Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007054.1 Hibiscus syriacus cultivar Beakdansim tig00018292_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: 67903
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:472 original size:57 final size:56
Alignment explanation
Indices: 409--535 Score: 145
Period size: 57 Copynumber: 2.2 Consensus size: 56
399 GTATTGGGAT
409 TAATTTAGAATGATGGTCATAATTTGA-AGAGTG-AATTGAAA-TTCAAAAATTC-AGGAC
1 TAATTTAGAATGAT--TC-TAATTT-ATAGA-TGAAATTGAAAGTTCAAAAATTCAAGGAC
* * *
466 TAATTTAGAATGATTCTAGTTTATAGATGAAATTGAAATGTTCAAAAGTTCAATGAC
1 TAATTTAGAATGATTCTAATTTATAGATGAAATTGAAA-GTTCAAAAATTCAAGGAC
523 TAATTTAGAATGA
1 TAATTTAGAATGA
536 GAGTCATGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
53 3 0.05
54 16 0.26
55 2 0.03
56 10 0.16
57 31 0.50
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (56 bp):
TAATTTAGAATGATTCTAATTTATAGATGAAATTGAAAGTTCAAAAATTCAAGGAC
Found at i:16512 original size:29 final size:29
Alignment explanation
Indices: 16479--16537 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
16469 CGCCTTGCCT
16479 AGGATTTTAAAATTCCATCCTTGATATAA
1 AGGATTTTAAAATTCCATCCTTGATATAA
16508 AGGATTTTAAAATTCCATCCTTGATATAA
1 AGGATTTTAAAATTCCATCCTTGATATAA
16537 A
1 A
16538 ATCATGCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (29 bp):
AGGATTTTAAAATTCCATCCTTGATATAA
Found at i:17490 original size:31 final size:31
Alignment explanation
Indices: 17452--17529 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
17442 AATTTTAAAA
**
17452 GTAACAAATC-AGTCACTATTATTATTGATTC
1 GTAACAAATCGA-TCACTAACATTATTGATTC
17483 GTAACAAATCGATCACTAACATTATTGATTC
1 GTAACAAATCGATCACTAACATTATTGATTC
*
17514 -TAACAAATCCATCACT
1 GTAACAAATCGATCACT
17530 GACGTTATCG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.35
31 27 0.63
32 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (31 bp):
GTAACAAATCGATCACTAACATTATTGATTC
Found at i:20696 original size:18 final size:18
Alignment explanation
Indices: 20669--20706 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
20659 AATATTAAGC
20669 CTATAATTT-ACCATAAA
1 CTATAATTTAACCATAAA
*
20686 CTATCAATTTAACCATTAA
1 CTAT-AATTTAACCATAAA
20705 CT
1 CT
20707 TATTGTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (18 bp):
CTATAATTTAACCATAAA
Found at i:24302 original size:2 final size:2
Alignment explanation
Indices: 24297--24336 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24287 AAATCAAAAC
24297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24337 TATCAAGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28110 original size:5 final size:5
Alignment explanation
Indices: 28100--28124 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28090 GCTAGGTTAC
28100 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
28125 CGTTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:30599 original size:31 final size:31
Alignment explanation
Indices: 30557--30617 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
30547 TAACCCGTGG
*
30557 TGATCACATCTTAGTTAAATAAAAACGAAAA
1 TGATCACATCTTAATTAAATAAAAACGAAAA
* *
30588 TGATCATATCTTAATTAAATGAAAACGAAA
1 TGATCACATCTTAATTAAATAAAAACGAAA
30618 GTGACTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (31 bp):
TGATCACATCTTAATTAAATAAAAACGAAAA
Found at i:38952 original size:14 final size:13
Alignment explanation
Indices: 38909--38949 Score: 64
Period size: 14 Copynumber: 3.0 Consensus size: 13
38899 ATTTTTTAAG
38909 AAGTATATAAATTT
1 AAGTAT-TAAATTT
38923 AAGTATTAAACTTT
1 AAGTATTAAA-TTT
38937 AAGTATTAAATTT
1 AAGTATTAAATTT
38950 TAAATACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (13 bp):
AAGTATTAAATTT
Found at i:43544 original size:23 final size:22
