Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold328
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: 936272
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 2 of 6
Found at i:254833 original size:16 final size:17
Alignment explanation
Indices: 254814--254850 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
254804 AAATCTGATT
254814 TAATCTAAATTTAA-AA
1 TAATCTAAATTTAATAA
*
254830 TAATTTAAATTTAATAA
1 TAATCTAAATTTAATAA
254847 TAAT
1 TAAT
254851 AATAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATCTAAATTTAATAA
Found at i:254849 original size:3 final size:3
Alignment explanation
Indices: 254841--254870 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
254831 AATTTAAATT
254841 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
254871 ATTCAACGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:256438 original size:23 final size:24
Alignment explanation
Indices: 256412--256456 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
256402 GAATTATTGA
256412 TATTAAAAATTA-AATTTTAAATT
1 TATTAAAAATTATAATTTTAAATT
*
256435 TATTAAATATTATAATTTTAAA
1 TATTAAAAATTATAATTTTAAA
256457 ATTAATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTAAAAATTATAATTTTAAATT
Found at i:256439 original size:16 final size:17
Alignment explanation
Indices: 256420--256452 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
256410 GATATTAAAA
*
256420 ATTAAATTTTA-AATTT
1 ATTAAATATTATAATTT
256436 ATTAAATATTATAATTT
1 ATTAAATATTATAATTT
256453 TAAAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAAATATTATAATTT
Found at i:256913 original size:15 final size:16
Alignment explanation
Indices: 256893--256922 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
256883 ATTTTATTTA
256893 AATTTTTA-TAAAAAT
1 AATTTTTATTAAAAAT
256908 AATTTTTATTAAAAA
1 AATTTTTATTAAAAA
256923 ATACTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTTTATTAAAAAT
Found at i:256971 original size:18 final size:17
Alignment explanation
Indices: 256948--256990 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
256938 TCTAATTCAG
*
256948 TTTTTTAAATAAATCTCA
1 TTTTTTAAATAAATAT-A
**
256966 TTTTTTATTTAAATATA
1 TTTTTTAAATAAATATA
256983 TTTTTTAA
1 TTTTTTAA
256991 TTTTAATACT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTTAAATAAATATA
Found at i:261668 original size:28 final size:28
Alignment explanation
Indices: 260766--261672 Score: 978
Period size: 28 Copynumber: 32.3 Consensus size: 28
260756 CTTATGTAGA
* * * *
260766 CTTTAAAAGGATACCACTAATTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
** * * *
260794 CTTCAAAAGGGTGCCACTAACTTATGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
** * *
260822 CTTCAAAAGGGTGCCACTGACTTATGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
** *
260850 CTTCAAAAGGGTGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* * * *
260878 CTTCGAATGGGTGCCACTAACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* * *
260906 CTTTAAAAGGGTGCCACTGATTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
260934 CTTTGAGAGAGATTGCCACTGACTTGTGTGGG
1 CTTTGAAAG-GA-TGCCACTGAC-T-TGTGGG
*
260966 C-TT-AAAGGGGTGCCACTGAC-TGTGGG
1 CTTTGAAA-GGATGCCACTGACTTGTGGG
260992 CTTTGAGAAGGATGCCACTGACTTGTGGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
* *
261021 CTTTGAGAAAGATGCCACTGACTTTTGGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
*
261050 CTTTGAGAAAGATGCCACTGACTTGTGGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
* * *
261079 CTTTAAAAGGATGCCACTGATTTATGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
** * * * *
261107 CTCCGAAAGGGTGCCAGTAACTTATGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
261135 CTTTGAAAATG-TGCCACTGACTTGTGGG
1 CTTTG-AAAGGATGCCACTGACTTGTGGG
* ** *
261163 CTTTGAAA-GAGTGCTACTGACACGTGAG
1 CTTTGAAAGGA-TGCCACTGACTTGTGGG
261191 CTTTGAGAA-GATGCCACTGACTTGTGGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
* *
261219 CTTT-AAAAGTTGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* * *
261246 CTTTTAGAAGGATGCCACAGACTTGTTGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
*
261275 CTTTGAAAGGATGCCACTGACATGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* *
261303 CTTTGAAAAGG-TGCCCCTGACTTATGGG
1 CTTTG-AAAGGATGCCACTGACTTGTGGG
* ** *
261331 CTTTGAAAAGG-TGCCACTAACACGTGAG
1 CTTTG-AAAGGATGCCACTGACTTGTGGG
* *
261359 CTTTGAGAGGATGTCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
261387 CTTT-AAA-GAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGA-TGCCACTGACTTGTGGG
261414 CTTTGAAAAGG-TGCCACTGACTTGTGGG
1 CTTTG-AAAGGATGCCACTGACTTGTGGG
*
261442 CTTTTAGAAGGATGCCACTGACTTGTGGG
1 CTTTGA-AAGGATGCCACTGACTTGTGGG
*
261471 CTTTGAAAGGATGCCACTGACATGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
261499 CTTT-AAAGGATGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
261526 CTTTGAAAGGATGCCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
* *
261554 CTTTGAAAGGATGCCACTGACATGTGAG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
** *
261582 CTTT-AAAGGATGCCACCAACTTGTGGT
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
261609 CTTTGAAAGGATGCCACTAACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
*
261637 CTTTGAAAGGATACCACTGACTTGTGGG
1 CTTTGAAAGGATGCCACTGACTTGTGGG
261665 CTTTGAAA
1 CTTTGAAA
261673 AAGGTCGTAT
Statistics
Matches: 762, Mismatches: 91, Indels: 52
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.02
27 103 0.14
28 483 0.63
29 140 0.18
30 13 0.02
31 4 0.01
32 7 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (28 bp):
CTTTGAAAGGATGCCACTGACTTGTGGG
Found at i:262932 original size:8 final size:8
Alignment explanation
Indices: 262919--262975 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
262909 TACACCCTTC
262919 TTTTTTGT
1 TTTTTTGT
262927 TTTTTTGT
1 TTTTTTGT
262935 TTGTTTT-T
1 TT-TTTTGT
*
262943 TTTTTGGT
1 TTTTTTGT
*
262951 TTTTTGTTT
1 TTTTT-TGT
262960 TTCTTTTGT
1 TT-TTTTGT
262969 TTTTTTG
1 TTTTTTG
262976 GGTACAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 3 0.07
8 24 0.59
9 11 0.27
10 3 0.07
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (8 bp):
TTTTTTGT
Found at i:262939 original size:12 final size:12
Alignment explanation
Indices: 262922--262974 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 12
262912 ACCCTTCTTT
262922 TTTGTTTTTTTG
1 TTTGTTTTTTTG
262934 TTTGTTTTTTT-
1 TTTGTTTTTTTG
*
262945 TTTGGTTTTTTG
1 TTTGTTTTTTTG
*
262957 TTT-TTCTTTTG
1 TTTGTTTTTTTG
262968 TTT-TTTT
1 TTTGTTTT
262975 GGGTACAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 22 0.61
12 14 0.39
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (12 bp):
TTTGTTTTTTTG
Found at i:262974 original size:19 final size:19
Alignment explanation
Indices: 262920--262975 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
262910 ACACCCTTCT
* *
262920 TTTTTGTTTT-TTTGTTTG
1 TTTTTCTTTTGTTTTTTTG
* *
262938 TTTTTTTTTTGGTTTTTTG
1 TTTTTCTTTTGTTTTTTTG
262957 TTTTTCTTTTGTTTTTTTG
1 TTTTTCTTTTGTTTTTTTG
262976 GGTACAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 9 0.28
19 23 0.72
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTGTTTTTTTG
Found at i:265475 original size:32 final size:32
Alignment explanation
Indices: 265439--265509 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
265429 TCCATAATAT
*
265439 AATTGAAAAATTGATTGATATATGCTATTTAA
1 AATTGAAAAATTAATTGATATATGCTATTTAA
265471 AATTGAAAAATTAATTGATATATGCTATTTAA
1 AATTGAAAAATTAATTGATATATGCTATTTAA
*
265503 ATTTGAA
1 AATTGAA
265510 TTTTATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (32 bp):
AATTGAAAAATTAATTGATATATGCTATTTAA
Found at i:265814 original size:21 final size:21
Alignment explanation
Indices: 265780--265825 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
265770 AGAGTTAAGT
265780 ATAAATGTTTTTCAAGCAATAA
1 ATAAATGTTTTTCAAGCAA-AA
*
265802 ATAAATG-TTTTCAAGTAAAA
1 ATAAATGTTTTTCAAGCAAAA
265822 ATAA
1 ATAA
265826 TTCAAAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 10 0.43
22 7 0.30
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (21 bp):
ATAAATGTTTTTCAAGCAAAA
Found at i:265946 original size:20 final size:19
Alignment explanation
Indices: 265922--265994 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
265912 CACACCCAGA
265922 TGTATCGATACATACTGCT
1 TGTATCGATACATACTGCT
* *
265941 TAGTATCGATACAT-GTTCT
1 T-GTATCGATACATACTGCT
* * *
265960 TGGTATCAATACACACTGAAT
1 T-GTATCGATACATACTG-CT
265981 TGTATCGATACATA
1 TGTATCGATACATA
265995 AAACAGGCAG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.37
20 24 0.59
21 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATACTGCT
Found at i:274055 original size:19 final size:18
