Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005712.1 Hibiscus syriacus cultivar Beakdansim tig00013353_pilon, whole genome shotgun sequence
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: 73161
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4902 original size:45 final size:45
Alignment explanation
Indices: 4853--5002 Score: 210
Period size: 45 Copynumber: 3.3 Consensus size: 45
4843 TATATGATAC
*
4853 TGACCTATGTGATTACATGAAAATGAGATATAAGGTATGTGGCAT
1 TGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGCAT
* * *
4898 TGACCTATATGATTATATGAAAATGAAATATAAGCTATGTGGCAT
1 TGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGCAT
* * * * *
4943 TGACCTATGTGATTACATGAAAATGTGATATAAGTTATATGACAA
1 TGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGCAT
*
4988 TGATCTATGTGATTA
1 TGACCTATGTGATTA
5003 TATGTCTATG
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (45 bp):
TGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGCAT
Found at i:4989 original size:22 final size:22
Alignment explanation
Indices: 4959--5034 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
4949 ATGTGATTAC
*
4959 ATGAAAATGTGATATAAGTTAT
1 ATGACAATGTGATATAAGTTAT
* **
4981 ATGACAATGAT-CTATGTGATTAT
1 ATGACAATG-TGATATAAG-TTAT
* *
5004 ATGTCTATGTGATATAAGTTAT
1 ATGACAATGTGATATAAGTTAT
*
5026 GTGA-AATGT
1 ATGACAATGT
5035 TATAAATGAT
Statistics
Matches: 39, Mismatches: 12, Indels: 7
0.67 0.21 0.12
Matches are distributed among these distances:
21 4 0.10
22 19 0.49
23 16 0.41
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (22 bp):
ATGACAATGTGATATAAGTTAT
Found at i:5012 original size:16 final size:15
Alignment explanation
Indices: 4965--5029 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
4955 TTACATGAAA
4965 ATGTGATATAAGT-T
1 ATGTGATATAAGTCT
* * *
4979 ATATGACA-ATGATCT
1 ATGTGATATAAG-TCT
*
4994 ATGTGATTATATGTCT
1 ATGTGA-TATAAGTCT
5010 ATGTGATATAAGT-T
1 ATGTGATATAAGTCT
5024 ATGTGA
1 ATGTGA
5030 AATGTTATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 2 0.05
14 14 0.34
15 12 0.29
16 10 0.24
17 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.42
Consensus pattern (15 bp):
ATGTGATATAAGTCT
Found at i:5014 original size:45 final size:44
Alignment explanation
Indices: 4843--5033 Score: 148
Period size: 45 Copynumber: 4.2 Consensus size: 44
4833 TATTTTATGC
* * * *
4843 TATATGATACTGACCTATGTGATTACATGAAAATGAGATATAAGG
1 TATATGA-AATGATCTATGTGATTACATGAAAATGTGATATAAGT
* * * * * * ** *
4888 TATGTGGCATTGACCTATATGATTATATGAAAATGAAATATAAGC
1 TATAT-GAAATGATCTATGTGATTACATGAAAATGTGATATAAGT
* * * *
4933 TATGTGGCATTGACCTATGTGATTACATGAAAATGTGATATAAGT
1 TATAT-GAAATGATCTATGTGATTACATGAAAATGTGATATAAGT
* ***
4978 TATATGACAATGATCTATGTGATTATATGTCTATGTGATATAAGT
1 TATATGA-AATGATCTATGTGATTACATGAAAATGTGATATAAGT
*
5023 TATGTGAAATG
1 TATATGAAATG
5034 TTATAAATGA
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
44 5 0.04
45 117 0.95
46 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.36
Consensus pattern (44 bp):
TATATGAAATGATCTATGTGATTACATGAAAATGTGATATAAGT
Found at i:11321 original size:45 final size:45
Alignment explanation
Indices: 11272--11423 Score: 205
Period size: 45 Copynumber: 3.4 Consensus size: 45
11262 GCTATATGAT
*
11272 ATTGACCTATATGATTACATGAAAATGAGATATAAGCTATGTGGC
1 ATTGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGC
* * * *
11317 ATTGACCTATGTGACTAAATGAAAATGAGATATAAACTATGTAGC
1 ATTGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGC
* * *
11362 ATTGACCTATGTGATTACATGAAAATGTGATATAAGTTATGTGAC
1 ATTGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGC
* * *
11407 AATGATCAATGTGATTA
1 ATTGACCTATGTGATTA
11424 TATGTTTATG
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (45 bp):
ATTGACCTATGTGATTACATGAAAATGAGATATAAGCTATGTGGC
Found at i:11577 original size:23 final size:23
Alignment explanation
Indices: 11551--11605 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
11541 TCGGGATAAT
11551 TCTACGTGGTCCTTGGGGACATA
1 TCTACGTGGTCCTTGGGGACATA
* * * *
11574 TCTATGTGGTCTTTTGGGACATT
1 TCTACGTGGTCCTTGGGGACATA
*
11597 TCCACGTGG
1 TCTACGTGG
11606 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (23 bp):
TCTACGTGGTCCTTGGGGACATA
Found at i:11750 original size:2 final size:2
Alignment explanation
Indices: 11743--11828 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
11733 TGATGATTAC
11743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11827 AT
1 AT
11829 GTTTTGTTCT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15118 original size:39 final size:39
Alignment explanation
Indices: 15075--15153 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
