTTA
Found at i:57085033 original size:24 final size:24
Alignment explanation
Indices: 57085001--57085267 Score: 387
Period size: 24 Copynumber: 11.1 Consensus size: 24
57084991 CTAGTTATAA
57085001 ATCAAAAGGGCTTATGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
57085025 ATCAAAAGGGCTTATGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
* *
57085049 ATAAAAAGGGCTTATGCCTCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
57085073 A-CTAAAAGGGCTTATGCCCCAGTT
1 ATC-AAAAGGGCTTATGCCCCAGTT
57085097 ATCAAAAGGGCTTATGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
* * *
57085121 ATAAAAAGGGCTTATGCTCCAATT
1 ATCAAAAGGGCTTATGCCCCAGTT
*
57085145 ATAAAAAGGGCTTATGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
57085169 A-CTAAAAGGGCTTATGCCCCAGTT
1 ATC-AAAAGGGCTTATGCCCCAGTT
57085193 ATCAAAAGGGCTTATGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
* *
57085217 ATTAAAAGGGCTTTTGCCCCAGTT
1 ATCAAAAGGGCTTATGCCCCAGTT
* *
57085241 ATTAAAAGAGG-TTAGGCCTCCAGTT
1 ATCAAAAG-GGCTTATGCC-CCAGTT
57085266 AT
1 AT
57085268 ATGATAAAGC
Statistics
Matches: 223, Mismatches: 14, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
24 211 0.95
25 12 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (24 bp):
ATCAAAAGGGCTTATGCCCCAGTT
Found at i:57088407 original size:47 final size:47
Alignment explanation
Indices: 57088354--57088623 Score: 443
Period size: 47 Copynumber: 5.7 Consensus size: 47
57088344 ATGTACACTT
*
57088354 TCACATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
57088401 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
57088448 TCACATATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
57088497 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
57088546 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* * *
57088593 TCTCATATATGCA-TGTTCACATCCATCACAT
1 TCACATATATACACT-TTCACATTCATCACAT
57088624 AGAATCCTAA
Statistics
Matches: 214, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 119 0.56
49 94 0.44
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:57088411 original size:49 final size:49
Alignment explanation
Indices: 57088358--57088602 Score: 435
Period size: 49 Copynumber: 5.1 Consensus size: 49
57088348 ACACTTTCAC
*
57088358 ATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
57088405 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
57088454 ATATATACACTTTCACATTCATCACATCGTCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
57088503 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
57088550 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
57088599 ATAT
1 ATAT
57088603 GCATGTTCAC
Statistics
Matches: 190, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
47 92 0.48
49 98 0.52
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:57088461 original size:96 final size:94
Alignment explanation
Indices: 57088354--57088623 Score: 436
Period size: 96 Copynumber: 2.8 Consensus size: 94
57088344 ATGTACACTT
57088354 TCACATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATACACTTTC
57088419 ACATTCATCACATCGGCCATTAGGCCTTA
66 ACATTCATCACATCGGCCATTAGGCCTTA
57088448 TCACATATATATACACTTTCACATTCATCACATC-GTCCATTAGGCCTTATCACATATATATACA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGT-CATTAGGCCTTATCAC--ATATATACA
57088512 CTTTCACATTCATCACATCGGCCATTAGGCCTTA
61 CTTTCACATTCATCACATCGGCCATTAGGCCTTA
* * *
57088546 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGCA-TGTT
1 TCACATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATACACT-TT
*
57088610 CACATCCATCACAT
65 CACATTCATCACAT
57088624 AGAATCCTAA
Statistics
Matches: 165, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
93 1 0.01
94 27 0.16
95 2 0.01
96 87 0.53
97 1 0.01
98 47 0.28
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
TCACATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTA
Found at i:57095679 original size:24 final size:24
Alignment explanation
Indices: 57095641--57095763 Score: 80
Period size: 23 Copynumber: 5.2 Consensus size: 24
57095631 TACCAATATA
* *
57095641 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCATATGAGCTTACTGTTT
* *
57095665 TCAGCTCAT-TGGAGCTTACCG-AT
1 TCAGCTCATAT-GAGCTTACTGTTT
*
57095688 TCAGCTCGTATGAGCTTACTG-TT
1 TCAGCTCATATGAGCTTACTGTTT
* **
57095711 T-AGCTTGATA-GAGCTTAC-CATT
1 TCAGC-TCATATGAGCTTACTGTTT
*
57095733 TCAGCTCA-ATAGAGCTTACTATTT
1 TCAGCTCATAT-GAGCTTACTGTTT
57095757 ATCAGCT
1 -TCAGCT
57095764 TAGGAGGAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
21 1 0.01
22 16 0.21
23 34 0.44
24 20 0.26
25 6 0.08
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (24 bp):
TCAGCTCATATGAGCTTACTGTTT
Found at i:57095702 original size:23 final size:23
Alignment explanation
Indices: 57095619--57095739 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 23
57095609 TTCACCACAA
*
57095619 CTCGTATGAGCTTACCAATATATCAG
1 CTCGTATGAGCTTACC--GAT-TCAG
* * *
57095645 CTCGTAAGAGCTTACTGTTTTCAG
1 CTCGTATGAGCTTACCG-ATTCAG
*
57095669 CTCAT-TGGAGCTTACCGATTCAG
1 CTCGTAT-GAGCTTACCGATTCAG
* *
57095692 CTCGTATGAGCTTACTG-TTTAG
1 CTCGTATGAGCTTACCGATTCAG
*
57095714 CTTG-ATAGAGCTTACC-ATTTCAG
1 CTCGTAT-GAGCTTACCGA-TTCAG
57095737 CTC
1 CTC
57095740 AATAGAGCTT
Statistics
Matches: 74, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.20
23 24 0.32
24 18 0.24
25 1 0.01
26 14 0.19
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (23 bp):
CTCGTATGAGCTTACCGATTCAG
Found at i:57095978 original size:20 final size:20
Alignment explanation
Indices: 57095955--57096007 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
57095945 GAAATGAATG
57095955 AATTACTGTTGA-TA-TAGATA
1 AATTACTGTT-ATTACTA-ATA
*
57095975 AATTACTATTATTACTAATA
1 AATTACTGTTATTACTAATA