Alignment explanation
Indices: 274033--274137 Score: 86
Period size: 19 Copynumber: 5.4 Consensus size: 18
274023 AGGGGGAGTA
*
274033 GTTATTAAAGGGAAGAAGT
1 GTTATTAAAGGGAA-AAAT
*
274052 GTTATTAAGAGAGAAAAAT
1 GTTATTAA-AGGGAAAAAT
*
274071 GTTATTAAAGGGAAGAA-
1 GTTATTAAAGGGAAAAAT
*
274088 GTCTCATTAAAAGAGAAAAAT
1 GT-T-ATT-AAAGGGAAAAAT
274109 GTTATTAAGAGGGAGAAAAAT
1 GTTATTAA-A-GG-GAAAAAT
*
274130 TTTATTAA
1 GTTATTAA
274138 GGGGGATTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.03
18 10 0.14
19 26 0.37
20 16 0.23
21 16 0.23
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.28
Consensus pattern (18 bp):
GTTATTAAAGGGAAAAAT
Found at i:274084 original size:38 final size:38
Alignment explanation
Indices: 274033--274122 Score: 144
Period size: 38 Copynumber: 2.3 Consensus size: 38
274023 AGGGGGAGTA
* * *
274033 GTTATTAAAGGGAAGAAGTGTTATTAAGAGAGAAAAAT
1 GTTATTAAAGGGAAGAAGTCTCATTAAAAGAGAAAAAT
274071 GTTATTAAAGGGAAGAAGTCTCATTAAAAGAGAAAAAT
1 GTTATTAAAGGGAAGAAGTCTCATTAAAAGAGAAAAAT
274109 GTTATTAAGAGGGA
1 GTTATTAA-AGGGA
274123 GAAAAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 43 0.90
39 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (38 bp):
GTTATTAAAGGGAAGAAGTCTCATTAAAAGAGAAAAAT
Found at i:274817 original size:13 final size:13
Alignment explanation
Indices: 274799--274823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274789 AAATTGCTTA
274799 GTATCGATACATT
1 GTATCGATACATT
274812 GTATCGATACAT
1 GTATCGATACAT
274824 GTTCTTGGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:274928 original size:13 final size:13
Alignment explanation
Indices: 274891--274928 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
274881 AACTCACTCA
*
274891 GTATCGATACAGT
1 GTATCGATACATT
*
274904 GTATCAATACATT
1 GTATCGATACATT
274917 GTATCGATACAT
1 GTATCGATACAT
274929 GGTAAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:275077 original size:23 final size:21
Alignment explanation
Indices: 275035--275078 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
275025 CACGAAAACA
* *
275035 AGCTCCAAACAAGTCAACAAC
1 AGCTACAAACAAATCAACAAC
275056 AGCTACAAACACAATCATACAAC
1 AGCTACAAACA-AATCA-ACAAC
275079 CTCCAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.50, C:0.32, G:0.07, T:0.11
Consensus pattern (21 bp):
AGCTACAAACAAATCAACAAC
Found at i:275877 original size:38 final size:38
Alignment explanation
Indices: 275824--275934 Score: 152
Period size: 40 Copynumber: 2.9 Consensus size: 38
275814 TAAAATATAA
* *
275824 ATTAAAATTATATTTATGTTAAATAAT-AATTAAAAGTT
1 ATTAAAATTATATTTATATTAAA-AATAAATTAAAAATT
*
275862 ATTAAAATTAAATTTATATTAAAAATAAATAATAAAAATT
1 ATTAAAATTATATTTATATTAAAAATAAAT--TAAAAATT
*
275902 ATGAAAATTATATTTATATTAAAAATAAATTAA
1 ATTAAAATTATATTTATATTAAAAATAAATTAA
275935 TAAACTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
37 3 0.05
38 27 0.42
40 35 0.54
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (38 bp):
ATTAAAATTATATTTATATTAAAAATAAATTAAAAATT
Found at i:281707 original size:36 final size:36
Alignment explanation
Indices: 281665--281770 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
281655 AACACATATC
* *
281665 CAATGAACCATATCTAAAACAATTAAAGCAAATTTA
1 CAATGAACCATATCTAAAACAATTAAAACAAATTCA
* *
281701 TAATGAACCATATCTAAAACAATTAAAACAAAGTCA
1 CAATGAACCATATCTAAAACAATTAAAACAAATTCA
281737 CAATGAACCATATCTAAAACAATTAAAACAAATT
1 CAATGAACCATATCTAAAACAATTAAAACAAATT
281771 AATTCACTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (36 bp):
CAATGAACCATATCTAAAACAATTAAAACAAATTCA
Found at i:282253 original size:271 final size:271
Alignment explanation
Indices: 281770--282314 Score: 1081
Period size: 271 Copynumber: 2.0 Consensus size: 271
281760 TAAAACAAAT
281770 TAATTCACTAAGATATATTAGAAATATTTAAATTATTATTTTCAACAAATACAACATTCATGTCA
1 TAATTCACTAAGATATATTAGAAATATTTAAATTATTATTTTCAACAAATACAACATTCATGTCA
281835 TAAACCACCTATATTTAGCAACCTCATTAAATGATGATTCATACAACACAATTAAATTGCAGCAA
66 TAAACCACCTATATTTAGCAACCTCATTAAATGATGATTCATACAACACAATTAAATTGCAGCAA
281900 GAATTTGGCAAACACTAATGGATGTTGCTCCATCATATAAAGCAATATTAACTTTGTATACCTAA
131 GAATTTGGCAAACACTAATGGATGTTGCTCCATCATATAAAGCAATATTAACTTTGTATACCTAA
281965 GAAAAACCATAGAAAAACATGATCTATCTCTATCCTTCATTTGACACCATGGATAAAAGTCATTG
196 GAAAAACCATAGAAAAACATGATCTATCTCTATCCTTCATTTGACACCATGGATAAAAGTCATTG
282030 CTCACTAGAAA
261 CTCACTAGAAA
282041 TAATTCACTAAGATATATTAGAAATATTTAAATTATTATTTTCAACAAATACAACATTCATGTCA
1 TAATTCACTAAGATATATTAGAAATATTTAAATTATTATTTTCAACAAATACAACATTCATGTCA
282106 TAAACCACCTATATTTAGCAACCTCATTAAATGATGATTCATACAACACAATTAAATTGCAGCAA
66 TAAACCACCTATATTTAGCAACCTCATTAAATGATGATTCATACAACACAATTAAATTGCAGCAA
282171 GAATTTGGCAAACACTAATGGATGTTGCTCCATCATATAAAGCAATATTAACTTTGTATACCTAA
131 GAATTTGGCAAACACTAATGGATGTTGCTCCATCATATAAAGCAATATTAACTTTGTATACCTAA
*
282236 GAAAAACTATAGAAAAACATGATCTATCTCTATCCTTCATTTGACACCATGGATAAAAGTCATTG
196 GAAAAACCATAGAAAAACATGATCTATCTCTATCCTTCATTTGACACCATGGATAAAAGTCATTG
282301 CTCACTAGAAA
261 CTCACTAGAAA
282312 TAA
1 TAA
282315 ATACGCCTCT
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 273 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (271 bp):
TAATTCACTAAGATATATTAGAAATATTTAAATTATTATTTTCAACAAATACAACATTCATGTCA
TAAACCACCTATATTTAGCAACCTCATTAAATGATGATTCATACAACACAATTAAATTGCAGCAA
GAATTTGGCAAACACTAATGGATGTTGCTCCATCATATAAAGCAATATTAACTTTGTATACCTAA
GAAAAACCATAGAAAAACATGATCTATCTCTATCCTTCATTTGACACCATGGATAAAAGTCATTG
CTCACTAGAAA
Found at i:286583 original size:2 final size:2
Alignment explanation
Indices: 286576--286600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
286566 AGAATTTCAT
286576 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
286601 TAAAATTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:287590 original size:22 final size:23
Alignment explanation
Indices: 287542--287591 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
287532 TTTAACGAAT
*
287542 TTAAT-ATATAAAATTTAATTTA
1 TTAATAATATAAAATTTAATATA
287564 TTAATAATA-AAAATTTAATA-A
1 TTAATAATATAAAATTTAATATA
287585 TATAATA
1 T-TAATA
287592 TGATATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 20 0.80
23 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATAATATAAAATTTAATATA
Found at i:287804 original size:33 final size:35
Alignment explanation
Indices: 287763--287834 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 35
287753 TTTTAAAATA
287763 AAAATTTAAATTT-TTTAATT-AAAAAAT-ATATTT
1 AAAATTT-AATTTATTTAATTCAAAAAATAATATTT
* *
287796 AAAATTTAATTTATTTAATTCATATAATAATATTT
1 AAAATTTAATTTATTTAATTCAAAAAATAATATTT
287831 AAAA
1 AAAA
287835 AGAATTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 5 0.15
33 14 0.41
34 5 0.15
35 10 0.29
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (35 bp):
AAAATTTAATTTATTTAATTCAAAAAATAATATTT
Found at i:288101 original size:2 final size:2
Alignment explanation
Indices: 288094--288119 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
288084 GCATTCATCC
288094 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
288120 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:288124 original size:2 final size:2
Alignment explanation
Indices: 288119--288148 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
288109 TCTCTCTCTC
288119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
288149 CACACATCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:288847 original size:34 final size:34
Alignment explanation
Indices: 288803--288892 Score: 162
Period size: 34 Copynumber: 2.6 Consensus size: 34
288793 TGAAATTTAC
*
288803 TTGCTCTCGTCTACTCCATGAAAAGATTTGTAAT
1 TTGCTTTCGTCTACTCCATGAAAAGATTTGTAAT
288837 TTGCTTTCGTCTACTCCATGAAAAGATTTGTAAT
1 TTGCTTTCGTCTACTCCATGAAAAGATTTGTAAT
*
288871 TTGCTTTCGTCTATTCCATGAA
1 TTGCTTTCGTCTACTCCATGAA
288893 GCAAAGATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (34 bp):
TTGCTTTCGTCTACTCCATGAAAAGATTTGTAAT
Found at i:289779 original size:34 final size:34
Alignment explanation
Indices: 289733--289798 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
289723 CTCCCTCTAC
*
289733 ATTCCTTAACTCATGATTTGTGACAATTTCATGT
1 ATTCCTTAACTCATGATTTGTAACAATTTCATGT
*
289767 ATTCCATT-ACTCATGATTTGTAACGATTTCAT
1 ATTCC-TTAACTCATGATTTGTAACAATTTCAT
289799 AAGAGAGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (34 bp):
ATTCCTTAACTCATGATTTGTAACAATTTCATGT
Found at i:291190 original size:22 final size:22
Alignment explanation
Indices: 291171--291219 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
291161 TTTTCGTATA
291171 GGTCAT-TCAAATTTCACGTACT
1 GGTCATCT-AAATTTCACGTACT
*
291193 GGTCATCTATATTTCACGTACT
1 GGTCATCTAAATTTCACGTACT
*