15065 TAATACATAG
15075 GACAATTTGTCCAGATTAATGATTCTTATGAGCGACCAA
1 GACAATTTGTCCAGATTAATGATTCTTATGAGCGACCAA
*
15114 GACAATTTGTCCAGATTTATGATTCTTATGAGCGACCAA
1 GACAATTTGTCCAGATTAATGATTCTTATGAGCGACCAA
15153 G
1 G
15154 GAAAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (39 bp):
GACAATTTGTCCAGATTAATGATTCTTATGAGCGACCAA
Found at i:17636 original size:2 final size:2
Alignment explanation
Indices: 17631--17682 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
17621 ACTATATACA
*
17631 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17673 AT AT AT AT AT
1 AT AT AT AT AT
17683 TTCTTCGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18272 original size:60 final size:61
Alignment explanation
Indices: 18189--18302 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 61
18179 AATGACCTTT
* * *
18189 TAACTATAAGGTGTTATTTTATTGAG-TCCATTGACTATT-AAAAGTTATAAAATGGTCTCC
1 TAACTATAAGGTATTATATTATTGAGTTCCATT-ACTATTAAAAAGTTACAAAATGGTCTCC
* * *
18249 TAACTATAGGGTATTGTATTATTGAGTTCCCTTACTATTAAAAAGTTACAAAAT
1 TAACTATAAGGTATTATATTATTGAGTTCCATTACTATTAAAAAGTTACAAAAT
18303 AGTCACCTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 28 0.61
61 18 0.39
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (61 bp):
TAACTATAAGGTATTATATTATTGAGTTCCATTACTATTAAAAAGTTACAAAATGGTCTCC
Found at i:22333 original size:15 final size:15
Alignment explanation
Indices: 22315--22353 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
22305 TAACCGGTTT
22315 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
22330 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
22345 CGATTTTAA
1 CGGTTTTAA
22354 TATTTCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:22526 original size:21 final size:21
Alignment explanation
Indices: 22502--22554 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
22492 ACACTTAGGG
22502 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
22523 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
22544 TACCGATTCCC
1 AACCGATTCCC
22555 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:22771 original size:13 final size:13
Alignment explanation
Indices: 22750--22804 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
22740 AAGTTCGATA
*
22750 AATTCAAATACTT
1 AATTGAAATACTT
22763 AATTGAAATACTT
1 AATTGAAATACTT
* *
22776 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
22790 AATTGAAATACTT
1 AATTGAAATACTT
22803 AA
1 AA
22805 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:22886 original size:32 final size:33
Alignment explanation
Indices: 22790--22888 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
22780 AACTCAACAT
* * *
22790 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22823 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22856 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
22888 A
1 A
22889 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:22907 original size:21 final size:21
Alignment explanation
Indices: 22883--22922 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22873 ACTTCAAGTT
22883 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
22904 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
22923 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:31228 original size:11 final size:11
Alignment explanation
Indices: 31212--31243 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31202 TCCGTTACAT
*
31212 TTTTATTTTTG
1 TTTTATTTTTA
31223 TTTTATTTTTA
1 TTTTATTTTTA
31234 TTTTATTTTT
1 TTTTATTTTT
31244 TCTTTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:33014 original size:25 final size:24
Alignment explanation
Indices: 32982--33048 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 24
32972 AAAATGATGA
32982 AAAAAAGAAAAAAAATAGCAGTTCG
1 AAAAAAGAAAAAAAAT-GCAGTTCG
* *
33007 AAAAAAGAAAAAAGGGATGTAGTTCG
1 AAAAAAGAAAAAA--AATGCAGTTCG
33033 AAAAAAGAAGAAAAAA
1 AAAAAAGAA-AAAAAA
33049 AGACGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 14 0.39
26 16 0.44
27 6 0.17
ACGTcount: A:0.66, C:0.04, G:0.19, T:0.10
Consensus pattern (24 bp):
AAAAAAGAAAAAAAATGCAGTTCG
Found at i:35828 original size:16 final size:16
Alignment explanation
Indices: 35807--35838 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35797 GGAAACCCAG
35807 TTTGATTAAAAGTATA
1 TTTGATTAAAAGTATA
*
35823 TTTGATTAAGAGTATA
1 TTTGATTAAAAGTATA
35839 AAACTTTATT
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:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
TTTGATTAAAAGTATA
Found at i:39814 original size:16 final size:16
Alignment explanation
Indices: 39788--39842 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
