Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004457.1 Hibiscus syriacus cultivar Beakdansim tig00009816_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: 76242
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:14186 original size:22 final size:22
Alignment explanation
Indices: 14158--14242 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
14148 TTTTGGTGCA
14158 GAGGGAACCGATCCCCCCTCAT
1 GAGGGAACCGATCCCCCCTCAT
* *
14180 GAGGGAACCGATTCCCCCT-TT
1 GAGGGAACCGATCCCCCCTCAT
*
14201 GAAGGGGAACCGATTCCCCCCACA-
1 G-A-GGGAACCGA-TCCCCCCTCAT
* *
14225 G-GGGAATCGATACCCCCT
1 GAGGGAACCGATCCCCCCT
14243 GGGGTTCTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
20 6 0.12
21 10 0.20
22 19 0.37
23 9 0.18
24 7 0.14
ACGTcount: A:0.24, C:0.36, G:0.25, T:0.15
Consensus pattern (22 bp):
GAGGGAACCGATCCCCCCTCAT
Found at i:14208 original size:23 final size:22
Alignment explanation
Indices: 14158--14220 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
14148 TTTTGGTGCA
*
14158 GAGGGAACCGATCCCCCCTCAT
1 GAGGGAACCGATTCCCCCTCAT
*
14180 GAGGGAACCGATTCCCCCT-TT
1 GAGGGAACCGATTCCCCCTCAT
14201 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
14221 CACAGGGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 2 0.05
22 19 0.51
23 16 0.43
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCTCAT
Found at i:14229 original size:21 final size:21
Alignment explanation
Indices: 14160--14241 Score: 69
Period size: 23 Copynumber: 3.8 Consensus size: 21
14150 TTGGTGCAGA
*
14160 GGGAACCGA-TCCCCCCTCATG
1 GGGAACCGATTCCCCCCACA-G
*
14181 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
14205 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
14226 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
14242 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 16 0.32
22 9 0.18
23 22 0.44
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:19713 original size:33 final size:33
Alignment explanation
Indices: 19661--19982 Score: 286
Period size: 33 Copynumber: 9.9 Consensus size: 33
19651 GTAATGAATA
* *
19661 TATCATAACAT-AAGTTTTCATGGAAAGAAATTC
1 TATCATAACATGAA-CTTTCATGGAAAGAAATTG
* *
19694 TATCATACCATGAACTTTCAT-GACAA-AAACTTA
1 TATCATAACATGAACTTTCATGGA-AAGAAA-TTG
* * *
19727 TATTATAACATGAACTGTCAT-GACAA-AAAGTTAA
1 TATCATAACATGAACTTTCATGGA-AAGAAA-TT-G
* * * *
19761 TACCATAACATGAACTTTCATAGCAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* *
19794 TATCATAACATGAACTTTCACGGAAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* * * *
19827 TACCATAACATGAACTTCCATGGTAAGAAATAG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* * * * *
19860 TATCTTAACATGAACGTTCATGGCAAGTACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
*
19893 --T-AT--CATGAACTTTCATGGAAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* *
19921 TATCACAACATGAACTTTCATGAAAAGAAATTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
*
19954 TATCATAACATGAACTTTCATGGCAAGAA
1 TATCATAACATGAACTTTCATGGAAAGAA
19983 CTTTTATAAC
Statistics
Matches: 237, Mismatches: 41, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
28 22 0.09
30 2 0.01
31 2 0.01
32 5 0.02
33 178 0.75
34 25 0.11
35 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (33 bp):
TATCATAACATGAACTTTCATGGAAAGAAATTG
Found at i:19808 original size:18 final size:17
Alignment explanation
Indices: 19764--19811 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
19754 AAGTTAATAC
19764 CATAACATGAAC-TT-T
1 CATAACATGAACTTTAT
* *
19779 CATAGCAAGAACTTGTAT
1 CATAACATGAACTT-TAT
19797 CATAACATGAACTTT
1 CATAACATGAACTTT
