Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 27
Found at i:5833573 original size:142 final size:137
Alignment explanation
Indices: 5833321--5833659 Score: 506
Period size: 142 Copynumber: 2.4 Consensus size: 137
5833311 CGGAAAATAC
* * *
5833321 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAACA-GAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
5833384 TGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
5833449 GCGAAATGAA
128 GCGAAATGAA
5833459 AATCGCAATGCGAAATGAAAATCGAACAGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACAGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
5833524 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 --TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
5833589 ATGCGAAATGAA
126 ATGCGAAATGAA
5833601 AATCGCAATGCGAAATGAAAATCGCAAC-GAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACAGA-ATAATCGCAATGCGAAATTA-AAATCGCA
5833660 TTGCGATTTT
Statistics
Matches: 186, Mismatches: 6, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 19 0.10
138 33 0.18
139 3 0.02
142 123 0.66
143 6 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACAGAATAATCGCAATGCGAAATTAAAATCGCAAACGTGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:5833765 original size:19 final size:19
Alignment explanation
Indices: 5833656--5833757 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5833646 AAATTATAAA
5833656 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5833675 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
5833695 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
5833711 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5833728 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5833747 CGCATTGCGAT
1 CGCATTGCGAT
5833758 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:5833889 original size:14 final size:14
Alignment explanation
Indices: 5833870--5833906 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5833860 CATCAATTAC
5833870 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5833884 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5833898 ACAAATCAA
1 ACAAATCAA
5833907 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5833918 original size:12 final size:12
Alignment explanation
Indices: 5833901--5833972 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
5833891 ATCTTTTACA
5833901 AATCAATTAAAC
1 AATCAATTAAAC
*
5833913 AATCAA--AAATTG
1 AATCAATTAAA--C
**
5833925 AATCAACTTTTAC
1 AATCAA-TTAAAC
5833938 AAATCAATTAAAC
1 A-ATCAATTAAAC
5833951 AATCAA--AAAC
1 AATCAATTAAAC
5833961 AATCAATTAAAC
1 AATCAATTAAAC
5833973 TATTGAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
10 13 0.28
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:5833935 original size:38 final size:38
Alignment explanation
Indices: 5833887--5833959 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
5833877 AACTTTTACA
*
5833887 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
5833925 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
5833960 CAATCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:5835846 original size:14 final size:14
Alignment explanation
Indices: 5835827--5835883 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5835817 GCGAAATGAA
*
5835827 AATCGCAACGACAG
1 AATCGCAACGAAAG
5835841 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5835858 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5835874 AATCGCAACG
1 AATCGCAACG
5835884 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5835854 original size:33 final size:33
Alignment explanation
Indices: 5835808--5835900 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5835798 GCGAAACCAA
*
5835808 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5835841 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5835874 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5835901 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5835865 original size:19 final size:19
Alignment explanation
Indices: 5835771--5835905 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5835761 TAGTTTACTT
* *
5835771 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5835791 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5835810 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5835829 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5835843 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5835862 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5835876 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5835895 TCGCAATGCGA
1 TCGCAACGCGA
5835906 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5835923 original size:19 final size:18
Alignment explanation
Indices: 5835901--5836028 Score: 92
Period size: 19 Copynumber: 7.3 Consensus size: 18
5835891 AAAATCGCAA
5835901 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
5835920 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
* *
5835934 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCGT
*
5835953 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
5835967 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
5835986 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
* *
5836005 TGCGATTTAAGTTTCGTGT
1 TGCGATTT-TGTTTCGCGT
5836024 TGCGA
1 TGCGA
5836029 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
14 21 0.25
16 2 0.02
17 2 0.02
18 1 0.01
19 59 0.69
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:5835949 original size:33 final size:33
Alignment explanation
Indices: 5835901--5835992 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
5835891 AAAATCGCAA
**
5835901 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTC-TGTCGT
*
5835934 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
5835967 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
5835993 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:5836347 original size:93 final size:93
Alignment explanation
Indices: 5836072--5836542 Score: 921
Period size: 92 Copynumber: 5.1 Consensus size: 93
5836062 TTGAATGGAT
5836072 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836137 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5836165 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836229 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5836257 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836322 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5836350 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836414 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5836442 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAA-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836506 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5836534 AAATTTACT
1 AAATTTACT
5836543 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
92 228 0.61
93 148 0.39
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5836395 original size:185 final size:185
Alignment explanation
Indices: 5836072--5836542 Score: 919
Period size: 185 Copynumber: 2.6 Consensus size: 185
5836062 TTGAATGGAT
5836072 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836137 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
5836202 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5836257 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836322 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
5836387 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5836442 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAA-AATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5836506 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
5836543 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 44 0.15
185 226 0.79
186 15 0.05
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5838265 original size:14 final size:14
Alignment explanation
Indices: 5838246--5838335 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5838236 TTGAAATGAA
5838246 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5838260 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5838277 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5838293 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5838312 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5838326 AATCGCAACG
1 AATCGCAACG
5838336 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5838283 original size:33 final size:33
Alignment explanation
Indices: 5838238--5838352 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5838228 TCTTTTGGTT
5838238 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5838271 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5838304 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5838337 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5838353 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5838284 original size:19 final size:18
Alignment explanation
Indices: 5838245--5838357 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5838235 GTTGAAATGA
5838245 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5838260 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5838277 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5838293 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5838310 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