39778 TTGAAAAAAA
39788 AATATTAATAACA-ATAT
1 AATA-TAATAA-ATATAT
39805 AATATAATAAATATAT
1 AATATAATAAATATAT
39821 AATA-AATAATATATAT
1 AATATAATAA-ATATAT
*
39837 ACTATA
1 AATATA
39843 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 6 0.18
16 23 0.68
17 5 0.15
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATAATAAATATAT
Found at i:39820 original size:11 final size:12
Alignment explanation
Indices: 39803--39833 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
39793 TAATAACAAT
39803 ATAATATAATAA
1 ATAATATAATAA
39815 AT-ATATAATAA
1 ATAATATAATAA
39826 ATAATATA
1 ATAATATA
39834 TATACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:39954 original size:24 final size:26
Alignment explanation
Indices: 39926--39982 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
39916 AATATTTAAA
39926 AAAAATCTATA-TAT-TATATGTTTTC
1 AAAAAT-TATATTATATATATGTTTTC
39951 AAAAATTATATTATATATATGTTTTC
1 AAAAATTATATTATATATATGTTTTC
39977 AAAAAT
1 AAAAAT
39983 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 17 0.57
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (26 bp):
AAAAATTATATTATATATATGTTTTC
Found at i:39957 original size:62 final size:62
Alignment explanation
Indices: 39884--40018 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 62
39874 TTTCAAAACC
*
39884 ATTTT-AAAAATTATA-TA-CTATATGTTTTCAAAAATATTTAAAAAAAATCTATATATTATAT
1 ATTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTT-AAAAAAA-CTATATATTATAT
* *
39945 GTTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTTTAAAAAACTATATATTATAT
1 ATTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTTAAAAAAACTATATATTATAT
40007 ATTTTCAAAAAT
1 ATTTTCAAAAAT
40019 GTGTTTTCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
61 4 0.06
62 34 0.51
63 8 0.12
64 21 0.31
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (62 bp):
ATTTTCAAAAATTATATTATATATATGTTTTCAAAAATATTTAAAAAAACTATATATTATAT
Found at i:40073 original size:39 final size:37
Alignment explanation
Indices: 39941--40131 Score: 215
Period size: 37 Copynumber: 5.0 Consensus size: 37
39931 TCTATATATT
* *
39941 ATATGTTTTCAAAAATTATATTATATATATGTTTTCAAAA
1 ATATGTTTT-AAAAACTATA-TAT-TATATATTTTCAAAA
*
39981 ATAT-TTTAAAAAACTATATATTATATATTTTCAAAA
1 ATATGTTTTAAAAACTATATATTATATATTTTCAAAA
* *
40017 ATGTGTTTTCAAAACTATATATTATATATTTTCCAAAA
1 ATATGTTTTAAAAACTATATATTATATATTTT-CAAAA
40055 ATGAT-TTTTAAAATACTATATATTATATACGTTTTCAAAA
1 AT-ATGTTTTAAAA-ACTATATATTATATA--TTTTCAAAA
** **
40095 ATATGTTTTCTAAACTATATATTATACGTTTTCAAAA
1 ATATGTTTTAAAAACTATATATTATATATTTTCAAAA
40132 CCATATATAT
Statistics
Matches: 132, Mismatches: 12, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
36 17 0.13
37 37 0.28
38 23 0.17
39 34 0.26
40 17 0.13
41 4 0.03
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (37 bp):
ATATGTTTTAAAAACTATATATTATATATTTTCAAAA
Found at i:40132 original size:23 final size:24
Alignment explanation
Indices: 40099--40144 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
40089 TCAAAAATAT
* *
40099 GTTTTCTAAACTATATAT-TATAC
1 GTTTTCAAAACCATATATATATAC
40122 GTTTTCAAAACCATATATATATA
1 GTTTTCAAAACCATATATATATA
40145 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (24 bp):
GTTTTCAAAACCATATATATATAC
Found at i:40141 original size:2 final size:2
Alignment explanation
Indices: 40134--40193 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
40124 TTTCAAAACC
40134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40176 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
40194 TCAAAACCCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44862 original size:16 final size:16
Alignment explanation
Indices: 44835--44889 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
44825 AATTGAAAAT
44835 TAATATTAATAACA-ATA
1 TAATA-TAATAA-ATATA
44852 TAATATAATAAATATA
1 TAATATAATAAATATA
44868 TAATA-AATAATATATA
1 TAATATAATAA-ATATA
44884 TAATAT
1 TAATAT
44890 GTATACTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.17
16 24 0.69
17 5 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAATATA
Found at i:44868 original size:11 final size:12
Alignment explanation
Indices: 44851--44886 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
44841 TAATAACAAT
44851 ATAATATAATAA
1 ATAATATAATAA
44863 AT-ATATAATAA
1 ATAATATAATAA
44874 ATAATATATATAA
1 ATAATATA-ATAA
44887 TATGTATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 7 0.32
13 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:44972 original size:36 final size:34
Alignment explanation
Indices: 44922--45087 Score: 116
Period size: 35 Copynumber: 4.6 Consensus size: 34
