Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005026.1 Hibiscus syriacus cultivar Beakdansim tig00011280_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: 66343
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2236 original size:21 final size:21
Alignment explanation
Indices: 2186--2254 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
2176 TAGAATGATT
2186 TAATTA-TTT-AATAGAGTTTAA
1 TAATTATTTTAAATA-A-TTTAA
2207 TAATT-TTTTAAATAATTTAA
1 TAATTATTTTAAATAATTTAA
*
2227 TAATTATTTTTAAATAATTAAA
1 TAATTA-TTTTAAATAATTTAA
2249 T-ATTAT
1 TAATTAT
2255 AAATATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 11 0.26
21 13 0.30
22 19 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TAATTATTTTAAATAATTTAA
Found at i:2236 original size:22 final size:22
Alignment explanation
Indices: 2202--2254 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2192 TTTAATAGAG
2202 TTTAATAA-T-TTTTTAAATAA
1 TTTAATAATTATTTTTAAATAA
2222 TTTAATAATTATTTTTAAATAA
1 TTTAATAATTATTTTTAAATAA
*
2244 TTAAAT-ATTAT
1 TTTAATAATTAT
2255 AAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.27
21 6 0.20
22 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATAATTATTTTTAAATAA
Found at i:2948 original size:19 final size:19
Alignment explanation
Indices: 2920--2956 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2910 TTTTGTCCGG
2920 ATTATCATTAATATTTAAC
1 ATTATCATTAATATTTAAC
* *
2939 ATTATTATTATTATTTAA
1 ATTATCATTAATATTTAA
2957 TATAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTATCATTAATATTTAAC
Found at i:4211 original size:18 final size:19
Alignment explanation
Indices: 4169--4217 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
4159 CGATGAACAA
*
4169 TATCGATACTGATGCAATTAG
1 TATCGATACTGATG--ATGAG
4190 TATCGATACTGATG-TGAG
1 TATCGATACTGATGATGAG
4208 TATCGATACT
1 TATCGATACT
4218 AAGATAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 13 0.48
21 14 0.52
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (19 bp):
TATCGATACTGATGATGAG
Found at i:4804 original size:49 final size:49
Alignment explanation
Indices: 4750--5197 Score: 461
Period size: 49 Copynumber: 9.1 Consensus size: 49
4740 TGCCTAACGA
* *
4750 TGCATTTTTTGTAGAAAGGTACCACTAATGCAAGTTAGATAACGAATGG
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
* * * ** * * * *
4799 TGCATTTTTGGCAAAAATGTGTCACTAATGCAAGTTA-ATTGCCTAACGA
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGA-TGACGAATGG
* *
4848 TGTATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGA
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
* * * * * * * **
4897 TGCATTTTTGGCATAAATGTACCATTAATGCAAGTTAAATGCCTAACAG
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
* * *
4946 TGTATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGATGAATGG
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
* * * * * *
4995 TGCATTTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTG-ACGA
1 TGCA-TTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGAC-GAATGG
*
5045 TACATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
* * * * *
5094 TGCATTTTTGGTAGAAAGGTGA-CATTAATGCAAGTTAAATGCCTAACGG
1 TGCATTTTTGGTAGAAAGGT-ACCACTAATGCAAGTTAGATGACGAATGG
* * * * *
5143 TGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTATATGACAAATGA
1 TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
5192 TGCATT
1 TGCATT
5198 ATCGACATGG
Statistics
Matches: 321, Mismatches: 71, Indels: 14
0.79 0.17 0.03
Matches are distributed among these distances:
48 2 0.01
49 278 0.87
50 40 0.12
51 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (49 bp):
TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGG
Found at i:4901 original size:98 final size:98
Alignment explanation
Indices: 4727--5197 Score: 674
Period size: 98 Copynumber: 4.8 Consensus size: 98
4717 ACTGCTCTAA
* * *
4727 AATGAAAGTTAAATGCCTAACGATGCATTTTTTGTAGAAAGGTACCACTAATGCAAGTTAGATAA
1 AATGCAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
* * *
4792 CGAATGGTGCATTTTTGGCAAAAATGTGTCACT
66 CGAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* *
4825 AATGCAAGTTAATTGCCTAACGATGTATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
* * * * *
4890 CGAATGATGCATTTTTGGCATAAATGTACCATT
66 CGAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* *
4923 AATGCAAGTTAAATGCCTAAC-AGTGTATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATG
1 AATGCAAGTTAAATGCCTAACGA-TGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATG
*
4987 ATGAATGGTGCATTTTTTGGCAGAAAGGTGCCACT
65 ACGAATGGTGCA-TTTTTGGCAGAAAGGTGCCACT
* *
5022 AATGCAAGTTAAATGCCTGACGATACATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
* * *
5087 CGAATGGTGCATTTTTGGTAGAAAGGTGACATT
66 CGAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * *
5120 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTATATGA
1 AATGCAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
* *
5185 CAAATGATGCATT
66 CGAATGGTGCATT
5198 ATCGACATGG
Statistics
Matches: 336, Mismatches: 34, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
97 1 0.00
98 247 0.74
99 87 0.26
100 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (98 bp):
AATGCAAGTTAAATGCCTAACGATGCATTTTTGGTAGAAAGGTACCACTAATGCAAGTTAGATGA
CGAATGGTGCATTTTTGGCAGAAAGGTGCCACT
Found at i:5082 original size:197 final size:195
Alignment explanation
Indices: 4727--5197 Score: 701
Period size: 197 Copynumber: 2.4 Consensus size: 195
4717 ACTGCTCTAA
* * * *
4727 AATGAAAGTTAAATGCCTAACGATGCATTTTTTGTAGAAAGGTACCACTAATGCAAGTTAGATAA
1 AATGCAAGTTAAATGCCTAACG-TGCATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGA
* * * **
4792 CGAATGGTGCATTTTTGGCAAAAATGTGTCACTAATGCAAGTTAATTGCCTAACGATGTATTTTT
65 CGAATGGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGATACATTTTT
* *
4857 GGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGATGCATTTTTGGCATAAATGT-ACCA
130 GGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGATGCATTTTTGGCAGAAAGGTGA-CA
4921 TT
194 TT
*
4923 AATGCAAGTTAAATGCCTAACAGTGTATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAAC-GTGCATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGA
* * *
4988 TGAATGGTGCATTTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTGACGATACATTTT
65 CGAATGGTGCA-TTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGATACATTTT
* *
5053 TGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGGTGCATTTTTGGTAGAAAGGTGACA
129 TGGTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGATGCATTTTTGGCAGAAAGGTGACA
5118 TT
194 TT
* *
5120 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAATGTGCCACTAATGCAAGTTATATGA
1 AATGCAAGTTAAATGCCTAAC-GTGCATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGA
* *
5185 CAAATGATGCATT
65 CGAATGGTGCATT
5198 ATCGACATGG
Statistics
Matches: 248, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
196 70 0.28
197 177 0.71
198 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (195 bp):
AATGCAAGTTAAATGCCTAACGTGCATTTTTGGTAGAAATGTACCACTAATGCAAGTTAGATGAC
GAATGGTGCATTTTTGGCAAAAAGGTGCCACTAATGCAAGTTAAATGCCTAACGATACATTTTTG
GTAGAAAGGTACCACTAATGCAAGTTAGATGACGAATGATGCATTTTTGGCAGAAAGGTGACATT
Found at i:5296 original size:46 final size:46
Alignment explanation
