Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007277.1 Hibiscus syriacus cultivar Beakdansim tig00019299_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: 62996
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1666 original size:22 final size:23
Alignment explanation
Indices: 1618--1666 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1608 ATAAATTATT
*
1618 TAAATAAATCAATCTATATTTAA
1 TAAATAAATCAATCTATATCTAA
1641 -AAATAAATCAATAC-ATA-CTAA
1 TAAATAAATCAAT-CTATATCTAA
1662 TAAAT
1 TAAAT
1667 TATTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 3 0.13
22 19 0.83
23 1 0.04
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATAAATCAATCTATATCTAA
Found at i:1669 original size:53 final size:52
Alignment explanation
Indices: 1606--2263 Score: 385
Period size: 53 Copynumber: 12.6 Consensus size: 52
1596 ACAACTACAA
*
1606 TAATAAATTATTTAAATAAATCAATCTATATTTAAAAATAAATCAATACATAC
1 TAATAAATTATTTAAATAAATCAATCTATATTT-AAAATAAATCAATCCATAC
* **
1659 TAATAAATTA-TTAAATAAATCAATTCTTACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAATAAATCAA-TC-TA-TA-TTTAA-AATAAATCAATCCATAC
** * * ** **
1714 TTTTAAA-TA-ATCAATCCATACAAATAAATATTTAAAATAAATCAAT-C-TAC
1 TAATAAATTATTTAAATAAAT-C-AATCTATATTTAAAATAAATCAATCCATAC
1764 TAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAATAAATCAATCT-ATA-TTTAAAATAAATCAATCCATAC
** *
1818 TAAT-AATTATTTAAA-AAATC-ATCTATACAACTACAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAATAAATCAATCTAT---A-TTTAA-AATAAATCAATCCATA--C
* ** * * *
1874 TAAAATAAATCATCCATACAAAT-AA-AT-TATTTAAAATAAATCAAT-CATAC
1 T--AATAAATTATTTAAATAAATCAATCTATATTTAAAATAAATCAATCCATAC
*
1924 TAATAAA-TATTTAAAATAAATCAAT-TCATATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTT-AAATAAATCAATCT-ATATTTAAAATAAATCAATCCATAC
* *
1976 AAATAAATTATTTAAAATAAATCAATCCATATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTT-AAATAAATCAATCTATATTTAAAATAAATCAATCCATAC
* *
2029 TAATAAATTATTTAAAATAAATCAATCCATA--CAACCAATAAAATC-ATCCATA-
1 TAATAAATTATTT-AAATAAATCAATCTATATTTAA--AAT-AAATCAATCCATAC
** * ** * ** ** *
2081 TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAATAAAT-C-AATCTA-TATTTAAAATAAATCAATCCATAC
*
2136 TAAT-AATTATTT--A-AAATAAATC-AT-TTT-AAATAAATCAATCCATAC
1 TAATAAATTATTTAAATAAATCAATCTATATTTAAAATAAATCAATCCATAC
* *
2181 T-A-AAATTATTT--A-AAATAAATC-AT-TTTAAAATAAATCAATCCATATTTA
1 TAATAAATTATTTAAATAAATCAATCTATATTTAAAATAAATCAATCCATA---C
* *
2229 TAATAATTTATTTTAAAATAAATCAATCCATATTT
1 TAATAAATTA-TTT-AAATAAATCAATCTATATTT
2264 TATAATATTT
Statistics
Matches: 477, Mismatches: 69, Indels: 114
0.72 0.10 0.17
Matches are distributed among these distances:
44 24 0.05
45 35 0.07
46 3 0.01
47 3 0.01
48 14 0.03
49 9 0.02
50 16 0.03
51 55 0.12
52 62 0.13
53 133 0.28
54 59 0.12
55 21 0.04
56 23 0.05
57 3 0.01
58 4 0.01
59 8 0.02
60 5 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (52 bp):
TAATAAATTATTTAAATAAATCAATCTATATTTAAAATAAATCAATCCATAC
Found at i:1800 original size:22 final size:22
Alignment explanation
Indices: 1774--1816 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1764 TAATAAATTA
*
1774 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
1796 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1817 CTAATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1832 original size:159 final size:164
Alignment explanation
Indices: 1606--2134 Score: 642
Period size: 159 Copynumber: 3.2 Consensus size: 164
1596 ACAACTACAA
*
1606 TAATAAATTATTT-AAATAAATCAA-TCTATATTTAAAAATAAATCAATACATACTAATAAATTA
