Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001217.1 Hibiscus syriacus cultivar Beakdansim tig00002404_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: 69073
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1786 original size:42 final size:42
Alignment explanation
Indices: 1679--1965 Score: 199
Period size: 42 Copynumber: 6.7 Consensus size: 42
1669 AAAAATTGTA
* * * *
1679 ATTGAAAAAATTAGAGGTCTCAATTATAAAAGTAAAAAAAATAAG
1 ATTGAAAAAATTAGGGGCCTTAATTATAAAAGT--AAAAAGT-AG
* * *
1724 ATTGAAAAAAATAGGTGCCTTAATTATAAAAGTAAAAAGTACT
1 ATTGAAAAAATTAGGGGCCTTAATTATAAAAGTAAAAAGTA-G
* *
1767 ATTG-AAAAATTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAG
1 ATTGAAAAAATTAGGGGCCTTAATTATAAAAGTAAAAAGT-AG
* * * * *
1809 ATT-AAAAAACTA-GGGCCTTTATTAT-AAGGTAGAAAGTGAA
1 ATTGAAAAAATTAGGGGCCTTAATTATAAAAGTAAAAAGT-AG
* * *** *
1849 ATTAAAAAGAATTAGAGATATTAATTATAAAGGTAAAAAGTGAG
1 ATTGAAAA-AATTAGGGGCCTTAATTATAAAAGTAAAAAGT-AG
* * * * *
1893 ATTGAAAAAAATGAGAGACCTTAATTATAAAGGTAAAATGTAAG
1 ATTG-AAAAAATTAGGGGCCTTAATTATAAAAGTAAAAAGT-AG
*
1937 ATTGAAAAAAGTAGGGGTCC--AATTATAAA
1 ATTGAAAAAATTAGGGG-CCTTAATTATAAA
1966 GATAAATGTG
Statistics
Matches: 198, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
40 16 0.08
41 15 0.08
42 55 0.28
43 28 0.14
44 52 0.26
45 32 0.16
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (42 bp):
ATTGAAAAAATTAGGGGCCTTAATTATAAAAGTAAAAAGTAG
Found at i:1853 original size:40 final size:42
Alignment explanation
Indices: 1728--1953 Score: 147
Period size: 44 Copynumber: 5.3 Consensus size: 42
1718 AATAAGATTG
* * * * *
1728 AAAAAAATAGGTGCCTTAATTATAAAAGTAAAAAGT-ACTATT
1 AAAAAACTAGGGGCCTTAGTTATAAAGGTAAAAAGTGA-AATT
* * *
1770 GAAAAATTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAGATT
1 AAAAAACTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAAATT
*
1812 AAAAAACTA-GGGCCTTTA-TTAT-AAGGTAGAAAGTGAAATT
1 AAAAAACTAGGGGCC-TTAGTTATAAAGGTAAAAAGTGAAATT
* * *** * *
1852 AAAAAGAATTAGAGATATTAATTATAAAGGTAAAAAGTGAGATT
1 -AAAA-AACTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAAATT
* * * * *
1896 GAAAAAAATGAGAGACCTTAATTATAAAGGTAAAATGT-AAGATT
1 -AAAAAACT-AGGGGCCTTAGTTATAAAGGTAAAAAGTGAA-ATT
*
1940 GAAAAAAGTAGGGG
1 -AAAAAACTAGGGG
1954 TCCAATTATA
Statistics
Matches: 149, Mismatches: 26, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
40 16 0.11
41 13 0.09
42 51 0.34
43 13 0.09
44 56 0.38
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAACTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAAATT
Found at i:1889 original size:44 final size:42
Alignment explanation
Indices: 1789--2117 Score: 195
Period size: 44 Copynumber: 7.7 Consensus size: 42
1779 GGGGCCTTAG
* * *
1789 TTATAAAGGTAAAAAGTGAGATT-AAAAAACTAGGGCCTTT-A
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAG-ATTTAA
* *
1830 TTAT-AAGGTAGAAAGTGAAATTAAAAAGAATTAGAGATATTAA
1 TTATAAAGGTAAAAAGTGAGATTAAAAA-AATTAGAGAT-TTAA
* *
1873 TTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGAGACCTTAA
1 TTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGAGA-TTTAA
* * * * * * **
1917 TTATAAAGGTAAAATGTAAGATTGAAAAAAGTAGGGGTCCAA
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGATTTAA
* * * * *
1959 TTATAAAGAT-AAATGTGAGATTACAAAAATTA-AGGGTTTCAC
1 TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGA-GATTT-AA
* * * *
2001 TTATAAAGATAGAAAA-TGAAATTTAAAAAAATTAGAGACATCAA
1 TTATAAAGGTA-AAAAGTGAGA-TTAAAAAAATTAGAGA-TTTAA
* * * * *
2045 TTATAAAGATTAAAAAATAAGATT-AAAAAATTAGAGACATCAA
1 TTATAAAG-GTAAAAAGTGAGATTAAAAAAATTAGAGA-TTTAA
* * * *
2088 TTATGAAGATTAAAAAATAAGATTAAAAAA
1 TTATAAAG-GTAAAAAGTGAGATTAAAAAA
2118 TAAGATTAAA
Statistics
Matches: 232, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
40 16 0.07
41 30 0.13
42 30 0.13
43 60 0.26
44 84 0.36
45 12 0.05
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.26
Consensus pattern (42 bp):
TTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGATTTAA
Found at i:1987 original size:41 final size:42
Alignment explanation
Indices: 1915--2011 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1905 GAGAGACCTT
*
1915 AATTATAAAGGTAAAATGTAAGATTGAAAAAAGT-AGGGGTCC
1 AATTATAAAGAT-AAATGTAAGATTGAAAAAAGTAAGGGGTCC