Alignment explanation
Indices: 43496--43544 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
43486 CCATAATGTC
43496 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
43517 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
43540 AAGGA
1 AAGGA
43545 AAATTGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:45482 original size:103 final size:103
Alignment explanation
Indices: 45159--45461 Score: 543
Period size: 103 Copynumber: 2.9 Consensus size: 103
45149 GGGTCTACGC
* * *
45159 GGTCTTTCGGGACATATATGTATTCTTTGAAATATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
45224 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
45262 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
45327 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
45365 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
45430 CCCTAGTATATGTATATGATTCTTAAGGAATG
66 CCTTGGCATATGTATATGATTCTTAAGGAATG
45462 GTATATAGTC
Statistics
Matches: 192, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 192 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:45524 original size:23 final size:23
Alignment explanation
Indices: 45491--45558 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
45481 ATTATTATAT
45491 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
45514 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
45537 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
45559 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:47158 original size:19 final size:19
Alignment explanation
Indices: 47129--47175 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
47119 TTATTATTTA
* *
47129 AAAAGTATAAAATCAAACTT
1 AAAA-TATAAAATAAAAATT
47149 AAAATATAAAATAAAAATT
1 AAAATATAAAATAAAAATT
*
47168 TAAATATA
1 AAAATATA
47176 CTAAAATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATAAAATAAAAATT
Found at i:59831 original size:21 final size:20
Alignment explanation
Indices: 59812--59931 Score: 138
Period size: 21 Copynumber: 5.8 Consensus size: 20
59802 GACTATCGCA
*
59812 TTGCGATAG-TCCAAGTTCGCG
1 TTGCGATAGCTCCAAATT--CG
*
59833 TTGCGATAGTCTCCAAATTGG
1 TTGCGATAG-CTCCAAATTCG
59854 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAATTCG
59875 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAATTCG
*
59896 TTGCGATAG-TCCCAAGTTCG
1 TTGCGATAGCT-CCAAATTCG
59916 TTGCGATAG-TCCAAAT
1 TTGCGATAGCTCCAAAT
59932 CGCAACGACT
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
19 6 0.07
20 18 0.20
21 60 0.66
23 7 0.08
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGCTCCAAATTCG
Found at i:59859 original size:42 final size:40
Alignment explanation
Indices: 59812--59926 Score: 167
Period size: 42 Copynumber: 2.8 Consensus size: 40
59802 GACTATCGCA
*
59812 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCTCCAAATTGG
1 TTGCGATAGTCCAAGTT--CGTTGCGATAGTCTCCAAATTCG
*
59854 TTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAATTCG
1 TTGCGATAG--TCCAAGTTCGTTGCGATAGTCTCCAAATTCG
59896 TTGCGATAGTCCCAAGTTCGTTGCGATAGTC
1 TTGCGATAGT-CCAAGTTCGTTGCGATAGTC
59927 CAAATCGCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
40 1 0.01
41 19 0.28
42 40 0.60
44 7 0.10
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGTTGCGATAGTCTCCAAATTCG
Found at i:60019 original size:21 final size:21
Alignment explanation
Indices: 59989--60309 Score: 355
Period size: 21 Copynumber: 15.6 Consensus size: 21
59979 GGTGATTTTG
*
59989 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
60010 GACTACCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
60031 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
60052 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
60073 GACTATCGCAACGAACTT-GA