1 TAATAAATTATTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATACATACTAATAAATTA
1669 -TTAAATAAATCAATTCT-TACAACTACAATAATAAATCAATCCATATTTT-AAAT-AATCAATC
65 TTTAAATAAATCAATTCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATC-ATC
1730 CATACAAATAAA-TATTTAAAATAAATCAATC-TAC
129 CATACAAATAAATTATTTAAAATAAATCAATCATAC
*
1764 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAAT-AATTAT
1 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTAT
1828 TTAAA-AAATC-A-TCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCATCCA
66 TTAAATAAATCAATTCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCATCCA
1890 TACAAATAAATTATTTAAAATAAATCAATCATAC
131 TACAAATAAATTATTTAAAATAAATCAATCATAC
* *
1924 TAATAAA-TATTTAAAATAAATCAATTCATA-TTTAAAATAAATCAATTCATACAAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTAT
* * ** **
1987 TTAAAATAAATCAATCCATATTTA-AAATA-AATCAATCCATACTAATAAAT-TATTTAAAATAA
66 TT-AAATAAATCAATTC-TA--TACAACTACAAT-AATAAAT-C-AATCCATAT-TTTAAAATAA
2049 ATCAATCCATACAACCAATAAAATCATCCATATTTTAAAATAAATCAATCCATAC
123 ATC-ATCCATAC-A--AAT--AA--AT---TA-TTTAAAATAAATCAAT-CATAC
2104 TAATAAATTATTTAAAATAAATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATTCATA
2135 CTAATAATTA
Statistics
Matches: 327, Mismatches: 10, Indels: 45
0.86 0.03 0.12
Matches are distributed among these distances:
156 3 0.01
157 33 0.10
158 66 0.20
159 98 0.30
160 15 0.05
161 5 0.02
162 1 0.00
163 1 0.00
164 5 0.02
165 9 0.03
166 4 0.01
167 18 0.06
168 8 0.02
169 1 0.00
171 3 0.01
173 2 0.01
175 2 0.01
178 2 0.01
179 16 0.05
180 12 0.04
181 23 0.07
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (164 bp):
TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTAT
TTAAATAAATCAATTCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCATCCA
TACAAATAAATTATTTAAAATAAATCAATCATAC
Found at i:1956 original size:21 final size:21
Alignment explanation
Indices: 1930--2027 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 21
1920 ATACTAATAA
*
1930 ATATTTAAAATAAATCAATTC
1 ATATTTAAAATAAATCAATCC
*
1951 ATATTTAAAATAAATCAATTC
1 ATATTTAAAATAAATCAATCC
*
1972 ATA---CAAAT--A--AAT--
1 ATATTTAAAATAAATCAATCC
1984 -TATTTAAAATAAATCAATCC
1 ATATTTAAAATAAATCAATCC
2004 ATATTTAAAATAAATCAATCC
1 ATATTTAAAATAAATCAATCC
2025 ATA
1 ATA
2028 CTAATAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
11 2 0.03
14 7 0.11
16 2 0.03
18 7 0.11
21 47 0.72
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATTTAAAATAAATCAATCC
Found at i:1993 original size:14 final size:15
Alignment explanation
Indices: 1952--1998 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
1942 AATCAATTCA
1952 TATTTAAAATAAATC
1 TATTTAAAATAAATC
*
1967 AATTCATACAAATAAAT-
1 TATT--TA-AAATAAATC
1984 TATTTAAAATAAATC
1 TATTTAAAATAAATC
1999 AATCCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
17 5 0.19
18 8 0.31
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
TATTTAAAATAAATC
Found at i:2096 original size:75 final size:77
Alignment explanation
Indices: 1992--2202 Score: 278
Period size: 75 Copynumber: 2.8 Consensus size: 77
1982 ATTATTTAAA
1992 ATAAATCAATCCATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 ATAAATC-ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
2056 CATAC-AACCAA-T
65 CATACTAA-CAATT
*
2068 A-AAATCATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTC
1 ATAAATCATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
*
2132 ATACTAATAATT
66 ATACTAACAATT
**
2144 ATTTAAA--ATAAATCATTTT-AAATAAATCAATCCATACT-A-AAATTATTTAAAATAAATCA
1 A--TAAATCATCCAT-ATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