291215 TGTCA
1 GGTCA
291220 AAATTGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (22 bp):
GGTCATCTAAATTTCACGTACT
Found at i:298083 original size:28 final size:27
Alignment explanation
Indices: 298046--298140 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 27
298036 ATCATATAAA
* *
298046 ATATTATATAATTTATATGATATTTTTT
1 ATATTTTATAATTTAT-TTATATTTTTT
* * * *
298074 ATATTTTAT-ATATATTTAAAATTTTG
1 ATATTTTATAATTTATTTATATTTTTT
298100 ATATATTTATAATTTATTTTATATTTATATT
1 ATAT-TTTATAATTTA-TTTATATTT-T-TT
298131 A-ATTTTATAA
1 ATATTTTATAA
298141 ATATAACAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
26 11 0.21
27 10 0.19
28 12 0.23
29 14 0.27
30 3 0.06
31 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATATTTTATAATTTATTTATATTTTTT
Found at i:306596 original size:78 final size:78
Alignment explanation
Indices: 306467--306619 Score: 270
Period size: 78 Copynumber: 2.0 Consensus size: 78
306457 TTATGATAAC
* *
306467 TTTATCTACAGTAAAGGCTTTAGCTTTCTCTTATTATTAGTTCACCTTAACCCTAGTAAAAACAG
1 TTTATCTACAATAAAGGCTTTAGCCTTCTCTTATTATTAGTTCACCTTAACCCTAGTAAAAACAG
306532 TAATCTTTTGTAA
66 TAATCTTTTGTAA
* *
306545 TTTATCTACAATAAAGGCTTTAGCCTTCTCTTTTTATTAGTTCACCTTAACCCTAGTAAAAATAG
1 TTTATCTACAATAAAGGCTTTAGCCTTCTCTTATTATTAGTTCACCTTAACCCTAGTAAAAACAG
306610 TAATCTTTTG
66 TAATCTTTTG
306620 GCTGTCTGCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (78 bp):
TTTATCTACAATAAAGGCTTTAGCCTTCTCTTATTATTAGTTCACCTTAACCCTAGTAAAAACAG
TAATCTTTTGTAA
Found at i:308543 original size:2 final size:2
Alignment explanation
Indices: 308536--308570 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
308526 ATTTGTCGTG
308536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
308571 CTTTTACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:315503 original size:19 final size:19
Alignment explanation
Indices: 315458--315503 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
315448 ATATAAATAA
*
315458 AATATTAATAATAATTTTT
1 AATATTTATAATAATTTTT
*
315477 AA-ATTTATAA-ATTTTTT
1 AATATTTATAATAATTTTT
315494 GAATATTTAT
1 -AATATTTAT
315504 TTAATGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AATATTTATAATAATTTTT
Found at i:319729 original size:19 final size:18
Alignment explanation
Indices: 319704--319768 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
319694 ATTTCAACGA
319704 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
319722 TGTTGTATTGATAC--AA-
1 T-TTGTATCGATACATAAG
319738 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
319754 TTTTGTATCGATACA
1 -TTTGTATCGATACA
319769 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:319747 original size:32 final size:32
Alignment explanation
Indices: 319706--319776 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
319696 TTCAACGATT
*
319706 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
319738 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
319770 TGTATCG
1 TGTATCG
319777 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:319839 original size:13 final size:13
Alignment explanation
Indices: 319821--319845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319811 ATTACTCAAA
319821 TGTATCGATACAT
1 TGTATCGATACAT
319834 TGTATCGATACA
1 TGTATCGATACA
319846 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:319898 original size:52 final size:51
Alignment explanation
Indices: 319834--319982 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
319824 ATCGATACAT
** * *
319834 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGAAAATTTGCCTAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
319886 TGTATCGATACACTA-CAAAATGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
319938 TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
319983 TCATATTTCG
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 84 0.98
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:323517 original size:53 final size:53
Alignment explanation
Indices: 323456--323556 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
323446 TTATTTTGGA
*
323456 TTTGGGTCATT-TCAGATTCGGGTCAATCGGGTTTAACACTCTAGTTAATCAAG
1 TTTGGGTCATTCT-AGATTCGGGTCAATCGGGTTTAACACTCGAGTTAATCAAG
* * *
323509 TTTGGGTCATTCTGGATTCGGGTCAATTGGGTTTAACATTCGAGTTAA
1 TTTGGGTCATTCTAGATTCGGGTCAATCGGGTTTAACACTCGAGTTAA
323557 ATCAGGTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 42 0.98
54 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (53 bp):
TTTGGGTCATTCTAGATTCGGGTCAATCGGGTTTAACACTCGAGTTAATCAAG
Found at i:324331 original size:16 final size:16
Alignment explanation
Indices: 324293--324338 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
324283 CAGGTTAATT
*
324293 GTCATTTTGGGTTCAA
1 GTCATTTTGGGTTTAA
*
324309 GTCATTTTGGGTTTAG
1 GTCATTTTGGGTTTAA
* *
324325 GTTATTTCGGGTTT
1 GTCATTTTGGGTTT
324339 TGGATCGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.50
Consensus pattern (16 bp):
GTCATTTTGGGTTTAA
Found at i:326188 original size:80 final size:77
Alignment explanation
Indices: 325983--326218 Score: 217
Period size: 80 Copynumber: 3.0 Consensus size: 77
325973 ATATCCTCTC
** * * ** *
325983 AGAGATGGTTAGGTTGGAGTATCCCTAGAGATGAAAAATTCAGCATTTTGGAAGTGAAACGGGTT
1 AGAGATGGTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAGTGTTTTGAAAGT-AAACGGGTT
* *
326048 GGAGTATCTCTTA
65 AGAGTATCCCTTA
** * * **
326061 AGAGATGGTGGGACTAGAGTATTCCCAAAGATGAAAAATTTGGTGTTTTGAAAGTAACATCGGGG
1 AGAGATGGTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAGTGTTTTGAAAGTAA-A-C-GGG
326126 TTAGAGTATTCCCTT-
63 TTAGAGTA-TCCCTTA
* *
326141 GGAGATGGTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAATGTTTT-AGAAGTAAAAACAGG
1 AGAGATGGTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAGTGTTTTGA-AAGT--AAAC-GG
326205 GTTAGAGTA-CCCTT
62 GTTAGAGTATCCCTT
326219 TTTGATATTT
Statistics
Matches: 127, Mismatches: 24, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
77 2 0.02
78 48 0.38
79 2 0.02
80 67 0.53
81 6 0.05
82 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (77 bp):
AGAGATGGTGGGGTTGGAGTATCCCCAAAGATGAAAAATTCAGTGTTTTGAAAGTAAACGGGTTA
GAGTATCCCTTA
Found at i:328590 original size:20 final size:20
Alignment explanation
Indices: 328565--328619 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
328555 AATAGCATGT
328565 ATGTATCAATACATTGAAGA
1 ATGTATCAATACATTGAAGA
328585 ATGTATCAATACATTGAAGA
1 ATGTATCAATACATTGAAGA
328605 ATGTATCAATACATT
1 ATGTATCAATACATT
328620 TGGGTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCAATACATTGAAGA
Found at i:328706 original size:20 final size:20
Alignment explanation
Indices: 328635--328708 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
328625 CAAAAACCTA
* *
328635 GAATGTATCGATACAATGAGT
1 GAATGTATCGATAC-ATAAAT
***
328656 G-ATGTATCGATACATTGTT
1 GAATGTATCGATACATAAAT
* *
328675 AGCATTTATCGATACATAAAT
1 -GAATGTATCGATACATAAAT
328696 GAATGTATCGATA
1 GAATGTATCGATA
328709 AAATATTTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.07
20 24 0.57
21 15 0.36
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
GAATGTATCGATACATAAAT
Found at i:328794 original size:20 final size:20
Alignment explanation
Indices: 328769--328822 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
328759 CATCATAAGC
*
328769 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTAACTT
*
328789 ATGTATTGATACATTAACTT
1 ATGTATCGATACATTAACTT
328809 ATTGTATCGATACA
1 A-TGTATCGATACA
328823 AATTCCAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:329499 original size:32 final size:32
Alignment explanation
Indices: 329463--329601 Score: 109
Period size: 32 Copynumber: 4.3 Consensus size: 32
329453 TGTTGTTCAT
* *
329463 AATAGCTCATATTCAAAATAATTCTTGTTTAG
1 AATAGCTCATATTCAAAATAACTCTTGTTTAA
* * * * * *
329495 AATAGCCCACATTTAGAATAACTATTGTTTAG
1 AATAGCTCATATTCAAAATAACTCTTGTTTAA
* * *
329527 AATAGCTTA-AGTTCAAAACAACTCTCGTTTAA
1 AATAGCTCATA-TTCAAAATAACTCTTGTTTAA
* ** * *
329559 AATAGCTCATGTTCAAAATAGTTTTTGTTGAA
1 AATAGCTCATATTCAAAATAACTCTTGTTTAA
*
329591 AACAGCTCATA
1 AATAGCTCATA
329602 ATTAGAATAG
Statistics
Matches: 81, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
31 1 0.01
32 80 0.99
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (32 bp):
AATAGCTCATATTCAAAATAACTCTTGTTTAA
Found at i:331102 original size:43 final size:43
Alignment explanation
Indices: 331041--331167 Score: 123
Period size: 43 Copynumber: 3.0 Consensus size: 43
331031 TTGGTAAACA
* ** *
331041 CCACTAAATTTGA-ATATTTAGTGGTGTTTATAGC-TTAAAAATG
1 CCACTAAATTT-ATTTATTTAGCAGTGTTTATA-CATCAAAAATG
* *
331084 CCACTAAATTTATTTATTTAGCAGTGTTTATACATCGAAAATT
1 CCACTAAATTTATTTATTTAGCAGTGTTTATACATCAAAAATG
* * ** *