44912 ACTATATAAC
* * *
44922 ATACATTATATTTTCAAAAACCATTTTAAAAATTAT
1 ATACA-TATGTTTTCAAAAA-CATTTAAAAAACTAT
*
44958 ATACAGTATGTTTTCAAAAATATTTAAAAAACTAT
1 ATACA-TATGTTTTCAAAAACATTTAAAAAACTAT
* * *
44993 ATATTATATGTTTTCAAAAATACGTTTTCAAAAACTAT
1 ATA-CATATGTTTTC-AAAA-AC-ATTTAAAAAACTAT
* * * *
45031 ATTATATATACATTTTCAAAAATATTTTAAAAACTAT
1 A-TACATAT--GTTTTCAAAAACATTTAAAAAACTAT
* *
45068 ATATTATATATTTTCAAAAA
1 ATA-CATATGTTTTCAAAAA
45088 TGTGTTTTCA
Statistics
Matches: 109, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
35 35 0.32
36 25 0.23
37 19 0.17
38 19 0.17
39 6 0.06
40 5 0.05
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (34 bp):
ATACATATGTTTTCAAAAACATTTAAAAAACTAT
Found at i:44995 original size:35 final size:34
Alignment explanation
Indices: 44928--45345 Score: 221
Period size: 38 Copynumber: 11.0 Consensus size: 34
44918 TAACATACAT
* * *
44928 TATATTTTCAAAAACCATTTTAAAAATTATATACA
1 TATATTTTCAAAAA-TATTTTAAAAACTATATATA
* *
44963 GTATGTTTTCAAAAATATTTAAAAAACTATATATTA
1 -TATATTTTCAAAAATATTTTAAAAACTATATA-TA
*
44999 TATGTTTTCAAAAATACGTTTTCAAAAACTATATTATA
1 TATATTTTCAAAAATA--TTTT-AAAAACTATA-TATA
45037 TATACATTTTCAAAAATATTTTAAAAACTATATATTA
1 TAT--ATTTTCAAAAATATTTTAAAAACTATATA-TA
*
45074 TATATTTTCAAAAATGTGTTTTCAAAAA-TATATATTA
1 TATATTTTCAAAAA--TATTTT-AAAAACTATATA-TA
*
45111 TATGTTTTCCAAAACCGAT-TTTTAAAAAACTATATATTA
1 TATATTTT-CAAAA---ATATTTT-AAAAACTATATA-TA
*
45150 TATATGTTTTCAAAAAATATTTTTTCAAAACTATATATTA
1 TATA--TTTTC-AAAAATA--TTTTAAAAACTATATA-TA
* * * *
45190 TATGTTTTTAAAAACATGTTTTCAAAACCATATTATATA
1 TAT-ATTTTCAAAA-ATATTTT-AAAAAC-TA-TATATA
* * *
45229 TATATTTTTTCAAAACCCGGTTTTTTAAAAATTATATAT-
1 TATA--TTTTCAAAA----ATATTTTAAAAACTATATATA
* *
45268 TATATTCTTTCAAAAACCATTTTCTAAAAATTATATATTA
1 TATA-T-TTTCAAAAA-TA-TTT-TAAAAACTATATA-TA
* *
45308 TATTTTTTTCAAAAATATTTTCAAAATCTATACTATA
1 TA-TATTTTCAAAAATATTTT-AAAAACTATA-TATA
45345 T
1 T
45346 TAATATATAT
Statistics
Matches: 310, Mismatches: 31, Indels: 81
0.73 0.07 0.19
Matches are distributed among these distances:
35 42 0.14
36 17 0.05
37 60 0.19
38 66 0.21
39 50 0.16
40 50 0.16
41 16 0.05
42 4 0.01
43 5 0.02
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (34 bp):
TATATTTTCAAAAATATTTTAAAAACTATATATA
Found at i:45039 original size:38 final size:38
Alignment explanation
Indices: 44964--45339 Score: 294
Period size: 38 Copynumber: 9.9 Consensus size: 38
44954 TTATATACAG
*
44964 TATGTTTTCAAAAATA---TTTAAAAAACTATATATTA
1 TATGTTTTCAAAAATACGTTTTCAAAAACTATATATTA
44999 TATGTTTTCAAAAATACGTTTTCAAAAACTATATTATATA
1 TATGTTTTCAAAAATACGTTTTCAAAAACTATA-TAT-TA
**
45039 TACATTTTCAAAAATA--TTTT-AAAAACTATATATTA
1 TATGTTTTCAAAAATACGTTTTCAAAAACTATATATTA
* **
45074 TATATTTTCAAAAATGTGTTTTCAAAAA-TATATATTA
1 TATGTTTTCAAAAATACGTTTTCAAAAACTATATATTA
* * *
45111 TATGTTTTCCAAAA-CCGATTTTTAAAAAACTATATATTATA
1 TATGTTTTCAAAAATACG--TTTTCAAAAACTATATA-T-TA
**
45152 TATGTTTTCAAAAAATATTTTTTC-AAAACTATATATTA
1 TATGTTTTC-AAAAATACGTTTTCAAAAACTATATATTA
* * * *
45190 TATGTTTTTAAAAACATGTTTTCAAAACCATATTATATATA
1 TATGTTTTCAAAAATACGTTTTCAAAAAC-TA-TATAT-TA
* ** * *
45231 TATTTTTTC-AAAACCCGGTTTTTTAAAAATTATATATTA
1 TATGTTTTCAAAAATAC-G-TTTTCAAAAACTATATATTA
* * *
45270 TAT-TCTTTCAAAAA-CCATTTTCTAAAAATTATATATTA
1 TATGT-TTTCAAAAATACGTTTTC-AAAAACTATATATTA
* *
45308 TATTTTTTTCAAAAATA--TTTTCAAAATCTATA
1 TA-TGTTTTCAAAAATACGTTTTCAAAAACTATA
45340 CTATATTAAT
Statistics
Matches: 283, Mismatches: 31, Indels: 52
0.77 0.08 0.14
Matches are distributed among these distances:
35 32 0.11
36 4 0.01
37 59 0.21
38 68 0.24
39 33 0.12
40 48 0.17
41 27 0.10
42 12 0.04
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (38 bp):
TATGTTTTCAAAAATACGTTTTCAAAAACTATATATTA
Found at i:45051 original size:75 final size:74
Alignment explanation
Indices: 44968--45191 Score: 276
Period size: 75 Copynumber: 3.0 Consensus size: 74
44958 ATACAGTATG
*
44968 TTTTCAAAAATATTTAAAAAACTATATATTATATGTTTTCAAAAATACGTTTTCAAAAACTATAT
1 TTTTCAAAAATATTTAAAAAACTATATATTATATGTTTTCAAAAATATGTTTTCAAAAACTATAT
45033 TATATATACA
66 TAT-TATACA
* * *
45043 TTTTCAAAAATATTTTAAAAACTATATATTATATATTTTCAAAAATGTGTTTTCAAAAA-TATA-
1 TTTTCAAAAATATTTAAAAAACTATATATTATATGTTTTCAAAAATATGTTTTCAAAAACTATAT
**
45106 TATTATATG
66 TATTATACA
* *
45115 TTTTCCAAAACCGATTTTTAAAAAACTATATATTATATATGTTTTCAAAAAATATTTTTTC-AAA
1 TTTT-CAAAA---ATATTTAAAAAACTATATA-T-TATATGTTTTC-AAAAATATGTTTTCAAAA
45179 ACTATA-TATTATA
59 ACTATATTATTATA
45192 TGTTTTTAAA
Statistics
Matches: 130, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
72 8 0.06
73 8 0.06
74 4 0.03
75 55 0.42
76 17 0.13
77 1 0.01
78 14 0.11
79 23 0.18
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (74 bp):