Indices: 5195--5297 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
5185 CAAATGATGC
** * *
5195 ATTATCGACATGGAAGGATTCCATAAATGAAAATGCATAACGGTGA
1 ATTATCGACATGGAAGGAGGCCACAAATGAAAATACATAACGGTGA
* * * *
5241 ATAATCGACATGTAAGGAGGCCACAAATGAAAATACATAATGGTGT
1 ATTATCGACATGGAAGGAGGCCACAAATGAAAATACATAACGGTGA
*
5287 ATTAGCGACAT
1 ATTATCGACAT
5298 AAAAGGTGTC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATTATCGACATGGAAGGAGGCCACAAATGAAAATACATAACGGTGA
Found at i:10243 original size:22 final size:22
Alignment explanation
Indices: 10215--10282 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
10205 GTATAAGTAA
10215 GAGAATTAAACGAAAATTTGGT
1 GAGAATTAAACGAAAATTTGGT
10237 GAGAATTAAACGAAAATTTGGT
1 GAGAATTAAACGAAAATTTGGT
*
10259 GAGAATTAAATGAAAATTTGGT
1 GAGAATTAAACGAAAATTTGGT
10281 GA
1 GA
10283 AAATCGAGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.28
Consensus pattern (22 bp):
GAGAATTAAACGAAAATTTGGT
Found at i:11036 original size:49 final size:49
Alignment explanation
Indices: 10964--11137 Score: 186
Period size: 49 Copynumber: 3.5 Consensus size: 49
10954 CTAAAAGTGC
* * *
10964 ATTTTTGGTAGAAAGGTACCACTAATGCATGTTAGACGACGAATGGTGT
1 ATTTTTGGCAGAAAGGTACCACTAATGCAAGTTAGACGACAAATGGTGT
* * * * * * *
11013 ATTTTTGGCATAAAGGTGCCACTAATGCAAGTTAAATGCCTAATGATGT
1 ATTTTTGGCAGAAAGGTACCACTAATGCAAGTTAGACGACAAATGGTGT
* * * * *
11062 ATTTTTTAGTAGAAAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGC
1 A-TTTTTGGCAGAAAGGTACCACTAATGCAAGTTAGACGACAAATGGTGT
* *
11112 ATTTTTGGCAGAAATGTGCCACTAAT
1 ATTTTTGGCAGAAAGGTACCACTAAT
11138 AAAAGTTAAA
Statistics
Matches: 99, Mismatches: 25, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
49 62 0.63
50 37 0.37
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (49 bp):
ATTTTTGGCAGAAAGGTACCACTAATGCAAGTTAGACGACAAATGGTGT
Found at i:11080 original size:99 final size:98
Alignment explanation
Indices: 10965--11155 Score: 283
Period size: 99 Copynumber: 1.9 Consensus size: 98
10955 TAAAAGTGCA
* * ** * *
10965 TTTTTGGTAGAAAGGTACCACTAATGCATGTTAGACGACGAATGGTGTATTTTTGGCATAAAGGT
1 TTTTTAGTAGAAAGGTACCACTAATGCAAGTTAGACGAAAAATGGTGCATTTTTGGCAGAAAGGT
**
11030 GCCACTAATGCAAGTTAAATGCCTAATGATGTAT
66 GCCACTAATAAAAGTTAAATGCC-AATGATGTAT
* *
11064 TTTTTAGTAGAAAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGCATTTTTGGCAGAAATGT
1 TTTTTAGTAGAAAGGTACCACTAATGCAAGTTAGACGAAAAATGGTGCATTTTTGGCAGAAAGGT
11129 GCCACTAATAAAAGTTAAATGCCAATG
66 GCCACTAATAAAAGTTAAATGCCAATG
11156 GTAAGGTACC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
98 4 0.05
99 78 0.95
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (98 bp):
TTTTTAGTAGAAAGGTACCACTAATGCAAGTTAGACGAAAAATGGTGCATTTTTGGCAGAAAGGT
GCCACTAATAAAAGTTAAATGCCAATGATGTAT
Found at i:11173 original size:83 final size:84
Alignment explanation
Indices: 11075--11235 Score: 234
Period size: 83 Copynumber: 1.9 Consensus size: 84
11065 TTTTAGTAGA
* *
11075 AAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGCA-TTTTTGGCAGAAATGTGCCACTAATA
1 AAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGCATTTTTTGGCAGAAAAGCGCCACTAATA
11139 AAAGTTAAATGCCAATGGT
66 AAAGTTAAATGCCAATGGT
* * ** * *
11158 AAGGTACCATTAATGTAAGTTAGATGACGAATGGTGCATTTTTTGGCAGAAAAGCGTCACTAATG
1 AAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGCATTTTTTGGCAGAAAAGCGCCACTAATA
*
11223 CAAGTTAAATGCC
66 AAAGTTAAATGCC
11236 TAACAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 34 0.50
84 34 0.50
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (84 bp):
AAGGTACCACTAATGTAAGTTAGACGAAAAATGGTGCATTTTTTGGCAGAAAAGCGCCACTAATA
AAAGTTAAATGCCAATGGT
