Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 13 of 208
Found at i:5221760 original size:5 final size:5
Alignment explanation
Indices: 5221735--5221807 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
5221725 TTACTTTATT
*
5221735 TAATA TATATAA TAATA TAATG TAATA TAAT- TAATA TAATA TAATA TATTATA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
*
5221788 TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TA
5221808 CATAACATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 37 0.65
6 4 0.07
7 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:5221763 original size:22 final size:22
Alignment explanation
Indices: 5221735--5221817 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
5221725 TTACTTTATT
*
5221735 TAATATATATAATAATATAATG
1 TAATATATATAATAATATAATA
5221757 TAATATA-AT--TAATATAATA
1 TAATATATATAATAATATAATA
*
5221776 TAATATAT-TATATTATATAATA
1 TAATATATATA-ATAATATAATA
* *
5221798 AAATA-ATATACATAACATAA
1 TAATATATATA-ATAATATAA
5221818 AAATCTCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 17 0.34
21 4 0.08
22 29 0.58
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (22 bp):
TAATATATATAATAATATAATA
Found at i:5221793 original size:17 final size:19
Alignment explanation
Indices: 5221735--5221807 Score: 84
Period size: 17 Copynumber: 4.1 Consensus size: 19
5221725 TTACTTTATT
5221735 TAATAT-ATATAA-TAATA
1 TAATATAATATAATTAATA
*
5221752 TAATGTAATATAATTAATA
1 TAATATAATATAATTAATA
5221771 TAATATAATAT-ATT-ATA
1 TAATATAATATAATTAATA
* *
5221788 TTATATAATA-AAATAATA
1 TAATATAATATAATTAATA
5221806 TA
1 TA
5221808 CATAACATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
17 19 0.40
18 13 0.28
19 15 0.32
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
TAATATAATATAATTAATA
Found at i:5241090 original size:15 final size:15
Alignment explanation
Indices: 5241066--5241099 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5241056 TAAATTAGAA
5241066 ATTACCATTATTATT
1 ATTACCATTATTATT
*
5241081 ATTACTATTATTATT
1 ATTACCATTATTATT
5241096 ATTA
1 ATTA
5241100 TATATAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTACCATTATTATT
Found at i:5255050 original size:24 final size:24
Alignment explanation
Indices: 5254988--5255053 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
5254978 AATATAATTT
*
5254988 ATATATATTAAAATTAA-AATTTAA
1 ATATAT-TTAAAATTAATAACTTAA
* * *
5255012 AAATAATTT-ATATTAATTACTTAA
1 ATAT-ATTTAAAATTAATAACTTAA
5255036 ATATATTTAAAATTAATA
1 ATATATTTAAAATTAATA
5255054 TTTCATTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
23 10 0.31
24 20 0.62
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATTTAAAATTAATAACTTAA
Found at i:5260948 original size:18 final size:18
Alignment explanation
Indices: 5260915--5260949 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5260905 ATTGAAATTG
* *
5260915 AATTTGATTTTTTTTTTT
1 AATTTGATATTATTTTTT
5260933 AATTTGATATTATTTTT
1 AATTTGATATTATTTTT
5260950 ATCGTAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
AATTTGATATTATTTTTT
Found at i:5281224 original size:45 final size:46
Alignment explanation
Indices: 5281157--5281280 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
5281147 CATATGACCT
*
5281157 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
5281200 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
5281246 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
5281281 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:5281263 original size:46 final size:45
Alignment explanation
Indices: 5281157--5281354 Score: 207
Period size: 37 Copynumber: 4.8 Consensus size: 45
5281147 CATATGACCT
*
5281157 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
5281200 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
5281246 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
5281283 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
5281320 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
5281355 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:5281284 original size:37 final size:37
Alignment explanation
Indices: 5281243--5281381 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
5281233 GCTGAAGCTA
* *
5281243 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
5281280 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
5281317 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
5281354 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
5281382 AGTACTCAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:5292547 original size:20 final size:20
Alignment explanation
Indices: 5292522--5292571 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5292512 TGGCTTAAAA
5292522 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
5292542 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
5292559 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5292572 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:5297186 original size:20 final size:20
Alignment explanation
Indices: 5297161--5297210 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5297151 TGGCTTAAAA
5297161 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
5297181 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
5297198 GTGGTAGTGGATT
1 TTGGTAGTGGATT
5297211 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:5318635 original size:16 final size:17
Alignment explanation
Indices: 5318608--5318639 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5318598 AAATAAATCT
5318608 AAAAATATTAATTTTTG
1 AAAAATATTAATTTTTG
5318625 AAAAATA-TAATTTTT
1 AAAAATATTAATTTTT
5318640 CTTTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAAAATATTAATTTTTG
Found at i:5324665 original size:15 final size:15
Alignment explanation
Indices: 5324645--5324678 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5324635 CCACTATATA
5324645 TAATAATAATAATAG
1 TAATAATAATAATAG
*
5324660 TAATAATAATAATGG
1 TAATAATAATAATAG
5324675 TAAT
1 TAAT
5324679 TTCTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:5339977 original size:85 final size:85
Alignment explanation
Indices: 5339834--5340001 Score: 282
Period size: 85 Copynumber: 2.0 Consensus size: 85
5339824 CTGGTTATGG
* *
5339834 GGGTCATTTGAAGGTGCGACCGTTCAGGAGGCTAAAAGGAATTCAAAATATTATTTCTCAGTTAT
1 GGGTCATTTGAAGGTGCGACCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
5339899 TAAGCAGCCCAAATAAACTT
66 TAAGCAGCCCAAATAAACTT
* * *
5339919 GGGTCATTTGAATGTGCGGCCATTCAGGAGGCTGAAAGGAATTCAAAATATTACTTCTCAGTTAT
1 GGGTCATTTGAAGGTGCGACCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
*
5339984 TAAGCGGCCCAAATAAAC
66 TAAGCAGCCCAAATAAAC
5340002 ATTTCTTTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (85 bp):
GGGTCATTTGAAGGTGCGACCATTCAGGAGGCTAAAAGGAATTCAAAATATTACTTCTCAGTTAT
TAAGCAGCCCAAATAAACTT
Found at i:5340077 original size:30 final size:30
Alignment explanation
Indices: 5340043--5340111 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5340033 TCTTTTACCC
*
5340043 ACTTTTAATCGGTCCAAAAAGCTTTTATTA
1 ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
* ****
5340073 ACTTTTAAGGGGTCCAAATTTTTTTTATTA
1 ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
5340103 ACTTTTAAG
1 ACTTTTAAG
5340112 GGACCTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (30 bp):
ACTTTTAAGCGGTCCAAAAAGCTTTTATTA
Found at i:5344834 original size:33 final size:32
Alignment explanation
Indices: 5344788--5344849 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
5344778 TCCCCATAAT
5344788 ATTAAAAAATATAT-AAATTAAAAATAAAAAAA
1 ATTAAAAAATATATAAAATT-AAAATAAAAAAA
*
5344820 ATTAGAAAATTATATAAAATTAAAATAAAA
1 ATTA-AAAAATATATAAAATTAAAATAAAA
5344850 CAATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 4 0.15
33 18 0.67
34 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (32 bp):
ATTAAAAAATATATAAAATTAAAATAAAAAAA
Found at i:5344868 original size:24 final size:23
Alignment explanation
Indices: 5344841--5344896 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
5344831 ATATAAAATT
5344841 AAAATAAAA-CAATAAAATACTAAA
1 AAAATAAAATCAATAAAA-A-TAAA
*
5344865 AAAATAAAATTAATAAAAATAAA
1 AAAATAAAATCAATAAAAATAAA
5344888 AATAATAAA
1 AA-AATAAA
5344897 TAGGTATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.21
24 16 0.55
25 7 0.24
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAATAAAATCAATAAAAATAAA
Found at i:5344884 original size:15 final size:15
