Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 63 of 135
Found at i:21003946 original size:11 final size:11
Alignment explanation
Indices: 21003930--21003973 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
21003920 TCTAAAAAGA
*
21003930 TAAATATAAAT
1 TAAATACAAAT
21003941 TAAATACAAAT
1 TAAATACAAAT
21003952 TAAATACAAAT
1 TAAATACAAAT
*
21003963 TAAATATAAAT
1 TAAATACAAAT
21003974 AATATCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAATACAAAT
Found at i:21014382 original size:25 final size:25
Alignment explanation
Indices: 21014329--21014403 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
21014319 AAGAGTTTAA
* * * *
21014329 CTCTTATGAGCCCAAACAGAGTATTG
1 CTCTTACGAG-CCAGACAGAATATCG
21014355 CTCTTACGAGCCAGACAGAATATCG
1 CTCTTACGAGCCAGACAGAATATCG
* **
21014380 CTCTTACAAGCTTGACAGAATATC
1 CTCTTACGAGCCAGACAGAATATC
21014404 TTCATCGTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 33 0.79
26 9 0.21
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAGAATATCG
Found at i:21017373 original size:32 final size:32
Alignment explanation
Indices: 21017323--21017386 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
21017313 AGCGAGAGTC
* *
21017323 AATTGACTTAAAAGTGGGGATAAAAACACAAG
1 AATTAACTCAAAAGTGGGGATAAAAACACAAG
21017355 AATTAACTCAAAAGTGGGGATAAAAACACAAG
1 AATTAACTCAAAAGTGGGGATAAAAACACAAG
21017387 TTTTTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.17
Consensus pattern (32 bp):
AATTAACTCAAAAGTGGGGATAAAAACACAAG
Found at i:21021150 original size:20 final size:18
Alignment explanation
Indices: 21021117--21021153 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
21021107 TTTTTTAAAA
21021117 ATTAAAAAGTTAAAAATC
1 ATTAAAAAGTTAAAAATC
21021135 ATTAGAAAAGTATAAAAAT
1 ATTA-AAAAGT-TAAAAAT
21021154 AAAAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (18 bp):
ATTAAAAAGTTAAAAATC
Found at i:21024999 original size:43 final size:42
Alignment explanation
Indices: 21024850--21025041 Score: 181
Period size: 43 Copynumber: 4.5 Consensus size: 42
21024840 ATATCACAAT
** * * *
21024850 CGAGTCATAAGTCTTTCATTAAACATAATCTCATGTTCATCC
1 CGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATCC
* * * **
21024892 CGAGTCACGAGTCTTGCTTTAAACA-CATCTCATGCTCCTTT
1 CGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATCC
*
21024933 CGAGTCACAAGTCTTCCTTTTTAAACATAAATCTCATGCTCATCC
1 CGAGTCACGAGTCTTCC--TTTAAACAT-AATCTCATGCTCATCC
* *
21024978 CGAG-CTATGAGTCTTCCTTTAAAACATAATCTCATGCTCATCT
1 CGAGTC-ACGAGTCTTCCTTT-AAACATAATCTCATGCTCATCC
* * *
21025021 CGAGACATGAGTCTCCCTTTA
1 CGAGTCACGAGTCTTCCTTTA
21025042 TACGTCAAGT
Statistics
Matches: 124, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
41 26 0.21
42 22 0.18
43 43 0.35
44 8 0.06
45 25 0.20
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (42 bp):
CGAGTCACGAGTCTTCCTTTAAACATAATCTCATGCTCATCC
Found at i:21034604 original size:19 final size:19
Alignment explanation
Indices: 21034576--21034614 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
21034566 TTTATGGTTT
21034576 TAAATAATTTTTGGGTAAAA
1 TAAATAA-TTTTGGGTAAAA
*
21034596 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
21034614 T
1 T
21034615 TGGAGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 1 0.06
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:21034919 original size:14 final size:15
Alignment explanation
Indices: 21034900--21034928 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21034890 AATTAAGAGC
21034900 TTTTTCTCTC-TTTT
1 TTTTTCTCTCATTTT
21034914 TTTTTCTCTCATTTT
1 TTTTTCTCTCATTTT
21034929 CATAGACCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTCTCATTTT
Found at i:21039426 original size:195 final size:196
Alignment explanation
Indices: 21039167--21039530 Score: 554
Period size: 195 Copynumber: 1.9 Consensus size: 196
21039157 GTAAGCTGTC
*
21039167 CCCTGACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTGAAGCATAAATCCCAACCATCGT
1 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTGAAGCATAAATCCCAACCATCGT
21039232 AGGGCCTATAATCCATT-TAAGATTTTATATCTC-TTTCCTGACTCACGATGCTGCTCACACGAG
66 AGGGCCTATAATCCATTCTAAGA-TTTATATCTCATTTCCTGACTCACGATGCTGCTCACACGAG
* *
21039295 CTATAGAGGACCCTCAACATATGCGATACCTCAGCCATCGATACGGTATCTATGCATATAATTGT
130 CTATAGAGGACCCGCAACATATGCGATACCTCAACCATCGATACGGTATCTATGCATATAATTGT
21039360 TT
195 TT
* * * *
21039362 CCCTAACGATGTTGCTCACACGAGCTGTCGAGAATATGCACTT-ATGCATAAATCCTAGCCATCG
1 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCA-TTGAAGCATAAATCCCAACCATCG
* ** *
21039426 TAGGGCCTGTAATCCATTCTTGGATTTATTTCTCATTTCCTGACTCACGATGCTGCTCACACGAG
65 TAGGGCCTATAATCCATTCTAAGATTTATATCTCATTTCCTGACTCACGATGCTGCTCACACGAG
* * * *
21039491 CTATCGAGGACTCGCAACATATTCGGTACCTCAACCATCG
130 CTATAGAGGACCCGCAACATATGCGATACCTCAACCATCG
21039531 CGTCGGTTTC
Statistics
Matches: 151, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
195 82 0.54
196 69 0.46
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (196 bp):
CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTGAAGCATAAATCCCAACCATCGT
AGGGCCTATAATCCATTCTAAGATTTATATCTCATTTCCTGACTCACGATGCTGCTCACACGAGC
TATAGAGGACCCGCAACATATGCGATACCTCAACCATCGATACGGTATCTATGCATATAATTGTT
T
Found at i:21045096 original size:24 final size:24
Alignment explanation
Indices: 21045051--21045096 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
21045041 GATTCAAAGG
*
21045051 AGAAAAAGAGAAAGCACAAGGATA
1 AGAAAAAGAGAAAGCAAAAGGATA
*
21045075 AGAAAAAGA-AATGCAAAGAGGA
1 AGAAAAAGAGAAAGCAAA-AGGA
21045097 AGGCAAGCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.63, C:0.07, G:0.26, T:0.04
Consensus pattern (24 bp):
AGAAAAAGAGAAAGCAAAAGGATA
Found at i:21045229 original size:18 final size:18
Alignment explanation
Indices: 21045203--21045256 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
21045193 ATGTATTTTA
* *
21045203 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
21045221 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
* *
21045238 TTTATTTGTTAGTGCATT
1 TTTATTTGTCACTGCATT
21045256 T
1 T
21045257 GCATTGTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:21045242 original size:17 final size:17
Alignment explanation
Indices: 21045203--21045256 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
21045193 ATGTATTTTA
* *
21045203 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
21045221 TTTATTTGTCACTGCAT
1 TTTATTTGTCACTGCAT
* *
21045238 TTTATTTGTTAGTGCAT
1 TTTATTTGTCACTGCAT
21045255 TT
1 TT
21045257 GCATTGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:21045851 original size:21 final size:21
Alignment explanation
Indices: 21045822--21045879 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
21045812 TCAGTGACTT
21045822 AAAA-AAGAAAAAGAAAAGA-
1 AAAAGAAGAAAAAGAAAAGAG
*
21045841 AAAAGGAAGAAAAGGAAAAGAG
1 AAAA-GAAGAAAAAGAAAAGAG
21045863 AAAAGAAGAAAAA-AAAA
1 AAAAGAAGAAAAAGAAAA
21045880 TATTCCTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 22 0.65
22 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAGAAGAAAAAGAAAAGAG
Found at i:21045852 original size:15 final size:16
Alignment explanation
Indices: 21045832--21045875 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
21045822 AAAAAAGAAA
21045832 AAGAAAAGAAAAAG-G
1 AAGAAAAGAAAAAGAG
*
21045847 AAGAAAAGGAAAAGAG
1 AAGAAAAGAAAAAGAG
21045863 AA-AAGAAGAAAAA
1 AAGAA-AAGAAAAA
21045876 AAAATATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAG
Found at i:21045877 original size:11 final size:10
Alignment explanation
Indices: 21045822--21045879 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
21045812 TCAGTGACTT
21045822 AAAAAAGAAA
1 AAAAAAGAAA
21045832 AAGAAAAGAAA
1 AA-AAAAGAAA
**
21045843 AAGGAAGAAA
1 AAAAAAGAAA
* *
21045853 AGGAAAAGAGA
1 A-AAAAAGAAA
*
21045864 AAAGAAGAAA
1 AAAAAAGAAA
21045874 AAAAAA
1 AAAAAA
21045880 TATTCCTAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
10 20 0.56
11 16 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:21049457 original size:17 final size:17
Alignment explanation
Indices: 21049426--21049460 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21049416 AAAAACAATT
21049426 ACCTGAACCCAAACCTA
1 ACCTGAACCCAAACCTA
21049443 ACCT-AACCCACAACCTA
1 ACCTGAACCCA-AACCTA
21049460 A
1 A
21049461 ATACAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.43, G:0.03, T:0.11
Consensus pattern (17 bp):
ACCTGAACCCAAACCTA
Found at i:21051424 original size:14 final size:14
Alignment explanation
Indices: 21051405--21051431 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21051395 TTTCGGTGTT
21051405 TTACTATTCATCTA
1 TTACTATTCATCTA
21051419 TTACTATTCATCT
1 TTACTATTCATCT
21051432 TTAATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (14 bp):
TTACTATTCATCTA
Found at i:21051667 original size:21 final size:21
Alignment explanation
Indices: 21051643--21051683 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21051633 ATCAATATAA
*
21051643 GTGACAGCTCTACCGATACAT
1 GTGACACCTCTACCGATACAT
*
21051664 GTGACTCCTCTACCGATACA
1 GTGACACCTCTACCGATACA
21051684 AGTCTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (21 bp):
GTGACACCTCTACCGATACAT
Found at i:21057481 original size:49 final size:50
Alignment explanation
Indices: 21057409--21057542 Score: 175
Period size: 49 Copynumber: 2.7 Consensus size: 50
21057399 GCACCACACA
* * * *
21057409 GCCGTGTGAGGCATACAGTCGTGTGAAAACATGTAGATC-GTGTAGGTAG
1 GCCGTGTGGGGCACACAGTCGTGTGAAAACATGTAGAGCTGTATAGGTAG
* *
21057458 GCCGTGAGGGGCACACAGTCGTGTGAAAACATGCA-AGCTGTATAGGTAG
1 GCCGTGTGGGGCACACAGTCGTGTGAAAACATGTAGAGCTGTATAGGTAG
*
21057507 ACCGTGTGGGGCACAC-GATCGTGTGAAAACATGTAG
1 GCCGTGTGGGGCACACAG-TCGTGTGAAAACATGTAG
21057543 GCCATGTGGG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 3 0.04
49 70 0.96
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (50 bp):
GCCGTGTGGGGCACACAGTCGTGTGAAAACATGTAGAGCTGTATAGGTAG
Found at i:21058884 original size:25 final size:25
Alignment explanation
Indices: 21058856--21058904 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
21058846 AATTATTTCA
*
21058856 TTAATAAATTGGGTTTATTAAATTG