TTTTCAAAAATATTTAAAAAACTATATATTATATGTTTTCAAAAATATGTTTTCAAAAACTATAT
TATTATACA
Found at i:45108 original size:39 final size:38
Alignment explanation
Indices: 44928--45353 Score: 201
Period size: 37 Copynumber: 11.1 Consensus size: 38
44918 TAACATACAT
*** *
44928 TATATTTTCAAAAACCATTTT-AAAAAT-TATATA-CA
1 TATATTTTCAAAAAATGTTTTCAAAAATATATATATTA
* *
44963 GTATGTTTTC-AAAAAT-ATTT-AAAAA-ACTATATATTA
1 -TATATTTTCAAAAAATGTTTTCAAAAATA-TATATATTA
* *
44999 TATGTTTTCAAAAATACGTTTTCAAAAACTATAT-TATATA
1 TATATTTTCAAAAA-ATGTTTTCAAAAA-TATATATAT-TA
* * *
45039 TACATTTTC-AAAAATATTTT-AAAAA-CTATATATTA
1 TATATTTTCAAAAAATGTTTTCAAAAATATATATATTA
*
45074 TATATTTTCAAAAATGTGTTTTC-AAAA-ATATATATTA
1 TATATTTTCAAAAA-ATGTTTTCAAAAATATATATATTA
* * ** *
45111 TATGTTTTCCAAAACCGATTTTTAAAAA-ACTATATATTA
1 TATATTTTCAAAAAATG-TTTTCAAAAATA-TATATATTA
* *
45150 TATATGTTTTCAAAAAATATTTTTTC-AAAA-CTATATATTA
1 TATA--TTTTC-AAAAA-ATGTTTTCAAAAATATATATATTA
* *
45190 TATGTTTTTAAAAACATGTTTTCAAAACCATAT-TATATATA
1 TATATTTTCAAAAA-ATGTTTTCAAAA--ATATATATAT-TA
* *** *
45231 TATTTTTTCAAAACCCGGTTTTTTAAAAAT-TATATATTA
1 TATATTTTCAAAA-AATG-TTTTCAAAAATATATATATTA
***
45270 TAT-TCTTTCAAAAACCATTTTCTAAAAAT-TATATATTA
1 TATAT-TTTCAAAAAATGTTTTC-AAAAATATATATATTA
* * *
45308 TATTTTTTTC-AAAAATATTTTCAAAATCTATACTATATTAA
1 TA-TATTTTCAAAAAATGTTTTCAAAA-ATATA-TATATT-A
45349 TATAT
1 TATAT
45354 ATACTAAATA
Statistics
Matches: 306, Mismatches: 47, Indels: 70
0.72 0.11 0.17
Matches are distributed among these distances:
34 8 0.03
35 32 0.10
36 21 0.07
37 60 0.20
38 50 0.16
39 45 0.15
40 46 0.15
41 28 0.09
42 16 0.05
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATTTTCAAAAAATGTTTTCAAAAATATATATATTA
Found at i:49661 original size:42 final size:42
Alignment explanation
Indices: 49614--50028 Score: 493
Period size: 42 Copynumber: 9.9 Consensus size: 42
49604 AAAATGCTGC
* **
49614 AATAGAGTAGTAATATAGTGGCGTTTATAGCAAAAACGCCGA
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
*
49656 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGC
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* *
49698 AATAGAGTAGTAATATAGCAGCGTTTATAGCTCAAACACC-A
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* *
49739 TAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCC-A
1 -AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* * * *
49781 TAATAGAGTTGTAATATAGCGTCGTTTATAGCAT-AAACGCTGC
1 -AATAGAGTAGTAATATAGCGGCGTTTATAGC-TCAAACGCCGA
* * *
49824 AATAGAGTAGTAATATAGCGACATTTATAGCTCAAACGCCGC
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* * *
49866 AATAGAGTAGTAATATATCGGCATTTATAGCTCAAACGCCGC
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* *
49908 AATAGAGTCGTAATATAGCGGCGTTTATAGCTCAAATGCC-A
1 AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
* **
49949 CAATATAGTAGTAATATAGCGGCGTTT-TA-CAAGAAACGCC-A
1 -AATAGAGTAGTAATATAGCGGCGTTTATAGC-TCAAACGCCGA
* * *
49990 CAATAGAGTAGTATTATAGCGGCATTTATAGTTCAAACG
1 -AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACG
50029 TCATAATAGG
Statistics
Matches: 327, Mismatches: 38, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.00
41 34 0.10
42 291 0.89
43 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (42 bp):
AATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGA
Found at i:49839 original size:126 final size:125
Alignment explanation
Indices: 49613--50037 Score: 545
Period size: 126 Copynumber: 3.4 Consensus size: 125
49603 AAAAATGCTG
* * **
49613 CAATAGAGTAGTAATATAGTGGCGTTTATAGCAAAAACGCCGA-AATAGAGTAGTAATATAGCGG
1 CAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCC-ATAATAGAGTAGTAATATAGCGG
*
49677 CGTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGCAGCGTTTATAGCTCAAACACCA
65 CGTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGC-GCGTTTATAGCTCAAACGCCA
* * *
49739 TAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCCATAATAGAGTTGTAATATAGCGTC
1 CAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCCATAATAGAGTAGTAATATAGCGGC
* * *
49804 GTTTATAGCAT-AAACGCTGCAATAGAGTAGTAATATAGCGACATTTATAGCTCAAACGCCG
66 GTTTATAGC-TCAAACGCCGCAATAGAGTAGTAATATAGCG-CGTTTATAGCTCAAACGCCA
* * ** *
49865 CAATAGAGTAGTAATATATCGGCATTTATAGCTCAAACGCCGCAATAGAGTCGTAATATAGCGGC
1 CAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCCATAATAGAGTAGTAATATAGCGGC
* * * **
49930 GTTTATAGCTCAAATGCCACAATATAGTAGTAATATAGCGGCGTTT-TA-CAAGAAACGCCA
66 GTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGC-GCGTTTATAGC-TCAAACGCCA
* *
49990 CAATAGAGTAGTATTATAGCGGCATTTATAG-TTCAAACGTCATAATAG
1 CAATAGAGTAGTAATATAGCGGCATTTATAGCTT-AAACGCCATAATAG
50038 GGTTAACATA
Statistics