19812 CACGGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 2 0.08
18 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (17 bp):
CATAACATGAACTTTAT
Found at i:19855 original size:66 final size:66
Alignment explanation
Indices: 19661--19985 Score: 324
Period size: 66 Copynumber: 5.0 Consensus size: 66
19651 GTAATGAATA
* * * * * *
19661 TATCATAACAT-AAGTTTTCATGGAAAGAAATTCTATCATACCATGAACTTTCATGACAAAAACT
1 TATCATAACATGAA-CTTTCATGGAAAGAAATTGTACCATAACATGAACTTTCATGGCAAGAACT
*
19725 TA
65 TG
* * * *
19727 TATTATAACATGAACTGTCAT-GACAA-AAAGTTAATACCATAACATGAACTTTCATAGCAAGAA
1 TATCATAACATGAACTTTCATGGA-AAGAAA-TT-GTACCATAACATGAACTTTCATGGCAAGAA
19790 CTTG
63 CTTG
* * * * * *
19794 TATCATAACATGAACTTTCACGGAAAGAACTTGTACCATAACATGAACTTCCATGGTAAGAAATA
1 TATCATAACATGAACTTTCATGGAAAGAAATTGTACCATAACATGAACTTTCATGGCAAGAACTT
19859 G
66 G
* * * * * *
19860 TATCTTAACATGAACGTTCATGGCAAGTACTTGT---AT--CATGAACTTTCATGGAAAGAACTT
1 TATCATAACATGAACTTTCATGGAAAGAAATTGTACCATAACATGAACTTTCATGGCAAGAACTT
19920 G
66 G
* * *
19921 TATCACAACATGAACTTTCATGAAAAGAAATTGTATCATAACATGAACTTTCATGGCAAGAACTT
1 TATCATAACATGAACTTTCATGGAAAGAAATTGTACCATAACATGAACTTTCATGGCAAGAACTT
19986 TTATAACATA
Statistics
Matches: 211, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
61 48 0.23
63 2 0.01
64 2 0.01
65 5 0.02
66 99 0.47
67 51 0.24
68 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (66 bp):
TATCATAACATGAACTTTCATGGAAAGAAATTGTACCATAACATGAACTTTCATGGCAAGAACTT
G
Found at i:19900 original size:28 final size:28
Alignment explanation
Indices: 19868--19925 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
19858 AGTATCTTAA
* *
19868 CATGAACGTTCATGGCAAGTACTTGTAT
1 CATGAACGTTCATGGAAAGAACTTGTAT
*
19896 CATGAACTTTCATGGAAAGAACTTGTAT
1 CATGAACGTTCATGGAAAGAACTTGTAT
19924 CA
1 CA
19926 CAACATGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (28 bp):
CATGAACGTTCATGGAAAGAACTTGTAT
Found at i:19931 original size:94 final size:97
Alignment explanation
Indices: 19764--19985 Score: 306
Period size: 94 Copynumber: 2.3 Consensus size: 97
19754 AAGTTAATAC
*
19764 CATAACATGAACTTTCATAGCAAGAACTTGTATCATAACATGAACTTTCACGGAAAGAACTTGTA
1 CATAACATGAACTTTCATGGCAAGAACTTG-ATCAT-ACATGAACTTTCACGGAAAGAACTTGTA
* **
19829 CCATAACATGAACTTCCATGGTAAGAAATAGTAT
64 CCACAACATGAACTTCCATGAAAAGAAATAGTAT
* * * * *
19863 CTTAACATGAACGTTCATGGCAAGTACTTG-T-AT-CATGAACTTTCATGGAAAGAACTTGTATC
1 CATAACATGAACTTTCATGGCAAGAACTTGATCATACATGAACTTTCACGGAAAGAACTTGTACC
* *
19925 ACAACATGAACTTTCATGAAAAGAAATTGTAT
66 ACAACATGAACTTCCATGAAAAGAAATAGTAT
19957 CATAACATGAACTTTCATGGCAAGAACTT
1 CATAACATGAACTTTCATGGCAAGAACTT
19986 TTATAACATA
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
94 80 0.73
96 2 0.02
97 1 0.01
99 26 0.24
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (97 bp):
CATAACATGAACTTTCATGGCAAGAACTTGATCATACATGAACTTTCACGGAAAGAACTTGTACC
ACAACATGAACTTCCATGAAAAGAAATAGTAT
Found at i:20371 original size:24 final size:25
Alignment explanation
Indices: 20337--20412 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
20327 TTATATCTCA
20337 TGAAA-TAACACATATTTACACAAG
1 TGAAAGTAACACATATTTACACAAG
* *
20361 T-AAAGTAACACATAATTCCACAAG
1 TGAAAGTAACACATATTTACACAAG
* *
20385 TGAAATTAACACGTATCTTAC-CAA-
1 TGAAAGTAACACATAT-TTACACAAG
20409 TGAA
1 TGAA
20413 CTTATGATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.07
24 23 0.53
25 14 0.33
26 3 0.07
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.25
Consensus pattern (25 bp):
TGAAAGTAACACATATTTACACAAG
Found at i:25670 original size:40 final size:42
Alignment explanation