Found at i:11262 original size:182 final size:182
Alignment explanation
Indices: 10976--11332 Score: 477
Period size: 182 Copynumber: 2.0 Consensus size: 182
10966 TTTTGGTAGA
* * * * *
10976 AAGGTACCACTAATGCATGTTAGACGACGAATGGTGTATTTTTGGCATAAAGGTGCCACTAATGC
1 AAGGTACCACTAATGCAAGTTAGACGACGAATGGTGCATTTTTGGCAGAAAAGCGCCACTAATGC
* * *
11041 AAGTTAAATGCCTAATGATGTATTTTTTAGTAGAAAGGTACCACTAATGTAAGTTAGACGAAAAA
66 AAGTTAAATGCCTAAAGATGCATTTTTTA-TAGAAAGGTACCACTAATGCAAGTTAGACGAAAAA
**
11106 TGGTGCATTTTTGGCAGAAATGTGC-CACTAATAAAAGTTAAATGCCAATGGT
130 TAATGCATTTTTGGCAGAAATGTGCGCACTAATAAAAGTTAAATGCCAATGGT
* * * *
11158 AAGGTACCATTAATGTAAGTTAGATGACGAATGGTGCATTTTTTGGCAGAAAAGCGTCACTAATG
1 AAGGTACCACTAATGCAAGTTAGACGACGAATGGTGCA-TTTTTGGCAGAAAAGCGCCACTAATG
* **
11223 CAAGTTAAATGCCTAACAG-TGCATTTTTGT-TAGAAAGGTACCACTAATGCAAGTTAGATGACG
65 CAAGTTAAATGCCTAA-AGATGCATTTTT-TATAGAAAGGTACCACTAATGCAAGTTAGACGAAA
* **
11286 AATAATGCATTTTTGGCAGAAATGTGCGGACTAATGCAAGTTAAATG
128 AATAATGCATTTTTGGCAGAAATGTGCGCACTAATAAAAGTTAAATG
11333 TCTAACGGTG
Statistics
Matches: 151, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
182 87 0.58
183 62 0.41
184 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (182 bp):
AAGGTACCACTAATGCAAGTTAGACGACGAATGGTGCATTTTTGGCAGAAAAGCGCCACTAATGC
AAGTTAAATGCCTAAAGATGCATTTTTTATAGAAAGGTACCACTAATGCAAGTTAGACGAAAAAT
AATGCATTTTTGGCAGAAATGTGCGCACTAATAAAAGTTAAATGCCAATGGT
Found at i:11269 original size:49 final size:49
Alignment explanation
Indices: 11168--11382 Score: 205
Period size: 49 Copynumber: 4.3 Consensus size: 49
11158 AAGGTACCAT
* * * ** * * * *
11168 TAATGTAAGTTAGATGACGAATGGTGCATTTTTTGGCAGAAAAGCGTCAC
1 TAATGCAAGTTAAATGACTAACAGTGCA-TTTTTGGTAGAAATGTGCCAC
* * * *
11218 TAATGCAAGTTAAATGCCTAACAGTGCATTTTTGTTAGAAAGGTACCAC
1 TAATGCAAGTTAAATGACTAACAGTGCATTTTTGGTAGAAATGTGCCAC
* * * * * *
11267 TAATGCAAGTTAGATGACGAATAATGCATTTTTGGCAGAAATGTGCGGAC
1 TAATGCAAGTTAAATGACTAACAGTGCATTTTTGGTAGAAATGTGC-CAC
* * *
11317 TAATGCAAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAATATGCCAC
1 TAATGCAAGTTAAATGACTAACAGTGCATTTTTGGTAGAAATGTGCCAC
*
11366 TAATGCAAGTTAGATGA
1 TAATGCAAGTTAAATGA
11383 AAAACGATGC
Statistics
Matches: 131, Mismatches: 33, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
49 69 0.53
50 62 0.47
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (49 bp):
TAATGCAAGTTAAATGACTAACAGTGCATTTTTGGTAGAAATGTGCCAC
Found at i:11286 original size:99 final size:98
Alignment explanation
Indices: 11158--11382 Score: 308
Period size: 99 Copynumber: 2.3 Consensus size: 98
11148 TGCCAATGGT
* * **
11158 AAGGTACCATTAATGTAAGTTAGATGACGAATGGTGCATTTTTTGGCAGAAA-AGCGTCACTAAT
1 AAGGTACCACTAATGCAAGTTAGATGACGAATAATGCA-TTTTTGGCAGAAAGAGCG-CACTAAT
*
11222 GCAAGTTAAATGCCTAACAGTGCATTTTTGTTAGA
64 GCAAGTTAAATGCCTAACAGTGCATTTTTGGTAGA
* *
11257 AAGGTACCACTAATGCAAGTTAGATGACGAATAATGCATTTTTGGCAGAAATGTGCGGACTAATG
1 AAGGTACCACTAATGCAAGTTAGATGACGAATAATGCATTTTTGGCAGAAA-GAGCGCACTAATG
* *
11322 CAAGTTAAATGTCTAACGGTGCATTTTTGGTAGA
65 CAAGTTAAATGCCTAACAGTGCATTTTTGGTAGA
** *
11356 AATATGCCACTAATGCAAGTTAGATGA
1 AAGGTACCACTAATGCAAGTTAGATGA
11383 AAAACGATGC
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
98 13 0.12
99 96 0.86
100 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (98 bp):
AAGGTACCACTAATGCAAGTTAGATGACGAATAATGCATTTTTGGCAGAAAGAGCGCACTAATGC
AAGTTAAATGCCTAACAGTGCATTTTTGGTAGA
Found at i:19856 original size:15 final size:15
Alignment explanation
Indices: 19833--19891 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
19823 TATTTTCAGG
* *
19833 TAGAGCATTTTCACT
1 TAGAACATTTTCACA
*