57095995 AATTACTGGTTAT
1 AATTACT-GTTAT
57096008 ACGGATGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.75
21 6 0.21
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (20 bp):
AATTACTGTTATTACTAATA
Found at i:57096035 original size:20 final size:20
Alignment explanation
Indices: 57095998--57096036 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57095988 ACTAATAAAT
*
57095998 TACTGGTTATACGGATGAAC
1 TACTGGTTATACGAATGAAC
*
57096018 TACTGGTTATATGAATGAA
1 TACTGGTTATACGAATGAA
57096037 TTATATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TACTGGTTATACGAATGAAC
Found at i:57111641 original size:16 final size:16
Alignment explanation
Indices: 57111604--57111635 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57111594 AATTAAATAC
*
57111604 AATAAGAATAGAATTT
1 AATAATAATAGAATTT
57111620 AATAATAATAGAATTT
1 AATAATAATAGAATTT
57111636 TCTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AATAATAATAGAATTT
Found at i:57111681 original size:3 final size:3
Alignment explanation
Indices: 57111673--57111701 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
57111663 TTAAAATTAA
57111673 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57111702 ACAGAGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57115468 original size:15 final size:15
Alignment explanation
Indices: 57115448--57115481 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57115438 AGCATATACA
*
57115448 CACAACCAATTCAAC
1 CACAACCAAGTCAAC
*
57115463 CACAACCAAGTCATC
1 CACAACCAAGTCAAC
57115478 CACA
1 CACA
57115482 CATCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.12
Consensus pattern (15 bp):
CACAACCAAGTCAAC
Found at i:57116311 original size:42 final size:42
Alignment explanation
Indices: 57116201--57116320 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 42
57116191 ACCATACCAA
* *
57116201 GCCATATCCCAGATATGGTCTTACATG-GGATCTCATATCGAT
1 GCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATCGAT
* * * *
57116243 GCCAATAGCCCAGCTTTGGTTTTACACGAAGTCTCATATCGAT
1 GCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGAT
*
57116286 GTCATATCCCAGATATGGTCTTACACGTAA-TCTCA
1 GCCATATCCCAGATATGGTCTTACACG-AAGTCTCA
57116321 ACTAACCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 28 0.44
43 35 0.55
44 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCGAT
Found at i:57117692 original size:9 final size:9
Alignment explanation
Indices: 57117674--57117746 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
57117664 TTTATTTAAG
57117674 TTAA-GTGT
1 TTAATGTGT
57117682 TTAATGTGT
1 TTAATGTGT
57117691 TT--TGTGT
1 TTAATGTGT
57117698 TTAATAAGTGT
1 TTAAT--GTGT
57117709 TTAAATGTGT
1 TT-AATGTGT
*
57117719 TTAATATG-
1 TTAATGTGT
57117727 TT--TGT-T
1 TTAATGTGT
57117733 TTAATGTGT
1 TTAATGTGT
57117742 TTAAT
1 TTAAT
57117747 TGCAGGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 9 0.17
9 18 0.34
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:57117719 original size:21 final size:22
Alignment explanation
Indices: 57117693--57117746 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
57117683 TAATGTGTTT
57117693 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
57117714 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
57117737 TGTGTTTAAT
1 TGTGTTTAAT
57117747 TGCAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:57119559 original size:7 final size:7
Alignment explanation
Indices: 57119530--57119583 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
57119520 TATAAATTTT
57119530 ATTTATA
1 ATTTATA
*
57119537 ATTTAGCA
1 ATTTA-TA
*
57119545 TATATATA
1 -ATTTATA
57119553 ATTTAT-
1 ATTTATA
57119559 ATTTATA
1 ATTTATA
57119566 ATTTATA
1 ATTTATA
*
57119573 ATTTATT
1 ATTTATA
57119580 ATTT
1 ATTT
57119584 GATCTAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 6 0.15
7 27 0.69
8 2 0.05
9 4 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (7 bp):
ATTTATA
Found at i:57130834 original size:2 final size:2
Alignment explanation
Indices: 57130827--57130854 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57130817 CCGAATTGAG
57130827 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
57130855 GAATCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:57133610 original size:9 final size:9
Alignment explanation
Indices: 57133596--57133626 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57133586 TAAATGAATT
57133596 GAGTTATTC
1 GAGTTATTC
57133605 GAGTTATTC
1 GAGTTATTC
*
57133614 AAGTTATTC
1 GAGTTATTC
57133623 GAGT
1 GAGT
57133627 CAACTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
GAGTTATTC
Found at i:57138516 original size:40 final size:40
Alignment explanation
Indices: 57138461--57138541 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
57138451 TGAGTGGAAG
*
57138461 TATGATATCCGTAGAAGATCATGACGAACTAAAGGAGGGA
1 TATGATATCCGTAGAAGATCATGAAGAACTAAAGGAGGGA
57138501 TATGATATCCGTAGAAGATCATGAAGAACTAAAGGAGGGA
1 TATGATATCCGTAGAAGATCATGAAGAACTAAAGGAGGGA
57138541 T
1 T
57138542 TGTTTCATAA
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:0.11, G:0.27, T:0.21
Consensus pattern (40 bp):
TATGATATCCGTAGAAGATCATGAAGAACTAAAGGAGGGA
Found at i:57141639 original size:22 final size:21
Alignment explanation
Indices: 57141592--57141639 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
57141582 GTTAACTTTT
* * *
57141592 TGTAAAAAAATTTAAACTCTA
1 TGTAAAAAAATATAAAATATA
*
57141613 AGTAAAAAAATATAAAATATA
1 TGTAAAAAAATATAAAATATA
57141634 GTGTAA
1 -TGTAA
57141640 CTTTTAATCT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (21 bp):
TGTAAAAAAATATAAAATATA
Found at i:57145605 original size:8 final size:8
Alignment explanation
Indices: 57145592--57145626 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