Matches: 260, Mismatches: 32, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
124 2 0.01
125 52 0.20
126 204 0.78
127 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (125 bp):
CAATAGAGTAGTAATATAGCGGCATTTATAGCTTAAACGCCATAATAGAGTAGTAATATAGCGGC
GTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGCGCGTTTATAGCTCAAACGCCA
Found at i:58066 original size:21 final size:21
Alignment explanation
Indices: 58042--58087 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58032 CAGAGAGAAC
* *
58042 AGCAGCGGAAGCACATAGAGA
1 AGCAGCGAAAGCACAAAGAGA
*
58063 AGCAGCGAAAGCACAAAGATA
1 AGCAGCGAAAGCACAAAGAGA
58084 AGCA
1 AGCA
58088 ACATATCAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.28, T:0.04
Consensus pattern (21 bp):
AGCAGCGAAAGCACAAAGAGA
Found at i:58494 original size:42 final size:44
Alignment explanation
Indices: 58405--58549 Score: 136
Period size: 44 Copynumber: 3.4 Consensus size: 44
58395 TCTTAGTTAT
* * ** * * *
58405 TTAGCGGCGTTTGTA-ACAAAAAATGCCGCAATATATCAAACAT-
1 TTAGCGGCGTTTGTATCCTAAAAACACCGCAATATAGC-GATATC
*
58448 TTAGCGGCGTTTGTAT-CT-AAAACACCGCAATATAGCGGTATC
1 TTAGCGGCGTTTGTATCCTAAAAACACCGCAATATAGCGATATC
* * * *
58490 TTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATAGCGATCTT
1 TTAGCGGCGTTTGTATCCTAAAAACACCGCAATATAGCGATATC
*
58534 TTTGCGGCGTTTGTAT
1 TTAGCGGCGTTTGTAT
58550 GAACAAACGC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.02
42 31 0.36
43 18 0.21
44 34 0.40
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (44 bp):
TTAGCGGCGTTTGTATCCTAAAAACACCGCAATATAGCGATATC
Found at i:58716 original size:85 final size:85
Alignment explanation
Indices: 58535--58883 Score: 246
Period size: 85 Copynumber: 4.1 Consensus size: 85
58525 AGCGATCTTT
* * ** * * **
58535 TTGCGGCGTTT-GTATGAACAAACGCCGCTAAAGCTCAACACCTATTGCGGCGTTTGTG-GGAAA
1 TTGCGGCGTTTCG-ATTAA-AAACACCGCTAAATATCAAAACCTACTGCGGCGTTTGTGAAAAAA
* *
58598 ATGCCGCTAAATTTCAACACTTA
64 ACGCCGCTAAATATCAACAC-TA
** *
58621 TTGCAACGTTTGCGA-TAAAAACACCGCT-AATCTCAATAACC-ACTGCGGCGTTTGTGAAAAAA
1 TTGCGGCGTTT-CGATTAAAAACACCGCTAAATATCAA-AACCTACTGCGGCGTTTGTGAAAAAA
*
58683 ACGCCGCTAAACATCAACATCTA
64 ACGCCGCTAAATATCAACA-CTA
** * * * * *
58706 TTGCGGCGTTTTTATTACAAACGCCGCTAAATATCAAAACCTATTGTGGCGTTTGT-AATACAAA
1 TTGCGGCGTTTCGATTAAAAACACCGCTAAATATCAAAACCTACTGCGGCGTTTGTGAA-AAAAA
* *
58770 CACCGTTAAATATCAACAACTA
65 CGCCGCTAAATATCAAC-ACTA
* * * * * * * *
58792 TTGCGGCGTTT-TAATACAAACGCC-CTTAAATATCAAAACCTATTGCGGCGTTTGTTATATAAA
1 TTGCGGCGTTTCGATTAAAAACACCGC-TAAATATCAAAACCTACTGCGGCGTTTGTGAAAAAAA
* *
58855 CTCTGCTAAATATCAACACTTA
65 CGCCGCTAAATATCAACAC-TA
*
58877 TTACGGC
1 TTGCGGC
58884 ATTTTTTGTT
Statistics
Matches: 217, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
84 25 0.12
85 125 0.58
86 64 0.29
87 2 0.01
88 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (85 bp):
TTGCGGCGTTTCGATTAAAAACACCGCTAAATATCAAAACCTACTGCGGCGTTTGTGAAAAAAAC
GCCGCTAAATATCAACACTA
Found at i:58728 original size:43 final size:43
Alignment explanation
Indices: 58535--58922 Score: 288
Period size: 43 Copynumber: 9.1 Consensus size: 43
58525 AGCGATCTTT
* **
58535 TTGCGGCGTTTGT-ATGAACAAACGCCGCTAAAGCTCAACACCTA
1 TTGCGGCGTTTTTAAT--ACAAACGCCGCTAAATATCAACACCTA
* *** * * *
58579 TTGCGGCGTTTGTGGGA-AAATGCCGCTAAATTTCAACACTTA
1 TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAACACCTA
** *** * * * *
58621 TTGCAACGTTTGCGATAAAAACACCGCT-AATCTCAATAACC-A
1 TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAA-CACCTA
* * * * *
58663 CTGCGGCGTTTGTGAA-AAAAACGCCGCTAAACATCAACATCTA
1 TTGCGGCGTTT-TTAATACAAACGCCGCTAAATATCAACACCTA
* *
58706 TTGCGGCGTTTTTATTACAAACGCCGCTAAATATCAAAACCTA
1 TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAACACCTA
* * * * *
58749 TTGTGGCGTTTGTAATACAAACACCGTTAAATATCAACAACTA
1 TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAACACCTA
*
58792 TTGCGGCG-TTTTAATACAAACGCC-CTTAAATATCAAAACCTA
1 TTGCGGCGTTTTTAATACAAACGCCGC-TAAATATCAACACCTA
* * * *
58834 TTGCGGCGTTTGTT-ATATAAACTCTGCTAAATATCAACACTTA
1 TTGCGGCGTTT-TTAATACAAACGCCGCTAAATATCAACACCTA
* * ** * *
58877 TTACGGCATTTTTTGTTCAAACGCCACTAAATATCAACACCTA
1 TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAACACCTA
58920 TTG
1 TTG
58923 TGGAATTTTT
Statistics
Matches: 270, Mismatches: 62, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
42 102 0.38
43 152 0.56
44 16 0.06
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTTTAATACAAACGCCGCTAAATATCAACACCTA
Found at i:58736 original size:128 final size:126
Alignment explanation
Indices: 58536--58878 Score: 343
Period size: 128 Copynumber: 2.7 Consensus size: 126
58526 GCGATCTTTT