Indices: 25597--25680 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
25587 GAAAAATATA
*
25597 TATATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
25639 TATATATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
25679 TA
1 TA
25681 CCCTCTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 12 0.31
41 7 0.18
42 20 0.51
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (42 bp):
TATATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:25893 original size:8 final size:8
Alignment explanation
Indices: 25866--25895 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
25856 TATAATAATG
25866 AATAAAAA
1 AATAAAAA
25874 AATGAAAAA
1 AAT-AAAAA
25883 AATAAAAA
1 AATAAAAA
25891 AATAA
1 AATAA
25896 CATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:26186 original size:18 final size:17
Alignment explanation
Indices: 26165--26207 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
26155 ATATATACGT
26165 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
26183 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
26200 ATAA-AATA
1 ATAATAATA
26208 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:27621 original size:106 final size:106
Alignment explanation
Indices: 27436--28189 Score: 942
Period size: 106 Copynumber: 7.0 Consensus size: 106
27426 GTATTGTTCC
* * * **
27436 GAGTCCAATATCCTCCG-TCATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACA
* * *
27500 ACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
* * **
27542 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
* * * *
27607 CCAGTCGTCCCTTCGTTGTGAATTTTAACTTGTGTCGTCTT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
* *
27648 GAGTCCAATATCCTTCGCTGTGAAGTTAAAACTGGCTCTGAAACT--GAAAGTGGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAA-TGGTTTGTTGACA
* * *
27711 ACCAGTCGTCCATTCGTTGTGAAATTGAACTTGTGTTGTCTT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
* * *
27753 GAGTCCAATATCCTTCGCTATGAAGTTAAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAA-TGGTTTGTTGACA
*
27818 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
** *
27860 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCACTCTGAATGAAACT-GAAAACTGGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TGGTTTGTT
* * *
27924 GACAACCAGCCGTCTCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
* * * * *
27970 GAGTCCAATATCCTTCACTTTGAAGTTGAAATTGGCTCTGAAATTGGGTAATGGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
* *
28035 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
* *
28076 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTGGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TGGTTTGTT
* * * * * *
28140 GAAAATCAGTCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTC
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
28186 GAGT
1 GAGT
28190 GGCGCGATAT
Statistics
Matches: 574, Mismatches: 60, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
104 4 0.01
105 92 0.16
106 229 0.40
107 92 0.16
109 3 0.01
110 147 0.26
111 7 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
Found at i:28086 original size:216 final size:216
Alignment explanation
Indices: 27490--28189 Score: 1014
Period size: 216 Copynumber: 3.3 Consensus size: 216
27480 TGGGAAATTA
* * * * *
27490 TTTGTTGACAACCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
* * * *
27555 TTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGACAACCAGTCGTCCCTT
66 TTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATGATTTGTTGACAACCAGCCGTCCCTT
* * * * * *
27620 CGTTGTGAATTTTAACTTGTGTCGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTAAAACTGGCT
131 CGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT
27685 C----TGAAACTG-AAAGTGG
196 CTGAATGAAACTGAAAAGTGG
* * * * *
27701 TTTGTTGACAACCAGTCGTCCATTCGTTGTGAAATTGAACTTGTGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
* * * *
27766 TTCGCTATGAAGTTAAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGACAACCAGCTGTCCCT
66 TTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGATTTGTTGACAACCAGCCGTCCCT
*
27831 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTCAC
130 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGAC
*
27896 TCTGAATGAAACTGAAAACTGG
195 TCTGAATGAAACTGAAAAGTGG
*
27918 TTTGTTGACAACCAGCCGTCTCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
1 TTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
* * * * * *
27983 TTCACTTTGAAGTTGAAATTGGCTCTGAAATTGGGTAATGGTTTGTTGATAACCAACCGTCCCTT
66 TTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATGATTTGTTGACAACCAGCCGTCCCTT
*
28048 CGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT
131 CGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT
28113 CTGAATGAAACTGAAAAGTGG
196 CTGAATGAAACTGAAAAGTGG
* * * *
28134 TTTGTTGAAAATCAGTCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTCGAGT
1 TTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGT
28190 GGCGCGATAT
Statistics
Matches: 438, Mismatches: 45, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
211 93 0.21
212 82 0.19
216 165 0.38
217 98 0.22
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (216 bp):
TTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
TTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATGATTTGTTGACAACCAGCCGTCCCTT
CGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACT
CTGAATGAAACTGAAAAGTGG
Found at i:29001 original size:36 final size:36
Alignment explanation
Indices: 28952--29023 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
28942 CAATTTCAAC
* *
28952 AGTTTTTTCCAAGGGAAACTGTCTCAATAGAGACAA
1 AGTTTTTTCCAAGGGAAACTGTCTCAAAAAAGACAA
28988 AGTTTGTTT-CAAGGGAAACTGTCTCAAAAAAGACAA
1 AGTTT-TTTCCAAGGGAAACTGTCTCAAAAAAGACAA
29024 TAGTGAGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 30 0.91
37 3 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (36 bp):
AGTTTTTTCCAAGGGAAACTGTCTCAAAAAAGACAA
Found at i:48874 original size:50 final size:51
Alignment explanation
Indices: 48777--48875 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
48767 GCATGAATCA
* *
48777 ATCTCCCTTTGGCTGAATAGTGATATGTTGGTTCATATTGGTACCAAAGGT
1 ATCTCCCTTTGGCTGAATAGTGATATGATGGTTCATATTGGCACCAAAGGT
* * *
48828 ATCTCCC-TTGGCTGAAT-GATGTTGTGATGGTTCATATTGGCGCCAAAG
1 ATCTCCCTTTGGCTGAATAG-TGATATGATGGTTCATATTGGCACCAAAG
48876 TCTTCATGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.02
50 34 0.81
51 7 0.17
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (51 bp):
ATCTCCCTTTGGCTGAATAGTGATATGATGGTTCATATTGGCACCAAAGGT
Found at i:49083 original size:20 final size:20
Alignment explanation
Indices: 49058--49095 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49048 CTTTCATGTT
*
49058 TGAGCTAGTTATAAGGTGAA
1 TGAGCTAGATATAAGGTGAA
*
49078 TGAGCTGGATATAAGGTG
1 TGAGCTAGATATAAGGTG
49096 GCCATAGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (20 bp):
TGAGCTAGATATAAGGTGAA
Found at i:49584 original size:2 final size:2
Alignment explanation
Indices: 49577--49622 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
49567 ATAGATGTAG
49577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49619 TA TA
1 TA TA
49623 GAATATAGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58091 original size:20 final size:21