57145582 TTTAAAAATT
57145592 ATATAAAA
1 ATATAAAA
57145600 ATATAAAA
1 ATATAAAA
*
57145608 TTATAAAA
1 ATATAAAA
*
57145616 TTATAAAA
1 ATATAAAA
57145624 ATA
1 ATA
57145627 ATAATATAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATATAAAA
Found at i:57149656 original size:27 final size:27
Alignment explanation
Indices: 57149626--57149801 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
57149616 ATATTGAGTC
* *
57149626 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
57149653 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
57149680 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
57149708 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
57149735 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
57149762 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
57149789 CG--CACTTAGTGCT
1 CGCACACTTAGTGCT
57149802 GTACAATTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.08
27 91 0.73
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:57153954 original size:46 final size:46
Alignment explanation
Indices: 57153901--57154073 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
57153891 TGGTTGAGCA
*
57153901 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
57153947 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
57153994 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
57154040 ACCGAGCTCGTTGATTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
57154074 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.56
47 28 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:57154059 original size:93 final size:93
Alignment explanation
Indices: 57153898--57154068 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
57153888 GGATGGTTGA
* * *
57153898 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGACCGAACTCGTTGAGT
57153963 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
57153991 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGACCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGACCGAACTCGTTGAGT
*
57154056 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
57154069 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGACCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:57156571 original size:16 final size:16
Alignment explanation
Indices: 57156547--57156585 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
57156537 GAGAAAAGAA
*
57156547 AGTACGCTTATAGCTT
1 AGTAAGCTTATAGCTT
57156563 AGTAAGCTTATAGCTT
1 AGTAAGCTTATAGCTT
57156579 AGTAAGC
1 AGTAAGC
57156586 AAGTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (16 bp):
AGTAAGCTTATAGCTT
Found at i:57157860 original size:10 final size:10
Alignment explanation
Indices: 57157845--57157869 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
57157835 ATAATTTTAA
57157845 TTTTTTAATT
1 TTTTTTAATT
57157855 TTTTTTAATT
1 TTTTTTAATT
57157865 TTTTT
1 TTTTT
57157870 CAACCTCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:57160512 original size:16 final size:16
Alignment explanation
Indices: 57160491--57160529 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
57160481 GAGAAAAGAA
57160491 AGTAAGCTTATAGCTT
1 AGTAAGCTTATAGCTT
57160507 AGTAAGCTTATAGCTT
1 AGTAAGCTTATAGCTT
57160523 AGTAAGC
1 AGTAAGC
57160530 AAGTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (16 bp):
AGTAAGCTTATAGCTT
Found at i:57166951 original size:12 final size:12
Alignment explanation
Indices: 57166934--57166958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57166924 ATGTAAGTGA
57166934 TCTTGATGATTT
1 TCTTGATGATTT
57166946 TCTTGATGATTT
1 TCTTGATGATTT
57166958 T
1 T
57166959 TATATTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:57167733 original size:47 final size:46
Alignment explanation
Indices: 57167659--57167921 Score: 187
Period size: 47 Copynumber: 5.6 Consensus size: 46
57167649 AATTACTTAT
*
57167659 GTGCTAGTGTAAGACATGTCTGGGACATGGCATCGACGTAGAGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACAT-GCATCGACGTAGAGATGA
* * *
57167706 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGACGTAGA-GATGA
* * * *
57167753 -TAGCCAGTGTAAGA-GTGTATGGGACATGCATCG--GTTGAGA-GTT
1 GT-GCCAGTGTAAGACATGTCTGGGACATGCATCGACGTAGAGATG-A
** * * * *
57167796 GTGATAGTGTAAGACATGTCTGGGACATACATCAGCACGTATATACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATC-G-ACGTAGAGATGA
* * * * * * *
57167844 GAGCTAGTGTAGGACCATGTCTAGGACATGACATCGGCCTTGATGATGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGACGTAGA-GATGA
*
57167893 -TAGCCAGTGTAAGACCCTGTCTGGGACAT
1 GT-GCCAGTGTAAGA-CATGTCTGGGACAT
57167922 AACATCGGCA
Statistics
Matches: 168, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
42 1 0.01
43 12 0.07
44 19 0.11
45 1 0.01
46 28 0.17
47 44 0.26
48 18 0.11
49 41 0.24
50 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGACGTAGAGATGA
Found at i:57167778 original size:46 final size:46
Alignment explanation
Indices: 57167659--57167930 Score: 196
Period size: 49 Copynumber: 5.8 Consensus size: 46
57167649 AATTACTTAT
* * *
57167659 GTGCTAGTGTAAGACATGTCTGGGACATGGCATCGACGTAGAGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTAGAGATGA
*
57167706 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGA-GATGA
* * * *
57167753 -TAGCCAGTGTAAGA-GTGTATGGGACATGCATCGG--TTGAGA-GTT
1 GT-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATG-A
** * * * * *
57167796 GTGATAGTGTAAGACATGTCTGGGACATACATCAGCACGTATATACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGC-C-TAGAGATGA
* * * * *
57167844 GAGCTAGTGTAGGACCATGTCTAGGACATGACATCGGCCTTGATGATGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTAGA-GATGA
* *
57167893 -TAGCCAGTGTAAGACCCTGTCTGGGACATAACATCGGC