19848 TAGCACATTTTCACA
1 TAGAACATTTTCACA
*
19863 TAGAACATTTTCATA
1 TAGAACATTTTCACA
* *
19878 TAAAACATATTCAC
1 TAGAACATTTTCAC
19892 GTACCAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (15 bp):
TAGAACATTTTCACA
Found at i:25979 original size:16 final size:17
Alignment explanation
Indices: 25958--25991 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25948 AGGTGTCACA
*
25958 TTGACT-TTTTAAAACT
1 TTGACTCTTTGAAAACT
25974 TTGACTCTTTGAAAACT
1 TTGACTCTTTGAAAACT
25991 T
1 T
25992 GCTGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (17 bp):
TTGACTCTTTGAAAACT
Found at i:26892 original size:82 final size:82
Alignment explanation
Indices: 26708--26959 Score: 310
Period size: 83 Copynumber: 3.0 Consensus size: 82
26698 TACATATATC
* * * * *
26708 GTGGCGTTTATAGACAAACACCGCTAAAACCTAGTACTTTAGTGACGTTTTAAGTAAAAACACCG
1 GTGGCGTTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTTAAG-ACAAACATCG
*
26773 CTAAATACTCATAGTTTA
65 CTAAATACTCATACTTTA
* * *
26791 GTGGCATTTTTAGACAAACGCCGCTAAAACCTAGTACTTTACTGGCGTTTTTAGACAAACATCGC
1 GTGGCGTTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTTAAGACAAACATCGC
*
26856 TAAATACTCGTACTTTA
66 TAAATACTCATACTTTA
* * * *
26873 GTGGCGTTTTTTGACAAACGCTGCTAAATACTTA-TACTTTAGTGGCGTTTTAAG-CAAAAATGC
1 GTGGCGTTTTTAGACAAACGCCGCTAAA-ACCTAGTACTTTAGTGGCGTTTTAAGACAAACAT-C
* *
26936 TGCTAAATACGCATACATTA
64 -GCTAAATACTCATACTTTA
26956 GTGG
1 GTGG
26960 TTTTTTTATT
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
81 6 0.04
82 68 0.47
83 72 0.49
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (82 bp):
GTGGCGTTTTTAGACAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTTAAGACAAACATCGC
TAAATACTCATACTTTA
Found at i:26957 original size:42 final size:41
Alignment explanation
Indices: 26545--26959 Score: 224
Period size: 41 Copynumber: 10.1 Consensus size: 41
26535 GTAACATTAA
* * * *
26545 TGGCGTTTTTCA-ACAAACGCTGCTAAA-GCTCGTACTTTAG
1 TGGCGTTTTT-AGAAAAACGCCGCTAAATACTCATACTTTAG
* * * * * *
26585 TGGTGTTTATTTGACAAACGCCACTAAAGA-TAAGTACTTTAG
1 TGGCGTTT-TTAGAAAAACGCCGCTAAATACTCA-TACTTTAG
* * * * * * *
26627 TGGCGTTTGTA-AACAAACGCCGCCATAGAATCGTTCTTTAG
1 TGGCGTTTTTAGAA-AAACGCCGCTAAATACTCATACTTTAG
* * * *
26668 TGGCGTTTTTA-AACAAACGCC-AT-AATAGGGTACATA-TATCG
1 TGGCGTTTTTAGAA-AAACGCCGCTAAATA--CT-CATACTTTAG
* * *
26709 TGGCGTTTATAGACAAACACCGCTAAA-AC-CTAGTACTTTAG
1 TGGCGTTTTTAGAAAAACGCCGCTAAATACTC-A-TACTTTAG
* * * *
26750 TGACGTTTTAAGTAAAAACACCGCTAAATACTCATAGTTTAG
1 TGGCGTTTTTAG-AAAAACGCCGCTAAATACTCATACTTTAG
* * *
26792 TGGCATTTTTAGACAAACGCCGCTAAA-AC-CTAGTACTTTAC
1 TGGCGTTTTTAGAAAAACGCCGCTAAATACTC-A-TACTTTAG
* ** *
26833 TGGCGTTTTTAGACAAACATCGCTAAATACTCGTACTTTAG
1 TGGCGTTTTTAGAAAAACGCCGCTAAATACTCATACTTTAG
* * * *
26874 TGGCGTTTTTTGACAAACGCTGCTAAATACTTATACTTTAG
1 TGGCGTTTTTAGAAAAACGCCGCTAAATACTCATACTTTAG
* * * * *
26915 TGGCGTTTTAAGCAAAAATGCTGCTAAATACGCATACATTAG
1 TGGCGTTTTTAG-AAAAACGCCGCTAAATACTCATACTTTAG
26957 TGG
1 TGG
26960 TTTTTTTATT
Statistics
Matches: 288, Mismatches: 64, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 4 0.01
40 13 0.05
41 183 0.64
42 80 0.28
43 6 0.02
44 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (41 bp):
TGGCGTTTTTAGAAAAACGCCGCTAAATACTCATACTTTAG
Found at i:35422 original size:29 final size:28
Alignment explanation
Indices: 35333--35456 Score: 106
Period size: 29 Copynumber: 4.4 Consensus size: 28
35323 CATTTTACAC
35333 AAATAGCACCATTTTCGAATTAATTCCCA
1 AAATAGCACCA-TTTCGAATTAATTCCCA
* *** * * *
35362 AAATATCATTTTTTCGAA-AAATTACTA
1 AAATAGCACCATTTCGAATTAATTCCCA
35389 AAATAGCAACCATTTCGAATTAATTCCCA
1 AAATAGC-ACCATTTCGAATTAATTCCCA