331127 CCATTAAATTTATTGATTTAGCAGCATTTATACATCGAAAA
1 CCACTAAATTTATTTATTTAGCAGTGTTTATACATCAAAAA
331168 CACTACTAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 70 0.97
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (43 bp):
CCACTAAATTTATTTATTTAGCAGTGTTTATACATCAAAAATG
Found at i:331178 original size:43 final size:43
Alignment explanation
Indices: 331084--331180 Score: 131
Period size: 43 Copynumber: 2.3 Consensus size: 43
331074 CTTAAAAATG
* ** **
331084 CCACTAAATTTATTTATTTAGCAGTGTTTATACATCGAAAATT
1 CCACTAAATTTATTGATTTAGCAGCATTTATACATCGAAAACA
*
331127 CCATTAAATTTATTGATTTAGCAGCATTTATACATCGAAAACA
1 CCACTAAATTTATTGATTTAGCAGCATTTATACATCGAAAACA
*
331170 CTACTAAATTT
1 CCACTAAATTT
331181 GGATATTTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (43 bp):
CCACTAAATTTATTGATTTAGCAGCATTTATACATCGAAAACA
Found at i:337422 original size:4 final size:5
Alignment explanation
Indices: 337396--337424 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
337386 ATTTTTAAAA
337396 ATTTT ATTTT ATTTT ATTTT A-TTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
337425 CTTCAACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:337747 original size:10 final size:10
Alignment explanation
Indices: 337732--337785 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
337722 AAGTAGAGAG
337732 AAAAAAAGAAA
1 AAAAAAAG-AA
337743 AAAAAAAGAA
1 AAAAAAAGAA
*
337753 GAAAAAAGAA
1 AAAAAAAGAA
* * *
337763 AGAAAAATAG
1 AAAAAAAGAA
*
337773 AGAAAAAGAA
1 AAAAAAAGAA
337783 AAA
1 AAA
337786 TTAAGGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
10 27 0.77
11 8 0.23
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:337757 original size:21 final size:20
Alignment explanation
Indices: 337728--337785 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
337718 AAAAAAGTAG
337728 AGAGAAAAAAAGAAAAAAAAA
1 AGAG-AAAAAAGAAAAAAAAA
*
337749 AGAAGAAAAAAGAAAGAAAAAT
1 AG-AGAAAAAAGAAA-AAAAAA
337771 AGAG-AAAAAGAAAAA
1 AGAGAAAAAAGAAAAA
337786 TTAAGGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 9 0.26
21 14 0.41
22 9 0.26
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AGAGAAAAAAGAAAAAAAAA
Found at i:337764 original size:14 final size:14
Alignment explanation
Indices: 337737--337785 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
337727 GAGAGAAAAA
*
337737 AAGAAAAAAAAAAG
1 AAGAAAAAAGAAAG
337751 AAGAAAAAAGAAAG
1 AAGAAAAAAGAAAG
*
337765 AA-AAATAGAGAAA-
1 AAGAAA-AAAGAAAG
337778 AAGAAAAA
1 AAGAAAAA
337786 TTAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAGAAAG
Found at i:341347 original size:33 final size:33
Alignment explanation
Indices: 341307--341375 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
341297 CCGTTACAAG
*
341307 CAATGTATCAATACAATT-CATCATGTATCGATA
1 CAATGTATCAATAC-ATTGCACCATGTATCGATA
** *
341340 CAATGTATTGATACATTGTACCATGTATCGATA
1 CAATGTATCAATACATTGCACCATGTATCGATA
341373 CAA
1 CAA
341376 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACATTGCACCATGTATCGATA
Found at i:341443 original size:13 final size:13
Alignment explanation
Indices: 341425--341451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
341415 ACAATTGTCC
341425 ATGTATCGATACA
1 ATGTATCGATACA
341438 ATGTATCGATACA
1 ATGTATCGATACA
341451 A
1 A
341452 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:344633 original size:17 final size:17
Alignment explanation
Indices: 344607--344640 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
344597 GTAGCATATG
*
344607 ATTTGTTCCTTGTCCTT
1 ATTTGCTCCTTGTCCTT
344624 ATTTGCTCCTTGTCCTT
1 ATTTGCTCCTTGTCCTT
344641 CTTACTTGTT
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:0.06, C:0.26, G:0.12, T:0.56
Consensus pattern (17 bp):
ATTTGCTCCTTGTCCTT
Found at i:346411 original size:13 final size:13
Alignment explanation
Indices: 346371--346423 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
346361 CCGTTACAAG
346371 CAATGTATCGATA
1 CAATGTATCGATA
346384 CAA--T-TC-AT-
1 CAATGTATCGATA
346392 C-ATGTATCGATA
1 CAATGTATCGATA
346404 CAATGTATCGATA
1 CAATGTATCGATA
*
346417 CATTGTA
1 CAATGTA
346424 CCATATATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:346437 original size:33 final size:33
Alignment explanation
Indices: 346371--346439 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
346361 CCGTTACAAG
* *
346371 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAATTCACCATATATCGATA
* *
346404 CAATGTATCGATAC-ATTGTACCATATATTGATA
1 CAATGTATCGATACAATT-CACCATATATCGATA
346437 CAA
1 CAA
346440 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATATATCGATA
Found at i:346512 original size:19 final size:19
Alignment explanation
Indices: 346468--346523 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
346458 CTGCTAGTTT
* **
346468 CATGTTTCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
346488 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
346507 CATGTATCGATACAATG
1 CATGTATCGATACAATG
346524 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:346526 original size:13 final size:13
Alignment explanation
Indices: 346508--346534 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
346498 TACAATGAAC
346508 ATGTATCGATACA
1 ATGTATCGATACA
346521 ATGTATCGATACA
1 ATGTATCGATACA
346534 A
1 A
346535 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:347096 original size:31 final size:31
Alignment explanation
Indices: 347058--347120 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
347048 GACTTAGGAT
*
347058 TTTTGCAAAAGGAAACACTTTTTTAAGAAAC
1 TTTTGCAAAAGGAAACACTTCTTTAAGAAAC
347089 TTTTGCAAAAGGAAACACTTCTTTAAGAAAC
1 TTTTGCAAAAGGAAACACTTCTTTAAGAAAC
347120 T
1 T
347121 CTAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (31 bp):
TTTTGCAAAAGGAAACACTTCTTTAAGAAAC
Found at i:351867 original size:20 final size:21
Alignment explanation
Indices: 351837--351881 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
351827 GTTCTAAGAT
* * *
351837 TTTTCATTTTTTTATTTATTC
1 TTTTCATTTTTATAGTTATTA
351858 TTTT-ATTTTTATAGTTATTA
1 TTTTCATTTTTATAGTTATTA
351878 TTTT
1 TTTT
351882 TGATTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCATTTTTATAGTTATTA
Found at i:353207 original size:13 final size:13
Alignment explanation
Indices: 353133--353260 Score: 59
Period size: 13 Copynumber: 9.8 Consensus size: 13
353123 AATAAAACCT
*
353133 ATTTAAATTTTAAA
1 ATTTAAAATTT-AA
*
353147 ATTTAAAATTTGA
1 ATTTAAAATTTAA
* *
353160 ATTTATATTTTGAA
1 ATTTAAAATTT-AA
**
353174 ATTT-TGA-TT-A
1 ATTTAAAATTTAA
*
353184 ATATTAGAATTTAA
1 AT-TTAAAATTTAA
353198 ATTTAAAATTTAA
1 ATTTAAAATTTAA
* *
353211 ATTTCAAA-TAACA
1 ATTTAAAATTTA-A
*
353224 ATCTTAAAATTCAA
1 AT-TTAAAATTTAA
*
353238 ATTGAATAA-TTAA
1 ATTTAA-AATTTAA
*
353251 TTTTAAAATT
1 ATTTAAAATT
353261 CAAACAGAAT
Statistics
Matches: 86, Mismatches: 18, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
10 3 0.03
11 2 0.02
12 7 0.08
13 44 0.51
14 28 0.33
15 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (13 bp):
ATTTAAAATTTAA
Found at i:358643 original size:14 final size:14
Alignment explanation
Indices: 358621--358651 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
358611 GTATCGATAA
*
358621 CTACGTTCAACAAC
1 CTACATTCAACAAC
358635 CTACATTCAACAAC
1 CTACATTCAACAAC
358649 CTA
1 CTA
358652 TGTATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.35, G:0.03, T:0.23
Consensus pattern (14 bp):
CTACATTCAACAAC
Found at i:359227 original size:20 final size:20
Alignment explanation
Indices: 359202--359239 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
359192 AATACAACAA
*
359202 GTGAATGCATCGATACATAG
1 GTGAATGCATAGATACATAG
*
359222 GTGAATGTATAGATACAT
1 GTGAATGCATAGATACAT
359240 GTCTAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
GTGAATGCATAGATACATAG
Found at i:359353 original size:48 final size:49
Alignment explanation
Indices: 359296--359430 Score: 148
Period size: 51 Copynumber: 2.7 Consensus size: 49
359286 TCTAGAAAGA
* *
359296 AAATGTATCGATACATTTTTATTGTATCGATA-ATTCTAGG-TTTGATCT
1 AAATGTATCGATACATTTTTATTGTATCGATACATTCT-GGCTTTGACCC
* *
359344 AAATGTATCGATACATTATTCATTTTATCGATACATTCTGGCTTTTGACCC
1 AAATGTATCGATACATT-TTTATTGTATCGATACATTCTGGC-TTTGACCC
* * * *
359395 AATTATATCAATACATTTTTCAATGTATCGATACAT
1 AAATGTATCGATACATTTTT-ATTGTATCGATACAT
359431 CCAATTAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
48 17 0.24
49 15 0.21
50 7 0.10
51 33 0.46
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (49 bp):
AAATGTATCGATACATTTTTATTGTATCGATACATTCTGGCTTTGACCC
Found at i:363034 original size:21 final size:22
Alignment explanation
Indices: 363010--363069 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