Alignment explanation
Indices: 5344825--5344896 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 15
5344815 AAAAAATTAG
*
5344825 AAAATTATATAAAATT
1 AAAATTA-ATAAAAAT
*
5344841 AAAA-TAA-AACAAT
1 AAAATTAATAAAAAT
5344854 AAAATACTAA-AAAAAT
1 AAAAT--TAATAAAAAT
5344870 AAAATTAATAAAAAT
1 AAAATTAATAAAAAT
*
5344885 AAAAATAATAAA
1 AAAATTAATAAA
5344897 TAGGTATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
13 8 0.17
14 4 0.08
15 19 0.40
16 17 0.35
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTAATAAAAAT
Found at i:5344890 original size:21 final size:21
Alignment explanation
Indices: 5344825--5344892 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
5344815 AAAAAATTAG
*
5344825 AAAATT-ATATAAAATTAAAAT
1 AAAATTAATA-AAAATAAAAAT
*
5344846 AAAA-CAATAAAATACTAAAAAAAT
1 AAAATTAATAAAA-A-T--AAAAAT
5344870 AAAATTAATAAAAATAAAAAT
1 AAAATTAATAAAAATAAAAAT
5344891 AA
1 AA
5344893 TAAATAGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 3 0.08
21 16 0.42
22 1 0.03
23 1 0.03
24 10 0.26
25 7 0.18
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAATTAATAAAAATAAAAAT
Found at i:5380296 original size:20 final size:20
Alignment explanation
Indices: 5380258--5380296 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5380248 AATATTTTAT
*
5380258 TAATAAATTAAATTATAAAA
1 TAATAAATTAAAATATAAAA
5380278 TAATAAATGTAAAAT-TAAA
1 TAATAAAT-TAAAATATAAA
5380297 TCATTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAATAAATTAAAATATAAAA
Found at i:5381810 original size:21 final size:21
Alignment explanation
Indices: 5381786--5381837 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5381776 CATTGTTTCT
*
5381786 AATCTCACCGCAACAGTACCC
1 AATCTCACCGCAACAGTAACC
* *
5381807 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCAACAGTAACC
5381828 AATCTCACCG
1 AATCTCACCG
5381838 TCAGCGCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.19
Consensus pattern (21 bp):
AATCTCACCGCAACAGTAACC
Found at i:5386938 original size:29 final size:28
Alignment explanation
Indices: 5386906--5386988 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
5386896 CAAGTCCTTC
*
5386906 AAAAGTTTTGAAAATTTTATTTAGACCCT
1 AAAAGTTTTGAAAATTTTAATTA-ACCCT
* * *
5386935 AAAA-TCCTTGAAAATTTTAATTAAGCTT
1 AAAAGT-TTTGAAAATTTTAATTAACCCT
*
5386963 ACAAATGTTTTGAAAATATTAATTAA
1 A-AAA-GTTTTGAAAATTTTAATTAA
5386989 AACCCTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 5 0.11
29 22 0.50
30 16 0.36
31 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (28 bp):
AAAAGTTTTGAAAATTTTAATTAACCCT
Found at i:5394915 original size:23 final size:23
Alignment explanation
Indices: 5394887--5394931 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5394877 GTTCAAAATT
*
5394887 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
5394910 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
5394932 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:5395018 original size:24 final size:24
Alignment explanation
Indices: 5394980--5395231 Score: 143
Period size: 24 Copynumber: 10.8 Consensus size: 24
5394970 TGGATTGGAT
* *
5394980 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
5395005 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
5395029 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
5395049 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
5395074 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
* *
5395098 AATTT-AAA-AATATTA-ATGACA
1 AATTTAAAATAATAATATATGATA
* *
5395119 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
5395143 AATTTAAAATAATGTTA-ACAATA
1 AATTTAAAATAATAATATATGATA
5395166 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
5395189 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
5395213 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
5395232 CAATATACAC
Statistics
Matches: 172, Mismatches: 37, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.03
21 12 0.07
22 19 0.11
23 50 0.29
24 72 0.42
25 14 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:5395076 original size:69 final size:69
Alignment explanation
Indices: 5395002--5395229 Score: 180
Period size: 69 Copynumber: 3.3 Consensus size: 69
5394992 ATAATATATA
* * * *
5395002 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGA-TAATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGACAAATT-TGA-AATAGAT
*
5395063 CATACGTG
63 -ATACATG
** * *
5395071 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
5395136 CATG
66 CATG
** * * * * **
5395140 ATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-ATA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGACAAATTTGAAATAGAT-
*
5395203 AAACATG
63 ATACATG
*
5395210 ATAAATCTAAAATAATAATA
1 ATAAATTTAAAATAATAATA
5395230 TACAATATAC
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
68 10 0.08
69 68 0.53
70 51 0.40
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.33
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGACAAATTTGAAATAGATATA
CATG
Found at i:5396091 original size:22 final size:21
Alignment explanation
Indices: 5396066--5396113 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
5396056 TACAAATTAA
*
5396066 ATCTCTAATATTACAAAATCTT
1 ATCTCTAAGATTAC-AAATCTT
* *
5396088 ATCTTCTAAGATTGCATATCTT
1 ATC-TCTAAGATTACAAATCTT
5396110 ATCT
1 ATCT
5396114 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCTT
Found at i:5397710 original size:79 final size:78
Alignment explanation
Indices: 5397575--5397736 Score: 227
Period size: 79 Copynumber: 2.1 Consensus size: 78
5397565 CCAAAATACT
* * *
5397575 ACTGT-ATATATACATCATGTTATACATCACATGATAAGCATGGATTTACTCCTAACACTATACA
1 ACTGTAATATATACATCATATTAAACATCACATGATAAGCATGGAATTACTCCTAACACTATACA
* *
5397639 CACTTATATAAAG
66 CACATATACAAAG
* * *
5397652 ACTGTAATATATATATCATATTAAAGATCACATGAATAAGCATGGAATTACTCCTAACACTATAT
1 ACTGTAATATATACATCATATTAAACATCACATG-ATAAGCATGGAATTACTCCTAACACTATAC
*
5397717 ACACATATACACAG
65 ACACATATACAAAG
5397731 ACTGTA
1 ACTGTA
5397737 TCCAGATCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 5 0.07
78 24 0.32
79 45 0.61
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (78 bp):
ACTGTAATATATACATCATATTAAACATCACATGATAAGCATGGAATTACTCCTAACACTATACA
CACATATACAAAG
Found at i:5408605 original size:14 final size:14
Alignment explanation
Indices: 5408586--5408616 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5408576 GATATTTTAC
5408586 CTTTCGAAGAACAA
1 CTTTCGAAGAACAA
5408600 CTTTCGAAGAACAA
1 CTTTCGAAGAACAA
5408614 CTT
1 CTT
5408617 ACGGATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (14 bp):
CTTTCGAAGAACAA
Found at i:5428307 original size:24 final size:22
Alignment explanation
Indices: 5428280--5428327 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
5428270 TGGTTACAAC
*
5428280 TTTATAAAATGTACATAAATTATT
1 TTTATAAAATATA-ATAAA-TATT
*
5428304 TTTATAATATATAATAAATATT
1 TTTATAAAATATAATAAATATT
5428326 TT
1 TT
5428328 ATCATAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATAAAATATAATAAATATT
Found at i:5433572 original size:18 final size:19
Alignment explanation
Indices: 5433544--5433583 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
5433534 TGAATATAAT
5433544 AAATATATTTTTATTTTTA
1 AAATATATTTTTATTTTTA
5433563 AAATAT-TTTTTATTTTTA
1 AAATATATTTTTATTTTTA
5433581 AAA
1 AAA
5433584 CAAATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATATATTTTTATTTTTA
Found at i:5433591 original size:19 final size:18
Alignment explanation
Indices: 5433550--5433592 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
5433540 TAATAAATAT
*
5433550 ATTTTTATTTTTAAAATA
1 ATTTTTATTTTTAAAAAA
*
5433568 TTTTTTATTTTTAAAACAA
1 ATTTTTATTTTTAAAA-AA
5433587 ATTTTT
1 ATTTTT
5433593 GGTGTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTATTTTTAAAAAA
Found at i:5436163 original size:14 final size:14
Alignment explanation
Indices: 5436146--5436189 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5436136 ATATATTCCA
5436146 GAAAATAATTTCTG
1 GAAAATAATTTCTG
* *
5436160 GAAAATGATTTACTA
1 GAAAATAATTT-CTG
*
5436175 GAAAATATTTTCTG
1 GAAAATAATTTCTG
5436189 G
1 G
5436190 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (14 bp):
GAAAATAATTTCTG
Found at i:5436180 original size:15 final size:13
Alignment explanation
Indices: 5436133--5436184 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
5436123 GTTTGACAGT
*
5436133 AAAATATATTCCAG
1 AAAATAT-TTCTAG