1 TTAATAAATTGGGTTAATTAAATTG
* *
21058881 TTAATTAATTGGGTTAATTTAATT
1 TTAATAAATTGGGTTAATTAAATT
21058905 AATTTGACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (25 bp):
TTAATAAATTGGGTTAATTAAATTG
Found at i:21082807 original size:18 final size:19
Alignment explanation
Indices: 21082767--21082808 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
21082757 TGAAATTTTT
* * *
21082767 ATTTTTCATTATTATTATT
1 ATTTTTAATTATTAATATA
21082786 ATTTTTAATT-TTAATATA
1 ATTTTTAATTATTAATATA
21082804 ATTTT
1 ATTTT
21082809 ATTTGTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTAATTATTAATATA
Found at i:21097565 original size:21 final size:21
Alignment explanation
Indices: 21097530--21097574 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21097520 AGGAGAACGT
*
21097530 AGAAGAGAAAGAAGAAGAAGA
1 AGAAGAGAAAGAAGAAGAAAA
*
21097551 AGAA-AGAAAGAAAGACGAAAA
1 AGAAGAGAAAG-AAGAAGAAAA
21097572 AGA
1 AGA
21097575 GGAAAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AGAAGAGAAAGAAGAAGAAAA
Found at i:21097574 original size:24 final size:25
Alignment explanation
Indices: 21097530--21097579 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
21097520 AGGAGAACGT
*
21097530 AGAAGAGAAAGAAGAAGAAGAAGAA
1 AGAAGAGAAAGAAGAAAAAGAAGAA
* *
21097555 AGAA-AGAAAGACGAAAAAGAGGAA
1 AGAAGAGAAAGAAGAAAAAGAAGAA
21097579 A
1 A
21097580 ACTTTGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (25 bp):
AGAAGAGAAAGAAGAAAAAGAAGAA
Found at i:21107787 original size:21 final size:21
Alignment explanation
Indices: 21107752--21107796 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21107742 AGGAGAAGGC
*
21107752 AGAAGAGAAAGAAGAAGAAGA
1 AGAAGAGAAAGAAGAAGAAAA
*
21107773 AGAA-AGAAAGAAAGACGAAAA
1 AGAAGAGAAAG-AAGAAGAAAA
21107794 AGA
1 AGA
21107797 GGAAGACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AGAAGAGAAAGAAGAAGAAAA
Found at i:21107802 original size:15 final size:16
Alignment explanation
Indices: 21107753--21107803 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
21107743 GGAGAAGGCA
*
21107753 GAAGA-GAAAGAAGAA
1 GAAGACGAAAGAAGAG
*
21107768 GAAGAAGAAAGAA-AG
1 GAAGACGAAAGAAGAG
*
21107783 AAAGACGAAA-AAGAG
1 GAAGACGAAAGAAGAG
21107798 GAAGAC
1 GAAGAC
21107804 TTTGTTGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 21 0.70
16 7 0.23
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAGACGAAAGAAGAG
Found at i:21113064 original size:24 final size:24
Alignment explanation
Indices: 21113037--21113088 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
21113027 TCCCTTTTTG
21113037 TTCTACTCCATCTCACC-TCCTTAT
1 TTCTACTCC-TCTCACCTTCCTTAT
* *
21113061 TTCTCCTTCTCTCACCTTCCTTAT
1 TTCTACTCCTCTCACCTTCCTTAT
21113085 TTCT
1 TTCT
21113089 CCATTTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.48
Consensus pattern (24 bp):
TTCTACTCCTCTCACCTTCCTTAT
Found at i:21115573 original size:15 final size:15
Alignment explanation
Indices: 21115553--21115598 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
21115543 ATCATAATTT
21115553 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
21115568 TTTTTCTTCCTTTTTC
1 TTTTTCTT-CTTTTTC
21115584 TCTTTT-TTCTTTTTC
1 T-TTTTCTTCTTTTTC
21115599 CAATGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.52
16 10 0.34
17 4 0.14
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:21124397 original size:16 final size:17
Alignment explanation
Indices: 21124376--21124414 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
21124366 TAATTAAAAC
21124376 TGTCAATGCAA-TAAAT
1 TGTCAATGCAAGTAAAT
21124392 TGTCAATGCAAGTTAAAT
1 TGTCAATGCAAG-TAAAT
21124410 TGTCA
1 TGTCA
21124415 GAGCAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (17 bp):
TGTCAATGCAAGTAAAT
Found at i:21125981 original size:19 final size:19
Alignment explanation
Indices: 21125957--21125993 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21125947 CTAAAAATTA
*
21125957 CAAGTCTTTAAAATAAATC
1 CAAGTCTTAAAAATAAATC
21125976 CAAGTCTTAAAAATAAAT
1 CAAGTCTTAAAAATAAAT
21125994 TAAAATTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
CAAGTCTTAAAAATAAATC
Found at i:21132403 original size:22 final size:22
Alignment explanation
Indices: 21132378--21132420 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21132368 ATTCACATAT
21132378 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
21132400 TTTCTTACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
21132421 CTTTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:21136975 original size:7 final size:7
Alignment explanation
Indices: 21136965--21136995 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
21136955 GTTGAATGTT
21136965 TGAGGGA
1 TGAGGGA
21136972 TGAGGGA
1 TGAGGGA
21136979 TGAGGGA
1 TGAGGGA
21136986 TGAGGGA
1 TGAGGGA
21136993 TGA
1 TGA
21136996 TTAGGAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.55, T:0.16
Consensus pattern (7 bp):
TGAGGGA
Found at i:21141735 original size:46 final size:46
Alignment explanation
Indices: 21141668--21141769 Score: 195
Period size: 46 Copynumber: 2.2 Consensus size: 46
21141658 TTCAAAGCCT
*
21141668 AATGAGCTTTATTCTCCAATTCTAATGGCAAATGGCATGCCTTTCC
1 AATGAGCTCTATTCTCCAATTCTAATGGCAAATGGCATGCCTTTCC
21141714 AATGAGCTCTATTCTCCAATTCTAATGGCAAATGGCATGCCTTTCC
1 AATGAGCTCTATTCTCCAATTCTAATGGCAAATGGCATGCCTTTCC
21141760 AATGAGCTCT
1 AATGAGCTCT
21141770 GTTCGATAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (46 bp):
AATGAGCTCTATTCTCCAATTCTAATGGCAAATGGCATGCCTTTCC
Found at i:21141929 original size:21 final size:21
Alignment explanation
Indices: 21141903--21141946 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21141893 GGGTGATAAG
21141903 CAGTAGCAATCTTGTGCTTCA
1 CAGTAGCAATCTTGTGCTTCA
21141924 CAGTAGCAATCTTGTGCTTCA
1 CAGTAGCAATCTTGTGCTTCA
21141945 CA
1 CA
21141947 TCATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
CAGTAGCAATCTTGTGCTTCA
Found at i:21148935 original size:15 final size:13
Alignment explanation
Indices: 21148912--21148945 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
21148902 TACATATATA
21148912 TTTTTTCTTTTCCT
1 TTTTTTCTTTT-CT
21148926 TTTTTCTCTTTTCT
1 TTTTT-TCTTTTCT
21148940 TTTTTT
1 TTTTTT
21148946 ATATGTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 12 0.63
15 6 0.32
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:21149536 original size:17 final size:17
Alignment explanation
Indices: 21149514--21149562 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
21149504 TAACAAATGG
* *
21149514 AAATGCAATGATAATTC
1 AAATGCAATGACAATTA
*
21149531 AAATGCAGTGACAATTA
1 AAATGCAATGACAATTA
*
21149548 AAATGTAATGACAAT
1 AAATGCAATGACAAT
21149563 GGGAATGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (17 bp):
AAATGCAATGACAATTA
Found at i:21151711 original size:93 final size:93
Alignment explanation
Indices: 21151582--21151767 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
21151572 AAATAAGAAT
*
21151582 CAAAGCAATCTAAAAATGAAAGATACTCTCGTATTCATTCAAATGTCATTAAAATTCATTAGCAT
1 CAAAGCAATCTAAAAATGAAAGATACTCTCGTATTCATTCAAATGTCATTAAAATTCATCAGCAT
21151647 AAAAGAGGGGTGAACGAATACAATCGAA
66 AAAAGAGGGGTGAACGAATACAATCGAA
*
21151675 CAAAGCAATCTAAAAATGAAAGATACTCTCGTATTCATTCAAATTTCATTAAAATTCATCAGCAT
1 CAAAGCAATCTAAAAATGAAAGATACTCTCGTATTCATTCAAATGTCATTAAAATTCATCAGCAT
*
21151740 AAAAGAGGGGTTAACGAATACAATCGAA
66 AAAAGAGGGGTGAACGAATACAATCGAA
21151768 GCTTACTATC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (93 bp):
CAAAGCAATCTAAAAATGAAAGATACTCTCGTATTCATTCAAATGTCATTAAAATTCATCAGCAT
AAAAGAGGGGTGAACGAATACAATCGAA
Found at i:21153900 original size:24 final size:24
Alignment explanation
Indices: 21153869--21153919 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21153859 CCAAATAAAA
* * *
21153869 TTAGCTCTCACGAGTCCAGAAAGG
1 TTAGCTCTCACAAGCCCAAAAAGG
*
21153893 TTAGCTCTTACAAGCCCAAAAAGG
1 TTAGCTCTCACAAGCCCAAAAAGG
21153917 TTA
1 TTA
21153920 ACCATTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
TTAGCTCTCACAAGCCCAAAAAGG
Found at i:21166996 original size:154 final size:154
Alignment explanation
Indices: 21166713--21167021 Score: 573
Period size: 154 Copynumber: 2.0 Consensus size: 154
21166703 TCCTAAAGGG
21166713 TTTGTAACTAATAATTCAACTTCAACCGACTCGACAGATAGATTTTATCAGTTATTAAGCAGTAT
1 TTTGTAACTAATAATTCAACTTCAACCGACTCGACAGATAGATTTTATCAGTTATTAAGCAGTAT
*
21166778 CAATATAAAAATAAATCAATCTTGAATCGTTCAAAGCATGCACAGTCACATCAAGGATAAAAGTT
66 CAATATAAAAATAAATCAATCTTGAATCGTTCAAAGCACGCACAGTCACATCAAGGATAAAAGTT
21166843 ACCAATCATCTCATTGGATACAGT
131 ACCAATCATCTCATTGGATACAGT
* *
21166867 TTTGTAACTAATATTTCAACTTCAACCGACTCGACAGATAGATTTTATCAGTTATTAAGCTGTAT
1 TTTGTAACTAATAATTCAACTTCAACCGACTCGACAGATAGATTTTATCAGTTATTAAGCAGTAT
* *
21166932 CGATATAAAAATAAATCAATCTTGAATCGTTCAAAGCACGCACAGTCACATCAAGGATAGAAGTT
66 CAATATAAAAATAAATCAATCTTGAATCGTTCAAAGCACGCACAGTCACATCAAGGATAAAAGTT
21166997 ACCAATCATCTCATTGGATACAGT
131 ACCAATCATCTCATTGGATACAGT
21167021 T
1 T
21167022 GCCTCTTCTT
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 150 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (154 bp):
TTTGTAACTAATAATTCAACTTCAACCGACTCGACAGATAGATTTTATCAGTTATTAAGCAGTAT
CAATATAAAAATAAATCAATCTTGAATCGTTCAAAGCACGCACAGTCACATCAAGGATAAAAGTT
ACCAATCATCTCATTGGATACAGT
Found at i:21171496 original size:15 final size:14
Alignment explanation
Indices: 21171472--21171501 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
21171462 GAAATTCCTC
21171472 ATAGCAAGGGAGTT
1 ATAGCAAGGGAGTT
21171486 ATAGACAAGGGAGTT
1 ATAG-CAAGGGAGTT
21171501 A
1 A
21171502 CAACAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (14 bp):
ATAGCAAGGGAGTT
Found at i:21174729 original size:20 final size:21
Alignment explanation
Indices: 21174704--21174742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21174694 GCAAGGAATT
21174704 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
21174724 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
21174743 TAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:21187887 original size:12 final size:12
Alignment explanation
Indices: 21187855--21187919 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
