Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003771.1 Hibiscus syriacus cultivar Beakdansim tig00008075_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: 113872
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4009 original size:19 final size:18
Alignment explanation
Indices: 3985--4109 Score: 77
Period size: 17 Copynumber: 7.1 Consensus size: 18
3975 ATTTTGCTTG
3985 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAAAGAGAA
*
4004 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAAAGAGAA
*
4022 AA-AAGAAAAAATGATGGAA
1 AAGAAGAAAAAAAGA--GAA
*
4041 AA-AACGAAAAGAAA-AAAA
1 AAGAA-GAAAA-AAAGAGAA
*
4059 AAG-AGAAAAAATG-GAA
1 AAGAAGAAAAAAAGAGAA
* *
4075 AA-AGGAAGGAAAAGAGAA
1 AAGAAGAA-AAAAAGAGAA
*
4093 AA-ATG-AAAAAAGAGAA
1 AAGAAGAAAAAAAGAGAA
4109 A
1 A
4110 TAAAAGGAGG
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
16 19 0.22
17 22 0.25
18 22 0.25
19 16 0.18
20 6 0.07
21 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAAAAGAGAA
Found at i:4029 original size:25 final size:25
Alignment explanation
Indices: 3995--4109 Score: 67
Period size: 25 Copynumber: 4.4 Consensus size: 25
3985 AAGAAGAAAT
*
3995 AAAAGAGAAAAGAAGAAAAAATGAG
1 AAAAAAGAAAAGAAGAAAAAATGAG
* * *
4020 AAAAAAGAAAAAATGATGGAAAAAACGAA
1 AAAAAAG--AAAA-GA-AGAAAAAATGAG
*
4049 AAGAAAAAAAAAG-AGAAAAAATG-G
1 AA-AAAAGAAAAGAAGAAAAAATGAG
*
4073 AAAAAGGAAGGAA-AAGAGAAAAATGA-
1 AAAAAAGAA--AAGAAGA-AAAAATGAG
4099 AAAAAGAGAAA
1 AAAAA-AGAAA
4110 TAAAAGGAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
23 5 0.07
24 2 0.03
25 20 0.29
26 12 0.18
27 8 0.12
28 6 0.09
29 11 0.16
30 4 0.06
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAAAGAAGAAAAAATGAG
Found at i:4032 original size:27 final size:25
Alignment explanation
Indices: 3990--4109 Score: 100
Period size: 27 Copynumber: 4.5 Consensus size: 25
3980 GCTTGAAGAA
*
3990 GAAATAAAAGAGAAAAGAAGAAAAAAT
1 GAAA-AAAAGAAAAAAG-AGAAAAAAT
*
4017 GAGAAAAAAGAAAAAATGATGGAAAAAAC
1 GA-AAAAAAGAAAAAA-GA--GAAAAAAT
4046 GAAAAGAAA-AAAAAAGAGAAAAAAT
1 GAAAA-AAAGAAAAAAGAGAAAAAAT
* *
4071 GGAAAAAGGAAGGAAAAGAG-AAAAAT
1 GAAAAAAAGAA--AAAAGAGAAAAAAT
4097 GAAAAAAGAGAAA
1 GAAAAAA-AGAAA
4110 TAAAAGGAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
24 2 0.03
25 14 0.18
26 12 0.16
27 25 0.32
28 12 0.16
29 12 0.16
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (25 bp):
GAAAAAAAGAAAAAAGAGAAAAAAT
Found at i:4050 original size:37 final size:33
Alignment explanation
Indices: 3988--4103 Score: 94
Period size: 36 Copynumber: 3.3 Consensus size: 33
3978 TTGCTTGAAG
3988 AAGAAATAAAA-GAGAAAAGAAGAAAAAATGAGAAAA
1 AAGAAA-AAAATG-GAAAA-AAGAAAAAA-GAGAAAA
4024 AAGAAAAAATGATGGAAAAAACGAAAAGAA-A-AAAA
1 AAGAAAAAA--ATGGAAAAAA-GAAAA-AAGAGAAAA
*
4059 AAGAGAAAAAATGGAAAAAGGAAGGAAAAGAGAAAA
1 AAGA-AAAAAATGGAAAAAAGAA--AAAAGAGAAAA
*
4095 ATGAAAAAA
1 AAGAAAAAA
4104 GAGAAATAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
33 3 0.04
34 11 0.16
35 19 0.28
36 21 0.31
37 11 0.16
38 3 0.04
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (33 bp):
AAGAAAAAAATGGAAAAAAGAAAAAAGAGAAAA
Found at i:4069 original size:45 final size:44
Alignment explanation
Indices: 3995--4115 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 44
3985 AAGAAGAAAT
* * * *
3995 AAAAGAGAAAAGAAGAAAAAATGAG-AAAAAAGAAAAAATGATGG
1 AAAAAAGAAAAGAA-AAAAAAAGAGAAAAAAAGAAAAAAGGAAGG
* *
4039 AAAAAACGAAAAGAAAAAAAAAGAGAAAAAATGGAAAAAGGAAGG
1 AAAAAA-GAAAAGAAAAAAAAAGAGAAAAAAAGAAAAAAGGAAGG
* **
4084 AAAAGAGAAAA-ATGAAAAAAGAGAAATAAAAG
1 AAAAAAGAAAAGAAAAAAAAAGAGAAA-AAAAG
4116 GAGGGTTCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
43 13 0.20
44 23 0.36
45 28 0.44
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (44 bp):
AAAAAAGAAAAGAAAAAAAAAGAGAAAAAAAGAAAAAAGGAAGG
Found at i:5488 original size:51 final size:51
Alignment explanation
Indices: 5422--6041 Score: 963
Period size: 51 Copynumber: 12.0 Consensus size: 51
5412 GAAGCAAATT
5422 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
5473 AGTTCGTTGAGGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
5524 AGTTCGTTGAGGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5574 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5625 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5676 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
5727 AGTTCGTTGAGGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5778 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* *
5829 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACT
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * *
5880 AGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* ** * * * *
5931 TGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* ** * * *
5986 CGTTTTATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 AG-TTCGTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
6042 CATTTTATGA
Statistics
Matches: 537, Mismatches: 22, Indels: 15
0.94 0.04 0.03
Matches are distributed among these distances:
50 49 0.09
51 409 0.76
52 1 0.00
53 2 0.00
54 2 0.00
55 33 0.06
56 41 0.08
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