*
5436147 AAAATAATTTCTGG
1 AAAAT-ATTTCTAG
5436161 AAAATGATTTACTAG
1 AAAAT-ATTT-CTAG
5436176 AAAATATTT
1 AAAATATTT
5436185 TCTGGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (13 bp):
AAAATATTTCTAG
Found at i:5447084 original size:22 final size:21
Alignment explanation
Indices: 5447033--5447111 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
5447023 CTAAATTAAT
*
5447033 AAAATCCTAAAATAAAAAGAA
1 AAAATCTTAAAATAAAAAGAA
* *
5447054 ATAAGCTTAACAATACAAAA-AA
1 AAAATCTTAA-AATA-AAAAGAA
* *
5447076 AAAATCTTAATATAAATAATAA
1 AAAATCTTAAAATAAA-AAGAA
*
5447098 AATAATCATAAAAT
1 AA-AATCTTAAAAT
5447112 CTTTATCTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.04
21 12 0.27
22 18 0.40
23 13 0.29
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATCTTAAAATAAAAAGAA
Found at i:5452866 original size:15 final size:14
Alignment explanation
Indices: 5452846--5452879 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
5452836 AAATAAACTG
5452846 TTTTTTCTTTCTTTCT
1 TTTTTTC-TTCTTT-T
5452862 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
5452876 TTTT
1 TTTT
5452880 AAGAATTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 6 0.33
16 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:5458596 original size:16 final size:17
Alignment explanation
Indices: 5458574--5458614 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
5458564 TATGTATGTA
5458574 TGTATGTACGTACATAC
1 TGTATGTACGTACATAC
5458591 -GTATGTACGTACATAC
1 TGTATGTACGTACATAC
5458607 TGTATGTA
1 TGTATGTA
5458615 TGAAGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (17 bp):
TGTATGTACGTACATAC
Found at i:5466282 original size:411 final size:411
Alignment explanation
Indices: 5465513--5466340 Score: 1410
Period size: 411 Copynumber: 2.0 Consensus size: 411
5465503 TGACTCTAAT
* * *
5465513 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCTGAAACGTTATGATGATTAGAAG
1 CTGAAGATTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCGAAACGTTATGATGAGTAGAAG
* * * *
5465578 TCATAGTCTCCAATTTTTCAGAAAGTTTATCCCTCTTAAGTGTAACTGATTGAAGGTCTGCCCCA
66 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACTGATTGAAGATCTGCCCCA
*
5465643 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCAAG
* *
5465708 ATTATCAATCTTCTTCTGCAAAGAGTTTCTTTCATGATTAGCCTCTGTAATCGCCCTCCCGAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAACC
*
5465773 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
*
5465838 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAAC-TGTTCATTTCGTT
326 TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAT-TTCATTTCGTT
* *
5465902 CTGCCAACCTATAAATCTTGCC
390 CTGCCAACCTATAAAACTTACC
*
5465924 CTGAAGATTTTCATTCTCAACTTCAAATTGAGCTGCCTTTGCCGAAA-GATTATGATGAGTAGAA
1 CTGAAGATTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCGAAACG-TTATGATGAGTAGAA
*
5465988 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACTGATTGAAGATCTGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACTGATTGAAGATCTGCCCC
5466053 AAGATCAGCTACTCTCTTTTCTGGAC-CCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCA
130 AAGATCAGCTACTCTCTTTTCT-GACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCA
* *
5466117 AGATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTTCCTAA
194 AGATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAA
* *
5466182 CCATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAGGGCATGTTGATTCCATCCAAAA
259 CCATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAA
* *
5466247 GCTCCTCCCATTTTTGCAACAAGTGGTTCCTTTCCATTAAGGATTGTTCCAGCATTTCATTTCGT
324 GCTCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACATTTCATTTCGT
5466312 TCTGCCAACCTATAAAACTTACC
389 TCTGCCAACCTATAAAACTTACC
5466335 CTGAAG
1 CTGAAG
5466341 GTCCTCATAT
Statistics
Matches: 392, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
410 1 0.00
411 387 0.99
412 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (411 bp):
CTGAAGATTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCGAAACGTTATGATGAGTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGCGTAACTGATTGAAGATCTGCCCCA
AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCAAAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAACGCCCTCCCGAACC
ATTCAATCTTTTCTTCAGGTTCCATGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGC
TCCTCCCATTTTTGCAACAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACATTTCATTTCGTTC
TGCCAACCTATAAAACTTACC
Found at i:5484291 original size:25 final size:25
Alignment explanation
Indices: 5484230--5484285 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
5484220 ACCTTAGCGC
5484230 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
5484255 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACATCAGT
5484280 GCTCTC
1 GCTCTC
5484286 CTATTAGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:5484315 original size:22 final size:22
Alignment explanation
Indices: 5484240--5484307 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5484230 GCTCTCTGAT
* *
5484240 TATTAGCACATCAGTGCTCTCTGAT
1 TATTAGCACATTAGTGCTCTC---C
*
5484265 TATTAGCACGTTAGTGCTCTCC
1 TATTAGCACATTAGTGCTCTCC
*
5484287 TATTAGCACATTTGTGCTCTC
1 TATTAGCACATTAGTGCTCTC
5484308 AGTATAGCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 19 0.50
25 19 0.50
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (22 bp):
TATTAGCACATTAGTGCTCTCC
Found at i:5498191 original size:4 final size:4
Alignment explanation
Indices: 5498182--5498208 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5498172 ATCCGGTGGT
5498182 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
5498209 ACTACACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:5513482 original size:2 final size:2
Alignment explanation
Indices: 5513477--5513509 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5513467 ACAAGCACAT
5513477 AG AG AG AG 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 AG AG AG AG A
5513510 ATTTTTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5521547 original size:6 final size:6
Alignment explanation
Indices: 5521525--5521604 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
5521515 CTGCCTTTGG
* * * * *
5521525 CTCTGT CTTTTT CTCTGT CTCTGT CTCTGT CTTTTT CTCTGC CTCTGT
1 CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT CTCTGT
* * **
5521573 ATCTGT CTTTTGT -TCTAC CTCTGT CTCTGT CT
1 CTCTGT C-TCTGT CTCTGT CTCTGT CTCTGT CT
5521605 TTTGCTGTGC
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
5 2 0.04
6 48 0.89
7 4 0.07
ACGTcount: A:0.03, C:0.30, G:0.12, T:0.55
Consensus pattern (6 bp):
CTCTGT
Found at i:5521552 original size:24 final size:24
Alignment explanation
Indices: 5521513--5521664 Score: 153
Period size: 24 Copynumber: 6.3 Consensus size: 24
5521503 TTTGCTCTGC
* *
5521513 CTCTGCCTTTGGCTCTGTCTTTTT
1 CTCTGCCTCTGTCTCTGTCTTTTT
*
5521537 CTCTGTCTCTGTCTCTGTCTTTTT
1 CTCTGCCTCTGTCTCTGTCTTTTT
*
5521561 CTCTGCCTCTGTATCTGTCTTTTGT
1 CTCTGCCTCTGTCTCTGTCTTTT-T
* *
5521586 -TCTACCTCTGTCTCTGTCTTTTG
1 CTCTGCCTCTGTCTCTGTCTTTTT
* * * *
5521609 CTGTGCCTCCGTCTCTGCCTTTTG
1 CTCTGCCTCTGTCTCTGTCTTTTT
* * * * *
5521633 GTCTGCCTCTGGCTCTGCCTCTAT
1 CTCTGCCTCTGTCTCTGTCTTTTT
5521657 CTCTGCCT
1 CTCTGCCT
5521665 TTTGCTCTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
24 105 0.99
25 1 0.01
ACGTcount: A:0.02, C:0.33, G:0.16, T:0.49
Consensus pattern (24 bp):
CTCTGCCTCTGTCTCTGTCTTTTT
Found at i:5521649 original size:12 final size:12
Alignment explanation
Indices: 5521621--5521686 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
5521611 GTGCCTCCGT
*
5521621 CTCTGCCTTTTGG
1 CTCTGCC-TCTGG
5521634 -TCTGCCTCTGG
1 CTCTGCCTCTGG
**
5521645 CTCTGCCTCTAT
1 CTCTGCCTCTGG
* *
5521657 CTCTGCCTTTTG
1 CTCTGCCTCTGG
**
5521669 CTCTTTCTCTGG
1 CTCTGCCTCTGG
5521681 CTCTGC
1 CTCTGC
5521687 GTCTAATTCT
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
11 4 0.10
12 36 0.90
ACGTcount: A:0.02, C:0.36, G:0.18, T:0.44
Consensus pattern (12 bp):
CTCTGCCTCTGG
Found at i:5521660 original size:36 final size:36
Alignment explanation
Indices: 5521620--5521691 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
5521610 TGTGCCTCCG
*
5521620 TCTCTGCCTTTTGGTCTGCCTCTGGCTCTGCCTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
** *
5521656 TCTCTGCCTTTTGCTCTTTCTCTGGCTCTGCGTCTA
1 TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
5521692 ATTCTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.03, C:0.35, G:0.18, T:0.44