21187845 GGAAAATGTG
**
21187855 GAAGAGAAAAAA
1 GAAGAGAAGGAA
21187867 GAAGAGAAGGAA
1 GAAGAGAAGGAA
*
21187879 GAAGAGAAGGGA
1 GAAGAGAAGGAA
21187891 GAAGAGAAGAAGAA
1 GAAGAGAAG--GAA
*
21187905 TGAAGAAAAGGAA
1 -GAAGAGAAGGAA
21187918 GA
1 GA
21187920 TGCCCTGACA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 32 0.71
13 3 0.07
14 2 0.04
15 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
GAAGAGAAGGAA
Found at i:21192460 original size:21 final size:23
Alignment explanation
Indices: 21192436--21192544 Score: 78
Period size: 24 Copynumber: 4.7 Consensus size: 23
21192426 CATAGCGTGA
21192436 TCACGAGCCCA-AAA-TTAGCTC
1 TCACGAGCCCAGAAAGTTAGCTC
*
21192457 TCACGAGTCCAGAAAGGTTAGCTC
1 TCACGAGCCCAGAAA-GTTAGCTC
* * * *
21192481 TTATGAACCCAGAAAGGTTAACTC
1 TCACGAGCCCAGAAA-GTTAGCTC
* * * *
21192505 TTATGAACCCAGAAAGGTTAACTC
1 TCACGAGCCCAGAAA-GTTAGCTC
* *
21192529 TTACGAGCCTAGAAAG
1 TCACGAGCCCAGAAAG
21192545 GTTAACCAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
21 10 0.13
22 3 0.04
23 1 0.01
24 62 0.82
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (23 bp):
TCACGAGCCCAGAAAGTTAGCTC
Found at i:21192480 original size:24 final size:24
Alignment explanation
Indices: 21192465--21192550 Score: 127
Period size: 24 Copynumber: 3.6 Consensus size: 24
21192455 TCTCACGAGT
* *
21192465 CCAGAAAGGTTAGCTCTTATGAAC
1 CCAGAAAGGTTAACTCTTACGAAC
*
21192489 CCAGAAAGGTTAACTCTTATGAAC
1 CCAGAAAGGTTAACTCTTACGAAC
*
21192513 CCAGAAAGGTTAACTCTTACGAGC
1 CCAGAAAGGTTAACTCTTACGAAC
*
21192537 CTAGAAAGGTTAAC
1 CCAGAAAGGTTAAC
21192551 CAGTATATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (24 bp):
CCAGAAAGGTTAACTCTTACGAAC
Found at i:21198767 original size:29 final size:30
Alignment explanation
Indices: 21198724--21198780 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
21198714 GAATTGGATC
21198724 AAATCAAAATTTCATGTATAAAATTATACA
1 AAATCAAAATTTCATGTATAAAATTATACA
*
21198754 AAATCAAAA-TTCATGTATATAATTATA
1 AAATCAAAATTTCATGTATAAAATTATA
21198781 TATTAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTATACA
Found at i:21215695 original size:233 final size:234
Alignment explanation
Indices: 21215362--21215813 Score: 667
Period size: 234 Copynumber: 1.9 Consensus size: 234
21215352 AATTTTTTTC
* * * * * *
21215362 AAAAAACAGATTAATAGAATCGAAATATTTCGGTTAATTCAATAGGTTAACTGAATTAATCGAAA
1 AAAAAAAAAATTAATAGAACCGAAATATTTCGATTAATTCAATAGATTAACTGAATTAACCGAAA
* *
21215427 TATATATGTTTACTTTTTTTTGTTAAAACAAGTATAAAACATA-TCAAAAATTAAATTGATAATG
66 TATATATGTTTACTTTTTTTTGTTAAAACAAGTATAAAACATATTAAAAAATTAAATTAATAATG
* * *
21215491 TTTATTTGA-CTGAATTAATCGAATTAATAATAGTCTAATACATATAATATATAATATTATTTAT
131 TTCATTTGATC-GAATTAACCGAATTAATAATAGTCTAATACATATAATATATAATAGTATTTAT
*
21215555 TAAGTTCGGTTAATTCGATTAATTAACTGAATTAAAATTT
195 TAAGTTCGATTAATTCGATTAATTAACTGAATTAAAATTT
* ** * *
21215595 AAAAAAAAAATTAATCGAACCGAAATATTTCGATTAATTTGATATATTAATTGAATTAACCGAAA
1 AAAAAAAAAATTAATAGAACCGAAATATTTCGATTAATTCAATAGATTAACTGAATTAACCGAAA
* * * *
21215660 TTTATATGTTTTGC-TTTTTTTGTTGAAATAAGTATAAAACATATTAAAAAATTAAATTAATAAT
66 TATATATG-TTTACTTTTTTTTGTTAAAACAAGTATAAAACATATTAAAAAATTAAATTAATAAT
*
21215724 GTTCATTTGATCGAATTAACCGAATTAGTAATAGTCTAATACATATAATATATAATAGTATTTAT
130 GTTCATTTGATCGAATTAACCGAATTAATAATAGTCTAATACATATAATATATAATAGTATTTAT
21215789 TAAGTTCGATTAATTCGATTAATTA
195 TAAGTTCGATTAATTCGATTAATTA
21215814 TTCGATTTCA
Statistics
Matches: 194, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
233 88 0.45
234 105 0.54
235 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (234 bp):
AAAAAAAAAATTAATAGAACCGAAATATTTCGATTAATTCAATAGATTAACTGAATTAACCGAAA
TATATATGTTTACTTTTTTTTGTTAAAACAAGTATAAAACATATTAAAAAATTAAATTAATAATG
TTCATTTGATCGAATTAACCGAATTAATAATAGTCTAATACATATAATATATAATAGTATTTATT
AAGTTCGATTAATTCGATTAATTAACTGAATTAAAATTT
Found at i:21217980 original size:33 final size:34
Alignment explanation
Indices: 21217943--21218015 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
21217933 ATCAAATTAC
21217943 TTTTTTATCCTTC-TTTTTCACGTTTCTTCTTC-A
1 TTTTTTATCCTTCTTTTTTCACGTTTCTTC-TCAA
* *
21217976 TTTTTTATTCTTCTTTTTTCATGTTTCTTCTCAA
1 TTTTTTATCCTTCTTTTTTCACGTTTCTTCTCAA
21218010 TTTTTT
1 TTTTTT
21218016 CTTCCAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 14 0.39
34 22 0.61
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.68
Consensus pattern (34 bp):
TTTTTTATCCTTCTTTTTTCACGTTTCTTCTCAA
Found at i:21219257 original size:48 final size:48
Alignment explanation
Indices: 21219178--21219317 Score: 190
Period size: 48 Copynumber: 2.9 Consensus size: 48
21219168 CAACTCATGT
*
21219178 ACGTTTATACTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCAC
** * ** * *
21219226 ACGTTTATGCTCGTCAGCTTATATATGTTTACACTCATCAGCTTGCAC
1 ACGTTTATGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCAC
* *
21219274 ACGTTTACGCTCATCAGCTTGCACACATTTACGCTCGTCAGCTT
1 ACGTTTATGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCTT
21219318 ATATACGTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (48 bp):
ACGTTTATGCTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCAC
Found at i:21219297 original size:72 final size:72
Alignment explanation
Indices: 21219177--21219329 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
21219167 ACAACTCATG
* * * * *
21219177 TACGTTTATACTCGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCACACGTTTATGCTCGTCA
1 TACGTTTACACTCATCAGCTTGCACACATTTACGCTCATCAGCTTGCACACATTTACGCTCGTCA
21219242 GCTTATA
66 GCTTATA
* *
21219249 TATGTTTACACTCATCAGCTTGCACACGTTTACGCTCATCAGCTTGCACACATTTACGCTCGTCA
1 TACGTTTACACTCATCAGCTTGCACACATTTACGCTCATCAGCTTGCACACATTTACGCTCGTCA
21219314 GCTTATA
66 GCTTATA
21219321 TACGTTTAC
1 TACGTTTAC
21219330 GTAGTTCAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (72 bp):
TACGTTTACACTCATCAGCTTGCACACATTTACGCTCATCAGCTTGCACACATTTACGCTCGTCA
GCTTATA
Found at i:21219330 original size:24 final size:24
Alignment explanation
Indices: 21219178--21219317 Score: 172
Period size: 24 Copynumber: 5.8 Consensus size: 24
21219168 CAACTCATGT
**
21219178 ACGTTTATACTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
21219202 ACATTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* ** *
21219226 ACGTTTATGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
* * *
21219250 ATGTTTACACTCATCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
21219274 ACGTTTACGCTCATCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
21219298 ACATTTACGCTCGTCAGCTT
1 ACGTTTACGCTCGTCAGCTT
21219318 ATATACGTTT
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 97 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTGCAC
Found at i:21222342 original size:18 final size:18
Alignment explanation
Indices: 21222319--21222368 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
21222309 AATGAGGGAC
*
21222319 ATGATGTTCACATTTTAA
1 ATGATGTTAACATTTTAA
* *
21222337 ATGATGTTTACACTTTAA
1 ATGATGTTAACATTTTAA
21222355 ATGATGTTAACATT
1 ATGATGTTAACATT
21222369 GATGGAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (18 bp):
ATGATGTTAACATTTTAA
Found at i:21222890 original size:72 final size:71
Alignment explanation
Indices: 21222704--21222902 Score: 317
Period size: 72 Copynumber: 2.7 Consensus size: 71
21222694 CAATGCTAAA
* *
21222704 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTG-CTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
21222769 GTGTAAT
65 GTGTAAT
* *
21222776 GTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGC-TATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
21222841 GTGTAAT
65 GTGTAAT
*
21222848 CTAGTTTTATCAATAGTTGACTATGTTTGGTTTTTGGATATTGAATATGATGTTC
1 CTAGTTTTATCAATAGTTG-CTATGTTTGGTTTTTGGATATTGAAT-TTATGTTC
21222903 ACATTTTAAA
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
72 109 0.93
73 8 0.07
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (71 bp):
CTAGTTTTATCAATAGTTGCTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
TGTAAT
Found at i:21222917 original size:18 final size:18
Alignment explanation
Indices: 21222894--21222943 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
21222884 GATATTGAAT
*
21222894 ATGATGTTCACATTTTAA
1 ATGATGTTAACATTTTAA
* *
21222912 ATGATGTTTACACTTTAA
1 ATGATGTTAACATTTTAA
21222930 ATGATGTTAACATT
1 ATGATGTTAACATT
21222944 GATGGAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (18 bp):
ATGATGTTAACATTTTAA
Found at i:21223368 original size:72 final size:72
Alignment explanation
Indices: 21223279--21223534 Score: 424
Period size: 72 Copynumber: 3.6 Consensus size: 72
21223269 CAATGCTAAA
*
21223279 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
21223344 GTGTAAT
66 GTGTAAT
* * * *
21223351 GTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATTTTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
21223416 GTGTAAT
66 GTGTAAT
* *
21223423 CTAGTTTTATCAATAGTTGTCTATGTTTGGTTTTTGGATATTGAATTTTTGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
21223488 GTGTAAT
66 GTGTAAT
* *
21223495 CTAGTTTTATCAATAGTTGTTTATATTT-GATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATAT
21223535 AAAATTTGTT
Statistics
Matches: 170, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
71 11 0.06
72 159 0.94
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:21223410 original size:575 final size:575
Alignment explanation
Indices: 21222319--21223468 Score: 2273
Period size: 575 Copynumber: 2.0 Consensus size: 575
21222309 AATGAGGGAC
21222319 ATGATGTTCACATTTTAAATGATGTTTACACTTTAAATGATGTTAACATTGATGGAAACGGTCAA
1 ATGATGTTCACATTTTAAATGATGTTTACACTTTAAATGATGTTAACATTGATGGAAACGGTCAA
21222384 CAAAGGAAAACACCTAAGATATCTACTTCACATTTGAAAACTGGAAGGAAGAAATCCTCAAAGCA
66 CAAAGGAAAACACCTAAGATATCTACTTCACATTTGAAAACTGGAAGGAAGAAATCCTCAAAGCA
21222449 AATTGGAGGGGCTACAAGATTGTCTAGTCAAATAGAAAAATTATGCAATGCAGCTGACAATATGA
131 AATTGGAGGGGCTACAAGATTGTCTAGTCAAATAGAAAAATTATGCAATGCAGCTGACAATATGA
21222514 GTCAAGTCACATCTTGTTTGACTCCTGTTATGGGTCCATATGGTATTCCACAAGTAGTCAAAGTG
196 GTCAAGTCACATCTTGTTTGACTCCTGTTATGGGTCCATATGGTATTCCACAAGTAGTCAAAGTG