* * * *
1957 AATTATAAAGATAAATGTGAGATT-ACAAAAATTAAGGGTTTC
1 AATTATAAAGATAAATGTAAGATTGA-AAAAAGTAAGGGGTCC
*
1999 ACTTATAAAGATA
1 AATTATAAAGATA
2012 GAAAATGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 17 0.36
42 29 0.62
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (42 bp):
AATTATAAAGATAAATGTAAGATTGAAAAAAGTAAGGGGTCC
Found at i:1990 original size:128 final size:127
Alignment explanation
Indices: 1743--2074 Score: 304
Period size: 128 Copynumber: 2.6 Consensus size: 127
1733 AATAGGTGCC
* * * * *
1743 TTAATTATAAAAGTAAAAAGT-ACTATTG--AAAAATTAGGGGCCTTAGTTATAAAGGTAAAAAG
1 TTAATTATAAAGGTAAAAAGTGA-AATTGAAAAAAATTAGAGACCTTAATTATAAAGGTAAAAAG
* * *
1805 TGAGATTAAAAAACTAGGGCCTTTATTATAAGGTAGAAAGTGAAATTAAAAAGAATT-AGAGAT
65 TAAGATTAAAAAACTAGGGCCATTATTATAAGATAGAAAGTGAAATTAAAAAGAATTAAG-GAT
* * *
1868 ATTAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGAGACCTTAATTATAAAGGTAAAATG
1 -TTAATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGAGACCTTAATTATAAAGGTAAAAAG
* * * *
1933 TAAGATTGAAAAAAGTAGGGGTCCA--ATTATAAAGATA-AATGTGAGATTACAAA-AATTAAGG
65 TAAGATT-AAAAAACTA-GGG-CCATTATTAT-AAGATAGAAAGTGAAATTAAAAAGAATTAAGG
*
1994 GT
126 AT
* * * * * *
1996 TTCACTTATAAAGATAGAAAA-TGAAATTTAAAAAAATTAGAGACATCAATTATAAAGATTAAAA
1 TT-AATTATAAAGGTA-AAAAGTGAAATTGAAAAAAATTAGAGACCTTAATTATAAAG-GTAAAA
*
2060 AATAAGATTAAAAAA
63 AGTAAGATTAAAAAA
2075 TTAGAGACAT
Statistics
Matches: 170, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
126 24 0.14
127 3 0.02
128 89 0.52
129 44 0.26
130 8 0.05
131 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.27
Consensus pattern (127 bp):
TTAATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGAGACCTTAATTATAAAGGTAAAAAGT
AAGATTAAAAAACTAGGGCCATTATTATAAGATAGAAAGTGAAATTAAAAAGAATTAAGGAT
Found at i:2066 original size:13 final size:13
Alignment explanation
Indices: 2050--2136 Score: 93
Period size: 13 Copynumber: 6.4 Consensus size: 13
2040 ATCAATTATA
2050 AAGATTAAAAAAT
1 AAGATTAAAAAAT
2063 AAGATTAAAAAATT
1 AAGATTAAAAAA-T
* * **
2077 AGAGACATCAATTAT
1 A-AGA-TTAAAAAAT
2092 GAAGATTAAAAAAT
1 -AAGATTAAAAAAT
2106 AAGATTAAAAAAT
1 AAGATTAAAAAAT
2119 AAGATTAAAAAAT
1 AAGATTAAAAAAT
*
2132 TAGAT
1 AAGAT
2137 AACCTGAACA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
13 42 0.69
14 7 0.11
15 7 0.11
16 5 0.08
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.25
Consensus pattern (13 bp):
AAGATTAAAAAAT
Found at i:2078 original size:43 final size:43
Alignment explanation
Indices: 2001--2118 Score: 177
Period size: 43 Copynumber: 2.7 Consensus size: 43
1991 AGGGTTTCAC
*
2001 TTATAAAGA-TAGAAAATGAA-ATTTAAAAAAATTAGAGACATCAA
1 TTATAAAGATTAAAAAAT-AAGA-TT-AAAAAATTAGAGACATCAA
2045 TTATAAAGATTAAAAAATAAGATTAAAAAATTAGAGACATCAA
1 TTATAAAGATTAAAAAATAAGATTAAAAAATTAGAGACATCAA
*
2088 TTATGAAGATTAAAAAATAAGATTAAAAAAT
1 TTATAAAGATTAAAAAATAAGATTAAAAAAT
2119 AAGATTAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
43 49 0.70
44 13 0.19
45 8 0.11
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.26
Consensus pattern (43 bp):
TTATAAAGATTAAAAAATAAGATTAAAAAATTAGAGACATCAA
Found at i:9395 original size:21 final size:21
Alignment explanation
Indices: 9356--9397 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9346 ATTTATCATG
*
9356 CTGTTGATCTAGCTTATCTTT
1 CTGTTGATCTAGCTCATCTTT
*
9377 CTGTTGATCTTGCTCATCTTT
1 CTGTTGATCTAGCTCATCTTT
9398 AAGTCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.14, T:0.52
Consensus pattern (21 bp):
CTGTTGATCTAGCTCATCTTT
Found at i:18898 original size:21 final size:21
Alignment explanation
Indices: 18872--18934 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
18862 ATTTATCGTG
*
18872 CTGTTGATCTTGCACATCTTT
1 CTGTTGATCTTGCTCATCTTT
18893 CTGTTGATCTTGCTCATCTTT
1 CTGTTGATCTTGCTCATCTTT
18914 CTGTTGATCTTGCTCATCTTT
1 CTGTTGATCTTGCTCATCTTT
18935 GAGTCTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.11, C:0.24, G:0.14, T:0.51
Consensus pattern (21 bp):
CTGTTGATCTTGCTCATCTTT
Found at i:28737 original size:19 final size:19
Alignment explanation
Indices: 28699--28755 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
28689 TTCGAGAATG
28699 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