2203 TTTTAAAATA
Statistics
Matches: 124, Mismatches: 4, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
74 7 0.06
75 80 0.65
76 6 0.05
77 23 0.19
78 5 0.04
79 3 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (77 bp):
ATAAATCATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
ATACTAACAATT
Found at i:2111 original size:22 final size:22
Alignment explanation
Indices: 2043--2111 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
2033 AAATTATTTA
*
2043 AAATAAATCAATCCATAC-AAC
1 AAATAAATCAATCCATACTAAT
* **
2064 CAATAAAATC-ATCCATA-TTTT
1 AAAT-AAATCAATCCATACTAAT
2085 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
2108 AAAT
1 AAAT
2112 TATTTAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
21 15 0.42
22 19 0.53
23 2 0.06
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:2121 original size:32 final size:31
Alignment explanation
Indices: 2082--2158 Score: 136
Period size: 32 Copynumber: 2.5 Consensus size: 31
2072 TCATCCATAT
2082 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAAT-AATTA
*
2114 TTTAAAATAAATCAATTCATACTAATAATTA
1 TTTAAAATAAATCAATCCATACTAATAATTA
2145 TTTAAAATAAATCA
1 TTTAAAATAAATCA
2159 TTTTAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAATTA
Found at i:2124 original size:14 final size:14
Alignment explanation
Indices: 2105--2215 Score: 62
Period size: 14 Copynumber: 7.5 Consensus size: 14
2095 AATCCATACT
2105 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
2119 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
2137 AAT-AATTATTTAA
1 AATAAATTATTTAA
* *
2150 AATAAATCATTTTA
1 AATAAATTATTTAA
* ** *
2164 AATAAATCAATCCAT
1 AATAAAT-TATTTAA
*
2179 ACTAAAATTATTTAA
1 AAT-AAATTATTTAA
*
2194 AATAAATCATTTTAA
1 AATAAATTA-TTTAA
2209 AATAAAT
1 AATAAAT
2216 CAATCCATAT
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
13 3 0.04
14 29 0.41
15 24 0.34
16 7 0.10
17 5 0.07
18 3 0.04
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:2140 original size:18 final size:18
Alignment explanation
Indices: 2087--2141 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
2077 CATATTTTAA
*
2087 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
2105 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
2119 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
2137 AATAA
1 AATAA
2142 TTATTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
17 4 0.14
18 12 0.43
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:2165 original size:15 final size:15
Alignment explanation
Indices: 2145--2217 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
2135 CTAATAATTA
2145 TTTAAAATAAATCAT
1 TTTAAAATAAATCAT
*
2160 TTT-AAATAAATCAA
1 TTTAAAATAAATCAT
** * * *
2174 TCCATACTAAAATTA-
1 TTTAAAAT-AAATCAT
2189 TTTAAAATAAATCAT
1 TTTAAAATAAATCAT
2204 TTTAAAATAAATCA
1 TTTAAAATAAATCA
2218 ATCCATATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
14 16 0.36
15 23 0.52
16 5 0.11
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAATAAATCAT
Found at i:2203 original size:44 final size:45
Alignment explanation
Indices: 2105--2253 Score: 201
Period size: 45 Copynumber: 3.2 Consensus size: 45
2095 AATCCATACT
* * *
2105 AATAAATTATTTAAAATAAATCAATTCATACTAATAATTATTTAA
1 AATAAATCATTTTAAATAAATCAATCCATACTAATAATTATTTAA
2150 AATAAATCATTTTAAATAAATCAATCCATACTAA-AATTATTTAA
1 AATAAATCATTTTAAATAAATCAATCCATACTAATAATTATTTAA
*
2194 AATAAATCATTTTAAAATAAATCAATCCATATTTATAATAATTTATTTTAA
1 AATAAATCATTTT-AAATAAATCAATCCATA---CTAATAA-TTA-TTTAA
2245 AATAAATCA
1 AATAAATCA
2254 ATCCATATTT
Statistics