Found at i:6092 original size:55 final size:54
Alignment explanation
Indices: 5844--6093 Score: 219
Period size: 55 Copynumber: 4.6 Consensus size: 54
5834 GTTGAAGATT
* * * **
5844 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CTAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCT--TTTATTGAAGATTGTTC
* * * * * *
5895 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCT-TTTATTGAAGATTGTTC
*
5950 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CC-TTTTATTGAAGATTGTTC
* * *
6006 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGCTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-C-TTTTATTGAAGATTGTTC
*
6061 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
6094 GCTCGTCATT
Statistics
Matches: 171, Mismatches: 17, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
51 42 0.25
52 2 0.01
54 3 0.02
55 69 0.40
56 53 0.31
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCTTTTATTGAAGATTGTTC
Found at i:22092 original size:27 final size:27
Alignment explanation
Indices: 22062--22116 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
22052 TTTATATTTT
* *
22062 AATAAAGAATAATTT-TATTGAATTAAA
1 AATAAA-AATAATTTATAATAAATTAAA
*
22089 AATAAAAATTATTTATAATAAATTAAA
1 AATAAAAATAATTTATAATAAATTAAA
22116 A
1 A
22117 GAAACAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
AATAAAAATAATTTATAATAAATTAAA
Found at i:23788 original size:2 final size:2
Alignment explanation
Indices: 23781--23817 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23771 AATACATTTA
23781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23818 ACATATTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24929 original size:37 final size:37
Alignment explanation
Indices: 24870--24973 Score: 133
Period size: 35 Copynumber: 2.9 Consensus size: 37
24860 ATCCCATTAT
* * *
24870 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAT
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
* *
24906 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
*
24942 CA-TTTTCAAAAAAATATTTACCAAACTTTGAA
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAA
24974 CTTAACAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 26 0.44
36 13 0.22
37 20 0.34
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAAC
Found at i:28124 original size:6 final size:6
Alignment explanation
Indices: 28113--29072 Score: 1852
Period size: 6 Copynumber: 159.7 Consensus size: 6
28103 GCATCACCTG
28113 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28161 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28209 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28257 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28305 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28353 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28401 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
28449 TACATA TTCATA TACATACA TACATA TACATA TATATA TACATA TACATATA
1 TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA TAC--ATA
28501 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28549 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28597 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28645 TACATA TACATA TAC--A TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28691 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28739 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28787 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28835 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28883 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28931 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
28979 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
29027 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACA
29073 GATGAGGGCG
Statistics
Matches: 944, Mismatches: 4, Indels: 12
0.98 0.00 0.01
Matches are distributed among these distances:
4 4 0.00
6 928 0.98
8 12 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:34747 original size:15 final size:15
Alignment explanation
Indices: 34727--34758 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34717 AGAGTGAACC
34727 TCCCAAAGAGGTTGA
1 TCCCAAAGAGGTTGA
34742 TCCCAAAGAGGTTGA
1 TCCCAAAGAGGTTGA
34757 TC
1 TC
34759 TTTATGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (15 bp):
TCCCAAAGAGGTTGA
Found at i:39851 original size:26 final size:25
Alignment explanation
Indices: 39804--39873 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 25
39794 TTTTAAAAAT
** * *
39804 TTAAACATTAACGATTACAAAAATGA
1 TTAAACATTAATTA-TAAAAAAAAGA
39830 TTAAACATTAATTATAAAAAAAAGA
1 TTAAACATTAATTATAAAAAAAAGA
* *
39855 -TAAA-AATACTTATAAAAAA
1 TTAAACATTAATTATAAAAAA
39874 TATTATCACT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 13 0.34
24 4 0.11
25 9 0.24
26 12 0.32
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.27
Consensus pattern (25 bp):
TTAAACATTAATTATAAAAAAAAGA
Found at i:49386 original size:38 final size:38
Alignment explanation
Indices: 49343--49458 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 38
49333 AAAGGAATTA
49343 TGTTCTAATGTGAAAGGGAAAGTAAACAAAAAGAACTC
1 TGTTCTAATGTGAAAGGGAAAGTAAACAAAAAGAACTC