1 GT-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
57167931 AACTTATCCC
Statistics
Matches: 176, Mismatches: 34, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
42 1 0.01
43 12 0.07
44 20 0.11
46 29 0.16
47 44 0.25
48 16 0.09
49 48 0.27
50 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGAGATGA
Found at i:57169846 original size:22 final size:23
Alignment explanation
Indices: 57169820--57169864 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
57169810 AACAATGTAA
*
57169820 TTTGATGAATTACTAA-TATTTT
1 TTTGAAGAATTACTAATTATTTT
57169842 TTTGAAGAATTACTAATTATTTT
1 TTTGAAGAATTACTAATTATTTT
57169865 ACACATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TTTGAAGAATTACTAATTATTTT
Found at i:57170079 original size:76 final size:76
Alignment explanation
Indices: 57169940--57170081 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
57169930 TTTGTTACAC
* **
57169940 AACATATCTTAAAAATTTGTAAAATGTAGTTCTTTTACCATAATAATCCAAGAAAATTAATTAAA
1 AACATATCTTAAAAATTTGTAAAATGTAGTTCTTTTACCACAATAATCCAAGAAAAAAAATTAAA
57170005 TTTTATTACGT
66 TTTTATTACGT
* * *
57170016 AACATATTTTTAACATTTGTAAAATGTAGTTCTTTTACCACAATAATCCAA-AAAAAAAGATTAA
1 AACATATCTTAAAAATTTGTAAAATGTAGTTCTTTTACCACAATAATCCAAGAAAAAAA-ATTAA
57170080 AT
65 AT
57170082 ATCAAAATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 5 0.08
76 54 0.92
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (76 bp):
AACATATCTTAAAAATTTGTAAAATGTAGTTCTTTTACCACAATAATCCAAGAAAAAAAATTAAA
TTTTATTACGT
Found at i:57172999 original size:84 final size:84
Alignment explanation
Indices: 57172840--57172998 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
57172830 TAGGAGATCT
* * * * *
57172840 AAAGTTTAATTTTACTATATATTAATGTATAATTTCTTTATTTATAAGAGGATTAAATTGAAATT
1 AAAGTGTAATTTCACTACATATTAATGTATAATTTCTCTATTTATAAGAGGACTAAATTGAAATT
*
57172905 CTTTTATTTTTAAGGGGCC
66 CTTTCATTTTTAAGGGGCC
* *
57172924 AAAGTGTAATTTCACTACATATTAATTTATAGTTTCTCTATTTATAAGAGGACTAAATTGAAA-T
1 AAAGTGTAATTTCACTACATATTAATGTATAATTTCTCTATTTATAAGAGGACTAAATTGAAATT
*
57172988 GTTTCATTTTT
66 CTTTCATTTTT
57172999 TTGGGGGTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 10 0.15
84 56 0.85
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (84 bp):
AAAGTGTAATTTCACTACATATTAATGTATAATTTCTCTATTTATAAGAGGACTAAATTGAAATT
CTTTCATTTTTAAGGGGCC
Found at i:57173126 original size:29 final size:30
Alignment explanation
Indices: 57173091--57173158 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
57173081 TGTTTACATT
*
57173091 TTGATCACTTAATT-T-CAAAAAGTTACAAA
1 TTGATCACTAAATTGTAC-AAAAGTTACAAA
*
57173120 TTGATCACTAAATTGTACAAAAGTTACAAG
1 TTGATCACTAAATTGTACAAAAGTTACAAA
57173150 TTGATCACT
1 TTGATCACT
57173159 GTCTTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 13 0.37
30 21 0.60
31 1 0.03
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (30 bp):
TTGATCACTAAATTGTACAAAAGTTACAAA
Found at i:57175855 original size:43 final size:43
Alignment explanation
Indices: 57175754--57175856 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 43
57175744 CACATATCAT
* *
57175754 ACAATGCCAACGTCCTAGACGTGGTCTTACATGTAATCACATA
1 ACAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA
* * *
57175797 ACAATACC-ACTGTCCCAGACAG-GGTCTTATACGTAATCATATA
1 ACAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATA
* *
57175840 TCGATGCCAACGTCCCA
1 ACAATGCCAACGTCCCA
57175857 AACATCGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
42 2 0.04
43 44 0.90
44 3 0.06
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
ACAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATA
Found at i:57185134 original size:93 final size:93
Alignment explanation
Indices: 57185022--57185193 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
57185012 CGCCCATAAG
* * *
57185022 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGGCTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
57185087 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
57185115 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
57185180 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
57185194 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:57185190 original size:46 final size:46
Alignment explanation
Indices: 57185015--57185190 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
57185005 TGTAACCCGC
* * *
57185015 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
57185061 CCATAAGTGAACTCGGGCTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* * *
57185111 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
57185154 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
57185191 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:57190561 original size:213 final size:213
Alignment explanation
Indices: 57190194--57190620 Score: 845
Period size: 213 Copynumber: 2.0 Consensus size: 213
57190184 TCTAAAATAG
57190194 TAGCAAAATTAATAATAAAACAATAGTTATACAATATCCAAACAATAACAACAAAATAGTAGCAA
1 TAGCAAAATTAATAATAAAACAATAGTTATACAATATCCAAACAATAACAACAAAATAGTAGCAA
57190259 TATAATAGTAAAATGACAGCAAACAACATAAAAAAGTAGTAAACGACAATGAAAAAATTTAGGCA
66 TATAATAGTAAAATGACAGCAAACAACATAAAAAAGTAGTAAACGACAATGAAAAAATTTAGGCA
57190324 AATTTGGGCAAGGCCAAAAAATCTTACCTGAGGCCCGACCAGTTTAGAAAATGGGCTTTATTTTT
131 AATTTGGGCAAGGCCAAAAAATCTTACCTGAGGCCCGACCAGTTTAGAAAATGGGCTTTATTTTT
57190389 GTGTCCAGACCTATTTTT
196 GTGTCCAGACCTATTTTT
*
57190407 TAGCAAAATTAATAATAAAACAATAGTTATACAATATCCAAACAATAACAATAAAATAGTAGCAA
1 TAGCAAAATTAATAATAAAACAATAGTTATACAATATCCAAACAATAACAACAAAATAGTAGCAA
57190472 TATAATAGTAAAATGACAGCAAACAACATAAAAAAGTAGTAAACGACAATGAAAAAATTTAGGCA
66 TATAATAGTAAAATGACAGCAAACAACATAAAAAAGTAGTAAACGACAATGAAAAAATTTAGGCA
57190537 AATTTGGGCAAGGCCAAAAAATCTTACCTGAGGCCCGACCAGTTTAGAAAATGGGCTTTATTTTT