363000 AATATTTTTT
363010 ATTAATTAAATAA-TAATTTAA
1 ATTAATTAAATAATTAATTTAA
363031 ATTAATTAAATTAGATTTAATTTAA
1 ATTAATTAAA-TA-A-TTAATTTAA
*
363056 TTTAAATTAAATAA
1 ATT-AATTAAATAA
363070 ATTATTAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 10 0.30
22 2 0.06
23 1 0.03
24 1 0.03
25 12 0.36
26 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAATTAAATAATTAATTTAA
Found at i:363085 original size:30 final size:29
Alignment explanation
Indices: 363010--363078 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
363000 AATATTTTTT
* *
363010 ATTAATTAAATAATAATTTAAATTAATTAA
1 ATTAATTAAAT-TTAATTTAAATTAAATAA
*
363040 ATTAGATTTAATTTAATTTAAATTAAATAA
1 ATTA-ATTAAATTTAATTTAAATTAAATAA
363070 ATT-ATTAAA
1 ATTAATTAAA
363079 CTTTTAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
30 23 0.68
31 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTAATTAAATTTAATTTAAATTAAATAA
Found at i:365864 original size:3 final size:3
Alignment explanation
Indices: 365856--365885 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
365846 ATTTCAAAGA
365856 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
365886 TTTGGTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:367733 original size:1 final size:1
Alignment explanation
Indices: 367727--367751 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
367717 AGGGGCACTC
367727 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
367752 ACCATTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:370745 original size:15 final size:15
Alignment explanation
Indices: 370727--370778 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
370717 ATTTTAAGTG
*
370727 TATATATTTTTTTAT
1 TATATATTTTTTAAT
*
370742 TATATTATATTTTAAT
1 TATA-TATTTTTTAAT
*
370758 TATTTA-TTTTTACAT
1 TATATATTTTTTA-AT
370773 TATATA
1 TATATA
370779 ATCATTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 5 0.17
15 13 0.43
16 12 0.40
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATATTTTTTAAT
Found at i:370765 original size:18 final size:18
Alignment explanation
Indices: 370729--370789 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
370719 TTTAAGTGTA
*
370729 TATATTTTTTTATTATAT
1 TATATTTTATTATTATAT
370747 TATATTTTA--ATTAT-T
1 TATATTTTATTATTATAT
*
370762 TAT-TTTTA-CATTATAT
1 TATATTTTATTATTATAT
*
370778 AATCATTTTATT
1 TAT-ATTTTATT
370790 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 5 0.14
15 9 0.26
16 8 0.23
18 13 0.37
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TATATTTTATTATTATAT
Found at i:370775 original size:31 final size:33
Alignment explanation
Indices: 370716--370787 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
370706 TATTTTCATT
** *
370716 TATTTTAAGTGTATATATTTTTTTATTATATTA
1 TATTTTAAGTGTATATATTTTTACATTATATAA
*
370749 TATTTTAA-T-TATTTATTTTTACATTATATAA
1 TATTTTAAGTGTATATATTTTTACATTATATAA
370780 TCATTTTA
1 T-ATTTTA
370788 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.56
32 7 0.21
33 8 0.24
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (33 bp):
TATTTTAAGTGTATATATTTTTACATTATATAA
Found at i:372383 original size:23 final size:23
Alignment explanation
Indices: 372328--372387 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
372318 AAAAATATTT
*
372328 TTATTTTAAATTATTTATAAATA
1 TTATTTTAAATAATTTATAAATA
* * *
372351 TTAATATAAAATAATTT-TTAATA
1 TT-ATTTTAAATAATTTATAAATA
372374 TTATTTTAAATAAT
1 TTATTTTAAATAAT
372388 AAAATTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 10 0.33
23 9 0.30
24 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATTTTAAATAATTTATAAATA
Found at i:373078 original size:17 final size:17
Alignment explanation
Indices: 373056--373088 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
373046 ATTAATTTAT
*
373056 ATAATATTTTTTTAAAA
1 ATAATATTTTTATAAAA
373073 ATAATATTTTTATAAA
1 ATAATATTTTTATAAA
373089 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATATTTTTATAAAA
Found at i:374459 original size:17 final size:17
Alignment explanation
Indices: 374427--374461 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
374417 ATATGAAAAT
**
374427 ATTTAAATAATTACATA
1 ATTTAAATAAAAACATA
374444 ATTTAAATAAAAACATA
1 ATTTAAATAAAAACATA
374461 A
1 A
374462 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAAATAAAAACATA
Found at i:374496 original size:31 final size:32
Alignment explanation
Indices: 374453--374519 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
374443 AATTTAAATA
*
374453 AAAACATAAATAAAA-ATAATTTAAAAATTTTT
1 AAAACATAAATAAAATATAA-ATAAAAATTTTT
*
374485 AAAA-ATAAATAAAATTTAAATAAAAATTTTT
1 AAAACATAAATAAAATATAAATAAAAATTTTT
374516 AAAA
1 AAAA
374520 TTTAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAACATAAATAAAATATAAATAAAAATTTTT
Found at i:376329 original size:7 final size:7
Alignment explanation
Indices: 376317--376341 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
376307 TGTAAAAGTA
376317 CTTGTGC
1 CTTGTGC
376324 CTTGTGC
1 CTTGTGC
376331 CTTGTGC
1 CTTGTGC
376338 CTTG
1 CTTG
376342 ACATGGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.28, T:0.44
Consensus pattern (7 bp):
CTTGTGC
Found at i:377539 original size:23 final size:23
Alignment explanation
Indices: 377513--377569 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
377503 TGGACATGTT
377513 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
*
377536 AAAAATGCATGAAACATAATCAA
1 AAAAATGCATGAAACATAATAAA
377559 AAAAATGCATG
1 AAAAATGCATG
377570 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:378532 original size:20 final size:20
Alignment explanation
Indices: 378485--378559 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
378475 AAAAAGACAT
* ** *
378485 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
378505 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
378525 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
378545 AATGTATCGATACAT
1 AATGTATCGATACAT
378560 CAGGGTATGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:378553 original size:40 final size:39
Alignment explanation
Indices: 378482--378559 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
378472 GGTAAAAAGA
* * *
378482 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
378521 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
378560 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:379142 original size:32 final size:32
Alignment explanation
Indices: 379087--379971 Score: 922
Period size: 32 Copynumber: 29.2 Consensus size: 32
379077 AAAATGGTGA
* * * **
379087 TTTGAAAAGGGTTACCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379119 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379151 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
379183 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
379215 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
379247 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379279 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379311 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379343 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379375 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
379407 TTTGGAATGGGTTGCCACAGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
379439 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379471 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379503 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
379535 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
379565 TCTGAAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379593 TTTGAAA-GGG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
379621 TTTGAAAAGAG-TGCCGCTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379650 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
**
379679 TTTGAAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
379707 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
379736 TTTGAAAAGAG-TGCCACTGGC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379765 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* ** *
379794 TTTGAAA--GGATGCCAATGA-GT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
379822 TTTGAAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
379850 TTTGAAAAGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379879 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
379907 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
379936 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
379965 TTTGAAA
1 TTTGAAA
379972 GGGATGAACA
Statistics
Matches: 792, Mismatches: 44, Indels: 37
0.91 0.05 0.04