*** *
58536 TGCGGCGTTTGTATGAACAAACGCCGCTAAAGC-TCAACACCTATTGCGGCGTTTGTGGGAAAAT
1 TGCGGCGTTTGTA--AACAAACGCCGCTAAA-CATCAACACCTATTGCGGCGTTT-TTATAAAAC
* * * *
58600 GCCGCTAAATTTCAACACTTATTGCAACGTTTGCGATAAAAACACCGCT-AATCTCAATAACCAC
62 GCCGCTAAATATCAACACTTATTGCAACGTTTGCAATAAAAACACCGCTAAATATCAACAACCAC
* *
58664 TGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAACATCTATTGCGGCGTTTTTATTACAAACG
1 TGCGGCGTTTGT-AAACAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTTA-TA-AAACG
* * *** * * * * *
58729 CCGCTAAATATCAAAACCTATTGTGGCGTTTGTAATACAAACACCGTTAAATATCAACAACTAT
63 CCGCTAAATATCAACACTTATTGCAACGTTTGCAATAAAAACACCGCTAAATATCAACAACCAC
* *
58793 TGCGGCGTTT-TAATACAAACGCC-CTTAAATATCAAAACCTATTGCGGCGTTTGTTATATAAAC
1 TGCGGCGTTTGTAA-ACAAACGCCGC-TAAACATCAACACCTATTGCGGCGTTT-TTATA-AAAC
* *
58856 TCTGCTAAATATCAACACTTATT
62 GCCGCTAAATATCAACACTTATT
58879 ACGGCATTTT
Statistics
Matches: 178, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
126 2 0.01
127 39 0.22
128 112 0.63
129 25 0.14
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (126 bp):
TGCGGCGTTTGTAAACAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTTTATAAAACGCCG
CTAAATATCAACACTTATTGCAACGTTTGCAATAAAAACACCGCTAAATATCAACAACCAC
Found at i:58793 original size:86 final size:85
Alignment explanation
Indices: 58667--58925 Score: 301
Period size: 85 Copynumber: 3.0 Consensus size: 85
58657 TAACCACTGC
* * *
58667 GGCGTTTGTGAA-AAAAACGCCGCTAAACATCAACATCTATTGCGGCGTTTTTATTACAAACGCC
1 GGCGTTTGT-AATAAAAACACCGCTAAATATCAACAACTATTGCGGCGTTTTTATTACAAACGCC
58731 GCTAAATATCAAAACCTATTGT
65 -CTAAATATCAAAACCTATTGT
* * *
58753 GGCGTTTGTAATACAAACACCGTTAAATATCAACAACTATTGCGGCG-TTTTAATACAAACGCCC
1 GGCGTTTGTAATAAAAACACCGCTAAATATCAACAACTATTGCGGCGTTTTTATTACAAACGCCC
*
58817 TTAAATATCAAAACCTATTGC
66 -TAAATATCAAAACCTATTGT
* * * * * * *
58838 GGCGTTTGTTATATAAACTCTGCTAAATATCAAC-ACTTATTACGGCATTTTT-TGTTCAAACGC
1 GGCGTTTGTAATAAAAACACCGCTAAATATCAACAAC-TATTGCGGCGTTTTTAT-TACAAACGC
*
58901 CACTAAATATCAACACCTATTGT
64 C-CTAAATATCAAAACCTATTGT
58924 GG
1 GG
58926 AATTTTTTGT
Statistics
Matches: 149, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
84 3 0.02
85 73 0.49
86 72 0.48
87 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (85 bp):
GGCGTTTGTAATAAAAACACCGCTAAATATCAACAACTATTGCGGCGTTTTTATTACAAACGCCC
TAAATATCAAAACCTATTGT
Found at i:58898 original size:128 final size:129
Alignment explanation
Indices: 58535--58922 Score: 288
Period size: 128 Copynumber: 3.0 Consensus size: 129
58525 AGCGATCTTT
* * * ***
58535 TTGCGGCGTTTGT-ATGAACAAACGCCGCTAAAGC-TCAACACCTATTGCGGCGTTTGTGGGA-A
1 TTGCGGCGTTTGTGA--AAAAAACGCCGCTAAA-CATCAAAACCTATTGCGGCGTTTTTATTACA
* * * * * ** * ** * * * *
58597 AATGCCGCTAAATTTCAACACTTATTGCAACGTTTGCGATAAAAACACCGCT-AATCTCAATAAC
63 AACGCCGCTAAATATCAAAACCTATTACGGCATTTGTAATACAAACACCACTAAATATCAACAAC
*
58661 CA
128 TA
* * *
58663 CTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAACATCTATTGCGGCGTTTTTATTACAAAC
1 TTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAAAACCTATTGCGGCGTTTTTATTACAAAC
** * **
58728 GCCGCTAAATATCAAAACCTATTGTGGCGTTTGTAATACAAACACCGTTAAATATCAACAACTA
66 GCCGCTAAATATCAAAACCTATTACGGCATTTGTAATACAAACACCACTAAATATCAACAACTA
* * *
58792 TTGCGGCGTTT-T-AATACAAACGCC-CTTAAATATCAAAACCTATTGCGGCGTTTGTTA-TATA
1 TTGCGGCGTTTGTGAA-AAAAACGCCGC-TAAACATCAAAACCTATTGCGGCGTTT-TTATTACA
* * * * * ** * * *
58853 AACTCTGCTAAATATCAACACTTATTACGGCATTTTTTGTTCAAACGCCACTAAATATCAACACC
63 AACGCCGCTAAATATCAAAACCTATTACGGCATTTGTAATACAAACACCACTAAATATCAACAAC
58918 TA
128 TA
58920 TTG
1 TTG
58923 TGGAATTTTT
Statistics
Matches: 211, Mismatches: 42, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
126 1 0.00
127 40 0.19
128 145 0.69
129 25 0.12
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (129 bp):
TTGCGGCGTTTGTGAAAAAAACGCCGCTAAACATCAAAACCTATTGCGGCGTTTTTATTACAAAC
GCCGCTAAATATCAAAACCTATTACGGCATTTGTAATACAAACACCACTAAATATCAACAACTA
Found at i:60085 original size:25 final size:25
Alignment explanation
Indices: 60052--60100 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
60042 TTTTCCCTTT
*
60052 ATTTTATTTATTTAT-TTTGATTAG
1 ATTTTATTTATTTATATTCGATTAG
*
60076 ATTTTGATTTTTTTATATTCGATTA
1 ATTTT-ATTTATTTATATTCGATTA
60101 AATTATCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (25 bp):
ATTTTATTTATTTATATTCGATTAG
Found at i:63644 original size:23 final size:23
Alignment explanation
Indices: 63618--63662 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
63608 TAAATGCAAC
*
63618 GAAGTGCCACGTAGGATTGCACT
1 GAAGTGCCACGTAGAATTGCACT
63641 GAAGTGCCACGTAGAATTGCAC
1 GAAGTGCCACGTAGAATTGCAC
63663 CGTAGTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