131 AATTTGGGCAAGGCCAAAAAATCTTACCTGAGGCCCGACCAGTTTAGAAAATGGGCTTTATTTTT
57190602 GTGTCCAGACCTATTTTT
196 GTGTCCAGACCTATTTTT
57190620 T
1 T
57190621 GGACCTATAT
Statistics
Matches: 213, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 213 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (213 bp):
TAGCAAAATTAATAATAAAACAATAGTTATACAATATCCAAACAATAACAACAAAATAGTAGCAA
TATAATAGTAAAATGACAGCAAACAACATAAAAAAGTAGTAAACGACAATGAAAAAATTTAGGCA
AATTTGGGCAAGGCCAAAAAATCTTACCTGAGGCCCGACCAGTTTAGAAAATGGGCTTTATTTTT
GTGTCCAGACCTATTTTT
Found at i:57195990 original size:10 final size:10
Alignment explanation
Indices: 57195972--57196053 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 10
57195962 ATTATTATTG
57195972 TTAAATTTTT
1 TTAAATTTTT
57195982 TT-AATTTTT
1 TTAAATTTTT
*
57195991 TTAACTTTATT
1 TTAAATTT-TT
* *
57196002 TATATATATTT
1 T-TAAATTTTT
57196013 TTAGAATCTTTT
1 TTA-AAT-TTTT
57196025 TTGAAATTTTT
1 TT-AAATTTTT
* *
57196036 ATAAA-TATT
1 TTAAATTTTT
57196045 TTAAATTTT
1 TTAAATTTT
57196054 AAAAATTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
9 16 0.29
10 13 0.24
11 13 0.24
12 12 0.22
13 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TTAAATTTTT
Found at i:57199545 original size:40 final size:40
Alignment explanation
Indices: 57199456--57199719 Score: 351
Period size: 40 Copynumber: 6.7 Consensus size: 40
57199446 TTGAATGCTG
* *
57199456 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
57199495 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
57199535 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
57199574 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
57199614 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
57199654 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
57199695 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
57199720 AACGAGGAGC
Statistics
Matches: 204, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
39 52 0.25
40 142 0.70
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:57199737 original size:120 final size:118
Alignment explanation
Indices: 57199456--57199752 Score: 329
Period size: 119 Copynumber: 2.5 Consensus size: 118
57199446 TTGAATGCTG
* *
57199456 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* * *
57199516 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
57199574 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
57199639 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
57199695 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
57199753 TACGTGATTT
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 63 0.41
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:57201970 original size:107 final size:103
Alignment explanation
Indices: 57201780--57202035 Score: 293
Period size: 107 Copynumber: 2.4 Consensus size: 103
57201770 ATACACGGGT
* * * * * * *
57201780 ACCTTACCATTGCCATGACTTGTCATGGTCTTACATGGCATCCTTTTGAAACTTACCATTGTCAT
1 ACCTCACCAATGCCATGCCTTGGCATGGTCTTACATGGCATCCTTTAGAAACTTACCAATGCCAT
57201845 GTCTCGACATGGTCTTACATGATAT-CTTGCCTTATG-A
66 GTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAA
* *
57201882 A-CTCACCAATGCCATGCCTTGGCATGGTCTTACATGAGACATTTGCCTTATAGTAACTTATCAA
1 ACCTCACCAATGCCATGCCTTGGCATGGTCTTACATG-G-CA--T-CCTT-TAGAAACTTACCAA
* * *
57201946 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAA
60 TGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAA
* *
57201990 ACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 ACCTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGCATCCTT
57202036 AAACCCTAAT
Statistics
Matches: 130, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
101 31 0.24
102 2 0.02
103 2 0.02
105 5 0.04
106 5 0.04
107 39 0.30
108 11 0.08
109 8 0.06
110 27 0.21
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (103 bp):
ACCTCACCAATGCCATGCCTTGGCATGGTCTTACATGGCATCCTTTAGAAACTTACCAATGCCAT
GTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAA
Found at i:57202030 original size:55 final size:54
Alignment explanation
Indices: 57201782--57202035 Score: 235
Period size: 55 Copynumber: 4.8 Consensus size: 54
57201772 ACACGGGTAC
* * *
57201782 CTTACC-ATTGCCATGACTTGTCATGGTCTTACATGGCATCC-T--TTT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
* * * * *
57201831 CTTACC-ATTGTCATGTCTCGACATGGTCTTACATGATAT-CTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTA-GAAA
* * * *
57201883 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGAG-A-CATTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATG-GTATC-CTTG-CTT-TAGAAA
* *
57201938 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
*
57201991 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
57202036 AAACCCTAAT
Statistics
Matches: 165, Mismatches: 24, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
48 1 0.01
49 34 0.21
51 2 0.01
52 31 0.19
53 10 0.06
54 14 0.08
55 72 0.44
56 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
Found at i:57204087 original size:27 final size:27
Alignment explanation
Indices: 57204057--57204289 Score: 265
Period size: 27 Copynumber: 8.7 Consensus size: 27
57204047 CCAAAGTACT
*
57204057 CTCGATTTATAAAATTATCGTTTTACC
1 CTCGATTTATAAAATTACCGTTTTACC
*
57204084 CTCGATTTA-AAGAATTACCATTTTACC
1 CTCGATTTATAA-AATTACCGTTTTACC
* *
57204111 TTCGATTTATAAAATTACCATTTTACC
1 CTCGATTTATAAAATTACCGTTTTACC
* * *
57204138 CTCGATTTATAGAATTACCGTCTCACC
1 CTCGATTTATAAAATTACCGTTTTACC
* **
57204165 CTCGATTTACAAAATTATTGTTTTA-C
1 CTCGATTTATAAAATTACCGTTTTACC
* *
57204191 CTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTATAAAATTACCGTTTTACC
*
57204218 CTCGATTTA-AAGAATTACTGTTTTACC
1 CTCGATTTATAA-AATTACCGTTTTACC
* *