Alignment explanation
Indices: 58053--58092 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58043 CAGCTTGCTC
58053 AGGGGGAACCGATTCCCCCCA
1 AGGGGGAACCGATTCCCCCCA
*
58074 AGGGGGTACCGATTCCCCC
1 AGGGGGAACCGATTCCCCC
58093 TGAATGGTTT
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:0.20, C:0.38, G:0.30, T:0.12
Consensus pattern (21 bp):
AGGGGGAACCGATTCCCCCCA
Found at i:63927 original size:21 final size:21
Alignment explanation
Indices: 63860--63939 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
63850 TTGGTGCAGA
* *
63860 GGGAACCGA-TCCCCCCTCATA
1 GGGAACCGATTCCCCCCACA-G
**
63881 GGGAACCGATTCCCCTTTGA-AG
1 GGGAACCGATTCCCC--CCACAG
63903 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
63924 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
63940 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
22 20 0.43
23 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:64343 original size:24 final size:26
Alignment explanation
Indices: 64299--64346 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
64289 AGAATTTTCC
*
64299 AAAATTTTAAATTTTCGAAATTATAA
1 AAAATGTTAAATTTTCGAAATTATAA
64325 AAAATGTT-AATTTTC-AAATTAT
1 AAAATGTTAAATTTTCGAAATTAT
64347 TGTGTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 7 0.33
26 7 0.33
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (26 bp):
AAAATGTTAAATTTTCGAAATTATAA
Found at i:69358 original size:33 final size:33
Alignment explanation
Indices: 69306--69625 Score: 268
Period size: 33 Copynumber: 9.9 Consensus size: 33
69296 GTAATGAATA
* *
69306 TATCATAACAT-AAGTTTTCATGGAAAGAAATTC
1 TATCATAACATGAA-CTTTCATGGAAAGAAATTG
* *
69339 TATCATACCATGAACTTTCAT-GACAA-AAACTTA
1 TATCATAACATGAACTTTCATGGA-AAGAAA-TTG
* * *
69372 TATTATAACATGAACTGTCAT-GACAA-AAAGTTAA
1 TATCATAACATGAACTTTCATGGA-AAGAAA-TT-G
* * * *
69406 TACCATAACATGAACTTTCATAGCAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* *
69439 TATCATAACATGAACTTTCACGGAAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* * * *
69472 TACCATAACATGAACTTCCATGGTAAGAAATAG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* * * * *
69505 TATCTTAACATGAACGTTCATGGCAAGTACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
*
69538 --T-AT--CATGAACTTTCATGGAAAGAACTTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
* *
69566 TATCA-CACATGAACTTTCATGAAAAG-AATTG
1 TATCATAACATGAACTTTCATGGAAAGAAATTG
*
69597 TATCATAACATGAACTTTCATGGCAAGAA
1 TATCATAACATGAACTTTCATGGAAAGAA
69626 CTTTTATAAC
Statistics
Matches: 234, Mismatches: 40, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
28 22 0.09
30 2 0.01
31 11 0.05
32 41 0.18
33 130 0.56
34 25 0.11
35 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (33 bp):
TATCATAACATGAACTTTCATGGAAAGAAATTG
Found at i:69437 original size:67 final size:66
Alignment explanation
Indices: 69342--69493 Score: 173
Period size: 67 Copynumber: 2.3 Consensus size: 66
69332 GAAATTCTAT
* * * *
69342 CATACCATGAACTTTCATGACAAAAACTTATATTATAACATGAACTGTCA-TGACAAAAAGTTAA
1 CATAACATGAACTTTCATGACAAAAACTTATATCATAACATGAACTGTCACGGA-AAAAACTT-A
69406 TAC
64 TAC
* * * * *
69409 CATAACATGAACTTTCAT-AGCAAGAACTTGTATCATAACATGAACTTTCACGGAAAGAACTTGT
1 CATAACATGAACTTTCATGA-CAAAAACTTATATCATAACATGAACTGTCACGGAAAAAACTTAT
69473 AC
65 AC
*
69475 CATAACATGAACTTCCATG
1 CATAACATGAACTTTCATG
69494 GTAAGAAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
66 21 0.29
67 49 0.68
68 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (66 bp):
CATAACATGAACTTTCATGACAAAAACTTATATCATAACATGAACTGTCACGGAAAAAACTTATA
C
Found at i:69453 original size:18 final size:17