** *
49381 TGTTCTAATGTG--AGGGAAAAAAAACTTAAGGAAAAAGGAACTT
1 TGTTCTAATGTGAAAGGGAAAGTAAAC------AAAAA-GAACTC
49424 TGTTCTAATGTGAAAGGGAAAGTAAACAAAAAGAA
1 TGTTCTAATGTGAAAGGGAAAGTAAACAAAAAGAA
49459 GACTTTAGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
36 11 0.17
38 15 0.23
39 5 0.08
42 5 0.08
43 17 0.27
45 11 0.17
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (38 bp):
TGTTCTAATGTGAAAGGGAAAGTAAACAAAAAGAACTC
Found at i:49430 original size:43 final size:43
Alignment explanation
Indices: 49320--49436 Score: 124
Period size: 43 Copynumber: 2.8 Consensus size: 43
49310 TATAGGGGGG
*
49320 AAAACTTAAGGAAAAAGGAA-TTATGTTCTAATGTGAAAGGGAAAG
1 AAAACTTAAGGAAAAAGGAACTT-TGTTCTAATGTG--AGGGAAAA
* *
49365 TAAAC------AAAAA-GAACTCTGTTCTAATGTGAGGGAAAA
1 AAAACTTAAGGAAAAAGGAACTTTGTTCTAATGTGAGGGAAAA
49401 AAAACTTAAGGAAAAAGGAACTTTGTTCTAATGTGA
1 AAAACTTAAGGAAAAAGGAACTTTGTTCTAATGTGA
49437 AAGGGAAAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
36 11 0.19
38 15 0.25
39 6 0.10
42 5 0.08
43 18 0.31
45 4 0.07
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (43 bp):
AAAACTTAAGGAAAAAGGAACTTTGTTCTAATGTGAGGGAAAA
Found at i:50435 original size:32 final size:32
Alignment explanation
Indices: 50396--50463 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
50386 GTAAGATTAC
50396 AATGTTTGGTTTGA-GAAATATAAGATTATTTA
1 AATGTTTGGTTTGATG-AATATAAGATTATTTA
*
50428 AATGTTTGGTTTGATGAATATAAGATTATTTG
1 AATGTTTGGTTTGATGAATATAAGATTATTTA
50460 AATG
1 AATG
50464 CATATTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (32 bp):
AATGTTTGGTTTGATGAATATAAGATTATTTA
Found at i:55329 original size:21 final size:21
Alignment explanation
Indices: 55303--55347 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55293 GATTTCTGGG
* *
55303 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
55324 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
55345 CAA
1 CAA
55348 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:56431 original size:15 final size:17
Alignment explanation
Indices: 56407--56450 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
56397 ATAAGCAATG
56407 TGAC-TATAAGTATATA
1 TGACTTATAAGTATATA
*
56423 TG-CTT-TAAGT-GATA
1 TGACTTATAAGTATATA
56437 TGACTTATAAGTAT
1 TGACTTATAAGTAT
56451 TTCTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 7
0.71 0.06 0.23
Matches are distributed among these distances:
14 5 0.23
15 9 0.41
16 8 0.36
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (17 bp):
TGACTTATAAGTATATA
Found at i:57069 original size:13 final size:13
Alignment explanation
Indices: 57051--57113 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
57041 TTATATGGCA
57051 CTACGGTGCAATT
1 CTACGGTGCAATT
57064 CTACGG-GC-A--
1 CTACGGTGCAATT
*
57073 CTTCGGTGCAATT
1 CTACGGTGCAATT
57086 CTACGG-GC-A--
1 CTACGGTGCAATT
*
57095 CTTCGGTGCAATT
1 CTACGGTGCAATT
57108 CTACGG
1 CTACGG
57114 GGCACTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:57079 original size:22 final size:22
Alignment explanation
Indices: 57047--57127 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
57037 ATCATTATAT
*
57047 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
57069 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
57091 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
*
57114 GGCACTTTGGTGCA
1 GGCACTTCGGTGCA
57128 TTTATACGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 42 0.75
23 14 0.25
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:60229 original size:21 final size:21
Alignment explanation
Indices: 60203--60247 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
60193 GATTTCTGGG
* *
60203 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
60224 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
60245 CAA
1 CAA
60248 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:61971 original size:13 final size:13
Alignment explanation
Indices: 61953--62015 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
61943 TTATATGGCA
61953 CTACGGTGCAATT
1 CTACGGTGCAATT
61966 CTACGG-GC-A--
1 CTACGGTGCAATT
*
61975 CTTCGGTGCAATT
1 CTACGGTGCAATT
61988 CTACGG-GC-A--
1 CTACGGTGCAATT
*
61997 CTTCGGTGCAATT
1 CTACGGTGCAATT
62010 CTACGG
1 CTACGG
62016 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:61981 original size:22 final size:22
Alignment explanation
Indices: 61949--62029 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
61939 ATCATTATAT
*
61949 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
61971 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
61993 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
62016 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
62030 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:67585 original size:8 final size:8
Alignment explanation
Indices: 67568--67596 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
67558 ATCCAAACAC
67568 AAAAAA-A
1 AAAAAAGA
67575 AAAAAAGA
1 AAAAAAGA
67583 AAAAAAGA
1 AAAAAAGA
67591 AAAAAA
1 AAAAAA
67597 AGGGAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:72147 original size:119 final size:119
Alignment explanation