1 GACTATCGCAACGAACTTGGA
* *
60093 GACTATCGC-ACAAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
60113 GACTACCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
60134 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
60155 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
60176 GACTATCGCAACGAATTTGTA
1 GACTATCGCAACGAACTTGGA
*
60197 -A-TAATCGTAACGCGAACTT-G-
1 GACT-ATCGCAA--CGAACTTGGA
*
60217 GACTATCGCAACGAA-TT-TA
1 GACTATCGCAACGAACTTGGA
*
60236 GAATAATCGCAACGCAACTT-G-
1 GACT-ATCGCAACG-AACTTGGA
*
60257 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
60278 -A-AATCGCAACGCGAACTT--C
1 GACTATCGCAA--CGAACTTGGA
60297 GACTATCGCAACG
1 GACTATCGCAACG
60310 CGAACTGGAC
Statistics
Matches: 259, Mismatches: 24, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
18 2 0.01
19 27 0.10
20 49 0.19
21 172 0.66
22 9 0.03
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:60115 original size:103 final size:104
Alignment explanation
Indices: 59989--60190 Score: 379
Period size: 103 Copynumber: 2.0 Consensus size: 104
59979 GGTGATTTTG
*
59989 GACTATCGCAACGAATTTGGAGACTACCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
1 GACTATCGCAACAAATTTGGAGACTACCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
60054 CTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGA
66 CTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGA
*
60093 GACTATCGC-ACAAATTTGGAGACTACCGCAACGAATTTGGAGACTATCGCAACGAACTTGGAGA
1 GACTATCGCAACAAATTTGGAGACTACCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
60157 CTATCGCAACGAACTTGGAGACTATCGCAACGAA
66 CTATCGCAACGAACTTGGAGACTATCGCAACGAA
60191 TTTGTAATAA
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 87 0.91
104 9 0.09
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (104 bp):
GACTATCGCAACAAATTTGGAGACTACCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
CTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGA
Found at i:60232 original size:41 final size:40
Alignment explanation
Indices: 60035--60309 Score: 218
Period size: 40 Copynumber: 6.8 Consensus size: 40
60025 CTTGGAGACT
*
60035 ATCGCAA--CGAACTTGGAGACTATCGCAACGAACTTGGAGACT-
1 ATCGCAACGCGAACTT-G-GACTATCGCAACGAA-TTTGA-A-TA
*
60077 ATCGCAA--CGAACTTGAGACTATCGC-ACAAATTTGGAGACT-
1 ATCGCAACGCGAACTTG-GACTATCGCAACGAATTT-GA-A-TA
* * *
60117 ACCGCAA--CGAATTTGGAGACTATCGCAACGAACTTGGAGACT-
1 ATCGCAACGCGAACTT-G-GACTATCGCAACGAA-TTTGA-A-TA
60159 ATCGCAA--CGAACTTGGAGACTATCGCAACGAATTTGTAATA
1 ATCGCAACGCGAACTT-G-GACTATCGCAACGAATTTG-AATA
*
60200 ATCGTAACGCGAACTTGGACTATCGCAACGAATTTAGAATA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATA
60241 ATCGCAACGC-AACTTGGACTATCGCAACGAATTTGGAA-A
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATA
*
60280 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAACGCGAACTTGGACTATCGCAACG
60310 CGAACTGGAC
Statistics
Matches: 210, Mismatches: 13, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
39 13 0.06
40 68 0.32
41 63 0.30
42 57 0.27
43 9 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATA
Found at i:60245 original size:103 final size:100
Alignment explanation
Indices: 60010--60327 Score: 328
Period size: 103 Copynumber: 3.1 Consensus size: 100
60000 CGAATTTGGA
* * *
60010 GACTACCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
1 GACTATCGCAACGAA-TTTGAGAATATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGA
* * * *
60075 CTATCGCAACGAACTTGAGACTATCG--CACAAATTTGG
65 CTATCGCAACGAATTTGA-A-TATCGAACGCGAACTT-G
* *
60112 AGACTACCGCAACGAATTTGGAGACTATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAG
1 -GACTATCGCAACGAATTT-GAGAATATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAG
60177 ACTATCGCAACGAATTTGTAATAATCGTAACGCGAACTTG
64 ACTATCGCAACGAATTTG-AAT-ATCG-AACGCGAACTTG
*
60217 GACTATCGCAACGAATTT-AGAATAATCGCAACGCAACTT-G-GACTATCGCAACGAATTTGGA-
1 GACTATCGCAACGAATTTGAGAAT-ATCGCAACG-AACTTGGAGACTATCGCAACGAACTTGGAG
* * *
60278 A-AATCGCAACGCGAACTTCGACTATCGCAACGCGAAC-TG
64 ACTATCGCAA--CGAA-TTTGAATATCG-AACGCGAACTTG
60317 GACTATCGCAA
1 GACTATCGCAA
60328 TGCTAATATG
Statistics
Matches: 192, Mismatches: 12, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
100 20 0.10
101 14 0.07
102 33 0.17
103 95 0.49
104 23 0.12
105 1 0.01
106 6 0.03
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (100 bp):
GACTATCGCAACGAATTTGAGAATATCGCAACGAACTTGGAGACTATCGCAACGAACTTGGAGAC
TATCGCAACGAATTTGAATATCGAACGCGAACTTG
Found at i:61296 original size:25 final size:25
Alignment explanation
Indices: 61247--61295 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
61237 GTAAGTTCTA
61247 AATTTGACACTTCAAAATATATTTT
1 AATTTGACACTTCAAAATATATTTT
*
61272 AATTT-ACATCTT-AAAATATTTTTT
1 AATTTGACA-CTTCAAAATATATTTT
61296 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTTGACACTTCAAAATATATTTT
Found at i:62913 original size:18 final size:18
Alignment explanation
Indices: 62890--62925 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62880 GGCATTTGTG
*
62890 TACTTTACCCTTGTTTTA
1 TACTTTACCCTTGGTTTA
*
62908 TACTTTACTCTTGGTTTA
1 TACTTTACCCTTGGTTTA
62926 ACGCCATCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (18 bp):
TACTTTACCCTTGGTTTA
Found at i:64791 original size:13 final size:13
Alignment explanation
Indices: 64773--64808 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
64763 GGCTTACGTA
64773 TATTTTTTTATCG
1 TATTTTTTTATCG
64786 TATTTTTTTATCG
1 TATTTTTTTATCG
64799 TATGTTTTTT
1 TAT-TTTTTT
64809 CATATGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (13 bp):
TATTTTTTTATCG
Found at i:64933 original size:65 final size:65
Alignment explanation
Indices: 64853--64983 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
64843 CCATCTCTTT
* *
64853 ATATATTTTTTTATTAATTATTTAGTTTCGAATTATTTAAAATTTTATAAAATTCGTATTTCGGA
1 ATATATTTTTTTATTAATGATTTAGTTTCGAATTATTTAAAA-TTTATAAAAATCGTATTTCGGA
64918 C
65 C
*
64919 ATAT-TTTTTTTATTAATGATTTAGTTTCGAATTCTTTAAAATTTATAAAAATCGTATTTCGGAC
1 ATATATTTTTTTATTAATGATTTAGTTTCGAATTATTTAAAATTTATAAAAATCGTATTTCGGAC
64983 A
1 A
64984 AAAAAATATG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 23 0.37
65 35 0.56
66 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (65 bp):
ATATATTTTTTTATTAATGATTTAGTTTCGAATTATTTAAAATTTATAAAAATCGTATTTCGGAC
Found at i:65606 original size:21 final size:20
Alignment explanation
Indices: 65576--65631 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
65566 TACTTTCAAT
* **
65576 TTTATCTTTTTAGATAGTTTG
1 TTTATATTTTTA-ATAGTTAA
65597 TTTATATTTTATAATAGTTAA
1 TTTATATTTT-TAATAGTTAA
65618 TTTATATATTTTAA
1 TTTATAT-TTTTAA
65632 ATAATTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTATATTTTTAATAGTTAA
Found at i:65881 original size:11 final size:11
Alignment explanation
Indices: 65865--65889 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65855 AAATTATATC
65865 ATAATAAATAA
1 ATAATAAATAA
65876 ATAATAAATAA
1 ATAATAAATAA
65887 ATA
1 ATA
65890 TTTAAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATAAATAA
Found at i:66416 original size:31 final size:30
Alignment explanation
Indices: 66376--66437 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
66366 TGTCAACATG
* *
66376 ATGACGAGGTATGATAGTCATTTGAGATTC
1 ATGACGAGGTACGATAGCCATTTGAGATTC
66406 ATGATCGAGGTACGATAGCCATTTGAGATTC
1 ATGA-CGAGGTACGATAGCCATTTGAGATTC
66437 A
1 A
66438 AAATCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (30 bp):
ATGACGAGGTACGATAGCCATTTGAGATTC
Done.