Matches: 93, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
44 23 0.25
45 48 0.52
48 3 0.03
49 2 0.02
50 3 0.03
51 14 0.15
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (45 bp):
AATAAATCATTTTAAATAAATCAATCCATACTAATAATTATTTAA
Found at i:2227 original size:36 final size:36
Alignment explanation
Indices: 2187--2316 Score: 159
Period size: 36 Copynumber: 3.8 Consensus size: 36
2177 ATACTAAAAT
* * *
2187 TATTTAAAATAAATCATTTTAAAATAAATCAATCCA
1 TATTTATAATAATTTATTTTAAAATAAATCAATCCA
2223 TATTTATAATAATTTATTTTAAAATAAATCAATCCA
1 TATTTATAATAATTTATTTTAAAATAAATCAATCCA
2259 TATTTTATAAT-ATTTATTTTAAAAT--A--AAT---
1 TA-TTTATAATAATTTATTTTAAAATAAATCAATCCA
*
2288 TATTTATAATAAATTATTTTAAAATAAAT
1 TATTTATAATAATTTATTTTAAAATAAAT
2317 AAACCTTATT
Statistics
Matches: 85, Mismatches: 4, Indels: 14
0.83 0.04 0.14
Matches are distributed among these distances:
28 8 0.09
29 15 0.18
31 1 0.01
32 3 0.04
34 1 0.01
36 49 0.58
37 8 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (36 bp):
TATTTATAATAATTTATTTTAAAATAAATCAATCCA
Found at i:2292 original size:15 final size:15
Alignment explanation
Indices: 2259--2316 Score: 75
Period size: 14 Copynumber: 4.0 Consensus size: 15
2249 AATCAATCCA
* *
2259 TATTTTATAAT-ATT
1 TATTTTAAAATAAAT
2273 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
2288 TA-TTTATAATAAAT
1 TATTTTAAAATAAAT
2302 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
2317 AAACCTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 23 0.61
15 15 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:2329 original size:29 final size:28
Alignment explanation
Indices: 2272--2335 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
2262 TTTATAATAT
* *
2272 TTATTTTAAAATAAATTATTTATAATAAA
1 TTATTTTAAAATAAATAACTTAT-ATAAA
2301 TTATTTTAAAATAAATAAACCTTAT-TAAA
1 TTATTTTAAAATAAAT-AA-CTTATATAAA
2330 TTATTT
1 TTATTT
2336 AAATTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 26 0.84
30 1 0.03
31 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATTTTAAAATAAATAACTTATATAAA
Found at i:7841 original size:51 final size:50
Alignment explanation
Indices: 7778--7904 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 50
7768 TTAACAGTAA
** *
7778 AGCGCGCCCCCTGCGCCGCGCTATACGATGATTTGGCGCCACGTGGAGTAT
1 AGCGCGCCCCCTGCGCCGCGCTATACGATGAGCTGGCGCCACGTAG-GTAT
* * * *
7829 AGTGCGCCCCCTGCACCGCTCTATACGGTGAGCTGGCGCCACGTAGGTAT
1 AGCGCGCCCCCTGCGCCGCGCTATACGATGAGCTGGCGCCACGTAGGTAT
* *
7879 AGCGCGTCCCTTGCAG-CGCGCTATAC
1 AGCGCGCCCCCTGC-GCCGCGCTATAC
7905 CTGTATATCT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 24 0.38
51 39 0.62
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGCGCCGCGCTATACGATGAGCTGGCGCCACGTAGGTAT
Found at i:10071 original size:48 final size:49
Alignment explanation
Indices: 9953--10076 Score: 144
Period size: 48 Copynumber: 2.5 Consensus size: 49
9943 AGTTATACAA
*
9953 AACGCGATACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTAT
1 AACGCGGTACCTGCCCCGCGCTATATAAAATTATGTC--GAGTAAAGGTAT
** * *
10004 GTCACGGTTCCTGCCCCGCGCTATATAAAAATTATG-C-AGTAAAGGTAT
1 AACGCGGTACCTGCCCCGCGCTATAT-AAAATTATGTCGAGTAAAGGTAT
**
10052 AACGCGGTACCTGATCCGCGCTATA
1 AACGCGGTACCTGCCCCGCGCTATA
10077 CCCCTACGTG
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
48 30 0.49
51 22 0.36
52 9 0.15
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (49 bp):
AACGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGAGTAAAGGTAT
Found at i:13967 original size:2 final size:2
Alignment explanation
Indices: 13962--13994 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13952 GATGTAATAT