5838326 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5838343 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5838358 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5838388 original size:14 final size:14
Alignment explanation
Indices: 5838369--5838423 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5838359 TTTGGTTTCG
5838369 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5838383 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
5838402 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5838416 CGTTGCGA
1 CGTTGCGA
5838424 CAGTCATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5838586 original size:33 final size:33
Alignment explanation
Indices: 5838544--5838614 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5838534 AATACTAACT
*
5838544 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5838577 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5838610 TGAAA
1 TGAAA
5838615 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5838845 original size:22 final size:22
Alignment explanation
Indices: 5838794--5838847 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5838784 TGGTTGTGAG
*
5838794 GGATTTC-GCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5838815 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5838837 GGATTTCTTCG
1 GGATTTCTTCG
5838848 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5839018 original size:20 final size:20
Alignment explanation
Indices: 5838993--5839186 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
5838983 CTTTAAATAT
5838993 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5839013 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5839035 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5839054 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5839074 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5839094 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5839114 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5839134 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5839154 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5839174 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5839187 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5839180 original size:60 final size:60
Alignment explanation
Indices: 5838993--5839186 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
5838983 CTTTAAATAT
**
5838993 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
5839054 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
5839114 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
5839174 CGCGTTGCGATTT
1 CGCGTTGCGATTT
5839187 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:5839203 original size:21 final size:20
Alignment explanation
Indices: 5839179--5839255 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
5839169 ATATTCGCGT
5839179 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
5839200 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
5839220 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
5839242 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
5839256 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:5839266 original size:20 final size:20
Alignment explanation
Indices: 5839241--5839292 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5839231 AAGAATCGCG
*
5839241 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5839261 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5839281 TTGCGATTCTGG
1 TTGCGATTCTGG
5839293 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:5847849 original size:5 final size:5
Alignment explanation
Indices: 5847841--5847872 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5847831 TATCTTATCA
5847841 TTCTG TTCTG TTCTG TTCTG TTCT- TTCT- TTCT
1 TTCTG TTCTG TTCTG TTCTG TTCTG TTCTG TTCT
5847873 ATAAACTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.00, C:0.22, G:0.12, T:0.66
Consensus pattern (5 bp):
TTCTG
Found at i:5856288 original size:16 final size:16
Alignment explanation
Indices: 5856267--5856300 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5856257 AAAAATAGTC
5856267 AAGGAATATAAATTAT
1 AAGGAATATAAATTAT
5856283 AAGGAATATAAATTAT
1 AAGGAATATAAATTAT
5856299 AA
1 AA
5856301 ACATGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (16 bp):
AAGGAATATAAATTAT
Found at i:5858153 original size:3 final size:3
Alignment explanation
Indices: 5858145--5858181 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5858135 AAATGTCAAC
5858145 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5858182 GTCAACTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5859713 original size:33 final size:33
Alignment explanation
Indices: 5859629--5859715 Score: 140
Period size: 34 Copynumber: 2.6 Consensus size: 33
5859619 AAACAAGTAC
5859629 AATGTCAACTTTTATTATTATTTTTTATTATCA
1 AATGTCAACTTTTATTATTATTTTTTATTATCA
5859662 AATGTCAAACTTTTATTATTATTTTCTT-TTATCA
1 AATGTC-AACTTTTATTATTATTTT-TTATTATCA
*
5859696 AATGTCAGCTTTTATTATTA
1 AATGTCAACTTTTATTATTA
5859716 AAGATTATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 19 0.37
34 30 0.59
35 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (33 bp):
AATGTCAACTTTTATTATTATTTTTTATTATCA
Found at i:5862162 original size:28 final size:28
Alignment explanation
Indices: 5862122--5862186 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
5862112 GTTTATATCA
*
5862122 CTCCCTTGATATGCCCAACTACAAACAG
1 CTCCCTGGATATGCCCAACTACAAACAG
5862150 CTCCCTGGATATGCCCAACTACAAACAG
1 CTCCCTGGATATGCCCAACTACAAACAG
5862178 CTCCCTGGA
1 CTCCCTGGA
5862187 AATTCGGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.37, G:0.14, T:0.20
Consensus pattern (28 bp):
CTCCCTGGATATGCCCAACTACAAACAG
Found at i:5864713 original size:15 final size:16
Alignment explanation
Indices: 5864694--5864730 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5864684 TATAAACCTT
5864694 AATAATA-AATATTAAC
1 AATAATATAAT-TTAAC
5864710 -ATAATATAATTTAAC
1 AATAATATAATTTAAC
5864725 AATAAT
1 AATAAT
5864731 GTATAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATATAATTTAAC
Found at i:5865170 original size:59 final size:60
Alignment explanation
Indices: 5865078--5865198 Score: 181
Period size: 59 Copynumber: 2.0 Consensus size: 60
5865068 AAGCAAATGT
** * *
5865078 ATGTTTCACGTAACGTGCCTTATTAGAAGGGTGCTAGATCAATAAAATT-AAAAAATGGC
1 ATGTTTCACGTAACACGCCTCATTAAAAGGGTGCTAGATCAATAAAATTAAAAAAATGGC
* *
5865137 ATGTTTCACGTAACACGTCTCATTAAAAGGGTGCTAGATTAATAAAATTAAAAAAATGGC
1 ATGTTTCACGTAACACGCCTCATTAAAAGGGTGCTAGATCAATAAAATTAAAAAAATGGC
5865197 AT
1 AT
5865199 CTGACAGGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
59 43 0.78
60 12 0.22
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (60 bp):
ATGTTTCACGTAACACGCCTCATTAAAAGGGTGCTAGATCAATAAAATTAAAAAAATGGC
Found at i:5865994 original size:18 final size:19
Alignment explanation
Indices: 5865954--5865997 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5865944 AAAACTAGTG
5865954 AATATTTTTAAAAAATTTA
1 AATATTTTTAAAAAATTTA
**
5865973 AATATTTTTTTAAAATTT-
1 AATATTTTTAAAAAATTTA
5865991 AATATTT
1 AATATTT
5865998 ACAAATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTTTTAAAAAATTTA
Found at i:5870269 original size:24 final size:26
Alignment explanation
Indices: 5870226--5870276 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
5870216 AAACACATTC
5870226 AAATTCAAGATTTATCTTTTAAAATT
1 AAATTCAAGATTTATCTTTTAAAATT
* *
5870252 AAATTCAA-A-TTATTTTTTAGAATT
1 AAATTCAAGATTTATCTTTTAAAATT
5870276 A
1 A
5870277 TCTTCTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 1 0.04
26 8 0.35
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (26 bp):
AAATTCAAGATTTATCTTTTAAAATT
Found at i:5870299 original size:23 final size:22
Alignment explanation
Indices: 5870262--5870311 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
5870252 AAATTCAAAT
5870262 TATTTTTTAGAATTATCTTCTA-
1 TATTTTTTAGAATTATCTT-TAG
*
5870284 TATTTTCTTAGGATTATCTTTAG
1 TATTTT-TTAGAATTATCTTTAG
5870307 TATTT
1 TATTT
5870312 CTAGGGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (22 bp):
TATTTTTTAGAATTATCTTTAG
Found at i:5875528 original size:22 final size:24
Alignment explanation
Indices: 5875503--5875552 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
5875493 AAATTCAAAT
* *
5875503 TATTTTTC-T-GAATTATGTTTTG
1 TATTTTTCTTAGAATTATCTTTAG
5875525 TA-TTTTCTTAGAATTATCTTTAG
1 TATTTTTCTTAGAATTATCTTTAG
5875548 TATTT
1 TATTT
5875553 CTAGGGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 3 0.13
23 13 0.57
24 2 0.09
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.62
Consensus pattern (24 bp):
TATTTTTCTTAGAATTATCTTTAG
Found at i:5883693 original size:21 final size:21
Alignment explanation
Indices: 5883644--5883694 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5883634 TTTTTAGCCG
5883644 TTTGTAACTCATATAATTACT
1 TTTGTAACTCATATAATTACT
* * *
5883665 TCTATAACTCATGTAATTA-T
1 TTTGTAACTCATATAATTACT
5883685 ATTTGTAACT
1 -TTTGTAACT
5883695 GACACCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTGTAACTCATATAATTACT
Found at i:5886178 original size:12 final size:12
Alignment explanation
Indices: 5886161--5886185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5886151 TTATATCGAT