Alignment explanation
Indices: 69409--69456 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
69399 AAGTTAATAC
69409 CATAACATGAAC-TT-T
1 CATAACATGAACTTTAT
* *
69424 CATAGCAAGAACTTGTAT
1 CATAACATGAACTT-TAT
69442 CATAACATGAACTTT
1 CATAACATGAACTTT
69457 CACGGAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 2 0.08
18 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (17 bp):
CATAACATGAACTTTAT
Found at i:69500 original size:66 final size:66
Alignment explanation
Indices: 69306--69628 Score: 313
Period size: 66 Copynumber: 5.0 Consensus size: 66
69296 GTAATGAATA
* * * * * * *
69306 TATCATAACAT-AAGTTTTCATGGAAAGAAATTCTATCATACCATGAACTTTCATGACAAAAACT
1 TATCATAACATGAA-CTTTCATGGAAAGAACTTGTACCATAACATGAACTTTCATGGCAAGAACT
*
69370 TA
65 TG
* * * * * *
69372 TATTATAACATGAACTGTCAT-GACAAAAAGTTAATACCATAACATGAACTTTCATAGCAAGAAC
1 TATCATAACATGAACTTTCATGGA-AAGAACTT-GTACCATAACATGAACTTTCATGGCAAGAAC
69436 TTG
64 TTG
* * * * *
69439 TATCATAACATGAACTTTCACGGAAAGAACTTGTACCATAACATGAACTTCCATGGTAAGAAATA
1 TATCATAACATGAACTTTCATGGAAAGAACTTGTACCATAACATGAACTTTCATGGCAAGAACTT
69504 G
66 G
* * * * *
69505 TATCTTAACATGAACGTTCATGGCAAGTACTTGT---AT--CATGAACTTTCATGGAAAGAACTT
1 TATCATAACATGAACTTTCATGGAAAGAACTTGTACCATAACATGAACTTTCATGGCAAGAACTT
69565 G
66 G
* * *
69566 TATCA-CACATGAACTTTCATGAAAAGAA-TTGTATCATAACATGAACTTTCATGGCAAGAACTT
1 TATCATAACATGAACTTTCATGGAAAGAACTTGTACCATAACATGAACTTTCATGGCAAGAACTT
69629 TTATAACATA
Statistics
Matches: 209, Mismatches: 39, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
59 4 0.02
60 18 0.09
61 25 0.12
62 2 0.01
63 2 0.01
64 23 0.11
65 2 0.01
66 78 0.37
67 53 0.25
68 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (66 bp):
TATCATAACATGAACTTTCATGGAAAGAACTTGTACCATAACATGAACTTTCATGGCAAGAACTT
G
Found at i:69545 original size:28 final size:28
Alignment explanation
Indices: 69513--69602 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
69503 AGTATCTTAA
* *
69513 CATGAACGTTCATGGCAAGTACTTGTAT
1 CATGAACGTTCATGGAAAGAACTTGTAT
*
69541 CATGAACTTTCATGGAAAGAACTTGTAT
1 CATGAACGTTCATGGAAAGAACTTGTAT
* *
69569 CACACATGAACTTTCATGAAAAGAA-TTGTAT
1 ----CATGAACGTTCATGGAAAGAACTTGTAT
69600 CAT
1 CAT
69603 AACATGAACT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.06
28 25 0.46
31 6 0.11
32 20 0.37
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (28 bp):
CATGAACGTTCATGGAAAGAACTTGTAT
Found at i:70009 original size:24 final size:25
Alignment explanation
Indices: 69975--70050 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
69965 TTATATCTCA
69975 TGAAA-TAACACATATTTACACAAG
1 TGAAAGTAACACATATTTACACAAG
* *
69999 T-AAAGTAACACATAATTCCACAAG
1 TGAAAGTAACACATATTTACACAAG
* *
70023 TGAAATTAACACGTATCTTAC-CAA-
1 TGAAAGTAACACATAT-TTACACAAG
70047 TGAA
1 TGAA
70051 CTTATGATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.07
24 23 0.53
25 14 0.33
26 3 0.07
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.25
Consensus pattern (25 bp):
TGAAAGTAACACATATTTACACAAG
Found at i:75236 original size:39 final size:38
Alignment explanation
Indices: 75190--75268 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
75180 AAATGAAAAA
*
75190 TATATATATATACATCAAAGTA-TTAATAAATA-AATAAGC
1 TATATATATATACAACAAA-TATTTAA-AAATAGAA-AAGC
75229 TATATATATATACAACAAATATTTAAAAATAGAAAAGC
1 TATATATATATACAACAAATATTTAAAAATAGAAAAGC
75267 TA
1 TA
75269 CCCTCTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 13 0.35
39 24 0.65
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.32
Consensus pattern (38 bp):
TATATATATATACAACAAATATTTAAAAATAGAAAAGC
Done.