Consensus pattern (36 bp):
TCTCTGCCTTTTGCTCTGCCTCTGGCTCTGCCTCTA
Found at i:5522079 original size:6 final size:6
Alignment explanation
Indices: 5522039--5522067 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5522029 CGGACTATGA
5522039 GGCTCG GGCTCG GGCTCG GGCTCG GGCTC
1 GGCTCG GGCTCG GGCTCG GGCTCG GGCTC
5522068 TGTCTCGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.48, T:0.17
Consensus pattern (6 bp):
GGCTCG
Found at i:5528260 original size:42 final size:42
Alignment explanation
Indices: 5528213--5528299 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
5528203 CTCTATAGGG
5528213 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
1 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
*
5528255 AGAGGCATATTGAAATCTTAGTAGTCTGTTTGTAGTATCATT
1 AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
5528297 AGA
1 AGA
5528300 TTATTGAAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (42 bp):
AGAGGCATATTGAAATATTAGTAGTCTGTTTGTAGTATCATT
Found at i:5545914 original size:22 final size:21
Alignment explanation
Indices: 5545889--5545947 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
5545879 AAATACATTG
*
5545889 TATTCAAATAAAATTTTACTCA
1 TATTCAAATAAAATTTCA-TCA
* *
5545911 TATTGAAATATAATTTCATCA
1 TATTCAAATAAAATTTCATCA
*
5545932 -AATCAAAATAAAATTT
1 TATTC-AAATAAAATTT
5545948 GGATTGAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.07
21 13 0.43
22 15 0.50
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (21 bp):
TATTCAAATAAAATTTCATCA
Found at i:5565534 original size:12 final size:12
Alignment explanation
Indices: 5565517--5565552 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5565507 ATAGTCGTAG
*
5565517 TCATCAAAATCA
1 TCATCATAATCA
*
5565529 TCATCATAACCA
1 TCATCATAATCA
5565541 TCATCATAATCA
1 TCATCATAATCA
5565553 ATTCCACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (12 bp):
TCATCATAATCA
Found at i:5567148 original size:21 final size:23
Alignment explanation
Indices: 5567106--5567148 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
5567096 GTTATTTGTT
* *
5567106 TATTATAATTATTTTTTTAATGA
1 TATTATAATTATTATTTGAATGA
5567129 TATTAT-A-TATTATTTGAATG
1 TATTATAATTATTATTTGAATG
5567149 TTAATACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTATAATTATTATTTGAATGA
Found at i:5568917 original size:20 final size:20
Alignment explanation
Indices: 5568884--5568932 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
5568874 ATACAACATT
5568884 TTAAAAATAAATAAATACAG-
1 TTAAAAATAAATAAA-ACAGA
**
5568904 TTAAAAATTTATAAAACAGAA
1 TTAAAAATAAATAAAACAG-A
5568925 TTAAAAAT
1 TTAAAAAT
5568933 GTAAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (20 bp):
TTAAAAATAAATAAAACAGA
Found at i:5572254 original size:21 final size:21
Alignment explanation
Indices: 5572221--5572265 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5572211 TACGAGACTA
* * * *
5572221 CAAAAGGATATGGGAGTTATG
1 CAAAAAGACATGGGACTGATG
5572242 CAAAAAGACATGGGACTGATG
1 CAAAAAGACATGGGACTGATG
5572263 CAA
1 CAA
5572266 CAGGAACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
CAAAAAGACATGGGACTGATG
Found at i:5578014 original size:63 final size:63
Alignment explanation
Indices: 5577915--5578036 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
5577905 GTTTCGATGA
* *
5577915 GTATGGGTTGGGTGAGATATCTCTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
1 GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
*
5577978 GTATGGGTTGGGCGAGATGTCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTG
1 GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTG
5578037 GGTCGTGCTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.29
Consensus pattern (63 bp):
GTATGGGTTGGGCGAGATATCACTGGAAGGACTAGAGAGTTGGCTTAAAATTAATACTGCTGG
Found at i:5585782 original size:21 final size:21
Alignment explanation
Indices: 5585757--5585812 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5585747 TGTTTCAAGC
5585757 TTTTTTTAATTAATTAATAT-A
1 TTTTTTTAATTAATTAAT-TCA
* **
5585778 TTTTTTCAATTTTTTAATTCA
1 TTTTTTTAATTAATTAATTCA
*
5585799 TCTTTTTAATTAAT
1 TTTTTTTAATTAAT
5585813 AACTCTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTTAATTAATTAATTCA
Found at i:5585957 original size:13 final size:14
Alignment explanation
Indices: 5585939--5585967 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5585929 AAACATTAGC
5585939 TAATTTT-TTTATA
1 TAATTTTCTTTATA
5585952 TAATTTTCTTTATA
1 TAATTTTCTTTATA
5585966 TA
1 TA
5585968 TAATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TAATTTTCTTTATA
Found at i:5586057 original size:18 final size:18
Alignment explanation
Indices: 5586036--5586070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5586026 TAATATTATA
5586036 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
5586054 AAATATAATTATTATTT
1 AAATAAAATAATTATTT
5586071 TTATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:5586129 original size:45 final size:47
Alignment explanation
Indices: 5586044--5586135 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 47
5586034 TAAAATAAAA
*
5586044 TAATTATTTCAAATATAATTATTATTTTTATATGTAAAATATTTCAAT
1 TAATTATTTCAAATATAATTATTATTTATATATG-AAAATATTTCAAT
* *
5586092 TAATTATTTCAAATATCATTA-TGTTTATATATG-AAATATTTCAA
1 TAATTATTTCAAATATAATTATTATTTATATATGAAAATATTTCAA
5586136 ATAAACATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
45 11 0.27
47 10 0.24
48 20 0.49
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (47 bp):
TAATTATTTCAAATATAATTATTATTTATATATGAAAATATTTCAAT
Found at i:5586252 original size:19 final size:20
Alignment explanation
Indices: 5586210--5586252 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5586200 TATTGCACAT
*
5586210 ATAAA-AATTATATTTACTA
1 ATAAATAATAATATTTACTA
5586229 A-AAATAATAATATTTA-TA
1 ATAAATAATAATATTTACTA
5586247 ATAAAT
1 ATAAAT
5586253 TATTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATAATAATATTTACTA
Found at i:5587382 original size:122 final size:124
Alignment explanation
Indices: 5587075--5587422 Score: 583
Period size: 124 Copynumber: 2.8 Consensus size: 124
5587065 TTATTTCGAG
* * * *
5587075 TTGACGTTTCCGAGCAAATAGTATAAAATCGCTTCTACCAGGTTGCTAGTTGAGAAGAAACTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
5587140 AAATCACGCCCTCATGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
*
5587199 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAATAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
5587264 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAAT-ATTTT-T
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
* *
5587321 TTGACGTTTCTAAGCATATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
5587386 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
5587423 CAAGTTTGGG
Statistics
Matches: 210, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
122 98 0.47
123 5 0.02
124 107 0.51
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTGT
Found at i:5590541 original size:10 final size:10
Alignment explanation
Indices: 5590526--5590550 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5590516 CAAATCTAAC
5590526 ATTATGTAAA
1 ATTATGTAAA
5590536 ATTATGTAAA
1 ATTATGTAAA
5590546 ATTAT
1 ATTAT
5590551 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:5590654 original size:30 final size:29
Alignment explanation
Indices: 5590599--5591050 Score: 568
Period size: 29 Copynumber: 15.6 Consensus size: 29
5590589 AAATTATGTA
*
5590599 AAATTAGGTTAGGGTTAAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5590628 AAATTAGGTTAGGG-CAGTGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAG-G-GTTTTTAATT
*
5590658 AAATTAGATTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
5590688 AAATTAAGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
5590717 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
**
5590746 AAATTAGGTT-GGGGCAGTGGATTTTTAATT
1 AAATTAGGTTAGGGTTAG-GG-TTTTTAATT
5590776 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
5590806 -AA--A--TTA-GGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5590829 AAATTAGGTTAGGG-CAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
5590859 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5590888 AAATTAGGTTAGGG-CAGTGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATT
** * *
5590918 AGGTTAGGTTAGAGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5590947 AAATTAGGTTATGACAG-T-GGGTTTTTAATT