Indices: 71936--72154 Score: 386
Period size: 119 Copynumber: 1.8 Consensus size: 119
71926 TCGTTCAAGA
* * * *
71936 AAACAAAAGAAGAAATACACTCAGCTAGATGTAAAACCGTTGAATCTGAATATATGAAGAAAAGA
1 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
72001 AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
66 AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
72055 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAA-AAAAGA
1 AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
72119 AAAATTAAGAAAGAGAGGGTTTTATATGTAAAGAAG
66 AAAATTAAGAAAGAGA-GGTTTTATATGTAAAGAAG
72155 TTAAGAAGAG
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 22 0.23
119 73 0.77
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (119 bp):
AAACAAAAGAAAAAATAAACTCAGCTAGATGTAAAAACGCTGAATCTGAATATATGAAGAAAAGA
AAAATTAAGAAAGAGAGGTTTTATATGTAAAGAAGAGCATAGAAATGAAAGAGG
Found at i:76823 original size:30 final size:30
Alignment explanation
Indices: 76761--76823 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
76751 AATTGTACAT
76761 ATTTTATTAAAAAAATAAAAACTATCTTATA
1 ATTTTATTAAAAAAATAAAAACTA-CTTATA
*
76792 ATTTTATTCAAAACAAATGAAAA-TA-TTATA
1 ATTTTATT-AAAA-AAATAAAAACTACTTATA
76822 AT
1 AT
76824 AATAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 7 0.24
31 8 0.28
32 6 0.21
33 8 0.28
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (30 bp):
ATTTTATTAAAAAAATAAAAACTACTTATA
Found at i:77334 original size:2 final size:2
Alignment explanation
Indices: 77327--77356 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
77317 ATGGTGTTTG
77327 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
77357 TCAAGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77950 original size:21 final size:20
Alignment explanation
Indices: 77864--78021 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
77854 AAATGACCAA
**
77864 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
77883 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
77903 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
77923 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
77944 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
77965 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
77985 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
78006 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
78022 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:78050 original size:20 final size:20
Alignment explanation
Indices: 77988--78257 Score: 260
Period size: 20 Copynumber: 13.5 Consensus size: 20
77978 CGATTTTCCA
* ** *
77988 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
78008 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
78028 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
78048 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
78068 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
78088 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
78108 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
78128 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
78148 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
78168 AAATCACAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
78188 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
78208 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
78228 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
78248 AAATCACAAC
1 AAATCGCAAC
78258 ACTGAAATTT
Statistics
Matches: 208, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 204 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:78074 original size:40 final size:40
Alignment explanation
Indices: 78027--78257 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
78017 CGCGAACACA
* * *
78027 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCG
* * *
78067 TATATCGCAACGCGTATCCGTAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAA--CGATAATCCG
* * *
78107 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
78147 TAAATCGCAACGAGAATCTGTAAATCACAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
78187 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
78227 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCCGTAAATCGCAAC
78258 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 173 0.97
42 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
Found at i:78979 original size:24 final size:24
Alignment explanation
Indices: 78940--78986 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
78930 AAATTTGGTC
78940 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
78964 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
78987 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:81518 original size:33 final size:34
Alignment explanation
Indices: 81467--81677 Score: 224
Period size: 33 Copynumber: 6.2 Consensus size: 34
81457 CGGAAATTAC
*
81467 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
81500 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
81534 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
81567 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
81600 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