21222579 CTTGATAACATGTTAGAGGAAGTTCTAGAAGCTAGTCCACTATACTTTTTCTCACTGAGATTATT
261 CTTGATAACATGTTAGAGGAAGTTCTAGAAGCTAGTCCACTATACTTTTTCTCACTGAGATTATT
21222644 ACTCATAAGGACAAGCAAATTATGTTTTTATCAACTATGTGATTGAACAACAATGCTAAACTAGT
326 ACTCATAAGGACAAGCAAATTATGTTTTTATCAACTATGTGATTGAACAACAATGCTAAACTAGT
21222709 TTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTATGTGTA
391 TTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTATGTGTA
21222774 ATGTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
456 ATGTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
21222839 ATGTGTAATCTAGTTTTATCAATAGTTGACTATGTTTGGTTTTTGGATATTGAAT
521 ATGTGTAATCTAGTTTTATCAATAGTTGACTATGTTTGGTTTTTGGATATTGAAT
21222894 ATGATGTTCACATTTTAAATGATGTTTACACTTTAAATGATGTTAACATTGATGGAAACGGTCAA
1 ATGATGTTCACATTTTAAATGATGTTTACACTTTAAATGATGTTAACATTGATGGAAACGGTCAA
21222959 CAAAGGAAAACACCTAAGATATCTACTTCACATTTGAAAACTGGAAGGAAGAAATCCTCAAAGCA
66 CAAAGGAAAACACCTAAGATATCTACTTCACATTTGAAAACTGGAAGGAAGAAATCCTCAAAGCA
21223024 AATTGGAGGGGCTACAAGATTGTCTAGTCAAATAGAAAAATTATGCAATGCAGCTGACAATATGA
131 AATTGGAGGGGCTACAAGATTGTCTAGTCAAATAGAAAAATTATGCAATGCAGCTGACAATATGA
21223089 GTCAAGTCACATCTTGTTTGACTCCTGTTATGGGTCCATATGGTATTCCACAAGTAGTCAAAGTG
196 GTCAAGTCACATCTTGTTTGACTCCTGTTATGGGTCCATATGGTATTCCACAAGTAGTCAAAGTG
21223154 CTTGATAACATGTTAGAGGAAGTTCTAGAAGCTAGTCCACTATACTTTTTCTCACTGAGATTATT
261 CTTGATAACATGTTAGAGGAAGTTCTAGAAGCTAGTCCACTATACTTTTTCTCACTGAGATTATT
*
21223219 ACTCATAAGGATAAGCAAATTATGTTTTTATCAACTATGTGATTGAACAACAATGCTAAACTAGT
326 ACTCATAAGGACAAGCAAATTATGTTTTTATCAACTATGTGATTGAACAACAATGCTAAACTAGT
21223284 TTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTATGTGTA
391 TTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTATGTGTA
*
21223349 ATGTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATTTTGAATTTATGTTCTACTTATTT
456 ATGTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
*
21223414 ATGTGTAATCTAGTTTTATCAATAGTTGTCTATGTTTGGTTTTTGGATATTGAAT
521 ATGTGTAATCTAGTTTTATCAATAGTTGACTATGTTTGGTTTTTGGATATTGAAT
21223469 TTTTGTTCTA
Statistics
Matches: 572, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
575 572 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (575 bp):
ATGATGTTCACATTTTAAATGATGTTTACACTTTAAATGATGTTAACATTGATGGAAACGGTCAA
CAAAGGAAAACACCTAAGATATCTACTTCACATTTGAAAACTGGAAGGAAGAAATCCTCAAAGCA
AATTGGAGGGGCTACAAGATTGTCTAGTCAAATAGAAAAATTATGCAATGCAGCTGACAATATGA
GTCAAGTCACATCTTGTTTGACTCCTGTTATGGGTCCATATGGTATTCCACAAGTAGTCAAAGTG
CTTGATAACATGTTAGAGGAAGTTCTAGAAGCTAGTCCACTATACTTTTTCTCACTGAGATTATT
ACTCATAAGGACAAGCAAATTATGTTTTTATCAACTATGTGATTGAACAACAATGCTAAACTAGT
TTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTCAATTTATGTTCTACTTATTTATGTGTA
ATGTAATTTTATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTT
ATGTGTAATCTAGTTTTATCAATAGTTGACTATGTTTGGTTTTTGGATATTGAAT
Found at i:21225273 original size:20 final size:20
Alignment explanation
Indices: 21225226--21225282 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
21225216 TATCAAAATA
* *
21225226 TAAATATTTAATGATTATATT
1 TAAATATTT-ATAAATATATT
21225247 TAAATATTTA-AAATATAGTT
1 TAAATATTTATAAATATA-TT
*
21225267 TATATATTTATAAATA
1 TAAATATTTATAAATA
21225283 ATTAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 5 0.16
20 12 0.39
21 14 0.45
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TAAATATTTATAAATATATT
Found at i:21230200 original size:58 final size:56
Alignment explanation
Indices: 21230105--21230227 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 56
21230095 CGAGAATTTG
** *
21230105 AAAAAAAAAATTTGGTGTTGGCCATACAATGGTCGACACCCCCTTTTTT-ATCTGAT
1 AAAAAAAAAATTTACTGTTGGCCATACAATGGCCGACA-CCCCTTTTTTAATCTGAT
* * *
21230161 AGGAAAAAAAAATTTACTGTTGGCTATTGC-ATGGCCGACACTCCTTTTTTAATCTGAT
1 A--AAAAAAAAATTTACTGTTGGCCA-TACAATGGCCGACACCCCTTTTTTAATCTGAT
21230219 AAAAAAAAA
1 AAAAAAAAA
21230228 TCAAATTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
56 9 0.16
57 9 0.16
58 37 0.65
59 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (56 bp):
AAAAAAAAAATTTACTGTTGGCCATACAATGGCCGACACCCCTTTTTTAATCTGAT
Found at i:21230339 original size:62 final size:60
Alignment explanation
Indices: 21230241--21230720 Score: 341
Period size: 61 Copynumber: 8.0 Consensus size: 60
21230231 AATTTTACAC
*** * *
21230241 CAAAAAAATTTTGAATTTTTTATTTCA-CAAAAAGGGGATGTCGACCATTGCATGGTCAACA
1 CAAAAAAA-TTTGAATTTTTTATCAGATAAAAAAGGGG-TGTCGACCATTGCATGGCCAACA
* *
21230302 CAAAAAAAATTTGATTTTTTTACCAGATAAAAAAGGGGGTGTCGACCA-TGACATGGCCAACA
1 C-AAAAAAATTTGAATTTTTTATCAGATAAAAAA-GGGGTGTCGACCATTG-CATGGCCAACA
* * * * * *
21230364 CAAAAAGATTCGAATTTTTTATCTGA-CAAAAAGGGGTATCGACCA-TGATATGGCCAACA
1 CAAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATTG-CATGGCCAACA
* * * * *
21230423 CCAAAAAATTTTAAAATTTTTTTATCTG--AAAAAAGGGGTATCGACTATTGCATGGCCAACA
1 -CAAAAAAATTT-GAA-TTTTTTATCAGATAAAAAAGGGGTGTCGACCATTGCATGGCCAACA
* ** * *
21230484 CCAAAAAATTTTGAAAATTTTCAATCTG--AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACA
1 -CAAAAAAATTTG--AATTTTTTATCAGATAAAAAAG-GGGTGTCGACCATTGCATGGCCAACA
** * * *
21230546 CTCAAAAGTTT-AATTTTTTTATCAGAT-AAATAGGGGTGTCGGCCATTGCATGGCCAACA
1 CAAAAAAATTTGAA-TTTTTTATCAGATAAAAAAGGGGTGTCGACCATTGCATGGCCAACA
* * ** *
21230605 CCAAAAAA-TTGAATTTTTTAT-ATGATAAAAAGGGGGTGTCGGTCATTGCATGGCCAATA
1 CAAAAAAATTTGAATTTTTTATCA-GATAAAAAAGGGGTGTCGACCATTGCATGGCCAACA
* * *
21230664 TC----AAATTT---TTTTTCTATTAGATAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACA
1 -CAAAAAAATTTGAATTTTT-TATCAGATA-AAAAAGGGGTGTCGACCATTGCATGGCCAACA
21230720 C
1 C
21230721 CAAATTTTTT
Statistics
Matches: 353, Mismatches: 44, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
54 5 0.01
55 8 0.02
56 34 0.10
57 3 0.01
58 15 0.04
59 94 0.27
60 19 0.05
61 101 0.29
62 70 0.20
63 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAAAAAATTTGAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATTGCATGGCCAACA
Found at i:21230545 original size:182 final size:182
Alignment explanation
Indices: 21230237--21230661 Score: 427
Period size: 182 Copynumber: 2.3 Consensus size: 182
21230227 ATCAAATTTT
* * * *
21230237 ACACCAAAAAAATTTTGAATTTTTTATTTCACAAAAAGGGGATGTCGACCATTGCATGGTCAACA
1 ACACC-AAAAAATTTTAAATTTTTTATCTCACAAAAAGGGGATATCGACCATTGCATGGCCAACA
*** * *
21230302 CAAAAAAAATTTGATTTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGACATGGCCAACAC-A
65 CAAAAAAAATTTGAAAATTTTACAAGATAAAAAAGAGGGTGTCGACCATGACATGGCCAACACTA
* *
21230366 AAAAGATTCGAA-TTTTTTATCTGACAAAAAGGGGTATCGACCA-TGATATGGCCA
130 AAAAG-TT-GAATTTTTTTATCAGACAAAAAGGGGTATCGACCATTG-CATGGCCA
* *
21230420 ACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAAGGGG-TATCGACTATTGCATGGCCAAC
1 ACACCAAAAAATTTT-AAA-TTTTTTATCTCACAAAAAGGGGATATCGACCATTGCATGGCCAAC
* * ** *
21230483 ACCAAAAAATTTTGAAAATTTT-CAATCTGAAAAAAGAGGGTGTCGGCCATTG-CATGGCCAACA
64 ACAAAAAAAATTTGAAAATTTTACAAGAT-AAAAAAGAGGGTGTCGACCA-TGACATGGCCAACA
* * * * * *
21230546 CTCAAAAGTTTAATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGCATGGCCA
127 CTAAAAAGTTGAATTTTTTTATCAGACAAAAAGGGGTATCGACCATTGCATGGCCA
* * * * * * **
21230602 ACACCAAAAAA--TTGAATTTTTTATATGATAAAAAGGGGGTGTCGGTCATTGCATGGCCAA
1 ACACCAAAAAATTTTAAATTTTTTATCTCACAAAAAGGGGATATCGACCATTGCATGGCCAA
21230662 TATCAAATTT
Statistics
Matches: 203, Mismatches: 30, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
178 11 0.05
179 11 0.05
180 19 0.09
181 5 0.02
182 122 0.60
183 25 0.12
184 10 0.05
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (182 bp):
ACACCAAAAAATTTTAAATTTTTTATCTCACAAAAAGGGGATATCGACCATTGCATGGCCAACAC
AAAAAAAATTTGAAAATTTTACAAGATAAAAAAGAGGGTGTCGACCATGACATGGCCAACACTAA
AAAGTTGAATTTTTTTATCAGACAAAAAGGGGTATCGACCATTGCATGGCCA
Found at i:21230641 original size:59 final size:60
Alignment explanation
Indices: 21230237--21230724 Score: 386
Period size: 59 Copynumber: 8.1 Consensus size: 60
21230227 ATCAAATTTT
* * * * *
21230237 ACACCAAAAAAATTTTGAATTTTTTATTTCACAAAAAGGGGATGTCGACCATTGCATGGTCA
1 ACACC-AAAAAA-TTTGAATTTTTTATATGATAAAAAGGGGGTGTCGACCATTGCATGGCCA
* * *
21230299 ACACAAAAAAAATTTGATTTTTTTACCA-GATAAAAAAGGGGGTGTCGACCA-TGACATGGCCA
1 ACAC-CAAAAAATTTGAATTTTTTA-TATGAT-AAAAAGGGGGTGTCGACCATTG-CATGGCCA
* * * * *
21230361 ACA-CAAAAAGATTCGAATTTTTTATCTGACAAAAA-GGGGTATCGACCA-TGATATGGCCA
1 ACACCAAAAA-ATTTGAATTTTTTATATGATAAAAAGGGGGTGTCGACCATTG-CATGGCCA
* * * *
21230420 ACACCAAAAAATTTTAAAATTTTTTTATCTGA-AAAAA-GGGGTATCGACTATTGCATGGCCA
1 ACACCAAAAAA-TTT-GAA-TTTTTTATATGATAAAAAGGGGGTGTCGACCATTGCATGGCCA
** * * *
21230481 ACACCAAAAAATTTTGAAAATTTTCAATCTGA-AAAAAGAGGGTGTCGGCCATTGCATGGCCA
1 ACACCAAAAAA-TTTG--AATTTTTTATATGATAAAAAGGGGGTGTCGACCATTGCATGGCCA
* * *
21230543 ACACTC-AAAAGTTT-AATTTTTT-TATCAGATAAATA-GGGGTGTCGGCCATTGCATGGCCA
1 ACAC-CAAAAAATTTGAATTTTTTATAT--GATAAAAAGGGGGTGTCGACCATTGCATGGCCA
**
21230602 ACACCAAAAAA-TTGAATTTTTTATATGATAAAAAGGGGGTGTCGGTCATTGCATGGCCA
1 ACACCAAAAAATTTGAATTTTTTATATGATAAAAAGGGGGTGTCGACCATTGCATGGCCA
* * *
21230661 ATATC---AAATTT---TTTTTCTAT-TAGATAGAAAAGGGGGTGTCGGCCATTGCATGGCCA
1 ACACCAAAAAATTTGAATTTTT-TATAT-GATA-AAAAGGGGGTGTCGACCATTGCATGGCCA
21230717 ACACCAAA
1 ACACCAAA
21230725 TTTTTTTTTC
Statistics
Matches: 356, Mismatches: 41, Indels: 61
0.78 0.09 0.13
Matches are distributed among these distances:
54 6 0.02
55 7 0.02
56 34 0.10
57 4 0.01
58 16 0.04
59 93 0.26
60 25 0.07
61 88 0.25
62 82 0.23
63 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (60 bp):
ACACCAAAAAATTTGAATTTTTTATATGATAAAAAGGGGGTGTCGACCATTGCATGGCCA
Found at i:21230721 original size:115 final size:118
Alignment explanation
Indices: 21230269--21230724 Score: 364
Period size: 121 Copynumber: 3.8 Consensus size: 118
21230259 TTTATTTCAC
* * ** * * *
21230269 AAAAAG-GGGATGTCGACCATTGCATGGTCAACACAAAAAAAATTTGATTTTTTTACCAGATAAA
1 AAAAAGAGGG-TGTCGGCCATTGCATGGCCAACAC-TCAAAAGTTT-ATTTTTCTATCAGAT-AA
* * ** *
21230333 AAAGGGGGTGTCGACCA-TGACATGGCCAACA-CAAAAAGATTCG-AATTTTTTATCTGA
62 AAA-GGGGTGTCGGCCATTG-CATGGCCAACACCAAAAA-ATTTGAAATTTTCAATATGA
* * * * * *
21230390 CAAAAAG-GGGTATCGACCA-TGATATGGCCAACAC-CAAAAAATTTTAAAATTTTTTTATCTGA