* ***
35418 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACC-ATTTCGAATTAATTCCCA
*
35447 GAATAGCACC
1 AAATAGCACC
35457 GGTCAACGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
27 12 0.16
28 18 0.24
29 44 0.59
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (28 bp):
AAATAGCACCATTTCGAATTAATTCCCA
Found at i:35489 original size:13 final size:13
Alignment explanation
Indices: 35471--35512 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
35461 AACGGTCAAC
35471 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35484 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
35496 GGTAAACGGGTCG
1 GGTCAACGGGTCG
35509 GGTC
1 GGTC
35513 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:35514 original size:18 final size:18
Alignment explanation
Indices: 35491--35544 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
35481 TCGGGTCAAC
35491 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
35509 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
35527 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
35545 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:35544 original size:13 final size:13
Alignment explanation
Indices: 35475--35511 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
35465 GTCAACGGTC
*
35475 AACGGGTCGGGTC
1 AACGGGTCGGGTA
35488 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
35500 AACGGGTCGGGT
1 AACGGGTCGGGT
35512 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:35567 original size:10 final size:10
Alignment explanation
Indices: 35547--35601 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
35537 ACGGGTCGTG
35547 ACCGGTC-AA
1 ACCGGTCAAA
35556 ACCGGTCAAA
1 ACCGGTCAAA
35566 ACCGGTTCAAA
1 ACCGG-TCAAA
*
35577 ACCGGT-TAA
1 ACCGGTCAAA
35586 ACCGGTCAAA
1 ACCGGTCAAA
35596 ACCGGT
1 ACCGGT
35602 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:35602 original size:19 final size:19
Alignment explanation
Indices: 35547--35602 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
35537 ACGGGTCGTG
*
35547 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
35566 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
35586 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
35603 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:35640 original size:9 final size:9
Alignment explanation
Indices: 35626--35651 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35616 CGCCTGCGGC
35626 GGCGCGTGT
1 GGCGCGTGT
35635 GGCGCGTGT
1 GGCGCGTGT
35644 GGCGCGTG
1 GGCGCGTG
35652 CGACGTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (9 bp):
GGCGCGTGT
Found at i:42752 original size:29 final size:29
Alignment explanation
Indices: 42662--42786 Score: 101
Period size: 29 Copynumber: 4.3 Consensus size: 29
42652 CATTTTACAC
42662 AAATAGCA-CCATTTTCGAATTAATTCCCA
1 AAATAGCACCCA-TTTCGAATTAATTCCCA
* **** * * *
42691 AAATATCATTTTTTTCGAA-AAATTACTA
1 AAATAGCACCCATTTCGAATTAATTCCCA
42719 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
* * ***
42748 GAATAGCACCAAAACCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAATTAATTCCCA
*
42777 GAATAGCACC
1 AAATAGCACC
42787 GGTTAACGGT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 20 0.27
29 54 0.73
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCGAATTAATTCCCA
Found at i:42826 original size:12 final size:13
Alignment explanation
Indices: 42801--42855 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
42791 AACGGTCAAC
42801 GGTCAACGGGTCG
1 GGTCAACGGGTCG
42814 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
42826 GGTAAACGGGTCG