* *
81638 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
81671 AATCGCA
1 AATCGCA
81678 TTGCGATTCT
Statistics
Matches: 156, Mismatches: 9, Indels: 26
0.82 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 93 0.60
34 31 0.20
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.13
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:81572 original size:19 final size:19
Alignment explanation
Indices: 81481--81683 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
81471 GCAACGAGAG
81481 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
81500 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
81514 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
81534 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
81548 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
81567 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
81586 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
81600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
81619 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
81638 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
81652 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
81671 AATCGCATTGCGA
1 AATCGCAATGCGA
81684 TTCTCCCGTT
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 42 0.27
15 3 0.02
16 7 0.05
17 6 0.04
18 4 0.03
19 78 0.51
20 13 0.08
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:81594 original size:52 final size:52
Alignment explanation
Indices: 81509--81683 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
81499 AAATCCCAAC
81509 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
81562 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
81614 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
81666 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
81684 TTCTCCCGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 104 0.87
53 16 0.13
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:81716 original size:19 final size:19
Alignment explanation
Indices: 81692--81788 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
81682 GATTCTCCCG
81692 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
81711 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
81730 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
81744 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81763 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
81782 TTGCGAT
1 TTGCGAT
81789 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 42 0.60
20 8 0.11
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:81716 original size:52 final size:52
Alignment explanation
Indices: 81654--81768 Score: 151
Period size: 52 Copynumber: 2.2 Consensus size: 52
81644 AACGAGAGAA
*
81654 TCGCAATGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGA-TTTCATT
1 TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
** * ** *
81705 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
81758 TCGCATTGCGA
1 TCGCATTGCGA
81769 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
51 1 0.02
52 46 0.84
53 8 0.15
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATTAAAATCGCATTGCGATTCTCCCGTTGCGATTTTCATT
Found at i:81769 original size:52 final size:52
Alignment explanation
Indices: 81673--81788 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
81663 GAAATTAAAA
81673 TCGCATTGCGATTCTCCCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
*
81725 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGA-TTTCATTTCCGCATTGCGATTTTCATT
81777 TCGCATTGCGAT
1 TCGCATTGCGAT
81789 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 54 0.87
53 8 0.13
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
Found at i:81914 original size:14 final size:14
Alignment explanation
Indices: 81895--81931 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
81885 CATCAATTAC
81895 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
81909 ACAAATCATCTTTT
1 ACAAATCAACTTTT
81923 ACAAATCAA
1 ACAAATCAA
81932 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:83891 original size:19 final size:19
Alignment explanation
Indices: 83851--83985 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
83841 TAGTTTACTT
* *
83851 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
83871 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
83890 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
83909 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
83923 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
83942 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
83956 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
83975 TCGCAATGCGA
1 TCGCAACGCGA
83986 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:83926 original size:14 final size:14
Alignment explanation
Indices: 83907--83963 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
83897 GCGAAATGAA
*
83907 AATCGCAACGACAG
1 AATCGCAACGAAAG
83921 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
83938 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
83954 AATCGCAACG
1 AATCGCAACG