Matches are distributed among these distances:
27 1 0.00
28 149 0.19
29 211 0.27
30 13 0.02
31 1 0.00
32 417 0.53
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:381214 original size:5 final size:5
Alignment explanation
Indices: 381204--381246 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
381194 TTTTTTGCTA
* *
381204 TTTT- TTTTT TTTTG TTTTT TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
381247 TTTGGTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (5 bp):
TTTTG
Found at i:381222 original size:15 final size:15
Alignment explanation
Indices: 381194--381248 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
381184 GACCCTTCTA
381194 TTTTTTGCTATTTTTTT
1 TTTTTTG-T-TTTTTTT
381211 TTTTTTGTTTTTTTT
1 TTTTTTGTTTTTTTT
*
381226 TGTTTTGTTTTGTTTT
1 TTTTTTGTTTT-TTTT
381242 GTTTTTT
1 -TTTTTT
381249 TGGTGTAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 17 0.50
16 5 0.15
17 12 0.35
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (15 bp):
TTTTTTGTTTTTTTT
Found at i:393083 original size:7 final size:7
Alignment explanation
Indices: 393071--393095 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
393061 TGTAAAAGTA
393071 CTTGTGC
1 CTTGTGC
393078 CTTGTGC
1 CTTGTGC
393085 CTTGTGC
1 CTTGTGC
393092 CTTG
1 CTTG
393096 ACATGGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.28, T:0.44
Consensus pattern (7 bp):
CTTGTGC
Found at i:394315 original size:24 final size:23
Alignment explanation
Indices: 394268--394320 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
394258 TGGACATGTT
394268 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
*
394291 AAAAATGCATGAAACATAATCAA
1 AAAAATGCATGAAACATAATAAA
394314 AAAAATG
1 AAAAATG
394321 TATGGTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.17
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:395286 original size:20 final size:20
Alignment explanation
Indices: 395239--395313 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
395229 AAAAAGACAT
* ** *
395239 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
395259 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
395279 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
395299 AATGTATCGATACAT
1 AATGTATCGATACAT
395314 CAGGGTATGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:395307 original size:40 final size:39
Alignment explanation
Indices: 395236--395313 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
395226 GGTAAAAAGA
* * *
395236 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
395275 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
395314 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:395967 original size:24 final size:24
Alignment explanation
Indices: 395940--395992 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
395930 ACTCTTATCA
395940 AATTATT-ATTTAATTAATAAAAAT
1 AATTATTAATTTAATT-ATAAAAAT
*
395964 AATT-TTAATTTAATTATAAATAT
1 AATTATTAATTTAATTATAAAAAT
395987 ATATTA
1 A-ATTA
395993 ATATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTATTAATTTAATTATAAAAAT
Found at i:397539 original size:16 final size:15
Alignment explanation
Indices: 397517--397559 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
397507 AATTATTCCC
*
397517 TTTATAATAATTATT
1 TTTATAATAATTATA
*
397532 TATTATAATGATTATA
1 T-TTATAATAATTATA
*
397548 TTTATAACAATT
1 TTTATAATAATT
397560 TTTGAGTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTATAATAATTATA
Found at i:397663 original size:3 final size:3
Alignment explanation
Indices: 397655--397685 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
397645 AGTTATAGAG
397655 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
397686 TGCAGGAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:398706 original size:13 final size:13
Alignment explanation
Indices: 398688--398717 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
398678 AAATGATATG
398688 ATTACTTGTTTTT
1 ATTACTTGTTTTT
*
398701 ATTACTTTTTTTT
1 ATTACTTGTTTTT
398714 ATTA
1 ATTA
398718 TCTATGTAAC
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:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (13 bp):
ATTACTTGTTTTT
Found at i:402294 original size:2 final size:2
Alignment explanation
Indices: 402287--402322 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
402277 CAAACTATTG
402287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402323 TATCCCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403673 original size:21 final size:21
Alignment explanation
Indices: 403644--403688 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
403634 CTATTCAGAT
403644 TATTATTTAATTAATAAAAAA
1 TATTATTTAATTAATAAAAAA
* * *
403665 TATTTTTTAATTATTATAAAA
1 TATTATTTAATTAATAAAAAA
403686 TAT
1 TAT
403689 AAATATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATTTAATTAATAAAAAA
Found at i:404842 original size:48 final size:48
Alignment explanation
Indices: 404771--404868 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
404761 ACAGCAATTA
*
404771 ATCCAGTCGGAAGGATTAATATTAATCTGCATGACAATCACTAAGTAT
1 ATCCAGTCGGAAGGATTAATATTAATCTGCATGAAAATCACTAAGTAT
*
404819 ATCCAGTTGGAAGGATTAATATTAATCTGCATGAAAATCACTAAGTAT
1 ATCCAGTCGGAAGGATTAATATTAATCTGCATGAAAATCACTAAGTAT
404867 AT
1 AT
404869 GATTGATACT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (48 bp):
ATCCAGTCGGAAGGATTAATATTAATCTGCATGAAAATCACTAAGTAT
Found at i:405349 original size:2 final size:2
Alignment explanation
Indices: 405337--405369 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
405327 AAGTATTAGG
*
405337 AT AT A- AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
405370 TTGATCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:405652 original size:3 final size:3
Alignment explanation
Indices: 405644--405674 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
405634 ATTAATTAAT
*
405644 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
405675 TTTTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:406589 original size:22 final size:22
Alignment explanation
Indices: 406540--406589 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
406530 ATGAATTAAA
* * *
406540 TATAATATATTTATATTTTATT
1 TATATTATATTTATATTATAAT
* *
406562 TGTATTATTTTTATATTATAAT
1 TATATTATATTTATATTATAAT
406584 TATATT
1 TATATT
406590 TAAAATACTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATATTATATTTATATTATAAT
Found at i:406984 original size:2 final size:2
Alignment explanation
Indices: 406979--407005 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
406969 TATTTTCCAT
406979 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
407006 GCGCAGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:407581 original size:3 final size:3
Alignment explanation
Indices: 407565--407598 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
407555 AAAAAAAAAA
* *
407565 TAT TAT GAT GAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
407599 TGCAGAGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:408247 original size:31 final size:31
Alignment explanation
Indices: 408212--408272 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
408202 TCAATATATA
408212 TATATAATT-AATT-TTTAATTTATAAAAAATT
1 TATAT-ATTAAATTATTTAA-TTATAAAAAATT
*
408243 TATATATTAAATTATTTTATTATAAAAAAT
1 TATATATTAAATTATTTAATTATAAAAAAT
408273 AAAGCCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 20 0.74
32 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TATATATTAAATTATTTAATTATAAAAAATT
Found at i:409045 original size:141 final size:142
Alignment explanation
Indices: 408889--409178 Score: 444
Period size: 142 Copynumber: 2.0 Consensus size: 142
408879 AGAAAAGTAA
*
408889 AAAATATATATAAATAAAGATATTTTATA-TCTGATACATAGTAGATTGATTATTGTTCCTCTTA
1 AAAA-ATATATAAATAAAGATATTTTATACT-TGATAAATAGTAGATTGATTATTGTTCCTCTTA
*
408953 TGGGTAGA-TTTGTTAAGGAATATCACTTCGAATAATAATA-TTTCTACC-AAAAGAAGATGATT
64 TGGGTAGATTTTGTTAAGGAATATCACTTCGAATAATAATATTTTC-ACCAAAAAG-AGATAATT
409015 CTTTTTTTTAAGCCAT
127 CTTTTTTTTAAGCCAT
* * * * *
409031 AAAAATATATAAATAAAGATATTTTATACTTGATAAATAGTGGGTTGATTGTTGTTTCTCTTATT
1 AAAAATATATAAATAAAGATATTTTATACTTGATAAATAGTAGATTGATTATTGTTCCTCTTATG
*
409096 GGTAGATTTTGTTAAGGAATATCACTTCGAATAATAATATTTTCATCAAAAAGAGATAATTCTTT
66 GGTAGATTTTGTTAAGGAATATCACTTCGAATAATAATATTTTCACCAAAAAGAGATAATTCTTT
409161 TTTTTAAGCCAT
131 TTTTTAAGCCAT
409173 AAAAAT
1 AAAAAT
409179 TTTGATGAGA
Statistics
Matches: 136, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
141 59 0.43
142 68 0.50
143 9 0.07
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (142 bp):
AAAAATATATAAATAAAGATATTTTATACTTGATAAATAGTAGATTGATTATTGTTCCTCTTATG