5886161 TATGTACGTATA
1 TATGTACGTATA
5886173 TATGTACGTATA
1 TATGTACGTATA
5886185 T
1 T
5886186 TTAGGAGATT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TATGTACGTATA
Found at i:5891066 original size:20 final size:21
Alignment explanation
Indices: 5891027--5891066 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5891017 ACAAGATAAA
*
5891027 AATAATTGCATTACTGCAAGGC
1 AATAATTG-ATTAATGCAAGGC
5891049 AATAATTG-TTAATGCAAG
1 AATAATTGATTAATGCAAG
5891067 CATCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
AATAATTGATTAATGCAAGGC
Found at i:5892313 original size:22 final size:22
Alignment explanation
Indices: 5892286--5892356 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
5892276 TTCATTTCGT
5892286 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
* * **
5892308 GTTGCGAT--TTTCCAAAT-TC
1 GTTGCGATAGTCTACAGTTGTC
5892327 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
5892349 GTTGCGAT
1 GTTGCGAT
5892357 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 18 0.47
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTTGTC
Found at i:5892330 original size:19 final size:19
Alignment explanation
Indices: 5892306--5892374 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
5892296 TCTACAGTTG
5892306 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
5892325 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
5892346 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
5892366 TCGTTGCGA
1 TCGTTGCGA
5892375 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:5892331 original size:41 final size:41
Alignment explanation
Indices: 5892286--5892374 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
5892276 TTCATTTCGT
5892286 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
5892327 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
5892368 GTTGCGA
1 GTTGCGA
5892375 AAATTCGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
GTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
Found at i:5892994 original size:6 final size:6
Alignment explanation
Indices: 5892985--5893009 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5892975 GTCGTGGTCG
5892985 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
5893010 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:5893166 original size:20 final size:20
Alignment explanation
Indices: 5893141--5893192 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5893131 ACTGTAGACT
*
5893141 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
5893161 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
5893181 ATAGCAACGCGA
1 ATCGCAACGCGA
5893193 TTTTCAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:5894980 original size:21 final size:21
Alignment explanation
Indices: 5894951--5895006 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5894941 ATTCTGACTA
5894951 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
5894972 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
5894993 TCGCATTGCGATTT
1 TCGCATTGCGATTT
5895007 ACATAGCGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:5895561 original size:20 final size:20
Alignment explanation
Indices: 5895536--5895645 Score: 127
Period size: 19 Copynumber: 5.5 Consensus size: 20
5895526 TTCTAAACTT
*
5895536 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
5895556 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
5895576 ACTATCGCACCGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
5895597 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
5895616 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
5895635 AAAATCGCAAC
1 AAAATCGCAAC
5895646 GAGAGAATCG
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
19 35 0.44
20 29 0.37
21 15 0.19
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:5895597 original size:41 final size:38
Alignment explanation
Indices: 5895536--5895645 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 38
5895526 TTCTAAACTT
5895536 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-G-AAATGAAAATCGCAACACG-AAATG
** * *
5895576 ACTATCGCACCGAGAGAAATGAAAATCGCAACGCGAAATG
1 AAAATCGCAAC--GAGAAATGAAAATCGCAACACGAAATG
*
5895616 AAAATCGCAACGCGAAATGAAAATCGCAAC
1 AAAATCGCAACGAGAAATGAAAATCGCAAC
5895646 GAGAGAATCG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
38 18 0.31
40 21 0.36
41 18 0.31
42 1 0.02
43 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (38 bp):
AAAATCGCAACGAGAAATGAAAATCGCAACACGAAATG
Found at i:5895632 original size:60 final size:60
Alignment explanation
Indices: 5895536--5895652 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
5895526 TTCTAAACTT
* ** *
5895536 AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAATGACTATCGCACCGAGAGAAATG
1 AAAATCGCAACACGAAAATGAAAATCGCAACACG-AAATGAAAATCGCAACGAGAGAAATG
* *
5895597 AAAATCGCAACGCG-AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAATGAAAATCGCAACGAGAGAA
5895653 TCGCAACTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 20 0.40
60 18 0.36
61 12 0.24
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.11
Consensus pattern (60 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACACGAAATGAAAATCGCAACGAGAGAAATG
Found at i:5895665 original size:33 final size:36
Alignment explanation
Indices: 5895536--5895676 Score: 99
Period size: 33 Copynumber: 3.8 Consensus size: 36
5895526 TTCTAAACTT
**
5895536 AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATGAAAATCGCAAC-CG--AATG
** * *
5895576 ACTATCGCACCGAGAGAAATGAAAATCGCAACGCGAAATG
1 AAAATCGCAAC--GCGAAATGAAAATCGCAAC-CG-AATG
5895616 AAAATCGCAACGCGAAATGAAAATCGCAA-CG-A-G
1 AAAATCGCAACGCGAAATGAAAATCGCAACCGAATG
* * **
5895649 AGAATCGCAACTCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAATGAAAATCGCA
5895677 TTGCGATTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
33 25 0.29
34 1 0.01
36 2 0.02
38 17 0.20
40 21 0.25
41 18 0.21
42 1 0.01
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.11
Consensus pattern (36 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACCGAATG
Found at i:5895780 original size:20 final size:19
Alignment explanation
Indices: 5895672--5895803 Score: 157
Period size: 19 Copynumber: 7.1 Consensus size: 19
5895662 GAAACCAAAA
*
5895672 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5895691 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
5895710 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5895729 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
5895743 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
5895762 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
5895782 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5895802 TC
1 TC
5895804 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 3 0.03
19 49 0.51
20 32 0.33
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5897500 original size:18 final size:18
Alignment explanation
Indices: 5897454--5897503 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
5897444 TTTACTCGTA
*
5897454 ATTTCACTTAAATTAACC
1 ATTTCACTTAGATTAACC
5897472 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
5897490 ATTTCACTTAGATT
1 ATTTCACTTAGATT
5897504 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:5897724 original size:94 final size:94
Alignment explanation
Indices: 5897508--5897975 Score: 761
Period size: 94 Copynumber: 5.1 Consensus size: 94
5897498 TAGATTGCTT
* *
5897508 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
5897569 ATTTGTCTTT-TGTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5897596 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
5897661 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
5897690 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
5897755 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5897784 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
5897849 ATTTGTCTTTGTTTTGTCCTTTGATTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* ** * *
5897878 AGTAAATTTGTTCATTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
5897943 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
5897971 AGTAA
1 AGTAA
5897976 TGCAATCCAT
Statistics
Matches: 354, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
88 34 0.10
90 3 0.01
91 2 0.01
92 29 0.08
93 21 0.06
94 265 0.75
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5898093 original size:19 final size:19
Alignment explanation
Indices: 5898066--5898181 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
5898056 TCTTTTGGTT
*
5898066 GAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
5898085 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
5898104 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
* * *
5898121 G--A-GAGAATCACAACAC
1 GAAACGAAAATCGCAACGC
*
5898137 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
*
5898157 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
5898177 GAAAC
1 GAAAC
5898182 TATAATCGCG
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 34 0.41
20 34 0.41
ACGTcount: A:0.50, C:0.25, G:0.18, T:0.07
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:5898190 original size:19 final size:19
Alignment explanation
Indices: 5898072--5898181 Score: 104
Period size: 20 Copynumber: 5.9 Consensus size: 19