1 -AAAAAGAGGGTGTCGGCCATTG-CATGGCCAACACTC--AAAAGTTT---ATTTTTCTATCAGA
* * * *
21230452 -AAAAAGGGGTATCGACTATTGCATGGCCAACACCAAAAAATTTTGAAAATTTTCAATCTGA
59 TAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCAAAAAA-TTTG-AAATTTTCAATATGA
* *
21230513 AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACTCAAAAGTTTAATTTTTTTATCAGATAAATA
1 AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACTCAAAAGTTT-ATTTTTCTATCAGATAAAAA
**
21230578 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAA-TTG-AATTTTTTATATGA
65 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTGAAATTTTCAATATGA
* * * *
21230630 TAAAAAGGGGGTGTCGGTCATTGCATGGCCAATA-TC-AAA-TTT-TTTTTCTATTAGATAGAAA
1 -AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACTCAAAAGTTTATTTTTCTATCAGATA-AAA
21230691 AGGGGGTGTCGGCCATTGCATGGCCAACACCAAA
64 A-GGGGTGTCGGCCATTGCATGGCCAACACCAAA
21230725 TTTTTTTTTC
Statistics
Matches: 286, Mismatches: 31, Indels: 41
0.80 0.09 0.11
Matches are distributed among these distances:
113 13 0.05
114 3 0.01
115 35 0.12
116 3 0.01
117 13 0.05
118 30 0.10
119 3 0.01
120 39 0.14
121 77 0.27
122 22 0.08
123 45 0.16
124 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (118 bp):
AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACTCAAAAGTTTATTTTTCTATCAGATAAAAAG
GGGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTGAAATTTTCAATATGA
Found at i:21232140 original size:28 final size:28
Alignment explanation
Indices: 21232098--21232152 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
21232088 TTATTCTTTA
* * *
21232098 AAAATTTCATGTTCATGTTCGTTTATTT
1 AAAATTACATATTCATATTCGTTTATTT
21232126 AAAATTACATATTCATATTCGTTTATT
1 AAAATTACATATTCATATTCGTTTATT
21232153 AACCGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (28 bp):
AAAATTACATATTCATATTCGTTTATTT
Found at i:21232724 original size:12 final size:12
Alignment explanation
Indices: 21232707--21232738 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
21232697 CACATTCTCC
21232707 AATATAATATGA
1 AATATAATATGA
21232719 AATATAATATGA
1 AATATAATATGA
21232731 AATA-AATA
1 AATATAATA
21232739 AATTCTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
AATATAATATGA
Found at i:21235230 original size:18 final size:19
Alignment explanation
Indices: 21235195--21235231 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21235185 GATAAAACTA
21235195 CGATCACCGACTTTTCGTT
1 CGATCACCGACTTTTCGTT
21235214 CGATCACCGAC-TTTCGTT
1 CGATCACCGACTTTTCGTT
21235232 TGCCAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (19 bp):
CGATCACCGACTTTTCGTT
Found at i:21242302 original size:41 final size:40
Alignment explanation
Indices: 21242256--21242415 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 40
21242246 CGCTAAAGGT
21242256 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGAGAAAACGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATG-GAAAACGCC
* * * * *
21242297 ACTAAATGTCAGAGCATTAGTGGCATTTATGGGAAAACACC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTAT-GGAAAACGCC
21242338 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGAAAAACGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGG-AAAACGCC
* *
21242379 GCTAAAGGTAAGAGCATTAGCGACGTTTATAGGAAAA
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTAT-GGAAAA
21242416 ATACCGTTAA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 99 0.95
42 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (40 bp):
GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGAAAACGCC
Found at i:21242792 original size:29 final size:29
Alignment explanation
Indices: 21242711--21242799 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
21242701 GATTACATCA
*
21242711 AAATTAAAGTTTCATGTATA-CATGTG-AGCC
1 AAATTAAAG-TTCATGTATATAAT-TGCA-CC
* * *
21242741 ACAATTAGAAATTCACGTGTATAATTGCACC
1 A-AATTA-AAGTTCATGTATATAATTGCACC
21242772 AAATTAAAGTTCATGTATATAATTGCAC
1 AAATTAAAGTTCATGTATATAATTGCAC
21242800 AGTAAATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 19 0.40
30 6 0.12
31 18 0.38
32 5 0.10
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATATAATTGCACC
Found at i:21245528 original size:26 final size:25
Alignment explanation
Indices: 21245454--21245530 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
21245444 TTTATCATCC
* *
21245454 ATATTCTATCCCAGTAAAATTTTG-
1 ATATTTTATCCCGGTAAAATTTTGA
* *
21245478 ATGATATTATCCCGATAAAATTTTGA
1 AT-ATTTTATCCCGGTAAAATTTTGA
21245504 ATATTTTATCCCTGGTAAAATTTTGA
1 ATATTTTATCCC-GGTAAAATTTTGA
21245530 A
1 A
21245531 AAAATATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.05
25 27 0.61
26 15 0.34
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (25 bp):
ATATTTTATCCCGGTAAAATTTTGA
Found at i:21248853 original size:21 final size:21
Alignment explanation
Indices: 21248828--21248900 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
21248818 TATTAGTAGA
* *
21248828 CTTCTACCGATACTAGTGATG
1 CTTCTACCGAAACAAGTGATG
* * **
21248849 TTTCTACAGAAACAAGTGACA
1 CTTCTACCGAAACAAGTGATG
* *
21248870 CTTCTACCTAAACAAGTCATG
1 CTTCTACCGAAACAAGTGATG
21248891 CTTCTACCGA
1 CTTCTACCGA
21248901 TACTAAAAAC
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (21 bp):
CTTCTACCGAAACAAGTGATG
Found at i:21251421 original size:19 final size:19
Alignment explanation
Indices: 21251376--21251426 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
21251366 ACCAGTAAAA
* *
21251376 CAGTTCAGAATACTTCCTT
1 CAGTTCATAATCCTTCCTT
21251395 CAGTTCATAATCCTTCCTT
1 CAGTTCATAATCCTTCCTT
21251414 CAGTTCATAATCC
1 CAGTTCATAATCC
21251427 CATCCCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.37
Consensus pattern (19 bp):
CAGTTCATAATCCTTCCTT
Found at i:21254046 original size:41 final size:41
Alignment explanation
Indices: 21253983--21254210 Score: 303
Period size: 41 Copynumber: 5.5 Consensus size: 41
21253973 ACTTGATGTA
21253983 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
*** * * *
21254025 CGGAGGAAGACTCGTGACTCGAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* *
21254066 TAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* *
21254107 TAAAGGAAGACTCATGTCTCGAGGTGAGAATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* * *
21254148 TAAAGGAAGACGCGTGTCTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-T
* *
21254190 TAAAGGAAGACTTATGACTCG
1 TAAAGGAAGACTCATGTCTCG
21254211 GTAGATCGTA
Statistics
Matches: 160, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 141 0.88
42 19 0.12
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
Found at i:21254225 original size:82 final size:80
Alignment explanation
Indices: 21253983--21254239 Score: 268
Period size: 82 Copynumber: 3.1 Consensus size: 80
21253973 ACTTGATGTA
* *** * **
21253983 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATCGGAGGAAGACTCGTGACTCGAA
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGGT
* *
21254048 ATGAGCATGAGATTATAT
65 A-GATCGT-AGATTATAT
* *
21254066 TAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTATATTAAAGGAAGACTCATGTCTCGAGG
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTC--GG
21254131 TGAGAAT-G-AGATTATAT
64 T-AG-ATCGTAGATTATAT
* * *
21254148 TAAAGGAAGACGCGTGTCTCGGGATGAGCATGAGATTATATTTAAAGGAAGACTTATGACTCGGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATA-TTAAAGGAAGACTCATGACTCGGT
*
21254213 AGATCGTAAGATTGT-T
65 AGATCGT-AGATTATAT
21254229 TAAAAGGAAGA
1 T-AAAGGAAGA
21254240 TCTACGACTC
Statistics
Matches: 148, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
79 2 0.01
80 3 0.02
81 5 0.03
82 111 0.75
83 23 0.16
84 2 0.01
85 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (80 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGGTA
GATCGTAGATTATAT
Found at i:21254225 original size:123 final size:121
Alignment explanation
Indices: 21253983--21254239 Score: 318
Period size: 123 Copynumber: 2.1 Consensus size: 121
21253973 ACTTGATGTA
* ** *
21253983 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATCGGAGGAAGACTCGTGACTCGAA
1 TAAA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATATCAAAGGAAGACGCGTGACTCGAA
* *
21254048 ATGAGCATGAGATTATATTAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTATAT
65 ATGAGCATGAGATTATATTAAAGGAAGACTCATGACTC-GGGTGAGCATAAGATTAT-T
* * * **
21254107 TAAAGGAAGACTCATGTCTCGAGGTGAGAATGAGATTATATTAAAGGAAGACGCGTGTCTCGGGA
1 TAAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATATCAAAGGAAGACGCGTGACTCGAAA
* * * *
21254172 TGAGCATGAGATTATATTTAAAGGAAGACTTATGACTC-GGTAGATCGTAAGATTGTT
66 TGAGCATGAGATTATA-TTAAAGGAAGACTCATGACTCGGGT-GAGCATAAGATTATT
21254229 TAAAAGGAAGA
1 T-AAAGGAAGA
21254240 TCTACGACTC
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
122 5 0.04
123 87 0.76
124 23 0.20
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (121 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATATCAAAGGAAGACGCGTGACTCGAAA
TGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGGGTGAGCATAAGATTATT
Found at i:21257084 original size:15 final size:14
Alignment explanation
Indices: 21257037--21257083 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 14
21257027 CAGTAAAAGA
21257037 TTTAAAATT--AA-
1 TTTAAAATTAAAAT
21257048 TTTAAAATTAAAAT
1 TTTAAAATTAAAAT
21257062 TTTAAAATATAAAAT
1 TTTAAAAT-TAAAAT
21257077 TATTAAA
1 T-TTAAA
21257084 TTTATTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.29
13 2 0.06
14 8 0.26
15 7 0.23
16 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAAATTAAAAT
Found at i:21257113 original size:38 final size:38
Alignment explanation
Indices: 21257061--21257137 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
21257051 AAAATTAAAA
* *
21257061 TTTTAAAATATAAAATTATTAAATTTATTATATTATTT
1 TTTTAAAATATAAAATTATTAAATTTATTAAATAATTT
*
21257099 TTTTGAAATATAAAATTATTAAATTTATTAAATAATTT
1 TTTTAAAATATAAAATTATTAAATTTATTAAATAATTT
21257137 T
1 T
21257138 AATCTTATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
TTTTAAAATATAAAATTATTAAATTTATTAAATAATTT
Found at i:21258272 original size:20 final size:20
Alignment explanation
Indices: 21258247--21258327 Score: 87
Period size: 20 Copynumber: 4.0 Consensus size: 20
21258237 TGATGATTTT