1 AAATTAGGTTA-G--GGTTAGGGTTTTTAATT
*
5590977 AAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
5591006 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
5591035 AAATTAGGTTACGGTT
1 AAATTAGGTTAGGGTT
5591051 TTTAATTAAA
Statistics
Matches: 372, Mismatches: 26, Indels: 50
0.83 0.06 0.11
Matches are distributed among these distances:
23 15 0.04
24 4 0.01
25 3 0.01
26 1 0.00
27 2 0.01
28 12 0.03
29 176 0.47
30 144 0.39
31 9 0.02
32 6 0.02
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.44
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:5590670 original size:59 final size:57
Alignment explanation
Indices: 5590599--5591045 Score: 552
Period size: 59 Copynumber: 7.7 Consensus size: 57
5590589 AAATTATGTA
* *
5590599 AAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGCAGTGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAG-G-GTTTTTAATT
* *
5590658 AAATTAGATTAGGGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG-TAGGGTTTTTAATT
* *
5590717 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTGGGGCAGTGGATTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAG-GG-TTTTTAATT
5590776 AAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGG-T----TAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTAGGGTTTTTAATT
*
5590829 AAATTAGGTTAGGG-CAGTGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATTAAATTAGGTTAGGG-TAGGGTTTTTAATT
* ** * *
5590888 AAATTAGGTTAGGG-CAGTGGGTTTTTAATTAGGTTAGGTTAGAGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTA--GGGTTTTTAATTAAATTAGGTTAG-GGTAGGGTTTTTAATT
* *
5590947 AAATTAGGTTATGACAG-T-GGGTTTTTAATTAAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTA-G--GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TAGGGTTTTTAATT
5591006 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
5591046 CGGTTTTTAA
Statistics
Matches: 345, Mismatches: 23, Indels: 41
0.84 0.06 0.10
Matches are distributed among these distances:
51 1 0.00
53 43 0.12
54 3 0.01
55 2 0.01
56 1 0.00
57 3 0.01
58 53 0.15
59 183 0.53
60 53 0.15
61 2 0.01
62 1 0.00
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.44
Consensus pattern (57 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTAGGGTTTTTAATT
Found at i:5590835 original size:18 final size:21
Alignment explanation
Indices: 5590791--5590842 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 21
5590781 AGGTTAGGGT
5590791 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAA-TA-G
5590814 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAA-TA-G
5590837 TTAGGG
1 TTAGGG
5590843 CAGTGGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTTAATTAAATAG
Found at i:5591068 original size:18 final size:18
Alignment explanation
Indices: 5591020--5591070 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 18
5591010 TAGGTTAGGG
5591020 TTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAATTAAA
5591038 TTAGGTTACGGTTTTTAATTAAA
1 TTA-G----GGTTTTTAATTAAA
5591061 TTAGGGTTTT
1 TTAGGGTTTT
5591071 ATTACATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
22 1 0.04
23 17 0.61
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:5591553 original size:9 final size:9
Alignment explanation
Indices: 5591539--5591569 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5591529 GTTAAACGAA
5591539 TCGAGTTAT
1 TCGAGTTAT
*
5591548 TCGAGTTAA
1 TCGAGTTAT
5591557 TCGAGTTAT
1 TCGAGTTAT
5591566 TCGA
1 TCGA
5591570 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5591640 original size:9 final size:9
Alignment explanation
Indices: 5591623--5591659 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5591613 TGAGTTTTCG
5591623 AATTCGAAT
1 AATTCGAAT
*
5591632 AACTCGAAT
1 AATTCGAAT
*
5591641 AATTCAAAT
1 AATTCGAAT
5591650 AATTCGAAT
1 AATTCGAAT
5591659 A
1 A
5591660 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5591906 original size:30 final size:31
Alignment explanation
Indices: 5591872--5591931 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5591862 AAACATTTTA
*
5591872 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
5591902 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
5591932 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:5593338 original size:7 final size:7
Alignment explanation
Indices: 5593328--5593352 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5593318 TTATATACAT
5593328 AATACTA
1 AATACTA
5593335 AATACTA
1 AATACTA
5593342 AATACTA
1 AATACTA
5593349 AATA
1 AATA
5593353 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:5593766 original size:195 final size:195
Alignment explanation
Indices: 5593434--5593825 Score: 712
Period size: 195 Copynumber: 2.0 Consensus size: 195
5593424 AATAGAAGCT
*
5593434 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCGGATGGTTCCACCTAATTAAATAA
1 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCAGATGGTTCCACCTAATTAAATAA
* *
5593499 ATTTTTAGCATACTTTTATTTTTTAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
66 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
5593564 CCTCGTTACGAGTAGGAATGTATATAGGTGGTTCACTCGAGGACGTAGAAATGGAAAGCGAAACC
131 CCTCGTTACGAGTAGGAATGTATATAGGTGGTTCACTCGAGGACGTAGAAATGGAAAGCGAAACC
5593629 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCAGATGGTTCCACCTAATTAAATAA
1 GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCAGATGGTTCCACCTAATTAAATAA
* *
5593694 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTTCAAAATGTAATATAAATTTTA
66 AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
* * *
5593759 CCTCGTTACGAGTGGGAATGTATATGGGTGGTTCACTCGATGACGTAGAAATGGAAAGCGAAACC
131 CCTCGTTACGAGTAGGAATGTATATAGGTGGTTCACTCGAGGACGTAGAAATGGAAAGCGAAACC
5593824 GT
1 GT
5593826 GCCCATGATT
Statistics
Matches: 189, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 189 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (195 bp):
GTATATCTTCAAGTTCAGACGGTAATCCACGATAACTTGCCAGATGGTTCCACCTAATTAAATAA
AATTTTAGCATACTTTTATTTTTAAAAAATCTACATAATAATTCCAAAATGTAATATAAAATTTA
CCTCGTTACGAGTAGGAATGTATATAGGTGGTTCACTCGAGGACGTAGAAATGGAAAGCGAAACC
Found at i:5594630 original size:10 final size:10
Alignment explanation
Indices: 5594611--5594675 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
5594601 GCCATTGATG
*
5594611 AAAATATAAA
1 AAAATTTAAA
5594621 AAAATTTAAA
1 AAAATTTAAA
* *
5594631 ATTATTTTAAA
1 A-AAATTTAAA
*
5594642 AAAA-TAAAA
1 AAAATTTAAA
*
5594651 AAAAATTAAA
1 AAAATTTAAA
**
5594661 ATTATTTAAA
1 AAAATTTAAA
5594671 AAAAT
1 AAAAT
5594676 GAAATTGAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
9 8 0.20
10 25 0.61
11 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:5594654 original size:30 final size:30
Alignment explanation
Indices: 5594611--5594675 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
5594601 GCCATTGATG
*
5594611 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTA-TTTAAA
5594642 AAAATA-AAAAAAAATTAAAATTATTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAA
5594671 AAAAT
1 AAAAT
5594676 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (30 bp):
AAAATATAAAAAAAATTAAAATTATTTAAA
Found at i:5594731 original size:29 final size:29
Alignment explanation
Indices: 5594699--5594782 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
5594689 AATTGAAATT
5594699 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
5594728 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
5594750 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
5594779 AAAT
1 AAAT
5594783 TTAGAAGGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:5594731 original size:51 final size:51
Alignment explanation
Indices: 5594676--5594794 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
5594666 TTAAAAAAAT
*
5594676 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
5594727 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
5594778 GAAATTTAGAAGGAAAT
1 GAAATTGAG-AGGAAAT
5594795 AGAGAGGAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 57 0.89
52 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:5594808 original size:10 final size:11
Alignment explanation
Indices: 5594784--5594816 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
5594774 GAAGGAAATT
5594784 TAGA-AGGAAA
1 TAGAGAGGAAA
5594794 TAGAGAGGAAA
1 TAGAGAGGAAA
5594805 -AGAGAGGAAA
1 TAGAGAGGAAA
5594815 TA
1 TA
5594817 TTAGATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (11 bp):