5898062 GGTTGAAATG
*
5898072 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAACA
**
5898091 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACA
*
5898110 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAACA
* * *
5898124 AGAATCACAACACGAAACCA
1 AAAATCGCAACGCGAAA-CA
5898144 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-CA
5898164 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
5898182 TATAATCGCG
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 29 0.37
20 34 0.44
ACGTcount: A:0.50, C:0.26, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:5898248 original size:19 final size:18
Alignment explanation
Indices: 5898224--5898303 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 18
5898214 CAATTCTCTC
5898224 GTTGCGATTTTCATTTCGT
1 GTTGCGATTTTCATTTC-T
*
5898243 GTTGCGA--TTC-TCTC-
1 GTTGCGATTTTCATTTCT
* *
5898257 GTTGCGATTTTCGTTTCGC
1 GTTGCGATTTTCATTTC-T
*
5898276 GTTACGATTTTCATTCTCT
1 GTTGCGATTTTCATT-TCT
5898295 CGTTGCGAT
1 -GTTGCGAT
5898304 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 7 0.15
16 6 0.12
17 6 0.12
19 20 0.42
20 9 0.19
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (18 bp):
GTTGCGATTTTCATTTCT
Found at i:5898274 original size:33 final size:33
Alignment explanation
Indices: 5898190--5898284 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 33
5898180 ACTATAATCG
* * *
5898190 CGTTGCGATTTTCATTCCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
5898223 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
5898256 CGTTGCGATTTTCGTTTCGCGTTACGATT
1 CGTTGCGATTTTCATTTCGCGTTGCGATT
5898285 TTCATTCTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:5898804 original size:21 final size:21
Alignment explanation
Indices: 5898780--5898846 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5898770 TCATTCCTCG
5898780 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5898801 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5898822 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5898843 AGAG
1 AGAG
5898847 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:5898804 original size:42 final size:42
Alignment explanation
Indices: 5898728--5898846 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
5898718 GACTCGCTTG
* * * * * * *
5898728 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
5898770 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
5898812 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
5898847 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:5900216 original size:14 final size:14
Alignment explanation
Indices: 5900197--5900232 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5900187 ATTGTTTAAT
5900197 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5900211 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5900225 TGATTTGT
1 TGATTTGT
5900233 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5900381 original size:33 final size:33
Alignment explanation
Indices: 5900339--5900470 Score: 203
Period size: 33 Copynumber: 4.0 Consensus size: 33
5900329 AAAAATGACT
*
5900339 ATCGCAATGCGAAATGAAAATCACAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
5900372 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
5900405 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
5900438 ATCGCAACGCGAAACT-AAAATCGCAACGCGAAA
1 ATCGCAATGCGAAA-TGAAAATCGCAACGAGAAA
5900471 CTAAATTCGC
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
33 90 0.99
34 1 0.01
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:5900390 original size:19 final size:18
Alignment explanation
Indices: 5900339--5900470 Score: 92
Period size: 19 Copynumber: 7.7 Consensus size: 18
5900329 AAAAATGACT
5900339 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5900358 ATCACAA-CG--A-GAAA
1 ATCGCAAGCGAAATGAAA
5900372 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5900391 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
5900405 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5900424 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
5900438 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
5900457 ATCGCAACGCGAAA
1 ATCGCAA-GCGAAA
5900471 CTAAATTCGC
Statistics
Matches: 92, Mismatches: 5, Indels: 32
0.71 0.04 0.25
Matches are distributed among these distances:
14 30 0.33
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 44 0.48
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:5900487 original size:19 final size:19
Alignment explanation
Indices: 5900404--5900481 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
5900394 GCAACGAGAG
*
5900404 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
5900423 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
5900437 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
5900456 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
5900475 ATTCGCA
1 AATCGCA
5900482 TTGCGATTCT
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 35 0.67
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:5900518 original size:33 final size:33
Alignment explanation
Indices: 5900476--5900554 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
5900466 CGAAACTAAA
* *
5900476 TTCGCATTGCGATTCTCTCGTTGCGATTTTCTT
1 TTCGCATTGCGATTCTCTCGTTGAGATTTTCAT
5900509 TTCGCATTGCGATTCTCTCGTTGAGATTTTCAT
1 TTCGCATTGCGATTCTCTCGTTGAGATTTTCAT
5900542 TTCGCATTGCGAT
1 TTCGCATTGCGAT
5900555 AGTCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
TTCGCATTGCGATTCTCTCGTTGAGATTTTCAT
Found at i:5900520 original size:19 final size:18
Alignment explanation
Indices: 5900476--5900554 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 18
5900466 CGAAACTAAA
5900476 TTCGCATTGCGA--TTCT
1 TTCGCATTGCGATTTTCT
*
5900492 CTCG--TTGCGATTTTCTT
1 TTCGCATTGCGATTTTC-T
5900509 TTCGCATTGCGA--TTCT
1 TTCGCATTGCGATTTTCT
* *
5900525 CTCG--TTGAGATTTTCAT
1 TTCGCATTGCGATTTTC-T
5900542 TTCGCATTGCGAT
1 TTCGCATTGCGAT
5900555 AGTCATTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 17
0.67 0.09 0.24
Matches are distributed among these distances:
14 11 0.23
16 13 0.28
17 11 0.23
19 12 0.26
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (18 bp):
TTCGCATTGCGATTTTCT
Found at i:5900581 original size:20 final size:19
Alignment explanation
Indices: 5900539--5900581 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5900529 TTGAGATTTT
* *
5900539 CATTTCGCATTGCGATAGT
1 CATTTCGCATTGCGAGAGA
*
5900558 CATTTCCGCGTTGCGAGAGA
1 CATTT-CGCATTGCGAGAGA
5900578 CATT
1 CATT
5900582 AAGATGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (19 bp):
CATTTCGCATTGCGAGAGA
Found at i:5900620 original size:20 final size:20
Alignment explanation
Indices: 5900548--5900620 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
5900538 TCATTTCGCA
* *
5900548 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTACGTG
* * *
5900568 TTGCGAGAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
5900588 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTACGTG
5900609 TTGCGATAGTCA
1 TTGCGATAGTCA
5900621 AATGAATGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:5903100 original size:24 final size:24
Alignment explanation
Indices: 5903066--5903119 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5903056 CTGAAAAATC
5903066 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
5903090 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
5903114 ATCAAA
1 ATCAAA
5903120 TTTTGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5904006 original size:20 final size:21
Alignment explanation
Indices: 5903983--5904111 Score: 115
Period size: 21 Copynumber: 6.3 Consensus size: 21
5903973 AGAATCTCGT
5903983 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
5904003 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
5904023 TGCGATTTTCCTAATTCG-AA
1 TGCGATTTACGTAAATCGCAA
*
5904043 TTGCGATTTACGT-AATCGCAT
1 -TGCGATTTACGTAAATCGCAA
* * *
5904064 TGCGATTTAGGAAAATCGTAA
1 TGCGATTTACGTAAATCGCAA
* * *
5904085 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
5904106 TGCGAT
1 TGCGAT
5904112 AGTCAGAATC
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.05
20 38 0.43
21 42 0.48
22 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:5904049 original size:21 final size:20
Alignment explanation
Indices: 5903982--5904072 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 20
5903972 CAGAATCTCG
5903982 TTGCGATTTA-CTAAATCGCAA
1 TTGCGATTTACCT-AATCG-AA
*
5904003 -TGCGA-TTACGTAAATCGCAA
1 TTGCGATTTACCT-AATCG-AA
*
5904023 -TGCGATTTTCCTAATTCGAA
1 TTGCGATTTACCTAA-TCGAA
* *
5904043 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACCTAATCGAA
5904063 TTGCGATTTA
1 TTGCGATTTA
5904073 GGAAAATCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.05
20 38 0.63
21 19 0.32
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACCTAATCGAA
Found at i:5918312 original size:2 final size:2
Alignment explanation
Indices: 5918305--5918329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5918295 GAATTCCTTA
5918305 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 A
5918330 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5918526 original size:20 final size:21
Alignment explanation
Indices: 5918501--5918539 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5918491 TTATATTGTG