13962 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13995 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:14259 original size:139 final size:133
Alignment explanation
Indices: 14032--14294 Score: 393
Period size: 139 Copynumber: 1.9 Consensus size: 133
14022 GGGAAACAAG
* * * * *
14032 CAATTAATTTTGAACCTAAACTTTTGAGTTACTTTTTTATCTTATTTTATACTTACATTTATTTA
1 CAATTAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTTA
*
14097 TAATGTAATAAATATGCAATATATATATATATATATTTAACCTAAATTCCAATATAATCATTTTT
66 TAATGTAATAAATATGC---A-ATATATA-A-ATATTTAAACTAAATTCCAATATAATCATTTTT
14162 TGTTTTAAT
125 TGTTTTAAT
*
14171 CAATATAATTTTCAACCTAAACTTTTGAGTTTC-TTTTAATCTTATTTAAAACTTAAATTTATTT
1 CAAT-TAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTT
14235 ATAATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTT
65 ATAATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTT
14295 AATCAATTGA
Statistics
Matches: 116, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
133 32 0.28
134 1 0.01
135 7 0.06
136 1 0.01
139 49 0.42
140 26 0.22
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (133 bp):
CAATTAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTTA
TAATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTTTGTTTT
AAT
Found at i:27651 original size:31 final size:31
Alignment explanation
Indices: 27570--27654 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
27560 TAAGTAATCG
** *
27570 TATCTTAATTAAATAAAAACAAACGTGATGA
1 TATCTTAATTAAATAAAAATGAACGTGATCA
* *
27601 TATCTTGATTAAATAAAAATGAATGTGATCA
1 TATCTTAATTAAATAAAAATGAACGTGATCA
*
27632 TATCTTAATAAAATAAAAATGAA
1 TATCTTAATTAAATAAAAATGAA
27655 AATGATAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (31 bp):
TATCTTAATTAAATAAAAATGAACGTGATCA
Found at i:29122 original size:176 final size:176
Alignment explanation
Indices: 28828--29168 Score: 538
Period size: 176 Copynumber: 1.9 Consensus size: 176
28818 TGCAAAATCT
28828 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
1 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
*
28893 AAGCTATCAACTAAAGACCATTATAAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCC
66 AAGCTATCAACTAAAGACCACTATAAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCC
** * *
28958 CCAATCCACACTCTGTTTCTTTTTCGTGATCAACAGTCTTTTATAG
131 CCAATCCACACTCCATTTCTTTTACATGATCAACAGTCTTTTATAG
* * * *
29004 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTATGAATAACCATAATAGTCTTATATCTG
1 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
* * * ** *
29069 ACGCTATCAGCTGAAGACCACTATAAATACCCTTAGTCAAGACTGATAAGGGGCTAGAACCTTCT
66 AAGCTATCAACTAAAGACCACTATAAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCC
*
29134 CCAATCCATACTCCATTTCTTTTACATGATCAACA
131 CCAATCCACACTCCATTTCTTTTACATGATCAACA
29169 ATCTCTCGTA
Statistics
Matches: 149, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
176 149 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (176 bp):
AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
AAGCTATCAACTAAAGACCACTATAAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCC
CCAATCCACACTCCATTTCTTTTACATGATCAACAGTCTTTTATAG
Found at i:30636 original size:18 final size:18
Alignment explanation
Indices: 30613--30648 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
30603 ATGTCATTGC
30613 TTACATCAATTTAGTTTT
1 TTACATCAATTTAGTTTT
30631 TTACATCAATTTAGTTTT
1 TTACATCAATTTAGTTTT
30649 GATGTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (18 bp):
TTACATCAATTTAGTTTT
Found at i:35336 original size:29 final size:29