GGTAGATTTTGTTAAGGAATATCACTTCGAATAATAATATTTTCACCAAAAAGAGATAATTCTTT
TTTTTAAGCCAT
Found at i:409249 original size:15 final size:15
Alignment explanation
Indices: 409214--409242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
409204 AAAAAAAATT
409214 GAGA-AAAAAAAGAG
1 GAGATAAAAAAAGAG
409228 GAGATAAAAAAAGAG
1 GAGATAAAAAAAGAG
409243 ATGATAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (15 bp):
GAGATAAAAAAAGAG
Found at i:410489 original size:2 final size:2
Alignment explanation
Indices: 410484--410512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
410474 AATTGTATTT
410484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
410513 GAACCTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:411225 original size:2 final size:2
Alignment explanation
Indices: 411218--411247 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
411208 ATAAACAAAT
411218 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
411248 TTGTAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:413170 original size:2 final size:2
Alignment explanation
Indices: 413098--413152 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
413088 TTCTTTTGTA
*
413098 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
413140 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
413153 GTATTTTGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:413725 original size:2 final size:2
Alignment explanation
Indices: 413718--413742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
413708 AGGGATAAAC
413718 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
413743 AAGAAGAATG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:414768 original size:2 final size:2
Alignment explanation
Indices: 414763--414794 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
414753 CATCTATACG
414763 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
414795 TGTTGAATTG
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:419642 original size:24 final size:23
Alignment explanation
Indices: 419614--419668 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
419604 TTATTAAAAA
419614 ATTTTAAAAGTAAATATATAATAT
1 ATTTTAAAA-TAAATATATAATAT
* *
419638 ATTTTTTAAATAAATATATGATAT
1 A-TTTTAAAATAAATATATAATAT
*
419662 AATTTAA
1 ATTTTAA
419669 TATATGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 4 0.15
24 15 0.58
25 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
ATTTTAAAATAAATATATAATAT
Found at i:419647 original size:26 final size:24
Alignment explanation
Indices: 419615--419662 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
419605 TATTAAAAAA
*
419615 TTTTAAAAGTAAATATATAATATAT
1 TTTTTAAA-TAAATATATAATATAT
*
419640 TTTTTAAATAAATATATGATATA
1 TTTTTAAATAAATATATAATATA
419663 ATTTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTTTAAATAAATATATAATATAT
Found at i:419670 original size:17 final size:17
Alignment explanation
Indices: 419648--419689 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
419638 ATTTTTTAAA
419648 TAAATATATGATATA-AT
1 TAAATATATG-TATACAT
*
419665 TTAATATATGTATACAT
1 TAAATATATGTATACAT
419682 TAAATATA
1 TAAATATA
419690 AATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (17 bp):
TAAATATATGTATACAT
Found at i:425095 original size:20 final size:20
Alignment explanation
Indices: 425070--425122 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
425060 TTTGCCTGAA
425070 TGTATCGATACATTTCATAG
1 TGTATCGATACATTTCATAG
425090 TGTATCGATACATTTCATAG
1 TGTATCGATACATTTCATAG
425110 TGTATCGATACAT
1 TGTATCGATACAT
425123 CTGGGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTCATAG
Found at i:425172 original size:52 final size:52
Alignment explanation
Indices: 425090--425205 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
425080 CATTTCATAG
425090 TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
1 TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
* * *
425142 TGTATCAATACATTTTATAGTGTATTGATACATCTGGGCAAATTTGCCTGCA
1 TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
425194 TGTATCGATACA
1 TGTATCGATACA
425206 AAGATCAGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
Found at i:425216 original size:52 final size:52
Alignment explanation
Indices: 425106--425225 Score: 179
Period size: 52 Copynumber: 2.3 Consensus size: 52
425096 GATACATTTC
***
425106 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATTTT
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
* *
425158 ATAGTGTATTGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAG
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
425209 ATCAGTGTATCGATACA
1 AT-AGTGTATCGATACA
425226 ATGTATCGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 2 0.03
52 59 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
Found at i:425232 original size:13 final size:13
Alignment explanation
Indices: 425214--425238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
425204 CAAAGATCAG
425214 TGTATCGATACAA
1 TGTATCGATACAA
425227 TGTATCGATACA
1 TGTATCGATACA
425239 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:425305 original size:19 final size:18
Alignment explanation
Indices: 425281--425378 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
425271 TAGCTTATAT
425281 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
425300 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
425313 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
425332 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
425345 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
425365 TGTATCGATACAAA
1 TGTATCGATACAAA
425379 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:425318 original size:13 final size:13
Alignment explanation
Indices: 425300--425356 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
425290 ACAAAACTTA
425300 TGTATCGATACAT
1 TGTATCGATACAT
425313 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
425331 ATGTATCGATACAT
1 -TGTATCGATACAT
425345 TGTATCGATACA
1 TGTATCGATACA
425357 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:425320 original size:32 final size:32
Alignment explanation
Indices: 425279--425376 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
425269 AGTAGCTTAT
*
425279 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
425311 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
425343 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
425376 A
1 A
425377 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:426426 original size:43 final size:43
Alignment explanation
Indices: 426365--427862 Score: 1207
Period size: 43 Copynumber: 32.0 Consensus size: 43
426355 GACAAAGACA
426365 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
426408 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTG
** * *
426457 CCAATATGCTGATTTGAGGCTAGCGATATTGGACTTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
426500 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-----T-TAAAGGTG
* *
426549 CAAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGTCAAAGG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-G-GT-----G
*
426599 CACCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 --CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * * *
426644 CCAATGTGCTGATTCAAGGCTAGTGATATTGGACTTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* *
426687 CCAATGTGCTGATTCAAGGCCAGCTG-CATTGGACTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGC-GATATTGGAC-T-----TAAAGGTG
* *
426736 CCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT---------G
426788 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
426831 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---A-A--A-GGTG
* * ** *
426881 CCAATATGCTGATTTAAGGCCAGCGATATTGGATTTGGAGTTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * * *
426924 CCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGATGATGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTG
* *
426973 CCAATATACTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGACAAAGG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT-------G
427023 CACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 --CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* *
427068 CCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
427111 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTG
*
427160 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGACAAAGG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT-------G
*
427210 CACCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTG
1 --CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