*
5918501 ATTTATTGAGA-AGAAAAACA
1 ATTTATTAAGAGAGAAAAACA
5918521 ATTTATTAAGAGAGAAAAA
1 ATTTATTAAGAGAGAAAAA
5918540 TTGTGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (21 bp):
ATTTATTAAGAGAGAAAAACA
Found at i:5920764 original size:2 final size:2
Alignment explanation
Indices: 5920757--5920786 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5920747 TAATTTTTAA
5920757 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
5920787 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5920804 original size:22 final size:22
Alignment explanation
Indices: 5920755--5920822 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
5920745 TATAATTTTT
* *
5920755 AAATATATATATATATATA-TA
1 AAATATATATATTTATAAATTA
*
5920776 TATATATATATTATTT-TAAATTA
1 -AAATATATA-TATTTATAAATTA
* *
5920799 AAATATTTATATTTATATATTA
1 AAATATATATATTTATAAATTA
5920821 AA
1 AA
5920823 GAAACTCGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.14
22 26 0.70
23 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATATATATTTATAAATTA
Found at i:5921737 original size:17 final size:17
Alignment explanation
Indices: 5921717--5921751 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5921707 ACTCTCAGTG
5921717 ACATAATCTTTAATTAA
1 ACATAATCTTTAATTAA
5921734 ACATAATCTTTAATTAA
1 ACATAATCTTTAATTAA
5921751 A
1 A
5921752 TAAAAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (17 bp):
ACATAATCTTTAATTAA
Found at i:5922812 original size:33 final size:30
Alignment explanation
Indices: 5922769--5922844 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
5922759 TATTAAGGTA
* * *
5922769 TATTTTATTATATTTAGTATTTTTTTAGTAATT
1 TATTTAATTATATTTA--A-TTGTTTAATAATT
*
5922802 TATTTAATTAT-TTTAATTGTTTAATATTT
1 TATTTAATTATATTTAATTGTTTAATAATT
5922831 TATTTAATTA-ATTT
1 TATTTAATTATATTT
5922845 TTTTTTGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 23 0.61
30 1 0.03
32 4 0.11
33 10 0.26
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
TATTTAATTATATTTAATTGTTTAATAATT
Found at i:5924294 original size:467 final size:468
Alignment explanation
Indices: 5923415--5924357 Score: 1703
Period size: 467 Copynumber: 2.0 Consensus size: 468
5923405 GCGTCTGACG
* *
5923415 ATGAAGTTAAACAGTATGCACGGGCATGCATACTGCAGCTGATAGGAGGGTTGCTGATGCCGGAC
1 ATGAATTTAAACAATATGCACGGGCATGCATACTGCAGCTGATAGGAGGGTTGCTGATGCCGGAC
*
5923480 AAATCGCGCAACCAAGTTCACTGTATGTGGTTGCAACATCTTGGCGACTTTTATCTGGCCGAATC
66 AAATCGCGCAACCAAGTTCACTGTATGTGGTTGCAACATCTTGGCGACTTTCATCTGGCCGAATC
5923545 ACTCAGTTGGGGCTCGGCAGTTTTGGCTTGCCTGTACAGGGAGATGTGTCGAGCCATTGACTACA
131 ACTCAGTTGGGGCTCGGCAGTTTTGGCTTGCCTGTACAGGGAGATGTGTCGAGCCATTGACTACA
* * * * * *
5923610 GGCGTAATGCTATCGGCGGATGTCTCCTGTTGCTGCAGTCTTGGGCAATGTATCGATTGTCCTTT
196 AGCGTAATACTATCCGCGGATGTCCCCTGCTGCTGCAGTCTTGGGCAATGTATCGATTGCCCTTT
*
5923675 TTATGTCCCGTTGTCAAGAACCCATTCGTATTTCCGCTACTCCTGAGGTAATTATAAAACTGATT
261 TTATGTCCCGTTGTCAAGAACCCATTCGTATTTCAGCTACTCCTGAGGTAATTATAAAACTGATT
*
5923740 TTGTATATTAATAATTTTATACAGTGAATAAGAAATTATTTTTCTTGAATATGTGGTCTACTGAT
326 TTGTATATTAATAATTTTATACAGTGAATAAGAAATTATTTTTCTTGAATAGGTGGTCTACTGAT
5923805 AGGAAAAATCATCAGGAGCTACCTAATGATTTAG-AAAAAATTAGGGTGTTAATCGATCAGAAGG
391 AGGAAAAATCATCAGGAGCTACCTAATGATTTAGAAAAAAATTAGGGTGTTAATCGATCAGAAGG
*
5923869 CTGACATACATGT
456 CTGACACACATGT
5923882 ATGAATTTAAACAATATGCACGGGCATGCATACTGCAGCTGATAGGAGGGTTGCTGATGCCGGAC
1 ATGAATTTAAACAATATGCACGGGCATGCATACTGCAGCTGATAGGAGGGTTGCTGATGCCGGAC
5923947 AAATCGCGCAACCAAGTTCACTGTATGTGGTTGCAACATCTTGGCGACTTTCATCTGGCC-AGAT
66 AAATCGCGCAACCAAGTTCACTGTATGTGGTTGCAACATCTTGGCGACTTTCATCTGGCCGA-AT
* *
5924011 CACTTAGTTGGGGCTCGGCAGTTTTGGCTTGCCTGTACAGTGAGATGTGTCGAGCCATTGACTAC
130 CACTCAGTTGGGGCTCGGCAGTTTTGGCTTGCCTGTACAGGGAGATGTGTCGAGCCATTGACTAC
5924076 AAGCGTAATACTATCCGCGGATGTCCCCTGCTGCTGCAGTCTTGGG-AATGGTATCGATTGCCCT
195 AAGCGTAATACTATCCGCGGATGTCCCCTGCTGCTGCAGTCTTGGGCAAT-GTATCGATTGCCCT
5924140 TTTTATGTCCCGTTGTCAAGAACCCATTCGTATTTCAGCTACTCCTGAGGTAATTATAAAACTGA
259 TTTTATGTCCCGTTGTCAAGAACCCATTCGTATTTCAGCTACTCCTGAGGTAATTATAAAACTGA
5924205 TTTTGTATATTAATAATTTTATACAGTGAATAAGAAATTATTTTTCTTGAATAGGTGGTCTACTG
324 TTTTGTATATTAATAATTTTATACAGTGAATAAGAAATTATTTTTCTTGAATAGGTGGTCTACTG
* *
5924270 ATAGGAAAAATCATTAGGAGCTACCTGATGATTTAGAAAAAAATTAGGGTGTTAATCGATCAGAA
389 ATAGGAAAAATCATCAGGAGCTACCTAATGATTTAGAAAAAAATTAGGGTGTTAATCGATCAGAA
5924335 GGCTGACACACATGT
454 GGCTGACACACATGT
5924350 ATGAATTT
1 ATGAATTT
5924358 TAATGTTTAA
Statistics
Matches: 457, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
466 4 0.01
467 403 0.88
468 50 0.11
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (468 bp):
ATGAATTTAAACAATATGCACGGGCATGCATACTGCAGCTGATAGGAGGGTTGCTGATGCCGGAC
AAATCGCGCAACCAAGTTCACTGTATGTGGTTGCAACATCTTGGCGACTTTCATCTGGCCGAATC
ACTCAGTTGGGGCTCGGCAGTTTTGGCTTGCCTGTACAGGGAGATGTGTCGAGCCATTGACTACA
AGCGTAATACTATCCGCGGATGTCCCCTGCTGCTGCAGTCTTGGGCAATGTATCGATTGCCCTTT
TTATGTCCCGTTGTCAAGAACCCATTCGTATTTCAGCTACTCCTGAGGTAATTATAAAACTGATT
TTGTATATTAATAATTTTATACAGTGAATAAGAAATTATTTTTCTTGAATAGGTGGTCTACTGAT
AGGAAAAATCATCAGGAGCTACCTAATGATTTAGAAAAAAATTAGGGTGTTAATCGATCAGAAGG
CTGACACACATGT
Found at i:5929367 original size:21 final size:23
Alignment explanation
Indices: 5929326--5929373 Score: 73
Period size: 21 Copynumber: 2.1 Consensus size: 23
5929316 TAGGTCAATA
5929326 ATAAAATATATTTAATAAGTTAAT
1 ATAAAATATATTT-ATAAGTTAAT
5929350 ATAAAA-ATATTT-TAAGTTAAT
1 ATAAAATATATTTATAAGTTAAT
5929371 ATA
1 ATA
5929374 TATAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.50
23 6 0.25
24 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
ATAAAATATATTTATAAGTTAAT
Found at i:5937024 original size:14 final size:14
Alignment explanation
Indices: 5937005--5937071 Score: 97
Period size: 14 Copynumber: 5.1 Consensus size: 14
5936995 CGTTTGTGAA
5937005 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5937019 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5937033 CGTTCGGTTATG-T
1 CGTTCGGTTATGTT
*
5937046 --TT-GTTTATGTT
1 CGTTCGGTTATGTT
5937057 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5937071 C
1 C
5937072 TTTTATGTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 6 0.13
11 3 0.06
13 3 0.06
14 35 0.74
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:5937053 original size:24 final size:24
Alignment explanation
Indices: 5937005--5937084 Score: 108
Period size: 24 Copynumber: 3.2 Consensus size: 24
5936995 CGTTTGTGAA
5937005 CGTTCGGTTATGTTCGTTCGGTTATGTT
1 CGTTCGGTTATGTTC-TT---TTATGTT
5937033 CGTTCGGTTATGTT-TGTTTATGTT
1 CGTTCGGTTATGTTCT-TTTATGTT
5937057 CGTTCGGTTATGTTCTTTTATGTT
1 CGTTCGGTTATGTTCTTTTATGTT
5937081 CGTT
1 CGTT
5937085 TATTTATGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
24 33 0.66
25 1 0.02
26 1 0.02
27 1 0.02
28 14 0.28
ACGTcount: A:0.07, C:0.12, G:0.25, T:0.55
Consensus pattern (24 bp):
CGTTCGGTTATGTTCTTTTATGTT
Found at i:5937091 original size:38 final size:38
Alignment explanation
Indices: 5937012--5937094 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
5937002 GAACGTTCGG
* * *
5937012 TTATGTTCGTTCGGTTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGGTTATGTTCGTTAGGTTACGTTTAT
* *
5937050 TTATGTTCGTTCGGTTATGTTCTTTTATGTT-CGTTTAT
1 TTATGTTCGTTCGGTTATGTTC-GTTAGGTTACGTTTAT
5937088 TTATGTT
1 TTATGTT
5937095 TAACTCAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.59
Consensus pattern (38 bp):
TTATGTTCGTTCGGTTATGTTCGTTAGGTTACGTTTAT
Found at i:5937463 original size:16 final size:16
Alignment explanation
Indices: 5937444--5937508 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
5937434 CCAATGTTTA
*
5937444 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
5937460 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
5937476 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5937492 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5937508 T
1 T
5937509 TTACTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:5937490 original size:10 final size:10
Alignment explanation
Indices: 5937439--5937511 Score: 57
Period size: 10 Copynumber: 7.5 Consensus size: 10
5937429 GGTCTCCAAT
*
5937439 GTTTATGTTT
1 GTTTATGTTC
5937449 GTTTATGTTC
1 GTTTATGTTC
*
5937459 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
*
5937471 GTTCATGTTC
1 GTTTATGTTC
5937481 GTTTATGTTC
1 GTTTATGTTC
5937491 G----TGTTC
1 GTTTATGTTC
5937497 GTTTATGTTC
1 GTTTATGTTC
5937507 GTTTA
1 GTTTA
5937512 CTTATTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
6 6 0.12
10 33 0.66
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:5937599 original size:16 final size:16
Alignment explanation
Indices: 5937578--5937610 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5937568 AAAAAAATTT
5937578 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5937594 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5937610 T
1 T
5937611 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:5940509 original size:18 final size:18
Alignment explanation
Indices: 5940474--5940521 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5940464 AATTGCGCTC
* *
5940474 AATTTAATTTTTTTTTAA
1 AATTTAATTTATTATTAA
*
5940492 AATTTTATTTATTATTAAA
1 AATTTAATTTATTATT-AA
5940511 GAATTTAATTT
1 -AATTTAATTT
5940522 TAATTAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTAATTTATTATTAA
Found at i:5940527 original size:19 final size:18
Alignment explanation
Indices: 5940474--5940528 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
5940464 AATTGCGCTC
* *
5940474 AATTTAATTTTTTTTTAA
1 AATTTAATTTTTATTAAA
*
5940492 AATTTTATTTATTATTAAA
1 AATTTAATTT-TTATTAAA
*
5940511 GAATTTAATTTTAATTAA
1 -AATTTAATTTTTATTAA
5940529 CTTGATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 9 0.30
19 12 0.40
20 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTTAATTTTTATTAAA
Found at i:5949162 original size:163 final size:164
Alignment explanation
Indices: 5948668--5949328 Score: 1209
Period size: 164 Copynumber: 4.0 Consensus size: 164
5948658 TACGGTCAAC
*
5948668 GACGACAGACCATTGCAGACAGAAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTAAAAAAA
1 GACGACAGACCATTGCAGACAG-AAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAA
5948733 TGAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGG
65 TGAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGG
5948798 GAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
130 GAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
5948833 GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAAA
1 GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTT-AAAAAA
5948898 TGAGACGCGAAAATAACCGAAGATTTTTTTT-TATAATTTAGCCGGCATAGTCTGCCATTCATGG
65 TGAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGG
5948962 GAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
130 GAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
*
5948997 GACTACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAAT
1 GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAAT
*
5949062 GAGACGCGAAAATAACCGCAGA-TTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGG
66 GAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGG
5949126 AAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
131 AAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
*** *
5949160 GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAATTTACTGAACACCAGTCTTTAAAAAAT
1 GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAAT
*
5949225 GAGAAGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGG
66 GAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGG
*
5949290 AAGCCACGTTGAAGAAGCTTTAATCAAAGTATAT
131 AAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
5949324 GACGA
1 GACGA
5949329 ATCAAACGGC
Statistics
Matches: 482, Mismatches: 11, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
162 7 0.01
163 176 0.37
164 240 0.50
165 59 0.12
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (164 bp):
GACGACAGACCATTGCAGACAGAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAAT
GAGACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGG
AAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
Found at i:5949286 original size:327 final size:329
Alignment explanation
Indices: 5948672--5949326 Score: 1208
Period size: 327 Copynumber: 2.0 Consensus size: 329
5948662 GTCAACGACG
5948672 ACAGACCATTGCAGACAGAAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTAAAAAAATGAG
1 ACAGACCATTGCAGACAGAAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTAAAAAAATGAG
5948737 ACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGGAAG
66 ACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGGAAG
5948802 CCACGTTGAAGAAGCTTTAATCAAAGTAGATGACGACAGACCATTGCAGACAGAAAAACGATCCG
131 CCACGTTGAAGAAGCTTTAATCAAAGTAGATGACGACAGACCATTGCAGACAGAAAAACGATCCG
* *
5948867 CTAAAGCACTGAACACTAGTCTTTAAAAAAATGAGACGCGAAAATAACCGAAGATTTTTTTTTAT
196 CTAAAGCACTGAACACCAGTCTTTAAAAAAATGAGAAGCGAAAATAACCGAAGATTTTTTTTTAT
5948932 AATTTAGCCGGCATAGTCTGCCATTCATGGGAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
261 AATTTAGCCGGCATAGTCTGCCATTCATGGGAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
5948997 GACT
326 GACT
*
5949001 ACAGACCATTGCAGACAG-AAAAACGATCCGCTAAAGCACTGAACACTAGTCTTTAAAAAATGAG
1 ACAGACCATTGCAGACAGAAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTAAAAAAATGAG
*
5949065 ACGCGAAAATAACCGCAGA-TTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGGAAG
66 ACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGGAAG
5949129 CCACGTTGAAGAAGCTTTAATCAAAGTAGATGACGACAGACCATTGCAGACAGAAAAACGATCCG
131 CCACGTTGAAGAAGCTTTAATCAAAGTAGATGACGACAGACCATTGCAGACAGAAAAACGATCCG
***
5949194 CTAATTTACTGAACACCAGTCTTT-AAAAAATGAGAAGCGAAAATAACCGAAGATTTTTTTTATA
196 CTAAAGCACTGAACACCAGTCTTTAAAAAAATGAGAAGCGAAAATAACCGAAGATTTTTTTT-TA
*
5949258 TAATTTAGCCGGCATAGTCTGCCATTCATGGGAAGCCACGTTGAAGAAGCTTTAATCAAAGTATA
260 TAATTTAGCCGGCATAGTCTGCCATTCATGGGAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGA
5949323 TGAC
325 TGAC
5949327 GAATCAAACG
Statistics
Matches: 317, Mismatches: 8, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
326 36 0.11
327 200 0.63
328 63 0.20
329 18 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (329 bp):
ACAGACCATTGCAGACAGAAAAAACGATCCGCTAAAGCACTGAACACTAGTCTTAAAAAAATGAG
ACGCGAAAATAACCGAAGATTTTTTTTATATAATTTAGCCGGCATAGTCTGCCATTCATGGGAAG
CCACGTTGAAGAAGCTTTAATCAAAGTAGATGACGACAGACCATTGCAGACAGAAAAACGATCCG
CTAAAGCACTGAACACCAGTCTTTAAAAAAATGAGAAGCGAAAATAACCGAAGATTTTTTTTTAT
AATTTAGCCGGCATAGTCTGCCATTCATGGGAAGCCACGTTGAAGAAGCTTTAATCAAAGTAGAT
GACT
Found at i:5958402 original size:12 final size:13
Alignment explanation
Indices: 5958365--5958401 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
5958355 AAATTTTAAG
5958365 AAAAATATTTTTA
1 AAAAATATTTTTA
5958378 AAAAATATTTTTA
1 AAAAATATTTTTA
5958391 AAAAATATTTT
1 AAAAATATTTT
5958402 ATTTCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATATTTTTA
Found at i:5959457 original size:24 final size:25
Alignment explanation
Indices: 5959410--5959457 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5959400 CACATGATAC
**
5959410 AGTCGTAACTGCCAAAACTGAACGT
1 AGTCGTAACTGCCAAAACAAAACGT
*
5959435 AGTCGTAAC-GCTAAAACAAAACG
1 AGTCGTAACTGCCAAAACAAAACG
5959458 CACCTGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (25 bp):
AGTCGTAACTGCCAAAACAAAACGT
Found at i:5960146 original size:23 final size:23
Alignment explanation
Indices: 5960120--5960164 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5960110 CACCACAGCT
*
5960120 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
5960143 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
5960165 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:5961122 original size:22 final size:21
Alignment explanation
Indices: 5961097--5961154 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
5961087 TAATTCAATT
5961097 TCATATAACTCATATAATCTTC-
1 TCATATAACTCATA-AAT-TTCA
5961119 TCATATAACTTCATAAATTTCTA
1 TCATATAAC-TCATAAATTTC-A
*
5961142 TCATACAACTCAT
1 TCATATAACTCAT
5961155 GTGTTATAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 13 0.41
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (21 bp):
TCATATAACTCATAAATTTCA
Found at i:5961146 original size:23 final size:23
Alignment explanation
Indices: 5961097--5961140 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
5961087 TAATTCAATT
5961097 TCATATAAC-TCATATAATCTTC
1 TCATATAACTTCATATAATCTTC
5961119 TCATATAACTTCATA-AAT-TTC
1 TCATATAACTTCATATAATCTTC
5961140 T
1 T
5961141 ATCATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (23 bp):
TCATATAACTTCATATAATCTTC
Found at i:5961218 original size:18 final size:18
Alignment explanation
Indices: 5961197--5961231 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5961187 TCCCATCTAG
5961197 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
5961215 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
5961232 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:5961821 original size:64 final size:63
Alignment explanation
Indices: 5961723--5961883 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
5961713 TAATGAAGGT
* *
5961723 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
5961786 GG
62 GC
* *
5961788 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
5961852 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
5961884 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:5966775 original size:54 final size:54
Alignment explanation
Indices: 5966685--5967236 Score: 589
Period size: 54 Copynumber: 10.2 Consensus size: 54
5966675 CAAGACCGGT
* * * *
5966685 GGTCCAAGTTCCAGTGGAAAAGGCCATGCATTCGTTGACT-CTGTCACCAACTCA
1 GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGA-TGCTGTCACCAACTCA
* * * ** *
5966739 GGCCCAACTTCCAGAGGACATGGTAATGCATTCGTTGATG-TGGTCACCAACTCG
1 GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCT-GTCACCAACTCA
* * *
5966793 GGTCCAAGC-TCCGGCGGAAAAGGCCATGCATTCGTTGATGCTTTCACCAACTCA
1 GGTCCAA-CTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* * *
5966847 GGTCCAAGTTCCGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
1 GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* * * *
5966901 GGTCCAAGTTCCGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCAACAACTC-
1 GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* * * * * *
5966954 GGTTTCC-AGTTCCAGAGGACAAGGCCATGCACTCGTTGTTGCAGTCACCAACTCG
1 GG--TCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
**
5967009 GGTCCAAGC-TCCGGAGGACAAGGTAATGCATTCGTTGATGCTGTCACCAACTCA
1 GGTCCAA-CTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* * * * *