21258247 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* *
21258267 AATAATTTTAAATTAATTTAAA
1 AATAATTTTATATT--TTAAAA
21258289 AAT-A-TTTATA-TTTAAAA
1 AATAATTTTATATTTTAAAA
21258306 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-AT-ATTTTAAAA
21258328 TAATTTCCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
17 8 0.16
18 1 0.02
19 4 0.08
20 20 0.40
21 2 0.04
22 15 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:21258303 original size:39 final size:38
Alignment explanation
Indices: 21258244--21258329 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 38
21258234 AGATGATGAT
*
21258244 TTTAATAAT-TTTATATTTTAAAAAATAATTTTAAATTAA
1 TTTAAAAATATTTATATTTTAAAAAATAATTTT-AA-TAA
21258283 TTTAAAAATATTTATA-TTTAAAAAATAATTTTAATAA
1 TTTAAAAATATTTATATTTTAAAAAATAATTTTAATAA
*
21258320 TTTTAAAATA
1 TTTAAAAATA
21258330 ATTTCCTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 12 0.27
38 2 0.05
39 24 0.55
40 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
TTTAAAAATATTTATATTTTAAAAAATAATTTTAATAA
Found at i:21258331 original size:11 final size:11
Alignment explanation
Indices: 21258265--21258333 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
21258255 TATATTTTAA
21258265 AAAATAATTTT
1 AAAATAATTTT
* *
21258276 AAATTAATTTA
1 AAAATAATTTT
21258287 AAAATATTTATATTT
1 AAAATA---AT-TTT
21258302 AAAAAATAATTTT
1 --AAAATAATTTT
21258315 --AATAATTTT
1 AAAATAATTTT
21258324 AAAATAATTT
1 AAAATAATTT
21258334 CCTGACGTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
9 9 0.20
11 22 0.48
13 3 0.07
14 4 0.09
15 2 0.04
17 6 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:21260768 original size:41 final size:41
Alignment explanation
Indices: 21260713--21260875 Score: 254
Period size: 41 Copynumber: 4.0 Consensus size: 41
21260703 GAAAGACTTG
21260713 TGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCA
1 TGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCA
* *
21260754 TGTCTCGGGGTGAGCATGAGATTATATTAAAGGAAGACTCA
1 TGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCA
*
21260795 TGTCTCGAGGTGAGCATGAGATTATATTAAAGGAAGACTCA
1 TGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCA
* * * *
21260836 TGTCTTGGGATGTGTATGAGATTATATTTAAAGGAAGACT
1 TGTCTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACT
21260876 GATGACTAGG
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
41 100 0.88
42 13 0.12
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (41 bp):
TGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCA
Found at i:21260899 original size:41 final size:39
Alignment explanation
Indices: 21260731--21260913 Score: 154
Period size: 41 Copynumber: 4.5 Consensus size: 39
21260721 GATGAGCATG
* * * *
21260731 AGATTATATTAAAGGAAGACTCATGTCTCGGGGTGAGCATG
1 AGATTATATTAAAGGAAGACTCATGTCT--AGGTGATCGTA
* * *
21260772 AGATTATATTAAAGGAAGACTCATGTCTCGAGGTGAGCATG
1 AGATTATATTAAAGGAAGACTCATGTCT--AGGTGATCGTA
* *
21260813 AGATTATATTAAAGGAAGACTCATGTCTTGG-GATGTGTA
1 AGATTATATTAAAGGAAGACTCATGTCTAGGTGAT-CGTA
* *
21260852 TGAGATTATATTTAAAGGAAGACTGATGACTAGGTAGATCGTA
1 --AGATTATA-TTAAAGGAAGACTCATGTCTAGGT-GATCGTA
*
21260895 AGATTGT-TTAAAAGGAAGA
1 AGATTATATT-AAAGGAAGA
21260914 TCTACGACTC
Statistics
Matches: 124, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.02
39 5 0.04
40 9 0.07
41 82 0.66
42 20 0.16
43 3 0.02
44 3 0.02
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (39 bp):
AGATTATATTAAAGGAAGACTCATGTCTAGGTGATCGTA
Found at i:21260899 original size:82 final size:81
Alignment explanation
Indices: 21260723--21260913 Score: 233
Period size: 82 Copynumber: 2.3 Consensus size: 81
21260713 TGTCTCGAGA
* *
21260723 TGAGCATGAGATTATATTAAAGGAAGACTCATGTCTCGGGGTGAGCATGAGATTATATTAAAGGA
1 TGAGCATAAGATTATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGA
*
21260788 AGACTCATGTCTCGAGG
66 AGACTCATGACTC-AGG
* * * *
21260805 TGAGCATGAGATTATATTAAAGGAAGACTCATGTCTTGGGATGTGTATGAGATTATATTTAAAGG
1 TGAGCATAAGATTATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATA-TTAAAGG
*
21260870 AAGACTGATGACT-AGG
65 AAGACTCATGACTCAGG
* * *
21260886 TAGATCGTAAGATTGT-TTAAAAGGAAGA
1 T-GAGCATAAGATTATATT-AAAGGAAGA
21260914 TCTACGACTC
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
81 6 0.06
82 72 0.75
83 18 0.19
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (81 bp):
TGAGCATAAGATTATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATATTAAAGGA
AGACTCATGACTCAGG
Found at i:21263727 original size:18 final size:19
Alignment explanation
Indices: 21263673--21263724 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
21263663 TGAAGAGTTT
*
21263673 AATTTTATTTATTTTAATTA
1 AATTTTATTTATTTT-ATAA
21263693 AATTTT-TTTATTTTATAA
1 AATTTTATTTATTTTATAA
*
21263711 AATTTTAGTTATTT
1 AATTTTATTTATTT
21263725 ATATGCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.31
19 14 0.48
20 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
AATTTTATTTATTTTATAA
Found at i:21266170 original size:57 final size:57
Alignment explanation
Indices: 21266109--21266615 Score: 247
Period size: 57 Copynumber: 9.0 Consensus size: 57
21266099 TAATGCTTTC
* * *
21266109 CAGAACTTGAACAACAATAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
** * * * * *
21266166 CAGAACATT----ACTGACAACAA--A-AATGCAAGTCAGAATGAGAAAGATGCTTCT
1 CAGAAC-TTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
* * * * * * **
21266217 CAGAACTTAAAGAGTAACATCAACAACAATGATAGTGCAGACCAAAATGAAAAAAATGCTGCT
1 CAGAACTT------CAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
* * * * * * ** * *
21266280 GAGAGCATT----ACCGACAAC---GAAAATGCAGGTCAGAATGAGAATAATGCTTCC
1 CAGAAC-TTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
* * * * * * * * *
21266331 CAAAACTTAAACAACAACAGCAATGAGAATGCAAGACAGAATGAGAACAATGATCCTGTT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAAC---GATGCTGCT
* *
21266391 CAG-A--TCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAG---AACGATGCTGCT
* * *
21266448 CAG-A--TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAG---AACGATGCTGCT
* *
21266505 CAG-A--TCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGGACAACGATCCTGTT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGA-G--AACGATGCTGCT
*
21266562 CAG-A--TCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAATGCTGCT
1 CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
21266616 GAGGGTGTTA
Statistics
Matches: 361, Mismatches: 60, Indels: 61
0.75 0.12 0.13
Matches are distributed among these distances:
50 4 0.01
51 58 0.16
52 1 0.00
54 29 0.08
56 1 0.00
57 218 0.60
58 3 0.01
59 1 0.00
60 17 0.05
62 1 0.00
63 26 0.07
64 2 0.01
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (57 bp):
CAGAACTTCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCT
Found at i:21266296 original size:114 final size:114
Alignment explanation
Indices: 21266069--21266341 Score: 310
Period size: 114 Copynumber: 2.4 Consensus size: 114
21266059 GCAGCGTTAT
* * * *
21266069 CGACAACGAAAATGC-AGTTCAGAATGAGAATAATGCTTTCCAGAACTT-----G-AACAACAAT
1 CGACAACAAAAATGCAAG-TCAGAATGAGAATAATGCTTCCCAAAACTTAAAGAGTAACAACAAC
* * **
21266127 AACAATGAGAATGCAGGCCAAAATGAGAACGATGCTGCTCAGAACATTAC
65 AACAATGAGAATGCAGACCAAAATGAAAAAAATGCTGCTCAGAACATTAC
* * * *
21266177 TGACAACAAAAATGCAAGTCAGAATGAGAA-AGATGCTTCTCAGAACTTAAAGAGTAACATCAAC
1 CGACAACAAAAATGCAAGTCAGAATGAGAATA-ATGCTTCCCAAAACTTAAAGAGTAACAACAAC
* * * *
21266241 AACAATGATAGTGCAGACCAAAATGAAAAAAATGCTGCTGAGAGCATTAC
65 AACAATGAGAATGCAGACCAAAATGAAAAAAATGCTGCTCAGAACATTAC
* *
21266291 CGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAAAACTTAAA
1 CGACAACAAAAATGCAAGTCAGAATGAGAATAATGCTTCCCAAAACTTAAA
21266342 CAACAACAGC
Statistics
Matches: 137, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
107 1 0.01
108 39 0.28
109 2 0.01
113 1 0.01
114 93 0.68
115 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (114 bp):
CGACAACAAAAATGCAAGTCAGAATGAGAATAATGCTTCCCAAAACTTAAAGAGTAACAACAACA
ACAATGAGAATGCAGACCAAAATGAAAAAAATGCTGCTCAGAACATTAC
Found at i:21266640 original size:114 final size:114
Alignment explanation
Indices: 21266338--21266608 Score: 452
Period size: 114 Copynumber: 2.4 Consensus size: 114
21266328 TCCCAAAACT
* * * * * * *
21266338 TAAACAACAACAGCAATGAGAATGCAAGACAGAATGAGAACAATGATCCTGTTCAGATCAACACC
1 TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTACAGATCAACACC
21266403 AACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGA
66 AACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGA
*
21266452 TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGATCAACACC
1 TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTACAGATCAACACC
*
21266517 AACAACAATGAGAATGCAGGCCAAAATGAGGACAACGATCCTGTTCAGA
66 AACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGA
*
21266566 TCAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAA
1 TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAA
21266609 TGCTGCTGAG
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 149 1.00
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.14
Consensus pattern (114 bp):
TAAACACCAACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTACAGATCAACACC
AACAACAATGAGAATGCAGGCCAAAATGAGAACAACGATCCTGTTCAGA
Found at i:21268159 original size:147 final size:147
Alignment explanation
Indices: 21267888--21268181 Score: 444
Period size: 147 Copynumber: 2.0 Consensus size: 147
21267878 CCAGCAAGGG
* * * * * * *
21267888 CCTTCACGCCTTCACCTGGTTTTAGGTAGAAAGAACAACATAATATGATGAGAGAATTGTATGAA
1 CCTTCACGCCTTCACCTGGTTTTAAGTAAAAAGAACAACATAATATAACGAAAAAATTGTATAAA
*
21267953 ACTGTGATTCCACATCATAAATCACAATTAATATAACTTATATAACTTAATCTCCAGTACTATTT
66 ACTGTAATTCCACATCATAAATCACAATTAATATAACTTATATAACTTAATCTCCAGTACTATTT
*
21268018 GTATGCGCTCAATTGAT
131 GTATGAGCTCAATTGAT
* *
21268035 CCTTCACGCTTTCACCTGGTTTTAAGTAAAAAGAACAATATAATATAACGAAAAAATTGTATAAA
1 CCTTCACGCCTTCACCTGGTTTTAAGTAAAAAGAACAACATAATATAACGAAAAAATTGTATAAA
* * * * *
21268100 ACTGTAATTTCACATCATAAATCATAGTTAATATACCTTATATAACTTAATCTCTAGTACTATTT
66 ACTGTAATTCCACATCATAAATCACAATTAATATAACTTATATAACTTAATCTCCAGTACTATTT