Alignment explanation
Indices: 35302--35360 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
35292 CCTAAATTAA
*
35302 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
35331 TTTGATGTAATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
35360 T
1 T
35361 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:35371 original size:29 final size:29
Alignment explanation
Indices: 35311--35368 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
35301 ATTTGATGTC
* *
35311 ATTGCTTACATCAATTTAGTTTTGATGTA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
*
35340 ATTGCTTACATCAATTTAG-TTAGGTGAA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
35368 A
1 A
35369 ATTAAGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (29 bp):
ATTGCTTACATCAATTTAGTTTAGATGAA
Found at i:35892 original size:57 final size:57
Alignment explanation
Indices: 35804--35921 Score: 211
Period size: 57 Copynumber: 2.1 Consensus size: 57
35794 ACAACATTCA
*
35804 ACATCGATTTATGTTAGTCAAAAGTTTAGATTGAATTTTTTTCT-TGTTTCAAGAGTC
1 ACATCGATTTATGTTAATCAAAAGTTTAGATTGAATTTTTTTCTCT-TTTCAAGAGTC
35861 ACATCGATTTATGTTAATCAAAAGTTTAGATTGAATTTTTTTCTCTTTTCAAGAGTC
1 ACATCGATTTATGTTAATCAAAAGTTTAGATTGAATTTTTTTCTCTTTTCAAGAGTC
35918 ACAT
1 ACAT
35922 TGTATGCAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 58 0.98
58 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (57 bp):
ACATCGATTTATGTTAATCAAAAGTTTAGATTGAATTTTTTTCTCTTTTCAAGAGTC
Found at i:54780 original size:60 final size:60
Alignment explanation
Indices: 54651--54763 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
54641 TGTGGGGACA
*
54651 AATTTAGAATGAGAGTCATAGTTAGAAGATGAACTTAGAACATTCAAAAGTTTGACGATC
1 AATTTAGAATGAGAGTCATAGTTAGAAGATGAAATTAGAACATTCAAAAGTTTGACGATC
* * * * *
54711 AAGTTAGAATGAGAGTCATAGTTTA-AGGATGAAATTGGAATATTGAAAAGTTT
1 AATTTAGAATGAGAGTCATAG-TTAGAAGATGAAATTAGAACATTCAAAAGTTT
54764 AGGGACTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (60 bp):
AATTTAGAATGAGAGTCATAGTTAGAAGATGAAATTAGAACATTCAAAAGTTTGACGATC
Found at i:58335 original size:47 final size:47
Alignment explanation
Indices: 58266--58365 Score: 200
Period size: 47 Copynumber: 2.1 Consensus size: 47
58256 TTATAAAATT
58266 AAAAAAAAAATTAGAGGTCTCAATTATAAAAGTAGAAAGTGATATTG
1 AAAAAAAAAATTAGAGGTCTCAATTATAAAAGTAGAAAGTGATATTG
58313 AAAAAAAAAATTAGAGGTCTCAATTATAAAAGTAGAAAGTGATATTG
1 AAAAAAAAAATTAGAGGTCTCAATTATAAAAGTAGAAAGTGATATTG
58360 AAAAAA
1 AAAAAA
58366 TATATGATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (47 bp):
AAAAAAAAAATTAGAGGTCTCAATTATAAAAGTAGAAAGTGATATTG
Found at i:58626 original size:15 final size:15
Alignment explanation
Indices: 58606--58646 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
58596 ATGATTCAGA
*
58606 GGCTCTTAATGATTT
1 GGCTCTGAATGATTT
58621 GGCTCTGAATGATTT
1 GGCTCTGAATGATTT
58636 GGCTCTGAATG
1 GGCTCTGAATG
58647 TGACATGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.39
Consensus pattern (15 bp):
GGCTCTGAATGATTT
Found at i:59555 original size:5 final size:5
Alignment explanation
Indices: 59545--59569 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
59535 TTATAGGATA
59545 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
59570 GTTAAAATTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:61086 original size:2 final size:2
Alignment explanation
Indices: 61081--61119 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
61071 AAATAATTTA
61081 AT 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 AT A
61120 ACTCATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.