57204245 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTATAAAATTACCGTTTTACC
* * *
57204272 TTCAATTTACAAAATTAC
1 CTCGATTTATAAAATTAC
57204290 TAAAATACCC
Statistics
Matches: 174, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
26 24 0.14
27 147 0.84
28 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (27 bp):
CTCGATTTATAAAATTACCGTTTTACC
Found at i:57204234 original size:107 final size:108
Alignment explanation
Indices: 57204057--57204288 Score: 342
Period size: 107 Copynumber: 2.2 Consensus size: 108
57204047 CCAAAGTACT
* *
57204057 CTCGATTTATAAAATTATCGTTTTACCCTCGATTTAAAGAATTACCATTTTACCTTCGATTTATA
1 CTCGATTTACAAAATTATCGTTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTATA
*
57204122 AAATTACCATTTTACCCTCGATTTATAGAATTACCGTCTCACC
66 AAATTACCATTTTACCCTCGATTTACAGAATTACCGTCTCACC
* *
57204165 CTCGATTTACAAAATTATTGTTTTA-CCTCGATTTATAGAATTACCATTTTACCCTCGATTTA-A
1 CTCGATTTACAAAATTATCGTTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTATA
** * *
57204228 AGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACC
66 A-AATTACCATTTTACCCTCGATTTACAGAATTACCGTCTCACC
* *
57204272 TTCAATTTACAAAATTA
1 CTCGATTTACAAAATTA
57204289 CTAAAATACC
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
106 2 0.02
107 87 0.78
108 23 0.21
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (108 bp):
CTCGATTTACAAAATTATCGTTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTATA
AAATTACCATTTTACCCTCGATTTACAGAATTACCGTCTCACC
Found at i:57204289 original size:54 final size:54
Alignment explanation
Indices: 57204057--57204290 Score: 303
Period size: 54 Copynumber: 4.4 Consensus size: 54
57204047 CCAAAGTACT
* *
57204057 CTCGATTTATAAAATTA-TCGTTTTACCCTCGATTTAAAGAATTACCATTTTACC
1 CTCGATTTACAAAATTACT-GTTTTACCCTCGATTTATAGAATTACCATTTTACC
* * ** * * *
57204111 TTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTCTCACC
1 CTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCATTTTACC
*
57204165 CTCGATTTACAAAATTATTGTTTTA-CCTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCATTTTACC
* *
57204218 CTCGATTTA-AAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAA-AATTACTGTTTTACCCTCGATTTATAGAATTACCATTTTACC
* *
57204272 TTCAATTTACAAAATTACT
1 CTCGATTTACAAAATTACT
57204291 AAAATACCCT
Statistics
Matches: 156, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.01
53 46 0.29
54 106 0.68
55 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (54 bp):
CTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACCATTTTACC
Found at i:57204298 original size:27 final size:27
Alignment explanation
Indices: 57204241--57204352 Score: 93
Period size: 27 Copynumber: 4.1 Consensus size: 27
57204231 ATTACTGTTT
* * ****
57204241 TACCCTCGATTTACAGAATTACCGTTT
1 TACCTTCGATTTACAAAATTACCAAAA
* *
57204268 TACCTTCAATTTACAAAATTACTAAAA
1 TACCTTCGATTTACAAAATTACCAAAA
*
57204295 TACCCTT-GGTTTACAAAATTACCAAAA
1 TA-CCTTCGATTTACAAAATTACCAAAA
* *
57204322 TACCCTCGA-TTAGTAAAATTACCAAAA
1 TACCTTCGATTTA-CAAAATTACCAAAA
57204349 TACC
1 TACC
57204353 CCTGGCTTGT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 6 0.09
27 58 0.85
28 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.31
Consensus pattern (27 bp):
TACCTTCGATTTACAAAATTACCAAAA
Found at i:57204299 original size:54 final size:54
Alignment explanation
Indices: 57204057--57204332 Score: 279
Period size: 54 Copynumber: 5.1 Consensus size: 54
57204047 CCAAAGTACT
* * *
57204057 CTCGATTTATAAAATTA-TCGTTTTACCCTCGATTTAAAGAATTACCATTTTACC
1 CTCGATTTACAAAATTACT-ATTTTACCCTCGATTTACAGAATTACCATTTTACC
* * * * * * *
57204111 TTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTCTCACC
1 CTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACC
* * *
57204165 CTCGATTTACAAAATTATTGTTTTA-CCTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACC
* *
57204218 CTCGATTTA-AAGAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAA-AATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACC
* * *** * * * ***
57204272 TTCAATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACC
1 CTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACC
57204326 CTCGATT
1 CTCGATT
57204333 AGTAAAATTA
Statistics
Matches: 185, Mismatches: 33, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
52 2 0.01
53 46 0.25
54 135 0.73
55 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (54 bp):
CTCGATTTACAAAATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACC
Found at i:57204300 original size:134 final size:134
Alignment explanation
Indices: 57204057--57204315 Score: 331
Period size: 134 Copynumber: 1.9 Consensus size: 134
57204047 CCAAAGTACT
* * * *
57204057 CTCGATTTATAAAATTATCGTTTTACCCTCGATTTAAAGAATTACCATTTTACCTTCGATTTATA
1 CTCGATTTATAAAATTACCATTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTACA
* * * ****
57204122 AAATTACCATTTTACCCTCGATTTATAGAATTACCGTCTCACCCTCGATTTACAAAATTATTGTT
66 AAATTACCATTTTACCCTCAATTTACAAAATTACAAAATCACCCTCGATTTACAAAATTATTGTT
57204187 TTAC
131 TTAC
* **
57204191 CTCGATTTATAGAATTACCATTTTACCCTCGATTTAAAGAATTACTGTTTTACCCTCGATTTACA
1 CTCGATTTATAAAATTACCATTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTACA
* * * * *
57204256 GAATTACCGTTTTACCTTCAATTTACAAAATTACTAAAAT-ACCCTTGGTTTACAAAATTA
66 AAATTACCATTTTACCCTCAATTTACAAAATTAC-AAAATCACCCTCGATTTACAAAATTA
57204316 CCAAAATACC
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
134 104 0.99
135 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (134 bp):
CTCGATTTATAAAATTACCATTTTACCCTCGATTTAAAGAATTACCATTTTACCCTCGATTTACA
AAATTACCATTTTACCCTCAATTTACAAAATTACAAAATCACCCTCGATTTACAAAATTATTGTT
TTAC
Found at i:57204353 original size:27 final size:26
Alignment explanation
Indices: 57204282--57204460 Score: 141
Period size: 27 Copynumber: 6.7 Consensus size: 26