28719 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
28738 AAAATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAT
28756 GCGATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:28779 original size:19 final size:19
Alignment explanation
Indices: 28755--28933 Score: 164
Period size: 19 Copynumber: 9.8 Consensus size: 19
28745 CAACGCGAAA
28755 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
28774 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
28793 TGCGATTTTTATTTCGCGGT
1 TGCGATTTTCATTTCGC-GT
28813 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
28832 TGCGA--TT-GTTT-G-GT
1 TGCGATTTTCATTTCGCGT
* *
28846 CGCGATAGTT-ATTTCGCGT
1 TGCGAT-TTTCATTTCGCGT
*
28865 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
28879 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
* *
28899 TGCGATTCTCATTATCTCGT
1 TGCGATTTTCATT-TCGCGT
28919 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
28934 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 13, Indels: 28
0.76 0.07 0.16
Matches are distributed among these distances:
14 16 0.12
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 51 0.38
20 49 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:28826 original size:39 final size:38
Alignment explanation
Indices: 28755--28933 Score: 164
Period size: 33 Copynumber: 4.9 Consensus size: 38
28745 CAACGCGAAA
28755 TGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGT
*
28793 TGCGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGC-GTTGCGATTTTCATTTCGCGT
* * *
28832 TGCGA--TT-GTTT-G-GTCGCGATAGTT-ATTTCGCGT
1 TGCGATTTTCATTTCGCGTTGCGAT-TTTCATTTCGCGT
* **
28865 TGCGA--TTC---TCTCGTTGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCATTT-CGCGT
* *
28899 TGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 TGCGATTTTCATT-TCGCGTTGCGATTTTCATTTC
28934 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 11, Indels: 25
0.76 0.07 0.16
Matches are distributed among these distances:
31 1 0.01
32 1 0.01
33 34 0.29
34 12 0.10
35 1 0.01
36 5 0.04
37 2 0.02
38 16 0.14
39 27 0.23
40 18 0.15
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (38 bp):
TGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGT
Found at i:28910 original size:20 final size:20
Alignment explanation
Indices: 28876--28933 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28866 GCGATTCTCT
**
28876 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
28896 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
28916 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
28934 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:30997 original size:42 final size:42
Alignment explanation
Indices: 30937--31059 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
30927 GCCTGACTCG
* * *
30937 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
30979 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
31021 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
31060 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:31017 original size:21 final size:21
Alignment explanation
Indices: 30993--31059 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30983 TCATTCCTCG
30993 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
31014 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
31035 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
31056 AGAG
1 AGAG
31060 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:32439 original size:14 final size:15
Alignment explanation
Indices: 32419--32455 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
32409 TATTGTTTAA
32419 TTGATTTGTAAAAAG
1 TTGATTTGTAAAAAG
*
32434 -TGATTTG-CAAAAG
1 TTGATTTGTAAAAAG
32447 TTGATTTGT
1 TTGATTTGT
32456 TTAATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (15 bp):
TTGATTTGTAAAAAG
Found at i:32656 original size:19 final size:19
Alignment explanation
Indices: 32634--32731 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
32624 CGAAATTAAA
*
32634 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32653 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