1 GGTCAACGGGTCG
* * *
42839 GGTAAACTGGTAG
1 GGTCAACGGGTCG
42852 GGTC
1 GGTC
42856 GGGTAAACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.30
13 26 0.70
ACGTcount: A:0.20, C:0.18, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:42892 original size:10 final size:10
Alignment explanation
Indices: 42872--42926 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
42862 ACGGGTCGTG
42872 ACCGGTC-AA
1 ACCGGTCAAA
42881 ACCGGTCAAA
1 ACCGGTCAAA
42891 ACCGGTTCAAA
1 ACCGG-TCAAA
*
42902 ACCGGT-TAA
1 ACCGGTCAAA
42911 ACCGGTCAAA
1 ACCGGTCAAA
42921 ACCGGT
1 ACCGGT
42927 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:42927 original size:19 final size:19
Alignment explanation
Indices: 42872--42927 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
42862 ACGGGTCGTG
*
42872 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
42891 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
42911 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
42928 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:43567 original size:25 final size:24
Alignment explanation
Indices: 43501--43567 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
43491 TGCCACATAG
43501 ATTTGTCCTGAAGTACCACGTAGAA
1 ATTTGTCCTGAAG-ACCACGTAGAA
* * *
43526 AATTATCCCGAAGGACCACGTAGAA
1 ATTTGTCCTGAA-GACCACGTAGAA
*
43551 TTTTGTCCTGAATGACC
1 ATTTGTCCTGAA-GACC
43568 GTCTAAAACC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (24 bp):
ATTTGTCCTGAAGACCACGTAGAA
Found at i:43724 original size:15 final size:14
Alignment explanation
Indices: 43706--43758 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
43696 CACATAGGGT
43706 ATTTTCATGTAGAAC
1 ATTTTCAT-TAGAAC
*
43721 ATTTTCACTTAGCAC
1 ATTTTCA-TTAGAAC
*
43736 ATTTTCACATAGAAC
1 ATTTTCA-TTAGAAC
43751 ATTTTCAT
1 ATTTTCAT
43759 AAAAAAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 32 0.97
16 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (14 bp):
ATTTTCATTAGAAC
Found at i:45857 original size:4 final size:4
Alignment explanation
Indices: 45848--45893 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
45838 TTAACACGTG
45848 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
45894 GAAAACTCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:46477 original size:20 final size:21
Alignment explanation
Indices: 46452--46491 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
46442 TACTATGAAA
46452 TGGTTGAACAA-TATCGATAT
1 TGGTTGAACAAGTATCGATAT
*
46472 TGGTTGAAGAAGTATCGATA
1 TGGTTGAACAAGTATCGATA
46492 CTGATGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTGAACAAGTATCGATAT
Found at i:46512 original size:20 final size:20
Alignment explanation
Indices: 46483--46534 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
46473 GGTTGAAGAA
* * *
46483 GTATCGATACTGATGTTAAG
1 GTATCAATACTGAGGATAAG
**
46503 GTATCAATACCAAGGATAAG
1 GTATCAATACTGAGGATAAG
46523 GTATCAATACTG
1 GTATCAATACTG
46535 TAAGTAAAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
GTATCAATACTGAGGATAAG
Found at i:47424 original size:46 final size:46
Alignment explanation
Indices: 47371--47461 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
47361 GTCGAGGGTT
* *
47371 CTATGTGGTCCTTCGGGACAAAATTATGTGGTCATACGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAACTATGTAGTCATACGGGACAAAA
* *
47417 CTATGTGGTCCTTCGGGACAAACCTATGTAGTCATTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAAACTATGTAGTCATACGGGACAAA
47462 TATATGGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (46 bp):
CTATGTGGTCCTTCGGGACAAAACTATGTAGTCATACGGGACAAAA