5967063 GGTCCAAGTTCCGGCGGAAAAGGCCATGCATTCGTTGACGCTGTCACCAACTCG
1 GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* ** *
5967117 GGTCCAAGC-TCCGGAAGACAAGGTAATGCATTCGTTGATGCTGTCACCAATTCA
1 GGTCCAA-CTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
** * * *
5967171 GGTCCAAGC-TCCGGAGGACAAGGTAATGCATTCGTTGACGCCGTCACCAAATCA
1 GGTCCAA-CTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
*
5967225 GGTCCAAGTTCC
1 GGTCCAACTTCC
5967237 AGTGGCGGTG
Statistics
Matches: 428, Mismatches: 57, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
53 7 0.02
54 414 0.97
55 7 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (54 bp):
GGTCCAACTTCCGGAGGACAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
Found at i:5966876 original size:108 final size:107
Alignment explanation
Indices: 5966685--5967232 Score: 652
Period size: 108 Copynumber: 5.1 Consensus size: 107
5966675 CAAGACCGGT
* * * * *
5966685 GGTCCAAGTTCCAGTGGAAAAGGCCATGCATTCGTTGACT-CTGTCACCAACTCAGGCCCAACTT
1 GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGA-TGCTGTCACCAACTCAGGTCCAAGTT
* * **
5966749 CCAGAGGACATGGTAATGCATTCGTTGATGTGGTCACCAACTCG
65 CCGGAGGACAAGGCCATGCATTCGTTGATGT-GTCACCAACTCG
* *
5966793 GGTCCAAGCTCCGGCGGAAAAGGCCATGCATTCGTTGATGCTTTCACCAACTCAGGTCCAAGTTC
1 GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
* * *
5966858 CGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCA
66 CGGAGGACAAGGCCATGCATTCGTTGATG-TGTCACCAACTCG
* * *
5966901 GGTCCAAGTTCCGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCAACAACTC-GGTTTCC-AGT
1 GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGG--TCCAAGT
* * * *
5966964 TCCAGAGGACAAGGCCATGCACTCGTTGTTGCAGTCACCAACTCG
64 TCCGGAGGACAAGGCCATGCATTCGTTGATG-TGTCACCAACTCG
* **
5967009 GGTCCAAGCTCCGGAGGACAAGGTAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
1 GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
* * *
5967074 CGGCGGAAAAGGCCATGCATTCGTTGACGCTGTCACCAACTCG
66 CGGAGGACAAGGCCATGCATTCGTTGATG-TGTCACCAACTCG
* * ** * *
5967117 GGTCCAAGCTCCGGAAGACAAGGTAATGCATTCGTTGATGCTGTCACCAATTCAGGTCCAAGCTC
1 GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
** * * * *
5967182 CGGAGGACAAGGTAATGCATTCGTTGACGCCGTCACCAAATCA
66 CGGAGGACAAGGCCATGCATTCGTTGATG-TGTCACCAACTCG
5967225 GGTCCAAG
1 GGTCCAAG
5967233 TTCCAGTGGC
Statistics
Matches: 387, Mismatches: 47, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
107 6 0.02
108 375 0.97
109 6 0.02
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.23
Consensus pattern (107 bp):
GGTCCAAGCTCCGGAGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
CGGAGGACAAGGCCATGCATTCGTTGATGTGTCACCAACTCG
Found at i:5966954 original size:162 final size:162
Alignment explanation
Indices: 5966685--5967241 Score: 706
Period size: 162 Copynumber: 3.4 Consensus size: 162
5966675 CAAGACCGGT
* * * * * *
5966685 GGTCCAAGTTCCAGTGGAAAAGGCCATGCATTCGTTGACT-CTGTCACCAACTCAGGCCCAACTT
1 GGTCCAAGCTCCGGAGGAAAAGGCAATGCATTCGTTGA-TGCTGTCACCAACTCAGGTCCAAGTT
* * * ** * *
5966749 CCAGAGGACATGGTAATGCATTCGTTGATG-TGGTCACCAACTCGGGTCCAAGCTCCGGCGGAAA
65 CCAGTGGAAAAGGCCATGCATTCGTTGATGCT-GTCACCAACTCGGGTCCAAGCTCCGGAGGACA
*
5966813 AGGCCATGCATTCGTTGATGCTTTCACCAACTCA
129 AGGCCATGCATTCGTTGATGCTGTCACCAACTCA
* * *
5966847 GGTCCAAGTTCCGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
1 GGTCCAAGCTCCGGAGGAAAAGGCAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
* * * * *
5966912 CGGTGGAAAAGGCCATGCATTCGTTGATGCTGTCAACAACTCGGTTTCC-AGTTCCAGAGGACAA
66 CAGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCGG-GTCCAAGCTCCGGAGGACAA
* * * *
5966976 GGCCATGCACTCGTTGTTGCAGTCACCAACTCG
130 GGCCATGCATTCGTTGATGCTGTCACCAACTCA
* *
5967009 GGTCCAAGCTCCGGAGGACAAGGTAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
1 GGTCCAAGCTCCGGAGGAAAAGGCAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
* * * *
5967074 CGGCGGAAAAGGCCATGCATTCGTTGACGCTGTCACCAACTCGGGTCCAAGCTCCGGAAGACAAG
66 CAGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCGGGTCCAAGCTCCGGAGGACAAG
** *
5967139 GTAATGCATTCGTTGATGCTGTCACCAATTCA
131 GCCATGCATTCGTTGATGCTGTCACCAACTCA
* * * * *
5967171 GGTCCAAGCTCCGGAGGACAAGGTAATGCATTCGTTGACGCCGTCACCAAATCAGGTCCAAGTTC
1 GGTCCAAGCTCCGGAGGAAAAGGCAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
5967236 CAGTGG
66 CAGTGG
5967242 CGGTGGACAT
Statistics
Matches: 347, Mismatches: 44, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
161 4 0.01
162 339 0.98
163 4 0.01
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.23
Consensus pattern (162 bp):
GGTCCAAGCTCCGGAGGAAAAGGCAATGCATTCGTTGATGCTGTCACCAACTCAGGTCCAAGTTC
CAGTGGAAAAGGCCATGCATTCGTTGATGCTGTCACCAACTCGGGTCCAAGCTCCGGAGGACAAG
GCCATGCATTCGTTGATGCTGTCACCAACTCA
Found at i:5982297 original size:26 final size:24
Alignment explanation
Indices: 5982244--5982293 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
5982234 TAATTTATCC
*
5982244 ATTGTTCTTTTTTAGTAATAGAGG
1 ATTGTTCGTTTTTAGTAATAGAGG
*
5982268 ATTGTTCGTTTTTAGTGATAGAGG
1 ATTGTTCGTTTTTAGTAATAGAGG
5982292 AT
1 AT
5982294 ATTGGGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (24 bp):
ATTGTTCGTTTTTAGTAATAGAGG
Found at i:5987060 original size:18 final size:17
Alignment explanation
Indices: 5987029--5987072 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5987019 TTTTAATATT
5987029 ATATATTTAATTTATTTA
1 ATAT-TTTAATTTATTTA
*
5987047 AGTATTTTATTTTATTTA
1 A-TATTTTAATTTATTTA
5987065 ATATTTTA
1 ATATTTTA
5987073 CTAATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
ATATTTTAATTTATTTA
Found at i:5989620 original size:21 final size:20
Alignment explanation
Indices: 5989534--5989691 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
5989524 AAATGACCAA
**
5989534 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5989553 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5989573 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5989593 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5989614 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5989635 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5989655 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5989676 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5989692 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5989682 original size:20 final size:20
Alignment explanation
Indices: 5989658--5989907 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
5989648 CGATTTTCCA
** *
5989658 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
5989678 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
5989698 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
5989718 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
5989738 AAATCGCAACGC-ATATGGGT
1 AAATCGCAACGCGA-ATCCGT
* *
5989758 AAATCGCAAAGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5989778 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5989798 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
5989818 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5989838 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
5989858 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
5989878 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
5989898 AAATCACAAC
1 AAATCGCAAC
5989908 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:5990629 original size:24 final size:24
Alignment explanation
Indices: 5990590--5990636 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5990580 AAATTTGGTC
5990590 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5990614 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5990637 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5990828 original size:12 final size:12
Alignment explanation
Indices: 5990811--5990835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5990801 ATATAATCCT
5990811 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5990823 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5990835 G
1 G
5990836 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5993235 original size:19 final size:20
Alignment explanation
Indices: 5993172--5993227 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
5993162 GATTCTCTCG
5993172 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
5993192 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
5993212 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5993228 GCAATGCGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:5993263 original size:14 final size:14
Alignment explanation
Indices: 5993244--5993298 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5993234 CGGAAATGAA
5993244 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5993258 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5993277 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5993291 AATCGCAA
1 AATCGCAA
5993299 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5993278 original size:33 final size:33
Alignment explanation
Indices: 5993226--5993317 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
5993216 GATTTTCATT
5993226 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
5993260 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
5993293 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