32669 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32686 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
32701 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
32719 TTCGCAGTGCGAT
1 TTCGCATTGCGAT
32732 AGTAATTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 16 0.26
16 9 0.15
17 9 0.15
19 27 0.44
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:32680 original size:33 final size:33
Alignment explanation
Indices: 32638--32731 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
32628 ATTAAATTCG
32638 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
32671 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
32704 CATTGCGATTTTCATTTCGCAGTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
32732 AGTAATTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:35046 original size:12 final size:12
Alignment explanation
Indices: 35029--35053 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35019 TCTTCGGGGA
35029 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35041 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35053 C
1 C
35054 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:35262 original size:24 final size:24
Alignment explanation
Indices: 35228--35281 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35218 CTAAAACATC
* *
35228 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
35252 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
35276 ATCAAA
1 ATCAAA
35282 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:36370 original size:20 final size:20
Alignment explanation
Indices: 36341--36391 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
36331 ATTCATTTGA
36341 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCAAAAATGG
* *
36361 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCAAAAATGG
*
36381 TTATCGCAACG
1 CTATCGCAACG
36392 AGAAAATCGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCAAAAATGG
Found at i:36396 original size:20 final size:20
Alignment explanation
Indices: 36341--36398 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
36331 ATTCATTTGA
36341 CTATCGCAACGCA-AAAATGG
1 CTATCGCAACG-AGAAAATGG
* *
36361 CTATCACAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
36381 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
36399 CGCAATGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:36457 original size:33 final size:33
Alignment explanation
Indices: 36420--36514 Score: 127
Period size: 39 Copynumber: 2.7 Consensus size: 33
36410 ATGAAAATCG
36420 CATTGCGATTTTCTCGTTGCGATTTTCATTTCA
1 CATTGCGATTTTCTCGTTGCGATTTTCATTTCA
*
36453 CATTGCGATTTTCATTTTCGCATTGCGATTTTCATTTCG
1 CATTGCGATTTTC----TCG--TTGCGATTTTCATTTCA
36492 CATTGCGATTTTCTCGTTGCGAT
1 CATTGCGATTTTCTCGTTGCGAT
36515 AGCCATTTCG
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
33 20 0.36
35 3 0.05
37 3 0.05
39 29 0.53
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCTCGTTGCGATTTTCATTTCA
Found at i:36476 original size:20 final size:19
Alignment explanation
Indices: 36417--36504 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
36407 GAAATGAAAA
36417 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
36433 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
36450 TCACATTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
36470 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36489 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
36505 TCGTTGCGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 2 0.03
19 30 0.47
20 18 0.28
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:36481 original size:39 final size:39
Alignment explanation
Indices: 36427--36504 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
36417 TCGCATTGCG
* *
36427 ATTTTCTCGTTGCGATTTTCATTTCACATTGCGATTTTC
1 ATTTTCGCATTGCGATTTTCATTTCACATTGCGATTTTC
*
36466 ATTTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTTCGCATTGCGATTTTCATTTCACATTGCGATTTTC
36505 TCGTTGCGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.15, C:0.21, G:0.14, T:0.50
Consensus pattern (39 bp):
ATTTTCGCATTGCGATTTTCATTTCACATTGCGATTTTC
Found at i:36522 original size:33 final size:33
Alignment explanation
Indices: 36417--36533 Score: 135