Found at i:47467 original size:23 final size:23
Alignment explanation
Indices: 47371--47461 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
47361 GTCGAGGGTT
*
47371 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* *
47394 TTATGTGGTCATACGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* *
47417 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAA
*
47440 CTATGTAGTCATTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
47462 TATATGGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:49053 original size:21 final size:21
Alignment explanation
Indices: 49019--49059 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49009 CCTGAACTTT
*
49019 TCAAATTTTCAAAATCATACC
1 TCAAATTTTCAAAAACATACC
49040 TCAAAGTTTT-AAAAACATAC
1 TCAAA-TTTTCAAAAACATAC
49060 TTTTTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (21 bp):
TCAAATTTTCAAAAACATACC
Found at i:49787 original size:19 final size:17
Alignment explanation
Indices: 49750--49788 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
49740 ATACACATCC
49750 CTTTTTATCATCTTAAA
1 CTTTTTATCATCTTAAA
*
49767 CTTTTCTATCAATCTTTAA
1 CTTTT-TATC-ATCTTAAA
49786 CTT
1 CTT
49789 CATTCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTTTTATCATCTTAAA
Found at i:53595 original size:36 final size:36
Alignment explanation
Indices: 53543--53645 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
53533 AGTTGAGTAT
*
53543 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* * *
53579 TATCAACTTTGGTACATTCATGTATCAATGTTATTA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
53615 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
53646 CTAGCAACGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:61109 original size:36 final size:36
Alignment explanation
Indices: 61062--61158 Score: 167
Period size: 36 Copynumber: 2.7 Consensus size: 36
61052 GTATTATTAG
*
61062 CTTTGATACATTCGTGTATCAATGTTACCATATCAA
1 CTTTGGTACATTCGTGTATCAATGTTACCATATCAA
* *
61098 CTTTGGTACATTCGTGTATCAATGTTATCATATCAG
1 CTTTGGTACATTCGTGTATCAATGTTACCATATCAA
61134 CTTTGGTACATTCGTGTATCAATGT
1 CTTTGGTACATTCGTGTATCAATGT
61159 CCAGCACCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTTGGTACATTCGTGTATCAATGTTACCATATCAA
Found at i:65906 original size:11 final size:11
Alignment explanation
Indices: 65890--65934 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
65880 GAAAACAACG
65890 AAAAGAAAAGA
1 AAAAGAAAAGA
65901 AAAAGAAAAGA
1 AAAAGAAAAGA
*
65912 AAGA-AAAAGA
1 AAAAGAAAAGA
*
65922 AAGAAAAAAAGA
1 AA-AAGAAAAGA
65934 A
1 A
65935 CAAATCAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 8 0.27
11 15 0.50
12 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:65907 original size:25 final size:25
Alignment explanation
Indices: 65879--65938 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
65869 AAATAGAGAG
*
65879 AGAAAACAACG-AAAAGAAAAGAAAA
1 AGAAAACAAAGAAAAAG-AAAGAAAA
*
65904 AGAAAAGAAAGAAAAAGAAAGAAAA
1 AGAAAACAAAGAAAAAGAAAGAAAA
65929 A-AAGAACAAA
1 AGAA-AACAAA
65939 TCAGTACTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 23 0.77
26 5 0.17
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (25 bp):
AGAAAACAAAGAAAAAGAAAGAAAA
Found at i:65919 original size:10 final size:10
Alignment explanation
Indices: 65891--65929 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
65881 AAAACAACGA
65891 AAAG-AAAAG
1 AAAGAAAAAG
*
65900 AAAAAGAAAAG
1 AAAGA-AAAAG
65911 AAAGAAAAAG
1 AAAGAAAAAG
65921 AAAGAAAAA
1 AAAGAAAAA
65930 AAGAACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 14 0.54
11 9 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Done.