TAGAGAGGAAA
Found at i:5594971 original size:28 final size:29
Alignment explanation
Indices: 5594933--5594993 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5594923 CGATTTCTCG
5594933 AAAAATAGACC-ATTCCAGTAAATAATAA
1 AAAAATAGACCTATTCCAGTAAATAATAA
* * **
5594961 AAAAATCGACCTATTTCAGTAAATTTTAA
1 AAAAATAGACCTATTCCAGTAAATAATAA
5594990 AAAA
1 AAAA
5594994 GAACGACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (29 bp):
AAAAATAGACCTATTCCAGTAAATAATAA
Found at i:5598926 original size:50 final size:50
Alignment explanation
Indices: 5598851--5598950 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5598841 TAATAAAGAA
5598851 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
1 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
5598901 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
1 AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
5598951 TACCAATCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (50 bp):
AAAAAATTTACCATTTGATTACAAATTACTGTTAAGATTAACGCTTGCTT
Found at i:5605884 original size:41 final size:43
Alignment explanation
Indices: 5605838--5605954 Score: 100
Period size: 43 Copynumber: 2.8 Consensus size: 43
5605828 TTACTCGGTG
* *
5605838 GAATCAGCACTTAGCAACCACCTT-ATATTC-AGTGATAC-G-A
1 GAATCAGCACTTAGCAACCACCTTCACAATCAAG-GATACAGTA
* ** *
5605878 GAAATCAACACAAAACAACC-CCTTTCACAATCAAGGATACAGTA
1 G-AATCAGCACTTAGCAACCACC-TTCACAATCAAGGATACAGTA
* *
5605922 GAATCAGCACTTAGCAACCACCTTTAGAATCAA
1 GAATCAGCACTTAGCAACCACCTTCACAATCAA
5605955 TAATTCGGGG
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
40 3 0.05
41 16 0.28
42 9 0.16
43 26 0.45
44 4 0.07
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (43 bp):
GAATCAGCACTTAGCAACCACCTTCACAATCAAGGATACAGTA
Found at i:5605940 original size:43 final size:41
Alignment explanation
Indices: 5605893--5605985 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
5605883 CAACACAAAA
* *
5605893 CAACCCCTTTCACAATCAAGGATACAGTAGAATCAGCACTTAG
1 CAACCCCTTT-ACAATCAAGAATAC-GGAGAATCAGCACTTAG
* * * * *
5605936 CAACCACCTTTAGAATCAATAATTCGGGGAATTAGCACTTAG
1 CAACC-CCTTTACAATCAAGAATACGGAGAATCAGCACTTAG
5605978 CAACCCCT
1 CAACCCCT
5605986 CGGGGAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 3 0.07
42 19 0.45
43 15 0.36
44 5 0.12
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (41 bp):
CAACCCCTTTACAATCAAGAATACGGAGAATCAGCACTTAG
Found at i:5605988 original size:26 final size:26
Alignment explanation
Indices: 5605959--5606011 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5605949 AATCAATAAT
*
5605959 TCGGGGAAT-TAGCACTTAGCAACCCC
1 TCGGGGAATCT-GCACTTACCAACCCC
5605985 TCGGGGAATCTGCACTTACCAACCCC
1 TCGGGGAATCTGCACTTACCAACCCC
5606011 T
1 T
5606012 TTTTTATCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.21
Consensus pattern (26 bp):
TCGGGGAATCTGCACTTACCAACCCC
Found at i:5612447 original size:19 final size:19
Alignment explanation
Indices: 5612412--5612450 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5612402 AATAGACTAA
*
5612412 TTTATAAATTTGTCGAATT
1 TTTATAAATTTGACGAATT
5612431 TTTATGAAATTT-ACGAATT
1 TTTAT-AAATTTGACGAATT
5612450 T
1 T
5612451 AGATTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TTTATAAATTTGACGAATT
Found at i:5617093 original size:6 final size:7
Alignment explanation
Indices: 5617056--5617092 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
5617046 AAATATAAAT
5617056 AAAATTA
1 AAAATTA
5617063 AAAATTA
1 AAAATTA
5617070 AAAATTA
1 AAAATTA
5617077 AAAATT-
1 AAAATTA
5617083 AAAATTA
1 AAAATTA
5617090 AAA
1 AAA
5617093 TATAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:5624109 original size:19 final size:19
Alignment explanation
Indices: 5624087--5624123 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5624077 AAAAAAACAA
5624087 AACA-AAATAAAATTACACT
1 AACATAAATAAAA-TACACT
5624106 AACATAAATAAAATACAC
1 AACATAAATAAAATACAC
5624124 AACTCCTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (19 bp):
AACATAAATAAAATACACT
Found at i:5631253 original size:3 final size:3
Alignment explanation
Indices: 5631245--5631281 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5631235 AAGCTTATTT
5631245 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5631282 ATATATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:5634659 original size:16 final size:16
Alignment explanation
Indices: 5634640--5634671 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5634630 TCAAGTCATG
*
5634640 CAAATATATTGTCAGA
1 CAAATATATTGACAGA
5634656 CAAATATATTGACAGA
1 CAAATATATTGACAGA
5634672 TTTTGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
CAAATATATTGACAGA
Found at i:5639317 original size:64 final size:64
Alignment explanation
Indices: 5639199--5639319 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
5639189 CTATTTCGAA
* ** * *
5639199 TGATGAAAAGGTTTAAATGTTCCAATATTGTTTGGGATGAGTGGAGCTATGTTGCTCCTGGGAC
1 TGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTACGTTGCTCCTGGGAC
*
5639263 TGATGAAAAGGTTTAAATGTTTCAATATTGTTGGGGATGAGAAGAACTACGTTGCTC
1 TGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTACGTTGCTC
5639320 TGACTCTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (64 bp):
TGATGAAAAGGTTTAAATGTTCCAATATTGTTGGGGATGAGAAGAACTACGTTGCTCCTGGGAC
Found at i:5645379 original size:30 final size:30
Alignment explanation
Indices: 5645345--5645405 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
5645335 TAGGTTGTCA
5645345 ACAGTAAAAACTAGGTGATGTACAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
*
5645375 ACAGTAAAAACTAGGTGATGTAGAACTTTG
1 ACAGTAAAAACTAGGTGATGTACAACTTTG
5645405 A
1 A
5645406 GAAACTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (30 bp):
ACAGTAAAAACTAGGTGATGTACAACTTTG
Found at i:5647792 original size:12 final size:12
Alignment explanation
Indices: 5647766--5647802 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5647756 CGTATCTAAA
*
5647766 ATATACA-AAAT
1 ATATACATATAT
5647777 ATATACATATAT
1 ATATACATATAT
5647789 ATATACATATAT
1 ATATACATATAT
5647801 AT
1 AT
5647803 TTTGCGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATACATATAT
Found at i:5651525 original size:23 final size:23
Alignment explanation
Indices: 5651495--5651555 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
5651485 AAAATAATAA
5651495 AGTAGATTATATATTATTTTTAT
1 AGTAGATTATATATTATTTTTAT
5651518 AGTAGATTATATATTATTTTTAT
1 AGTAGATTATATATTATTTTTAT
5651541 AGT--ATTATATATTAT
1 AGTAGATTATATATTAT
5651556 GATTTTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.32
23 26 0.68
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (23 bp):
AGTAGATTATATATTATTTTTAT
Found at i:5651614 original size:31 final size:30
Alignment explanation
Indices: 5651579--5651983 Score: 92
Period size: 31 Copynumber: 13.5 Consensus size: 30
5651569 TCATATAATA
5651579 ATATTTAATATTAAAAATTTTATTAAATTAT
1 ATATTTAATATTAAAAATTTTA-TAAATTAT
* *
5651610 ATATTT-TTATTAAATTATATTTA-ATAATTAT
1 ATATTTAATATTAAA-AAT-TTTATA-AATTAT
*
5651641 -TATTTTAA-ATT--AAATTTTATAGTATTAT
1 ATA-TTTAATATTAAAAATTTTATA-AATTAT
* * * * *
5651669 ATATATTATGATTTTAGTAAA-TTCATATAGTA-
1 ATAT-TTA--ATATTA-AAAATTTTATAAATTAT
*
5651701 ATATTTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATTAAAAATTTTA-TAAATTAT
* * *
5651732 ATATTT-TTATTAAATTATATTTA-ATAATAAT
1 ATATTTAATATTAAA-AAT-TTTATA-AATTAT
* *
5651763 -TATTTTAA-ATT--ATATTTTATATTATTAT
1 ATA-TTTAATATTAAAAATTTTATA-AATTAT
* * * * *
5651791 ATATTATGATTTTAGTAAA-TTCATATAA-GA-
1 ATATT-TAATATTA-AAAATTTTATA-AATTAT
*
5651821 ATATTTAATATTAAGAA-TTTATAAATTAT
1 ATATTTAATATTAAAAATTTTATAAATTAT
* * *
5651850 ATATTT-TTATTAAATTATATTTA-ATAATAAT
1 ATATTTAATATTAAA-AAT-TTTATA-AATTAT
*
5651881 -TATTTTAA-ATT--AAATTTTATATTATTAT
1 ATA-TTTAATATTAAAAATTTTATA-AATTAT
* * * *
5651909 ATATTATGATTTTAGTAAA-TTTATATAA-GA-
1 ATATT-TAATATTA-AAAATTTTATA-AATTAT
*
5651939 ATATTTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATTAAAAATTTTA-TAAATTAT
*
5651970 ATATTT-TTATTAAA
1 ATATTTAATATTAAA
5651984 TTATATTTAA
Statistics
Matches: 273, Mismatches: 53, Indels: 97
0.65 0.13 0.23
Matches are distributed among these distances:
27 14 0.05
28 48 0.18
29 49 0.18
30 50 0.18
31 66 0.24
32 29 0.11
33 9 0.03
34 5 0.02
35 3 0.01
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
ATATTTAATATTAAAAATTTTATAAATTAT
Found at i:5651617 original size:18 final size:18