Period size: 33 Copynumber: 3.4 Consensus size: 33
36407 GAAATGAAAA
36417 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
36450 TCACATTGCGATTTTCATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC----TCG--TTGCGATTTTCATT
***
36489 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
36522 TCGCGTTGCGAT
1 TCGCATTGCGAT
36534 AGTCTGTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
33 37 0.51
35 3 0.04
37 3 0.04
39 29 0.40
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:38548 original size:39 final size:37
Alignment explanation
Indices: 38505--38641 Score: 107
Period size: 32 Copynumber: 3.9 Consensus size: 37
38495 TAGTTTACTT
*
38505 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAATGA-AA
* ** *
38544 TCGCAACGCGGAAA-TGACTATCGCAATGCGAAATGAAAA
1 TCGCAACAC-GAAACT-AAAATCGCAACGCGAAATG-AAA
38583 TCGC-A-ACG--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
38615 TCGC-A-ACG--AC-AAAATCGCAACGCGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAA
38642 CACAAATCGC
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
32 30 0.35
33 16 0.19
34 1 0.01
36 1 0.01
37 1 0.01
38 2 0.02
39 29 0.34
40 5 0.06
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:38559 original size:20 final size:19
Alignment explanation
Indices: 38524--38590 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
38514 GAAACTTAAA
38524 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
38543 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
* **
38563 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
38582 ATCGCAACG
1 ATCGCAACG
38591 ACAAAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:38598 original size:14 final size:14
Alignment explanation
Indices: 38579--38636 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38569 ATGCGAAATG
38579 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
38593 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
38609 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
38625 AAAATCGCAACG
1 AAAATCGCAACG
38637 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:38621 original size:32 final size:33
Alignment explanation
Indices: 38563--38641 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
38553 GGAAATGACT
*
38563 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
38596 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
38628 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
38642 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:38670 original size:19 final size:18
Alignment explanation
Indices: 38648--38729 Score: 91
Period size: 19 Copynumber: 4.7 Consensus size: 18
38638 GAAACACAAA
*
38648 TCGCATTGCTATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
38667 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
38683 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
38699 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
38718 TCGCATTGCGAT
1 TCGCATTGCGAT
38730 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.17
16 8 0.15
18 10 0.19
19 27 0.50
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:38736 original size:19 final size:19
Alignment explanation
Indices: 38694--38757 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
38684 CGTTGCGATT
**
38694 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
38713 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
38732 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
38752 TCATTT
1 TCATTT
38758 TCGTGTTGCG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:38748 original size:20 final size:19
Alignment explanation
Indices: 38695--38768 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
38685 GTTGCGATTT
* ***
38695 CATTTCGCATTGCGATTTT
1 CATTTCGCGTTGCGATAGC
*
38714 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
38733 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
38753 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
38769 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 21 0.45
20 23 0.49
21 3 0.06
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:39267 original size:18 final size:18
Alignment explanation