83964 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:83930 original size:33 final size:33
Alignment explanation
Indices: 83888--83980 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
83878 GCGAAACCAA
*
83888 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
83921 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
83954 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
83981 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:83977 original size:52 final size:54
Alignment explanation
Indices: 83851--83985 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
83841 TAGTTTACTT
*
83851 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
83909 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
83956 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
83986 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:84003 original size:19 final size:18
Alignment explanation
Indices: 83981--84123 Score: 76
Period size: 19 Copynumber: 8.3 Consensus size: 18
83971 AAAATCGCAA
83981 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
84000 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
84014 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
84028 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
84047 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
84061 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
**
84080 TGCGATTTTGGTTTCGTTT
1 TGCGATTTT-GTTTCGCGT
* *
84099 TACGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
84119 TGCGA
1 TGCGA
84124 AAGTAAACTA
Statistics
Matches: 100, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
14 36 0.36
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 45 0.45
20 12 0.12
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:84016 original size:14 final size:14
Alignment explanation
Indices: 83997--84033 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
83987 TTTGGTTTCG
83997 CGTTGCGATCTTGT
1 CGTTGCGATCTTGT
84011 CGTTGCGATCTTGT
1 CGTTGCGATCTTGT
84025 CGTTGCGAT
1 CGTTGCGAT
84034 TTTGGTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
CGTTGCGATCTTGT
Found at i:84048 original size:33 final size:33
Alignment explanation
Indices: 84011--84086 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
84001 GCGATCTTGT
**
84011 CGTTGCGA-TCTTGTCGTTGCGATTTTGGTTTCG
1 CGTTGCGATTC-TGTCGTTGCGATTTTCATTTCG
84044 CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
1 CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
84077 CGTTGCGATT
1 CGTTGCGATT
84087 TTGGTTTCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.08, C:0.20, G:0.28, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTCTGTCGTTGCGATTTTCATTTCG
Found at i:84287 original size:93 final size:93
Alignment explanation
Indices: 84171--84731 Score: 1099
Period size: 93 Copynumber: 6.1 Consensus size: 93
84161 ATGGATTGCA
84171 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84235 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84263 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84328 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84356 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84421 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84449 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84514 TAGCAGAATTGG-AGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84541 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84606 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84634 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
84699 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
84727 TTACT
1 TTACT
84732 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 96 0.21
93 370 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:84653 original size:185 final size:186
Alignment explanation
Indices: 84171--84731 Score: 1099
Period size: 185 Copynumber: 3.0 Consensus size: 186
84161 ATGGATTGCA
84171 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84235 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
84300 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
84356 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84421 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
84486 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGG-AGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
84541 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84606 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
84671 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
84727 TTACT
1 TTACT
84732 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 189 0.51
186 184 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:84673 original size:278 final size:279
Alignment explanation
Indices: 84171--84731 Score: 1099
Period size: 278 Copynumber: 2.0 Consensus size: 279
84161 ATGGATTGCA
84171 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84235 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
84300 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
84365 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