5993318 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.84
34 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:5993320 original size:52 final size:52
Alignment explanation
Indices: 5993258--5993374 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
5993248 GCAACGAGAG
5993258 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
5993310 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
5993362 AATCGCATTGCGA
1 AATCGCAATGCGA
5993375 TTCTCCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:5993423 original size:19 final size:19
Alignment explanation
Indices: 5993381--5993480 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
5993371 GCGATTCTCC
5993381 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
5993401 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
5993420 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
5993436 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
5993453 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
5993472 CATTGCGAT
1 CATTGCGAT
5993481 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:5993477 original size:52 final size:53
Alignment explanation
Indices: 5993364--5993480 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
5993354 GAAATTAAAA
5993364 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
5993417 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
5993469 TCGCATTGCGAT
1 TCGCATTGCGAT
5993481 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:5993606 original size:14 final size:14
Alignment explanation
Indices: 5993587--5993623 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5993577 CATCAATTAC
5993587 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5993601 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5993615 ACAAATCAA
1 ACAAATCAA
5993624 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5995621 original size:14 final size:14
Alignment explanation
Indices: 5995602--5995658 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5995592 GCGAAATGAA
*
5995602 AATCGCAACGACAG
1 AATCGCAACGAAAG
5995616 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5995633 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5995649 AATCGCAACG
1 AATCGCAACG
5995659 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5995629 original size:33 final size:33
Alignment explanation
Indices: 5995583--5995675 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5995573 GCGAAACCAA
*
5995583 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5995616 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5995649 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5995676 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5995640 original size:19 final size:19
Alignment explanation
Indices: 5995546--5995680 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5995536 TAGTTTACTT
* *
5995546 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5995566 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5995585 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5995604 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5995618 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5995637 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5995651 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5995670 TCGCAATGCGA
1 TCGCAACGCGA
5995681 TTTGGTTTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5995721 original size:33 final size:33
Alignment explanation
Indices: 5995676--5995766 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
5995666 AAAATCGCAA
5995676 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5995708 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5995741 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5995767 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:5995729 original size:19 final size:19
Alignment explanation
Indices: 5995676--5995803 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
5995666 AAAATCGCAA
5995676 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5995694 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5995708 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5995727 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5995741 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5995760 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5995779 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5995799 TGCGA
1 TGCGA
5995804 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 42 0.47
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5996006 original size:93 final size:93
Alignment explanation
Indices: 5995847--5996413 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
5995837 TTGAATGGAT
5995847 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5995912 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5995940 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAATATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5996005 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5996033 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5996098 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5996126 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5996191 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5996219 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5996284 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5996312 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5996377 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5996405 AAATTTACT
1 AAATTTACT
5996414 AAGCAATCTA
Statistics
Matches: 469, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 469 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5998137 original size:14 final size:14
Alignment explanation
Indices: 5998118--5998207 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5998108 TTGAAATGAA
5998118 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5998132 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5998149 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5998165 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
5998184 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5998198 AATCGCAACG
1 AATCGCAACG
5998208 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5998155 original size:33 final size:33
Alignment explanation
Indices: 5998110--5998224 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
5998100 TCTTTTGGTT
5998110 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5998143 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
5998176 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5998209 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5998225 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5998156 original size:19 final size:18
Alignment explanation
Indices: 5998117--5998229 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5998107 GTTGAAATGA
5998117 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5998132 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5998149 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5998165 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5998182 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5998198 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5998215 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5998230 TTTTGGTTTG
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5998260 original size:14 final size:14
Alignment explanation
Indices: 5998241--5998297 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5998231 TTTGGTTTGG
*
5998241 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
5998255 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5998274 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5998288 CGTTGCGATT
1 CGTTGCGATT
5998298 GTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5998277 original size:33 final size:33
Alignment explanation
Indices: 5998225--5998305 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
5998215 AAAATCGCAA
** * *
5998225 TGCGATTTTGGTTTGGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5998258 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
5998291 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
5998306 TCTCGTTGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.09, C:0.20, G:0.26, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5998338 original size:41 final size:41
Alignment explanation
Indices: 5998281--5998358 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5998271 TCGCGTTGCG
*
5998281 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
5998322 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
5998359 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:5998343 original size:20 final size:21
Alignment explanation
Indices: 5998282--5998357 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5998272 CGCGTTGCGA
5998282 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
5998303 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
5998323 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
5998344 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
5998358 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Done.