Alignment explanation
Indices: 5651596--5651751 Score: 87
Period size: 18 Copynumber: 8.9 Consensus size: 18
5651586 ATATTAAAAA
5651596 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
5651614 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
*
5651629 -TTTAAT-AATTAT-TAT
1 TTTTATTAAATTATATAT
* * *
5651644 TTTAAATTAAATTTTATAG
1 TTT-TATTAAATTATATAT
* * *
5651663 TATTATATATATTAT-GA-
1 TTTTAT-TAAATTATATAT
* *
5651680 TTTTAGTAAATTCATATAG
1 TTTTATTAAATT-ATATAT
** * *
5651699 TAATATTTAATATTA-AGAA
1 TTTTA-TTAA-ATTATATAT
5651718 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
5651736 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
5651752 TTAATAATAA
Statistics
Matches: 101, Mismatches: 23, Indels: 28
0.66 0.15 0.18
Matches are distributed among these distances:
13 2 0.02
14 8 0.08
15 1 0.01
16 11 0.11
17 13 0.13
18 41 0.41
19 18 0.18
20 4 0.04
21 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:5651670 original size:118 final size:120
Alignment explanation
Indices: 5651535--5652009 Score: 830
Period size: 118 Copynumber: 4.0 Consensus size: 120
5651525 TATATATTAT
* *
5651535 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAATAATATTTAATATTAAAAATTTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
*
5651600 ATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAAATTAAA
66 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAA
5651655 TTTTATAGTATTATATATATTATGATTTTAGTAAATTCATAT-AGTAATATTTAATATTAAGAAT
1 TTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAG-AATATTTAATATTAAGAAT
*
5651719 TTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATA
63 TTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAA
*
5651777 TTTTATATTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA-TTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
5651841 A-TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAA
66 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAA
* *
5651895 TTTTATATTATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTT
1 TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
*
5651960 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
66 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
5652010 ATATGATTAA
Statistics
Matches: 341, Mismatches: 8, Indels: 12
0.94 0.02 0.03
Matches are distributed among these distances:
118 112 0.33
119 8 0.02
120 104 0.30
121 5 0.01
122 112 0.33
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (120 bp):
TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAAA
Found at i:5652209 original size:44 final size:45
Alignment explanation
Indices: 5652146--5652242 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
5652136 CTATTACAGC
*
5652146 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * *
5652190 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
5652235 TCCATTAC
1 TCCATTAC
5652243 GCCTCTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:5652243 original size:16 final size:16
Alignment explanation
Indices: 5652222--5652254 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5652212 TTGATTTGCT
5652222 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
5652238 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
5652254 A
1 A
5652255 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:5652767 original size:14 final size:14
Alignment explanation
Indices: 5652748--5652777 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5652738 TAAAATTGAA
5652748 AAAAATCGAAAATC
1 AAAAATCGAAAATC
5652762 AAAAATCGAAAATC
1 AAAAATCGAAAATC
5652776 AA
1 AA
5652778 GACAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAATCGAAAATC
Found at i:5653206 original size:20 final size:20
Alignment explanation
Indices: 5653173--5653214 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5653163 GCCAAGGTGG
*
5653173 AAAAAGCCTGATATTAGACT
1 AAAAAACCTGATATTAGACT
*
5653193 AAAAAACCTTATATTAGACT
1 AAAAAACCTGATATTAGACT
5653213 AA
1 AA
5653215 GTCTTGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAAACCTGATATTAGACT
Found at i:5654253 original size:11 final size:10
Alignment explanation
Indices: 5654228--5654252 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5654218 CAATCACCAC
5654228 TTTTTCTTTT
1 TTTTTCTTTT
5654238 TTTTTCTTTT
1 TTTTTCTTTT
5654248 TTTTT
1 TTTTT
5654253 TTTACAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5672188 original size:24 final size:25
Alignment explanation
Indices: 5672129--5672188 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5672119 AATAATCACC
5672129 AAAATTTTATTTTAAAAATAAAAAAT
1 AAAA-TTTATTTTAAAAATAAAAAAT
** *
5672155 AAAAAGTATTTTAAAATTAAAAAAT
1 AAAATTTATTTTAAAAATAAAAAAT
*
5672180 -ATATTTATT
1 AAAATTTATT
5672189 ATATTCGGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 6 0.21
25 18 0.64
26 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATTTATTTTAAAAATAAAAAAT
Found at i:5679051 original size:12 final size:12
Alignment explanation
Indices: 5679036--5679061 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5679026 TTAAGTAATA
5679036 ATCTTTTTTCTC
1 ATCTTTTTTCTC
5679048 ATCTTTTTTCTC
1 ATCTTTTTTCTC
5679060 AT
1 AT
5679062 TTATGTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (12 bp):
ATCTTTTTTCTC
Found at i:5683221 original size:35 final size:35
Alignment explanation
Indices: 5683172--5683275 Score: 172
Period size: 35 Copynumber: 3.0 Consensus size: 35
5683162 ATATGTTATC
*
5683172 TCACTATTACCATTACATTTGAATCCAAATACATA
1 TCACTATTATCATTACATTTGAATCCAAATACATA
* *
5683207 TCATTATTGTCATTACATTTGAATCCAAATACATA
1 TCACTATTATCATTACATTTGAATCCAAATACATA
*
5683242 TCACTATTATCATTACATTTGAATCCAAACACAT
1 TCACTATTATCATTACATTTGAATCCAAATACAT
5683276 TAATTAATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (35 bp):
TCACTATTATCATTACATTTGAATCCAAATACATA
Found at i:5696542 original size:23 final size:23
Alignment explanation
Indices: 5696515--5696559 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
5696505 TCTTAAGATT
*
5696515 AAAAAAAACAAAACAAGAGAATGG
1 AAAAGAAACAAAA-AAGAGAATGG
* *
5696539 AAAAGAAATATAAAAGAGAAT
1 AAAAGAAACAAAAAAGAGAAT
5696560 TCATAGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (23 bp):
AAAAGAAACAAAAAAGAGAATGG
Found at i:5696613 original size:19 final size:19
Alignment explanation
Indices: 5696589--5696625 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5696579 CGTACTTCGA
*
5696589 TGAAAAAATTTAAAATATT
1 TGAAAAAAGTTAAAATATT
*
5696608 TGAAAAACGTTAAAATAT
1 TGAAAAAAGTTAAAATAT
5696626 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (19 bp):
TGAAAAAAGTTAAAATATT
Found at i:5700997 original size:33 final size:33
Alignment explanation
Indices: 5700954--5701019 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
5700944 TTAAACTATT
5700954 TTCATATGTTAATTTTAATTAAAAGTTATTTTA
1 TTCATATGTTAATTTTAATTAAAAGTTATTTTA
* *
5700987 TTCATGTGTTAATTTTAATTAGAAGTTATTTTA
1 TTCATATGTTAATTTTAATTAAAAGTTATTTTA
5701020 AATTATTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (33 bp):
TTCATATGTTAATTTTAATTAAAAGTTATTTTA
Found at i:5701014 original size:17 final size:16
Alignment explanation
Indices: 5700965--5701020 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
5700955 TCATATGTTA
*
5700965 ATTTTAATTAAAAGTT
1 ATTTTAATTAGAAGTT
*
5700981 ATTTT-ATTCATG-TGTT
1 ATTTTAATT-A-GAAGTT
5700997 AATTTTAATTAGAAGTT
1 -ATTTTAATTAGAAGTT
5701014 ATTTTAA
1 ATTTTAA
5701021 ATTATTATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
17 9 0.28
18 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTTAATTAGAAGTT
Found at i:5703398 original size:2 final size:2
Alignment explanation
Indices: 5703391--5703447 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5703381 TTATAATTAT
5703391 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5703433 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
5703448 TTCTTTTCTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5703948 original size:29 final size:28
Alignment explanation
Indices: 5703907--5703961 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
5703897 TGATTTGGTC
5703907 TATGCAAAGATTATGAAAATTGTTTAGT
1 TATGCAAAGATTATGAAAATTGTTTAGT
5703935 TATGCAAAAGATTATGAAAATTGTTTA
1 TATGC-AAAGATTATGAAAATTGTTTA
5703962 TTTTCATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (28 bp):
TATGCAAAGATTATGAAAATTGTTTAGT
Found at i:5710819 original size:25 final size:25