84430 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
84449 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
84514 TAGCAGAATTGG-AGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
84578 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
84643 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
*
84708 TGGCAGCAACCGAATAAAT
261 TGGCAGCAACCGAACAAAT
84727 TTACT
1 TTACT
84732 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
278 209 0.74
279 72 0.26
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:86498 original size:19 final size:18
Alignment explanation
Indices: 86476--86534 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
86466 AAAATCGCAA
*
86476 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
86495 TGCGA--TTCTTT--CGT
1 TGCGATTTTATTTCGCGT
86509 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-ATTTCGCGT
86528 TGCGATT
1 TGCGATT
86535 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 8 0.24
16 5 0.15
17 5 0.15
19 15 0.45
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:86511 original size:14 final size:14
Alignment explanation
Indices: 86492--86548 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
86482 TTTGGTTTCG
86492 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
86506 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
86523 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
86539 CGTTGCGATT
1 CGTTGCGATT
86549 TTCATTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:86524 original size:33 final size:33
Alignment explanation
Indices: 86476--86556 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
86466 AAAATCGCAA
** *
86476 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
86509 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
86542 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
86557 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:86581 original size:23 final size:21
Alignment explanation
Indices: 86533--86588 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
86523 CGCGTTGCGA
86533 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
86554 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
86575 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
86589 CTCTTCTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:86710 original size:33 final size:33
Alignment explanation
Indices: 86668--86738 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
86658 AATACTAACT
*
86668 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
86701 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
86734 TGAAA
1 TGAAA
86739 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:86972 original size:22 final size:22
Alignment explanation
Indices: 86920--86974 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
86910 TGGTTGTGAG
**
86920 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
86942 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
86964 GGATTTCTTCG
1 GGATTTCTTCG
86975 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:87147 original size:20 final size:20
Alignment explanation
Indices: 87121--87274 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
87111 CTTTAAATAT
87121 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
87141 TGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
87163 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
87182 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
87202 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
87222 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
87242 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
87262 CGCGTTGCGATTT
1 CGCGTTGCGATTT
87275 TGATATTCGC
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:87248 original size:40 final size:40
Alignment explanation
Indices: 87120--87294 Score: 208
Period size: 40 Copynumber: 4.3 Consensus size: 40
87110 GCTTTAAATA
*
87120 TCGCGTTGCGATTTACGGATATGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTAT
** * * *
87161 TATCGTTGCGATTTACGGATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* * *
87201 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* ** *
87241 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT-TGATAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATG-TAT
87281 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
87295 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 2 0.02
40 83 0.73
41 28 0.25
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
Found at i:87295 original size:40 final size:39
Alignment explanation
Indices: 87120--87417 Score: 154
Period size: 40 Copynumber: 7.4 Consensus size: 39
87110 GCTTTAAATA
* *
87120 TCGCGTTGCGATTTACGGATAT-GCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTTCAGA-ATCGCGTTGCGA-TTT-TGTAT
** * * ** *
87161 TATCGTTGCGATTTAC-GGATACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTTCAGAAT-CGCGTTGCGAT-TTTGTAT
* * * * *
87201 ACACGTTGCGATTTAC-GGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTTCAGAAT-CGCGTTGCGATTT-TGTAT
* *
87241 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGATAT
1 TCGCGTTGCGATTTTCAGAATCGCGTTGCGATTTTG-TAT