21268165 GTATGAGCTCAATTGAT
131 GTATGAGCTCAATTGAT
21268182 TACATCTACT
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
147 131 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (147 bp):
CCTTCACGCCTTCACCTGGTTTTAAGTAAAAAGAACAACATAATATAACGAAAAAATTGTATAAA
ACTGTAATTCCACATCATAAATCACAATTAATATAACTTATATAACTTAATCTCCAGTACTATTT
GTATGAGCTCAATTGAT
Found at i:21268692 original size:17 final size:17
Alignment explanation
Indices: 21268672--21268715 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
21268662 ATCATATTAA
*
21268672 TAATTTTTTTTAATAAT
1 TAATTTTTTTAAATAAT
*
21268689 TAATATTTTTTAAATTAT
1 TAAT-TTTTTTAAATAAT
*
21268707 AAATTTTTT
1 TAATTTTTT
21268716 AACTGTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATTTTTTTAAATAAT
Found at i:21269328 original size:15 final size:16
Alignment explanation
Indices: 21269289--21269337 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
21269279 TTCTTCTTCC
* *
21269289 TTCTTCTTCCCTCTTT
1 TTCTTTTTCCCTCATT
21269305 TTCTTTTTCCCTCATT
1 TTCTTTTTCCCTCATT
21269321 TT-TTTTT--CTCATT
1 TTCTTTTTCCCTCATT
21269334 TTCT
1 TTCT
21269338 CTCTTATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
15 5 0.17
16 16 0.53
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (16 bp):
TTCTTTTTCCCTCATT
Found at i:21274480 original size:37 final size:37
Alignment explanation
Indices: 21274433--21274536 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
21274423 ACAATTTTAA
* *
21274433 TCCAGAATTGCGCCC-AAACATGTCGCTGCATGAGCACT
1 TCCAG-ATTGCGCCCAAAAC-TGTCACCGCATGAGCACT
* **
21274471 TCTAGATTGCGCATAAAACTGTCACCGCATGAGCACT
1 TCCAGATTGCGCCCAAAACTGTCACCGCATGAGCACT
*
21274508 TCCAGATTGCACCCAAAACTGTCACCGCA
1 TCCAGATTGCGCCCAAAACTGTCACCGCA
21274537 GGAATATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
37 48 0.86
38 8 0.14
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (37 bp):
TCCAGATTGCGCCCAAAACTGTCACCGCATGAGCACT
Found at i:21274609 original size:38 final size:37
Alignment explanation
Indices: 21274566--21274649 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
21274556 CCCAAGACTG
* *
21274566 TCGCTGCATAAATATTCTTCAAATTGCATCCAGAACTA
1 TCGCTGCATAAATATTCTTC-AATTGCACCCAGAAATA
* *
21274604 TCGCTGCATAAGTATTCTTCAATTGCACCCAGAAATG
1 TCGCTGCATAAATATTCTTCAATTGCACCCAGAAATA
21274641 TCGCTGCAT
1 TCGCTGCAT
21274650 GAACATGTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 23 0.55
38 19 0.45
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (37 bp):
TCGCTGCATAAATATTCTTCAATTGCACCCAGAAATA
Found at i:21274637 original size:37 final size:38
Alignment explanation
Indices: 21274552--21274649 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 38
21274542 ATTTTTGGAA
21274552 TGCACCCA-AGACTGTCGCTGCATAAATATTCTTCAAAT
1 TGCACCCAGA-ACTGTCGCTGCATAAATATTCTTCAAAT
* * *
21274590 TGCATCCAGAACTATCGCTGCATAAGTATTCTTC-AAT
1 TGCACCCAGAACTGTCGCTGCATAAATATTCTTCAAAT
*
21274627 TGCACCCAGAAATGTCGCTGCAT
1 TGCACCCAGAACTGTCGCTGCAT
21274650 GAACATGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 23 0.43
38 29 0.55
39 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (38 bp):
TGCACCCAGAACTGTCGCTGCATAAATATTCTTCAAAT
Found at i:21274669 original size:26 final size:26
Alignment explanation
Indices: 21274633--21274692 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
21274623 CAATTGCACC
*
21274633 CAGAAATGTCGCTGCATGAACATGTA
1 CAGAATTGTCGCTGCATGAACATGTA
* *
21274659 CAGAATTGTCGCTGCATGAACGTGTC
1 CAGAATTGTCGCTGCATGAACATGTA
21274685 CAGAATTG
1 CAGAATTG
21274693 CGCCTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
CAGAATTGTCGCTGCATGAACATGTA
Found at i:21279179 original size:37 final size:38
Alignment explanation
Indices: 21279118--21279210 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 38
21279108 ACAATTTTAA
* *
21279118 TCCAGAATTGTGCCC-AAACATGTCGCTGCATGAGCACT
1 TCCA-AATTGCGCCCAAAACATGTCGCCGCATGAGCACT
* *
21279156 TCTAGATTGCGCCCAAAAC-TGTCGCCGCATGAGCACT
1 TCCAAATTGCGCCCAAAACATGTCGCCGCATGAGCACT
*
21279193 TCCAAATTGCACCCAAAA
1 TCCAAATTGCGCCCAAAA
21279211 TAGTCACCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 40 0.85
38 7 0.15
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (38 bp):
TCCAAATTGCGCCCAAAACATGTCGCCGCATGAGCACT
Found at i:21279330 original size:37 final size:38
Alignment explanation
Indices: 21279237--21279330 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 38
21279227 ATTTCTGGAA
* * *
21279237 TGCACCCAAGACTGTCGCTGCATAAATATTCTTTAAAT
1 TGCACCCAAGAATATCGCTACATAAATATTCTTTAAAT
* * * *
21279275 TGCA-TCTAGAACTATCGCTACATAAGTATTC-TTCAAT
1 TGCACCCAAGAA-TATCGCTACATAAATATTCTTTAAAT
*
21279312 TGCACCCAAGAATCTCGCT
1 TGCACCCAAGAATATCGCT
21279331 GCATGAACAT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 19 0.43
38 25 0.57
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (38 bp):
TGCACCCAAGAATATCGCTACATAAATATTCTTTAAAT
Found at i:21283582 original size:30 final size:30
Alignment explanation
Indices: 21283523--21283591 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
21283513 AAGAAATTGG
* * * *
21283523 ATATTTCTAATATAGTGTTTTGTGCATTAA
1 ATATTTTTAATATAATATTTCGTGCATTAA
*
21283553 ATATTTTTAATATAATATTTCGTGTATTAA
1 ATATTTTTAATATAATATTTCGTGCATTAA
**
21283583 GCATTTTTA
1 ATATTTTTA
21283592 TTTGGGTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (30 bp):
ATATTTTTAATATAATATTTCGTGCATTAA
Found at i:21283988 original size:11 final size:10
Alignment explanation
Indices: 21283962--21284017 Score: 78
Period size: 10 Copynumber: 5.5 Consensus size: 10
21283952 CCATTTTATT
21283962 TTTCTCTCAA
1 TTTCTCTCAA
21283972 -TTCTCTCAA
1 TTTCTCTCAA
21283981 TTTCCTCTCAA
1 TTT-CTCTCAA
21283992 TTTTCTCTCAA
1 -TTTCTCTCAA
*
21284003 TTTCTCTCAC
1 TTTCTCTCAA
21284013 TTTCT
1 TTTCT
21284018 TTCTAAAGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
9 9 0.21
10 16 0.38
11 14 0.33
12 3 0.07
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:21283997 original size:22 final size:19
Alignment explanation
Indices: 21283962--21284011 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
21283952 CCATTTTATT
21283962 TTTCTCTCAATTCTCTCAA
1 TTTCTCTCAATTCTCTCAA
21283981 TTTCCTCTCAATTTTCTCTCAA
1 TTT-CTCTCAA--TTCTCTCAA
21284003 TTTCTCTCA
1 TTTCTCTCA
21284012 CTTTCTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 6 0.21
22 12 0.43
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCTCTCAATTCTCTCAA
Found at i:21284016 original size:20 final size:19
Alignment explanation
Indices: 21283962--21284017 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 19
21283952 CCATTTTATT
*
21283962 TTTCTCTCAATTCTCTCAA
1 TTTCTCTCATTTCTCTCAA
21283981 TTTCCTCTCAATTTTCTCTCAA
1 TTT-CTCTC-A-TTTCTCTCAA
21284003 TTTCTCTCACTTTCT
1 TTTCTCTCA-TTTCT
21284018 TTCTAAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 6 0.19
22 12 0.38
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTCTCTCATTTCTCTCAA
Found at i:21284217 original size:18 final size:16
Alignment explanation
Indices: 21284183--21284278 Score: 54
Period size: 17 Copynumber: 5.8 Consensus size: 16
21284173 AATTTTTTCT
*
21284183 ATTATTTATTTATTTTA
1 ATTATTT-TTTAATTTA
*
21284200 TTTTATTTTTATAATTTA
1 -ATTATTTTT-TAATTTA
21284218 ATTATTTTTTAA--TA
1 ATTATTTTTTAATTTA
* *
21284232 A-TATTTAATTATTTTA
1 ATTATTT-TTTAATTTA
* *
21284248 TATTAATTTTATAACTTA
1 -ATT-ATTTTTTAATTTA
21284266 ATTAATTTTTTAA
1 ATT-ATTTTTTAA
21284279 ATATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
13 5 0.08
14 6 0.10
16 5 0.08
17 23 0.38
18 18 0.30
19 4 0.07
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATTTTTTAATTTA
Found at i:21284244 original size:48 final size:49
Alignment explanation
Indices: 21284171--21284278 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 49
21284161 AGAGTTAATT
* * * * * *
21284171 TTAATTTTTT-CTATTATTTATTTATTTTATTTTATTTTTATAATTTAA
1 TTAATTTTTTAATAATATTTAATTATTTTATATTAATTTTATAACTTAA
21284219 TT-ATTTTTTAATAATATTTAATTATTTTATATTAATTTTATAACTTAA
1 TTAATTTTTTAATAATATTTAATTATTTTATATTAATTTTATAACTTAA
21284267 TTAATTTTTTAA
1 TTAATTTTTTAA
21284279 ATATTTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 7 0.13
48 36 0.69
49 9 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (49 bp):
TTAATTTTTTAATAATATTTAATTATTTTATATTAATTTTATAACTTAA
Found at i:21284254 original size:21 final size:21
Alignment explanation
Indices: 21284165--21284258 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
21284155 ATGGTAAGAG
*
21284165 TTAAT-TTTAATT-TTTTCTA
1 TTAATATTTAATTATTTTATA
* * *
21284184 TTATTTATTTATTTTATTTTATT
1 TTA-ATATTTA-ATTATTTTATA
* *
21284207 TTTATAATTTAATTATTTTTTA
1 TTAAT-ATTTAATTATTTTATA
*
21284229 ATAATATTTAATTATTTTATA
1 TTAATATTTAATTATTTTATA
21284250 TTAAT-TTTA
1 TTAATATTTA
21284259 TAACTTAATT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 3 0.05
20 5 0.09
21 23 0.40
22 14 0.25
23 12 0.21
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (21 bp):
TTAATATTTAATTATTTTATA
Found at i:21286029 original size:18 final size:18
Alignment explanation
Indices: 21286006--21286050 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
21285996 GGGAGCTCAA
*
21286006 CTCAATTTCGATCGCCAC
1 CTCAATTTCAATCGCCAC
** *
21286024 CTCAATACCAATTGCCAC
1 CTCAATTTCAATCGCCAC
21286042 CTCAATTTC
1 CTCAATTTC
21286051 CACCGCCTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.38, G:0.07, T:0.29
Consensus pattern (18 bp):
CTCAATTTCAATCGCCAC
Found at i:21300511 original size:22 final size:22
Alignment explanation
Indices: 21300468--21300511 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
21300458 AAAATTATTT
*
21300468 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
21300490 AATAATTTTAATAATTTTAAAA
1 AATAATTTT-ATAATTTCAAAA
21300512 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:21305455 original size:15 final size:15
Alignment explanation
Indices: 21305432--21305464 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
21305422 TGTAGACTTA
*
21305432 TTGGCTGTGACCCGG
1 TTGGATGTGACCCGG
21305447 TTGGATGTGACCCGG
1 TTGGATGTGACCCGG
21305462 TTG
1 TTG