Alignment explanation
Indices: 5710791--5710840 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5710781 CAGGTAAGGC
*
5710791 TCCTTCTCCTTCTTTCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* *
5710816 TCCTTTTTCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
5710841 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.34, G:0.04, T:0.58
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:5714839 original size:18 final size:18
Alignment explanation
Indices: 5714798--5714842 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5714788 ATATAATTGT
*
5714798 AATAATTTTTAATCATTT
1 AATAATTTTTAATCATTA
* **
5714816 ATTAATTTTTAATTGTTA
1 AATAATTTTTAATCATTA
5714834 AATAATTTT
1 AATAATTTT
5714843 AAAAACTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
AATAATTTTTAATCATTA
Found at i:5714981 original size:21 final size:21
Alignment explanation
Indices: 5714957--5715009 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5714947 CGCTGTTTCT
* *
5714957 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
5714978 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5714999 AATCTCACCGC
1 AATCTCACCGC
5715010 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5716211 original size:30 final size:29
Alignment explanation
Indices: 5716168--5716234 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
5716158 ATTACATTTT
5716168 ATTTTTTAATTAAA-AAATAGA-TAAATTA
1 ATTTTTTAATTAAATAAA-AGAGTAAATTA
*
5716196 ATTTTTATATATTAAATTAAAGAGTAAATTA
1 ATTTTT-TA-ATTAAATAAAAGAGTAAATTA
5716227 ATTTTTTA
1 ATTTTTTA
5716235 TTGAGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.18
29 2 0.06
30 11 0.32
31 15 0.44
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTTTTTAATTAAATAAAAGAGTAAATTA
Found at i:5716646 original size:29 final size:29
Alignment explanation
Indices: 5716583--5716646 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
5716573 TGTCTCCTGC
5716583 TGGTTAAGGTTTTGGGTTTTTTATGGTTTA
1 TGGTTAAGGTTTTGGG-TTTTTATGGTTTA
* * *
5716613 AGGTTAGGGTTTTGTGG-TTTTGTGGTTTA
1 TGGTTAAGGTTTTG-GGTTTTTATGGTTTA
5716642 TGGTT
1 TGGTT
5716647 TTAAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 15 0.52
30 12 0.41
31 2 0.07
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (29 bp):
TGGTTAAGGTTTTGGGTTTTTATGGTTTA
Found at i:5717026 original size:126 final size:126
Alignment explanation
Indices: 5716841--5717385 Score: 765
Period size: 126 Copynumber: 4.3 Consensus size: 126
5716831 AGTGTTAATT
* * * * * *
5716841 TAAAA-AAGCTCCCACGTAGACG-ATCTTCTGCTACAATAGCTACTGAAAAAATAATTTCGAGAA
1 TAAAAGAAGCTCCCACGTGGACGCA-CTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTA
* *
5716904 GACGTTTCCGAGCAAATAGTGTCAAAAATGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
65 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
*
5716966 TGAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
* * * *
5717031 ACGTTTTTGAGCAAATAGTGTCAAAAACACTTTAAGTAAGATGTTTTGTC-GCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
* ** * * ** *
5717091 TAAAATAATATCCTACGTGGAGGCGTTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCAAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
*
5717156 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAGGCATA-ATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCA-AGATGCTTTGTCAGCAAAAGTAC
* * *
5717217 TAAAAGAAGCTCCCACGTGGATGCACTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
* * * *
5717282 ACGTTTTTGAGAAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
* *
5717343 TGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTC
1 TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTC
5717386 TTGTTTGGCC
Statistics
Matches: 369, Mismatches: 46, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
125 113 0.31
126 255 0.69
127 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAG
ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAAAAGTAC
Found at i:5723436 original size:116 final size:117
Alignment explanation
Indices: 5723227--5723436 Score: 296
Period size: 116 Copynumber: 1.8 Consensus size: 117
5723217 ACTTTGTATT
* * * *
5723227 ATTTATATTTTTTTAAATCAAATAATATGGAAATATTCAGAATATTGACTTATTTAAAATAAAAT
1 ATTTATATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAAT
* *
5723292 CAATTTTATTAAAAATATTAAAGTAAATTACAATTATTTTATTCAAAACAAC
66 CAATTATATTAAAAATATAAAAGTAAATTACAATTATTTTATTCAAAACAAC
* ** **
5723344 ATTT-TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTGTTATTTAAAAGAATTT
1 ATTTATATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAAT
* *
5723408 CTATTATATTAAAAATGTAAAAGTAAATT
66 CAATTATATTAAAAATATAAAAGTAAATT
5723437 TCTATTTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
116 76 0.95
117 4 0.05
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (117 bp):
ATTTATATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAAT
CAATTATATTAAAAATATAAAAGTAAATTACAATTATTTTATTCAAAACAAC
Found at i:5724534 original size:7 final size:7
Alignment explanation
Indices: 5724522--5724553 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
5724512 TATTAGTTAT
5724522 ATACATA
1 ATACATA
5724529 ATACATA
1 ATACATA
5724536 ATACATA
1 ATACATA
5724543 ATACATA
1 ATACATA
5724550 ATAC
1 ATAC
5724554 TAAATACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:5725784 original size:11 final size:11
Alignment explanation
Indices: 5725768--5725815 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
5725758 AAGTTTTTTA
*
5725768 AGAGGAATTTG
1 AGAGGAAATTG
5725779 AGAGGAAATTG
1 AGAGGAAATTG
5725790 AGA-GAATATTG
1 AGAGGAA-ATTG
5725801 -GAGAGAAATTG
1 AGAG-GAAATTG
5725812 AGAG
1 AGAG
5725816 AAAGGATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.16
11 21 0.66
12 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:5725793 original size:22 final size:23
Alignment explanation
Indices: 5725768--5725815 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5725758 AAGTTTTTTA
5725768 AGAGGAAT-TT-GAGAGGAAATTG
1 AGAGGAATATTGGAGA-GAAATTG
5725790 AGA-GAATATTGGAGAGAAATTG
1 AGAGGAATATTGGAGAGAAATTG
5725812 AGAG
1 AGAG
5725816 AAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (23 bp):
AGAGGAATATTGGAGAGAAATTG
Found at i:5725814 original size:10 final size:10
Alignment explanation
Indices: 5725776--5725818 Score: 59
Period size: 11 Copynumber: 4.0 Consensus size: 10
5725766 TAAGAGGAAT
5725776 TTGAGAGGAAA
1 TTGAGA-GAAA
5725787 TTGAGAGAATA
1 TTGAGAGAA-A
5725798 TTGGAGAGAAA
1 TT-GAGAGAAA
5725809 TTGAGAGAAA
1 TTGAGAGAAA
5725819 GGATTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.37
11 12 0.40
12 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:5735983 original size:29 final size:28
Alignment explanation
Indices: 5735907--5735992 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
5735897 TAGCGCGCTC
* * *
5735907 TTTGTTTTGTTATTGCACTTTGGTGCTAA
1 TTTGTTTTG-GATTACACTTTAGTGCTAA
* *
5735936 TATGTTTT-GATTAAGCACTTTAGTGCTAT
1 TTTGTTTTGGATT-A-CACTTTAGTGCTAA
*
5735965 TTTGTTTTGGCATTACACTTCAGTGCTA
1 TTTGTTTTGG-ATTACACTTTAGTGCTA
5735993 CTCTATTCTG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
27 3 0.07
29 38 0.83
30 2 0.04
31 3 0.07
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (28 bp):
TTTGTTTTGGATTACACTTTAGTGCTAA
Found at i:5736140 original size:24 final size:24
Alignment explanation
Indices: 5736108--5736157 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5736098 CGAATGTTGT
*
5736108 GACGCGATTAAGTGTAAGTAATTG
1 GACGAGATTAAGTGTAAGTAATTG
5736132 GACGAGATTAAGTGTAAGTAATTG
1 GACGAGATTAAGTGTAAGTAATTG
5736156 GA
1 GA
5736158 ATGATAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (24 bp):
GACGAGATTAAGTGTAAGTAATTG
Found at i:5737810 original size:26 final size:26
Alignment explanation
Indices: 5737781--5737833 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5737771 AGTGTGAAAA
* *
5737781 TTTTGAACTTGAATATTGTTTGTTTTT
1 TTTTGAA-GTGAATATTGTTTATTTTT
*
5737808 TTTTGGAGTGAATATTGTTTATTTTT
1 TTTTGAAGTGAATATTGTTTATTTTT
5737834 ACAACTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (26 bp):
TTTTGAAGTGAATATTGTTTATTTTT
Found at i:5740604 original size:6 final size:6
Alignment explanation
Indices: 5740595--5740620 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5740585 CCCGAGAAGG
5740595 AGAGGA AGAGGA AGAGGA AGAGGA AG
1 AGAGGA AGAGGA AGAGGA AGAGGA AG
5740621 GCTCCTCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Done.