* * ** *
87281 TCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTACT
1 TCGCGTTGCGATTTT-CAGAATCGCGTTGCGATTTTGTA-T
* * *
87322 ATCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAA
1 -TCGCGTTGCGATTTTC-AGAATCGCGTTGCGATTTTGTAT
* ** * ** * *
87363 ACTGATTTGCGATTCTGGGGATCGCGTTGCAATTTT-TATT
1 TC-GCGTTGCGATTTTCAGAATCGCGTTGCGATTTTGTA-T
87403 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
87418 GTTGGTCATT
Statistics
Matches: 197, Mismatches: 48, Indels: 26
0.73 0.18 0.10
Matches are distributed among these distances:
39 16 0.08
40 99 0.50
41 51 0.26
42 31 0.16
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (39 bp):
TCGCGTTGCGATTTTCAGAATCGCGTTGCGATTTTGTAT
Found at i:87296 original size:20 final size:20
Alignment explanation
Indices: 87222--87359 Score: 118
Period size: 20 Copynumber: 6.8 Consensus size: 20
87212 TTTACGGATA
*
87222 CGCGTTGCGATTTATG-TGTT
1 CGCGTTGCGATTT-TGATATT
*
87242 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTGATATT
87262 CGCGTTGCGATTTTGATATT
1 CGCGTTGCGATTTTGATATT
* *
87282 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT-GATATT
** *
87303 CGCAATGCGAATTTG-TACTAT
1 CGCGTTGCGATTTTGATA-T-T
* * * *
87324 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTT-GATATT
87345 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
87360 GAAACTGATT
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
19 2 0.02
20 50 0.53
21 42 0.44
23 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTTGATATT
Found at i:87311 original size:21 final size:21
Alignment explanation
Indices: 87261--87363 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
87251 ATTTTCATAT
* * *
87261 TCGCGTTGCGATTTT-GATAT
1 TCGCATTGCGATTTTGGAAAA
*
87281 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
87302 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
87323 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
87344 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
87364 CTGATTTGCG
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.25
21 47 0.72
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:91832 original size:24 final size:23
Alignment explanation
Indices: 91784--91834 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
91774 AGTCTGAAAT
**
91784 ATTTAGTTTATAAAATATATTAA
1 ATTTAGTTTATAAAATATACCAA
*
91807 ATTTTGTTTATAAATATATACCAA
1 ATTTAGTTTATAAA-ATATACCAA
91831 ATTT
1 ATTT
91835 GGCAGTCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTAGTTTATAAAATATACCAA
Found at i:104348 original size:2 final size:2
Alignment explanation
Indices: 104341--104374 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
104331 ATTATTAATA
*
104341 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104375 ATTTAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104706 original size:24 final size:24
Alignment explanation
Indices: 104679--104762 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
104669 AATACAAATG
* *
104679 AATGAACATAAAAGAACGGATGTA
1 AATGAACATAAAAGAACGAACGTA
* *
104703 AATGAACACAAACGAACGAACGTA
1 AATGAACATAAAAGAACGAACGTA
** * *
104727 AACAAACATAAATGAACGAACATA
1 AATGAACATAAAAGAACGAACGTA
104751 AATGAACATAAA
1 AATGAACATAAA
104763 CCACAACAAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.13
Consensus pattern (24 bp):
AATGAACATAAAAGAACGAACGTA
Found at i:104748 original size:14 final size:14
Alignment explanation
Indices: 104731--104757 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
104721 AACGTAAACA
104731 AACATAAATGAACG
1 AACATAAATGAACG
104745 AACATAAATGAAC
1 AACATAAATGAAC
104758 ATAAACCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:111124 original size:9 final size:9
Alignment explanation
Indices: 111107--111182 Score: 62
Period size: 9 Copynumber: 8.4 Consensus size: 9
111097 TGCCCAGCAG
111107 CAGCAACAA
1 CAGCAACAA
*
111116 CAACAACAA
1 CAGCAACAA
* * *
111125 CACCAGCAG
1 CAGCAACAA
* * *
111134 CAACACCAG
1 CAGCAACAA
* *
111143 CAGCAGCAG
1 CAGCAACAA
111152 CAGCAACAA
1 CAGCAACAA
111161 CAGCAACAA
1 CAGCAACAA
*
111170 CAGCAACAG
1 CAGCAACAA
111179 CAGC
1 CAGC
111183 CGCCACCGCA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.47, C:0.37, G:0.16, T:0.00
Consensus pattern (9 bp):
CAGCAACAA
Found at i:111137 original size:12 final size:12
Alignment explanation
Indices: 111104--111162 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
111094 GCATGCCCAG
*
111104 CAGCAGCAACAA
1 CAGCAGCAACAC
* *
111116 CAACAACAACAC
1 CAGCAGCAACAC
111128 CAGCAGCAACAC
1 CAGCAGCAACAC
* *
111140 CAGCAGCAGCAG
1 CAGCAGCAACAC
*
111152 CAGCAACAACA
1 CAGCAGCAACA
111163 GCAACAACAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.47, C:0.37, G:0.15, T:0.00
Consensus pattern (12 bp):
CAGCAGCAACAC
Found at i:112557 original size:24 final size:24
Alignment explanation
Indices: 112530--112580 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
112520 AATGAAGGTA
112530 TTAATGTCCCTATGAAGTGTGCTT
1 TTAATGTCCCTATGAAGTGTGCTT
112554 TTAATGTCCCTATGAAGTGTGCTT
1 TTAATGTCCCTATGAAGTGTGCTT
112578 TTA
1 TTA
112581 CCTTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TTAATGTCCCTATGAAGTGTGCTT
Done.