GAAGTGCCACGTAGAATTGCACT
Found at i:64127 original size:15 final size:15
Alignment explanation
Indices: 64096--64137 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
64086 TTTATGATCA
* *
64096 TATAATCATATAACT
1 TATAATCACATATCT
*
64111 TATTATCACATATCT
1 TATAATCACATATCT
64126 TATAATCACATA
1 TATAATCACATA
64138 CCTAATTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAATCACATATCT
Found at i:65255 original size:64 final size:64
Alignment explanation
Indices: 65165--65288 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
65155 ATCCCTTGAC
* * *
65165 GGGTGCATCGGTGCACTATCTATGCATCGGTACA-TAAATCTCATTCGATGTTTGTATTTTAAGG
1 GGGTGCATCGATGCACTATCTATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAGG
* * * *
65229 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGACATTCGATGTTTTTATTTT
1 GGGTGCATCGATGCACTATC-TATGCATCGATACACTAATCACATTCGATGTTTGTATTTT
65289 TATTTTAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
63 1 0.02
64 49 0.96
65 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (64 bp):
GGGTGCATCGATGCACTATCTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAGG
Found at i:69169 original size:37 final size:37
Alignment explanation
Indices: 69128--69206 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
69118 AAATTCTCTG
*
69128 AAGAACCTGACTTAAACCCACGAAGGGAAGTCA-TCCA
1 AAGAACCTGACTTAAACCCACGAAAGGAAGTCACT-CA
* *
69165 AAGAACCTTACTTAAACCCACGAAAGTAAGTCACTCA
1 AAGAACCTGACTTAAACCCACGAAAGGAAGTCACTCA
69202 AAGAA
1 AAGAA
69207 TCATGTCGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.15
Consensus pattern (37 bp):
AAGAACCTGACTTAAACCCACGAAAGGAAGTCACTCA
Found at i:70183 original size:198 final size:197
Alignment explanation
Indices: 69644--70290 Score: 653
Period size: 200 Copynumber: 3.3 Consensus size: 197
69634 ATCATTTACA
** * * **
69644 ACATAGCTTAATTCGAGAAGAGCTATCTGTTAACCAAAGCTTTCAAGTTCGATTCAATTCAACTC
1 ACATAGCTTAAGACGAAAAGAGCTATCTGTCAACCAAAGCTTTCAAGTTCGATTC-CCTCAACTC
** * *
69709 GAA-AGCACATTGACCGCATGGTA-TCAACGAATAACTACCTATCGGTCAAAATTCAAACCAAGG
65 -AAGAGCACATTGACCGCATGGTAGT-AACGAGGAACTA-CTTTCGGTCAAAATTCAAACTAAGG
* * * * * * * * * *
69772 TCTTTAA-TCAGATAAGAAGACCCAAGTTAGTTGTGACTTGGAAACAATGAACCACTTCTCAATT
127 TCTTTAAGCCA-AGAA-AAGGCCCAAGTTGGTTGCGATTTGGCAACAAAGAACCACTTCCCAATC
*
69836 ATATTTCA
190 ATATTTCG
* ** * * *
69844 ACATAACTTAA-ATTAAGAAGAGCTATCTGCCTACCAAAACTTTCAAGTTCGATTCCACTCAACT
1 ACATAGCTTAAGACGAA-AAGAGCTATCTGTCAACCAAAGCTTTCAAGTTCGATTCC-CTCAACT
* * * * *
69908 TAAGAGCACATTGACCGCATGGTAGTAACAAGGAACTACCTTCATGTTAAAATTCAAACTAAGGT
64 CAAGAGCACATTGACCGCATGGTAGTAACGAGGAACTACTTTC-GGTCAAAATTCAAACTAAGGT
* * *
69973 CTTTAAGCCAAGAAAAGGGCCCAAGTTGGTTGCGGTTTGGCAACAAAGAACCACTTCCCAGTCAG
128 CTTTAAGCCAAGAAAA-GGCCCAAGTTGGTTGCGATTTGGCAACAAAGAACCACTTCCCAATCAT
70038 ATTTCG
192 ATTTCG
* * *
70044 ACATAGCTTAAGCCGAAAAGAGCTATCTATCGACCAAAGCTTTCAAGTTCGATTCCCTCAACTCA
1 ACATAGCTTAAGACGAAAAGAGCTATCTGTCAACCAAAGCTTTCAAGTTCGATTCCCTCAACTCA
* *
70109 AGAGCACATTGACCGCA-AGTAGTAACGAGGAACTATTTTTCGGTCAAAATTCAAACTAAGGTCT
66 AGAGCACATTGACCGCATGGTAGTAACGAGGAACTA-CTTTCGGTCAAAATTCAAACTAAGGTCT
* * * ** *
70173 TTAAGCCAAGAAGAATGCTCAGGTTGGTTGCGATTTTACAACAAAGAACCACTTCCCAACCATAT
130 TTAAGCCAAGAA-AAGGCCCAAGTTGGTTGCGATTTGGCAACAAAGAACCACTTCCCAATCATAT
*
70238 TTTG
194 TTCG
** * *
70242 -CATAGCTTAAG-TTAAGAAGAGCTATATGTC-ACTCAAAGCTTTAAAGTTC
1 ACATAGCTTAAGACGAA-AAGAGCTATCTGTCAAC-CAAAGCTTTCAAGTTC
70291 AACTCCACGA
Statistics
Matches: 371, Mismatches: 64, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
196 4 0.01
197 38 0.10
198 93 0.25
199 38 0.10
200 193 0.52
201 5 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (197 bp):
ACATAGCTTAAGACGAAAAGAGCTATCTGTCAACCAAAGCTTTCAAGTTCGATTCCCTCAACTCA
AGAGCACATTGACCGCATGGTAGTAACGAGGAACTACTTTCGGTCAAAATTCAAACTAAGGTCTT
TAAGCCAAGAAAAGGCCCAAGTTGGTTGCGATTTGGCAACAAAGAACCACTTCCCAATCATATTT
CG
Found at i:71078 original size:6 final size:6
Alignment explanation
Indices: 71067--71092 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
71057 TAATATTTTA
71067 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
71093 ATTGTTTCGG
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:71461 original size:12 final size:12
Alignment explanation
Indices: 71434--71484 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
71424 CATAATTTAT
71434 TTTTAATTT-A-
1 TTTTAATTTAAC
*
71444 TTTTAAGTTAAC
1 TTTTAATTTAAC
*
71456 TTTTAATTTTAAT
1 TTTTAA-TTTAAC
*
71469 TTTTATTTTAAC
1 TTTTAATTTAAC
71481 TTTT
1 TTTT
71485 TTTCTTTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 15 0.45
13 9 0.27
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTAATTTAAC
Done.