21305465 TATGCCCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.30
Consensus pattern (15 bp):
TTGGATGTGACCCGG
Found at i:21309287 original size:24 final size:24
Alignment explanation
Indices: 21309260--21309370 Score: 159
Period size: 24 Copynumber: 4.6 Consensus size: 24
21309250 TATTAGTTGG
* *
21309260 CGAGCGTAAACGCAAAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
21309284 CGAGCATAAACGTAAAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
* **
21309308 CAAGCATAAACGTAAAGTGTTTGA
1 CGAGCATAAACGTAAAGTGGCTGA
* *
21309332 TGAGCATAAACATAAAGTGGCTGA
1 CGAGCATAAACGTAAAGTGGCTGA
21309356 CGAGCATAAACGTAA
1 CGAGCATAAACGTAA
21309371 TTGAAACTTG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (24 bp):
CGAGCATAAACGTAAAGTGGCTGA
Found at i:21326388 original size:15 final size:15
Alignment explanation
Indices: 21326368--21326404 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
21326358 TGGTCTCGAA
21326368 ACCACTATTTTTGAT
1 ACCACTATTTTTGAT
21326383 ACCACTATTTTTGAT
1 ACCACTATTTTTGAT
21326398 ACCACTA
1 ACCACTA
21326405 AAAATCGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (15 bp):
ACCACTATTTTTGAT
Found at i:21334108 original size:21 final size:21
Alignment explanation
Indices: 21334083--21334123 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21334073 TAATTAATTA
**
21334083 TATAGATATATCCAACTTTTT
1 TATAGATATATAAAACTTTTT
21334104 TATAGATATATAAAACTTTT
1 TATAGATATATAAAACTTTT
21334124 ATCAGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (21 bp):
TATAGATATATAAAACTTTTT
Found at i:21348148 original size:24 final size:24
Alignment explanation
Indices: 21348121--21348169 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
21348111 AGAAGTGGAG
21348121 GAAG-AAGAAGAAGAAGGAAAAGAA
1 GAAGAAAG-AGAAGAAGGAAAAGAA
*
21348145 GAAGAAAGAGAGGAAGGAAAAGAA
1 GAAGAAAGAGAAGAAGGAAAAGAA
21348169 G
1 G
21348170 TCGAGGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAGAAGAAGGAAAAGAA
Found at i:21349161 original size:8 final size:8
Alignment explanation
Indices: 21349148--21349197 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
21349138 TCAGTCACAT
21349148 AAAAAAGA
1 AAAAAAGA
21349156 AAAAAA-A
1 AAAAAAGA
**
21349163 TGAAAAGA
1 AAAAAAGA
*
21349171 GAAAAAG-
1 AAAAAAGA
21349178 AAAAAA-A
1 AAAAAAGA
21349185 AAAAAAGA
1 AAAAAAGA
21349193 AAAAA
1 AAAAA
21349198 TATATATTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 16 0.47
8 18 0.53
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:21349167 original size:10 final size:9
Alignment explanation
Indices: 21349148--21349197 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
21349138 TCAGTCACAT
21349148 AAAAAAGAA
1 AAAAAAGAA
21349157 AAAAAATGAA
1 AAAAAA-GAA
21349167 AAGAGAAA-AA
1 AA-A-AAAGAA
*
21349177 GAAAAA-AA
1 AAAAAAGAA
21349185 AAAAAAGAA
1 AAAAAAGAA
21349194 AAAA
1 AAAA
21349198 TATATATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 10 0.29
9 13 0.37
10 8 0.23
11 1 0.03
12 3 0.09
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:21349182 original size:14 final size:14
Alignment explanation
Indices: 21349149--21349197 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
21349139 CAGTCACATA
21349149 AAAAAGAAAAAAAATG
1 AAAAA-AAAAAAAA-G
* *
21349165 -AAAAGAGAAAAAG
1 AAAAAAAAAAAAAG
21349178 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
21349192 AAAAAA
1 AAAAAA
21349198 TATATATTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 23 0.82
15 4 0.14
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:21357301 original size:12 final size:11
Alignment explanation
Indices: 21357284--21357320 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
21357274 TTGAGGCAGA
21357284 AGAAGAAGTAAG
1 AGAAGAAG-AAG
21357296 AGAAGAAGAA-
1 AGAAGAAGAAG
21357306 AGAA-AAGAAG
1 AGAAGAAGAAG
21357316 AGAAG
1 AGAAG
21357321 GAATAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.22
10 8 0.35
11 2 0.09
12 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:21357314 original size:15 final size:15
Alignment explanation
Indices: 21357281--21357333 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
21357271 GTATTGAGGC
*
21357281 AGAAGAAG-AAGTAAG
1 AGAAGAAGAAAG-AAA
21357296 AGAAGAAGAAAGAAA
1 AGAAGAAGAAAGAAA
*
21357311 AGAAG-AGAAGGAATA
1 AGAAGAAGAAAGAA-A
21357326 AGAAGAAG
1 AGAAGAAG
21357334 GAATTTCCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 7 0.21
15 21 0.64
16 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (15 bp):
AGAAGAAGAAAGAAA
Found at i:21359866 original size:24 final size:24
Alignment explanation
Indices: 21359833--21359879 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21359823 ATTCATCTCT
*
21359833 TATTAATTTGCTCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
21359856 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
21359880 TACTCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:21362436 original size:20 final size:20
Alignment explanation
Indices: 21362411--21362453 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
21362401 ATTAGGGATT
21362411 GGTCATTTGAAGCCTACTGC
1 GGTCATTTGAAGCCTACTGC
21362431 GGTCATTTGAAGCCTACTGC
1 GGTCATTTGAAGCCTACTGC
21362451 GGT
1 GGT
21362454 GACATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (20 bp):
GGTCATTTGAAGCCTACTGC
Found at i:21371461 original size:9 final size:9
Alignment explanation
Indices: 21371447--21371499 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
21371437 CAAATGATTT
21371447 TAAAAATTA
1 TAAAAATTA
*
21371456 TAAAAA-AA
1 TAAAAATTA
*
21371464 TTAAAATTCA
1 TAAAAATT-A
21371474 -AAAAATTA
1 TAAAAATTA
21371482 TAAAAATTCA
1 TAAAAATT-A
21371492 TAAAAATT
1 TAAAAATT
21371500 CAAAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
8 7 0.19
9 19 0.53
10 10 0.28
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:21371505 original size:9 final size:10
Alignment explanation
Indices: 21371466--21371505 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
21371456 TAAAAAAATT
21371466 AAAATTCA-A
1 AAAATTCATA
21371475 AAAATT-ATA
1 AAAATTCATA
21371484 AAAATTCATA
1 AAAATTCATA
21371494 AAAATTCA-A
1 AAAATTCATA
21371503 AAA
1 AAA
21371506 TTTAGCATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.03
9 17 0.59
10 11 0.38
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAATTCATA
Found at i:21372171 original size:31 final size:31
Alignment explanation
Indices: 21372083--21372194 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
21372073 TAATATTTAG
* * *
21372083 TACCTGAACTTGATACTTTTTCTTAATTTGGA
1 TACCTAAACTTGACACTTTTTCCTAATTT-GA
*
21372115 -ACCTAAACTTG----TTTTTGGTCTAATTTGA
1 TACCTAAACTTGACACTTTTT--CCTAATTTGA
*
21372143 TA-CTCAAACTTGACACTTTTTCCTAATTTGG
1 TACCT-AAACTTGACACTTTTTCCTAATTTGA
21372174 TACCTAAACTTGACACTTTTT
1 TACCTAAACTTGACACTTTTT
21372195 TTTAAGTTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
27 5 0.08
28 4 0.06
29 14 0.21
31 36 0.55
32 2 0.03
33 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (31 bp):
TACCTAAACTTGACACTTTTTCCTAATTTGA
Found at i:21372213 original size:30 final size:30
Alignment explanation
Indices: 21372134--21372214 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
21372124 TGTTTTTGGT
* *
21372134 CTAATTTGATACTCAAACTTGACACTTTTTC
1 CTAAGTTGGTACT-AAACTTGACACTTTTTC
* *
21372165 CTAATTTGGTACCTAAACTTGACACTTTTTT
1 CTAAGTTGGTA-CTAAACTTGACACTTTTTC
*
21372196 TTAAGTTGGTACTAAACTT
1 CTAAGTTGGTACTAAACTT
21372215 TTTAGGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 8 0.18
31 35 0.78
32 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (30 bp):
CTAAGTTGGTACTAAACTTGACACTTTTTC
Found at i:21372258 original size:89 final size:91
Alignment explanation
Indices: 21372077--21372269 Score: 239
Period size: 89 Copynumber: 2.1 Consensus size: 91
21372067 TTAATATAAT
* * * * * *
21372077 ATTTAGTACCTGAACTTGATACTTTTTCTTAATTTGGAACCTAAACTTGTTTTTGGTCTAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGAACCTAAACTTGTTTTAGGTCCAATTTG
21372142 ATACTCAAACTTGACACTTTTTCCTA
66 ATACTCAAACTTGACACTTTTTCCTA
* *
21372168 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGGTA-CTAAAC-T-TTTTAGGATCCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGAACCTAAACTTGTTTTAGG-TCCAATTT
* * * * *
21372230 GGTACTTAAACTTGCCTCTTTTTTCTA
65 GATACTCAAACTTGACACTTTTTCCTA
21372257 ATTTGGTACCTAA
1 ATTTGGTACCTAA
21372270 TATTTTTTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
88 6 0.07
89 43 0.49
90 6 0.07
91 33 0.38
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGAACCTAAACTTGTTTTAGGTCCAATTTG
ATACTCAAACTTGACACTTTTTCCTA
Found at i:21375447 original size:37 final size:35
Alignment explanation
Indices: 21375372--21375462 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 35
21375362 TCACGTTAGC
*
21375372 AATTATTTAATTTTTAATAA-ATAAAAAAATTTAA
1 AATTTTTTAATTTTTAATAATATAAAAAAATTTAA
* * * *
21375406 AATTTTTTGAAATTTTTAATAATGTCAATAAATTTAT
1 AATTTTTT--AATTTTTAATAATATAAAAAAATTTAA
21375443 AATTTTTTAA-TTTTAATAAT
1 AATTTTTTAATTTTTAATAAT
21375463 TTCATAATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 17 0.35
35 2 0.04
36 12 0.24
37 18 0.37
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (35 bp):
AATTTTTTAATTTTTAATAATATAAAAAAATTTAA
Found at i:21375470 original size:17 final size:17
Alignment explanation
Indices: 21375419--21375471 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
21375409 TTTTTGAAAT
*
21375419 TTTTAATAATGTCAATAA
1 TTTTAATAATTTC-ATAA
* **
21375437 ATTT-ATAATTTTTTAA
1 TTTTAATAATTTCATAA
21375453 TTTTAATAATTTCATAA
1 TTTTAATAATTTCATAA
21375470 TT
1 TT
21375472 GGGTAAATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 6 0.22
17 18 0.67
18 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAATAATTTCATAA
Found at i:21378883 original size:17 final size:18
Alignment explanation
Indices: 21378858--21378891 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21378848 ATAACAATTA
*
21378858 TGAAGATTTTGG-ATATG
1 TGAAAATTTTGGCATATG
21378875 TGAAAATTTTGGCATAT
1 TGAAAATTTTGGCATAT
21378892 TCCCTGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (18 bp):
TGAAAATTTTGGCATATG
Done.