427255 CCAATGTGCTGATTCAAGGCCAACGATATTGGACTTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* *
427298 CCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTG
*
427347 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT---------G
*
427399 CCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * * *
427442 CCAATGTGCTGATTCAAGGTCAGCGACATTGGGCTTAAAAGATGAGGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---A-A--A-GGTG
** *
427492 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGTTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * * *
427535 CCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGATGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTG
* * *
427584 CCAATTTGCTGATTCAAGGCCAGCTATATTGGATTTAAAGGTGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT---------G
*
427636 CCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * *
427679 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---A-A--A-GGTG
** *
427729 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGTTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
* * * *
427772 TCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTG
427821 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT
427863 AAAAAAAAAG
Statistics
Matches: 1197, Mismatches: 133, Indels: 250
0.76 0.08 0.16
Matches are distributed among these distances:
43 512 0.43
44 12 0.01
45 5 0.00
46 6 0.01
47 7 0.01
48 7 0.01
49 297 0.25
50 113 0.09
51 1 0.00
52 237 0.20
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
Found at i:426644 original size:187 final size:182
Alignment explanation
Indices: 426260--428154 Score: 1583
Period size: 187 Copynumber: 10.0 Consensus size: 182
426250 TGACAAAGAC
* *
426260 GCCAATATGCTGATTCAAGGCCAGGGATATTGGACTTAAAGATGACAAAGGTGCTAATATGCTGA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TG---AAGGTGCCAATATGCTGA
*** *
426325 TTCAAGGCCAGCGATATTGGACTTAAAGGTGACAAAGACACCAATATGCTGATTCAAGGCCAGCG
57 TTCAAGGCCAGCGATATTGGACTT--A--T---AAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * *
426390 ATATTGGAC-------T-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
115 ACATTGGACTTAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT---
426447 GATGAAGGT
177 -A--AAGGT
** * *
426456 GCCAATATGCTGATTTGAGGCTAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGATTCAAGGCC
* * * *
426521 AGCTACATTGGACTTAAATATAAAGGTGCAAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
66 AGCGATATTGGAC-T---TATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
** * *
426586 AAGGTGTCAAAGGCACCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGT
127 AAGGTGT-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* * * *
426643 GCCAATGTGCTGATTCAAGGCTAGTGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGATTCAAGGCC
* * *
426708 AGCTG-CATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
66 AGC-GATATTGGACTT----ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
426772 AAAGGTGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT
126 AAAGGTG-TAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* * *
426830 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGCTGATT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----GA--A-GGTGCCAATATGCTGATT
* ** * * *
426895 TAAGGCCAGCGATATTGGA-TT-TGGAGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGAC
59 CAAGGCCAGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC
* * *
426958 TTAAAGATG--ATGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
124 TTAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* *
427015 GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
1 -------G--CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGA
* *
427080 TTCAAGGCCAGCGATATTGGAC-T-TGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
57 TTCAAGGCCAGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGG
*
427143 ACTTAAA-G-ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
122 ACTTAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* * *
427202 GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGTGCTGA
1 -------G--CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGA
* *
427267 TTCAAGGCCAACGATATTGGAC-T-TGAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGG
57 TTCAAGGCCAGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGG
*
427330 ACTTAAA-G-ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
122 ACTTAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* * *
427389 GACAAAGGCGCCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
1 ---------GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGA
* * * * * *
427454 TTCAAGGTCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGAT
57 TTCAAGGCCAGCGATATTGGACTT-ATA-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCTAC
* * * *
427519 ATTGGACTT----G-G---AGTTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGA
117 ATTGGACTTAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-A
427576 TGATGGT
179 --A-GGT
* * * *
427583 GCCAATTTGCTGATTCAAGGCCAGCTATATTGGATTTAAAGGTGACAAAGGCGCCAATATGCTGA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGA-CT-----TG---AAGGTGCCAATATGCTGA
* * *
427648 TTCAAGGCCAGTGATATTGGAC-T-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
57 TTCAAGGCCAGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGG
* * * * ** *
427711 GCTTAAAAGATG--AGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGTT
122 ACTT-AAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
* * * *
427771 GTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GA--A-GGTGCCAATATGCTGATTC
* * * *
427836 AAGGCCAGCGATATTGGACTTAAAGGTAAAAAAAAAGATGTCAATGTGTTGATTCAAGGCCAGCT
60 AAGGCCAGCGATATTGGACTT--A--T------AAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * * * *
427901 ATATTGAACTTAAAGATGGAAAAGGTGCCAATCTGCTGATTCAAGGCCAGCTATATTGGACTTAA
115 ACATTGGACTTAAAGGT-GTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
427966 AGGT
179 AGGT
* * *
427970 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAATGTGCCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAAG---GTGCCAATATGCTGATTC
* * * * *
428035 AAGGCCAGCTATATTGGACTTAGAACGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
60 AAGGCCAGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACT
** ** *
428100 TAAA-G-ACAAAGAAGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGG
125 TAAAGGTGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGG
428155 AAGATGCCAC
Statistics
Matches: 1462, Mismatches: 143, Indels: 198
0.81 0.08 0.11
Matches are distributed among these distances:
182 2 0.00
183 1 0.00
184 37 0.03
185 112 0.08
186 47 0.03
187 663 0.45
188 117 0.08
189 47 0.03
190 5 0.00
191 10 0.01
192 2 0.00
193 45 0.03
194 175 0.12
195 1 0.00
196 38 0.03
197 39 0.03
199 121 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (182 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGG
TGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT
Found at i:426662 original size:21 final size:21
Alignment explanation
Indices: 426638--426705 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
426628 ATTGGACTTA
426638 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
** *
426659 AAGGCTAGTGATAT-TG--GACTTG
1 AAGG-T-GCCA-ATGTGCTGA-TTC
426681 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
426702 AAGG
1 AAGG
426706 CCAGCTGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 4 0.12
21 13 0.38
22 9 0.26
23 4 0.12
24 2 0.06
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:427086 original size:21 final size:21
Alignment explanation
Indices: 427062--427129 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
427052 ATTGGACTTA
427062 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* * *
427083 AAGGCCAGCGATAT-TG--GACTTG
1 AAGG--TGCCA-ATGTGCTGA-TTC
427105 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
427126 AAGG
1 AAGG
427130 CCAGCTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Found at i:427273 original size:21 final size:21
Alignment explanation
Indices: 427249--427316 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
427239 ATTAGACTTA
427249 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
* ** *
427270 AA-G-GCCAACGATATTGGACTTG
1 AAGGTGCCAATG-TGCT-GA-TTC
*
427292 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATGTGCTGATTC
427313 AAGG
1 AAGG
427317 CCAGCTACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 6 0.18
20 3 0.09
21 10 0.30
22 6 0.18
23 3 0.09
24 5 0.15
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATGTGCTGATTC
Done.