57204272 TTCAATTTAC
* * *
57204282 AAAATTACTAAAATACCCTTGGTT-T
1 AAAATTACCAAAATACCCTCGATTGT
57204307 ACAAAATTACCAAAATACCCTCGATTAGT
1 --AAAATTACCAAAATACCCTCGATT-GT
* *
57204336 AAAATTACCAAAATACCCCTGGCTTGT
1 AAAATTACCAAAATA-CCCTCGATTGT
* *
57204363 AAAATTACC-AAATACCCCTGGCTTGT
1 AAAATTACCAAAATA-CCCTCGATTGT
57204389 AAAATTACCAAAATACCC-CTGATTTGT
1 AAAATTACCAAAATACCCTC-GA-TTGT
* * * * *
57204416 GAAATTATCGAAATACTCTCAATTTGT
1 AAAATTACCAAAATACCCTCGA-TTGT
*
57204443 AAAA-TATCAAAATACCCT
1 AAAATTACCAAAATACCCT
57204461 TGTAGGGTAG
Statistics
Matches: 130, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
26 42 0.32
27 79 0.61
28 8 0.06
29 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTCGATTGT
Found at i:57204382 original size:26 final size:27
Alignment explanation
Indices: 57204282--57204409 Score: 170
Period size: 27 Copynumber: 4.8 Consensus size: 27
57204272 TTCAATTTAC
* * * **
57204282 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGCTTGT
* *
57204309 AAAATTACCAAAATA-CCCTCGATTAGT
1 AAAATTACCAAAATACCCCTGGCTT-GT
57204336 AAAATTACCAAAATACCCCTGGCTTGT
1 AAAATTACCAAAATACCCCTGGCTTGT
57204363 AAAATTACC-AAATACCCCTGGCTTGT
1 AAAATTACCAAAATACCCCTGGCTTGT
57204389 AAAATTACCAAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
57204410 ATTTGTGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
26 32 0.36
27 51 0.57
28 7 0.08
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGCTTGT
Found at i:57204491 original size:27 final size:27
Alignment explanation
Indices: 57204452--57204636 Score: 250
Period size: 27 Copynumber: 7.0 Consensus size: 27
57204442 TAAAATATCA
*
57204452 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
57204479 AAATACCCCTGTAGGGTAAAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
57204506 AAATAACCTTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
57204533 AAATACCCCTATAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
57204560 AAATACCCCTGTAGGGTAGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
57204587 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
57204614 AGATA-CCCT-T-GGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
57204637 ATTTTGCCCC
Statistics
Matches: 139, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
24 12 0.09
25 1 0.01
26 3 0.02
27 123 0.88
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:57204875 original size:25 final size:25
Alignment explanation
Indices: 57204841--57204910 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
57204831 AGGAAGTGCT
*
57204841 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
57204866 AAAAGGGCTTTACCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
57204891 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
57204911 ATTAACAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:57205013 original size:38 final size:38
Alignment explanation
Indices: 57204962--57205053 Score: 175
Period size: 38 Copynumber: 2.4 Consensus size: 38
57204952 ATGTTGCCAG
57204962 TGGAGAGTTTGGTTGGGTGGGTTGAGTTATTCCCCACA
1 TGGAGAGTTTGGTTGGGTGGGTTGAGTTATTCCCCACA
57205000 TGGAGAGTTTGGTTGGGTGGGTTGAGTTATTCCCCACA
1 TGGAGAGTTTGGTTGGGTGGGTTGAGTTATTCCCCACA
*
57205038 TGGAGAGCTTGGTTGG
1 TGGAGAGTTTGGTTGG
57205054 TACAGGTGGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.15, C:0.12, G:0.39, T:0.34
Consensus pattern (38 bp):
TGGAGAGTTTGGTTGGGTGGGTTGAGTTATTCCCCACA
Found at i:57205237 original size:30 final size:31
Alignment explanation
Indices: 57205169--57205251 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
57205159 CGTTTATAGT
57205169 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
57205200 AAAGGCTTCGGCCCAGTGATATGATTTATG-
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
57205230 GAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
57205252 TCAAGACTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 5 0.10
30 16 0.31
31 30 0.59
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:57205500 original size:12 final size:12
Alignment explanation
Indices: 57205483--57205513 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57205473 ATAAGTTTTA
57205483 TCTTATTAATAT
1 TCTTATTAATAT
57205495 TCTTATTAATAT
1 TCTTATTAATAT
*
57205507 TATTATT
1 TCTTATT
57205514 TGGTTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTTATTAATAT
Found at i:57207540 original size:27 final size:27
Alignment explanation
Indices: 57207521--57207704 Score: 215
Period size: 27 Copynumber: 6.8 Consensus size: 27
57207511 ATTACCAAAG
* *
57207521 TACAATCGATTTACAGAATTACCGTTT
1 TACACTCGATTTACAGAATTACCATTT
*
57207548 TACCCTCGATTTACAGAATTACCATTT
1 TACACTCGATTTACAGAATTACCATTT
* *
57207575 TACTCTCGATTTATAGAATTACCATTT
1 TACACTCGATTTACAGAATTACCATTT
* * **
57207602 TACCCTCGATTTATAGAATTACTGTTT
1 TACACTCGATTTACAGAATTACCATTT
* * *
57207629 CACCCTCGATTTACAGAATTATCATTT
1 TACACTCGATTTACAGAATTACCATTT
* *
57207656 TACCCTCAATTTACAGAATTACCATTT
1 TACACTCGATTTACAGAATTACCATTT
* * *
57207683 TACCCTTGATTTACAAAATTAC
1 TACACTCGATTTACAGAATTAC
57207705 TGAAATACCA
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
TACACTCGATTTACAGAATTACCATTT
Found at i:57207705 original size:81 final size:81
Alignment explanation
Indices: 57207526--57207706 Score: 281
Period size: 81 Copynumber: 2.2 Consensus size: 81
57207516 CAAAGTACAA
* * * * *
57207526 TCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACTCTCGATTTATAG
1 TCGATTTACAGAATTACTGTTTCACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
57207591 AATTACCATTTTACCC
66 AATTACCATTTTACCC
* *
57207607 TCGATTTATAGAATTACTGTTTCACCCTCGATTTACAGAATTATCATTTTACCCTCAATTTACAG
1 TCGATTTACAGAATTACTGTTTCACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