Indices: 39241--39285 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
39231 GTCGATCAGA
*
39241 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
39259 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
39277 TGATGGCTC
1 TGATGGCTC
39286 CTGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:40629 original size:20 final size:20
Alignment explanation
Indices: 40604--40641 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40594 AATAGTTTCT
40604 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
40624 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
40642 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:41161 original size:20 final size:20
Alignment explanation
Indices: 41136--41188 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
41126 GATTATGTAT
*
41136 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
41156 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
41176 TATCTCGTTGCGA
1 TATCGCGTTGCGA
41189 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:41226 original size:20 final size:20
Alignment explanation
Indices: 41116--41230 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
41106 CGCTTTGAAA
*
41116 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * *
41137 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
41157 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
41177 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
*
41198 ATTGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
41218 ATCGCATTGCGAT
1 ATCGCATTGCGAT
41231 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:41248 original size:21 final size:21
Alignment explanation
Indices: 41219--41294 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
41209 ATAGTAAGTA
41219 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
41240 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
41260 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
41281 TCGCATTGCGATTT
1 TCGCATTGCGATTT
41295 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:41249 original size:41 final size:41
Alignment explanation
Indices: 41158--41292 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
41148 AAAGTCAGTA
* * * * **
41158 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATTAT
1 TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCA--AT
41200 T-GCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* * **
41240 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
41281 TCGCATTGCGAT
1 TCGCATTGCGAT
41293 TTACTTATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
40 7 0.09
41 70 0.89
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:41263 original size:20 final size:20
Alignment explanation
Indices: 41219--41309 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
41209 ATAGTAAGTA
* **
41219 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
41240 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
41260 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
41281 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
41301 TCGCATTGC
1 TCGCATTGC
41310 TAATTGGGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 31 0.53
21 27 0.47
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:41293 original size:41 final size:41
Alignment explanation
Indices: 41219--41309 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
41209 ATAGTAAGTA
*
41219 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
41260 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
41301 TCGCATTGC
1 TCGCATTGC
41310 TAATTGGGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
Found at i:41326 original size:41 final size:41
Alignment explanation
Indices: 41219--41326 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
41209 ATAGTAAGTA
* * * * *
41219 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACTTAT
* * * *
41260 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
1 TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACTTAT
* **
41301 TCGCATTGCTAATTGGGAAAATCGCA
1 TCGCATTGCGAATTGCCAAAATCGCA
41327 ACGATACTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGAATTGCCAAAATCGCATTGCGATTTACTTAT
Done.