57207672 AATTACCATTTTACCC
66 AATTACCATTTTACCC
* *
57207688 TTGATTTACAAAATTACTG
1 TCGATTTACAGAATTACTG
57207707 AAATACCATT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 90 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (81 bp):
TCGATTTACAGAATTACTGTTTCACCCTCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
AATTACCATTTTACCC
Found at i:57207713 original size:27 final size:27
Alignment explanation
Indices: 57207664--57207801 Score: 102
Period size: 27 Copynumber: 5.1 Consensus size: 27
57207654 TTTACCCTCA
* ***
57207664 ATTTACAGAATTACCATTTTACCCTTG
1 ATTTACAAAATTACCAAAATACCCTTG
** *
57207691 ATTTACAAAATTACTGAAATACCATTG
1 ATTTACAAAATTACCAAAATACCCTTG
* *
57207718 GTTTACAAAATTACCAAAATACCCTCG
1 ATTTACAAAATTACCAAAATACCCTTG
* *
57207745 A-TCAGTAAAATTACCAAAATACTCC-TG
1 ATTTA-CAAAATTACCAAAATAC-CCTTG
* ** *
57207772 GTTTGTAAAATTA-CAAAATACCCCTG
1 ATTTACAAAATTACCAAAATACCCTTG
57207798 ATTT
1 ATTT
57207802 GTGAAATTAT
Statistics
Matches: 87, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
25 2 0.02
26 15 0.17
27 67 0.77
28 3 0.03
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (27 bp):
ATTTACAAAATTACCAAAATACCCTTG
Found at i:57207723 original size:81 final size:81
Alignment explanation
Indices: 57207526--57207733 Score: 229
Period size: 81 Copynumber: 2.6 Consensus size: 81
57207516 CAAAGTACAA
* * ** * * * * *
57207526 TCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACTCTCGATTTATAG
1 TCGATTTACAAAATTACTGAATCACCATCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
57207591 AATTACCATTTTACCC
66 AATTACCATTTTACCC
* * ** * *
57207607 TCGATTTATAGAATTACTGTTTCACCCTCGATTTACAGAATTATCATTTTACCCTCAATTTACAG
1 TCGATTTACAAAATTACTGAATCACCATCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
57207672 AATTACCATTTTACCC
66 AATTACCATTTTACCC
* * * *
57207688 TTGATTTACAAAATTACTGAAAT-ACCATTGGTTTACAAAATTACCA
1 TCGATTTACAAAATTACTG-AATCACCATCGATTTACAGAATTACCA
57207734 AAATACCCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 108 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (81 bp):
TCGATTTACAAAATTACTGAATCACCATCGATTTACAGAATTACCATTTTACCCTCAATTTACAG
AATTACCATTTTACCC
Found at i:57207797 original size:26 final size:27
Alignment explanation
Indices: 57207724--57207819 Score: 106
Period size: 27 Copynumber: 3.6 Consensus size: 27
57207714 ATTGGTTTAC
**
57207724 AAAATTACCAAAATA-CCCTCGATCAGT
1 AAAATTACCAAAATACCCCT-GATTTGT
* *
57207751 AAAATTACCAAAATACTCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
57207778 AAAATTA-CAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * *
57207804 GAAATTATCGAAATAC
1 AAAATTACCAAAATAC
57207820 TCTCAATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 23 0.39
27 33 0.56
28 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGATTTGT
Found at i:57207881 original size:27 final size:27
Alignment explanation
Indices: 57207838--57207970 Score: 173
Period size: 27 Copynumber: 5.0 Consensus size: 27
57207828 TTTAAAATAT
*
57207838 CGAAATACCCTTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
57207865 CGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
57207892 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
** *
57207919 CGAAATACCGTTGTAGGGTAGAAATAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
57207946 CGAGATA-CCCT-T-GGGTAAAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
57207970 C
1 C
57207971 ATTTTGCCCC
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
24 11 0.12
25 1 0.01
26 2 0.02
27 79 0.85
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:57208251 original size:25 final size:25
Alignment explanation
Indices: 57208175--57208244 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
57208165 AGGAAGTGCT
* *
57208175 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
57208200 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
57208225 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
57208245 ATTCAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:57208257 original size:24 final size:25
Alignment explanation
Indices: 57208178--57208255 Score: 106
Period size: 25 Copynumber: 3.1 Consensus size: 25
57208168 AAGTGCTAAA
*
57208178 AGGGCTTTGCCCCAGTTTACCGAAA-
1 AGGGCTTTGCCCCAGTTTATC-AAAG
*
57208203 AGGGCTTTGCCCCAGTTTATCAAAA
1 AGGGCTTTGCCCCAGTTTATCAAAG
57208228 AGGGCTTTGCCCCAG-TTATTCAAAG
1 AGGGCTTTGCCCCAGTTTA-TCAAAG
57208253 AGG
1 AGG
57208256 CTAGGCCTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.12
25 43 0.88
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
AGGGCTTTGCCCCAGTTTATCAAAG
Found at i:57208514 original size:31 final size:31
Alignment explanation
Indices: 57208465--57208610 Score: 240
Period size: 31 Copynumber: 4.7 Consensus size: 31
57208455 CGTTTACAGT
*
57208465 AAAGGCTTCGTCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
57208496 AAAGGTTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
57208527 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
57208558 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
57208589 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
57208611 TCAAGACTAA
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 5 0.05
31 102 0.95
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:57210601 original size:32 final size:32
Alignment explanation
Indices: 57210565--57210632 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
57210555 GAATAAGGGC
57210565 ACATTGGTTAGGCATTTAGGTTGAATCTTTTA
1 ACATTGGTTAGGCATTTAGGTTGAATCTTTTA
57210597 ACATTGGTTAGGCATTTAGGTTGAATCTTTTA
1 ACATTGGTTAGGCATTTAGGTTGAATCTTTTA
57210629 ACAT
1 ACAT
57210633 GTTTTGGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (32 bp):
ACATTGGTTAGGCATTTAGGTTGAATCTTTTA
Done.