Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004057.1 Hibiscus syriacus cultivar Beakdansim tig00008874_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: 170081
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3107 original size:31 final size:29
Alignment explanation
Indices: 3067--3170 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
3057 TCGAATTTAT
*
3067 GGGTTAAATTGATATATGATCTAAAGTTCAA
1 GGGTCAAATT-ATAT-TGATCTAAAGTTCAA
* * *
3098 AGGTCAAATTAATATTTTATCTAAAGTTTAA
1 GGGTCAAATT-ATA-TTGATCTAAAGTTCAA
* *
3129 GGGTTAAAATAGTATTGTATCTAAAGTTCAA
1 GGGTCAAATTA-TATTG-ATCTAAAGTTCAA
3160 GGGTCAAATTA
1 GGGTCAAATTA
3171 AAAATTAACT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 3 0.05
31 54 0.93
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (29 bp):
GGGTCAAATTATATTGATCTAAAGTTCAA
Found at i:12884 original size:29 final size:29
Alignment explanation
Indices: 12842--12899 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
12832 GATGTATACC
12842 CATGACTGACACCTCAAACCCAAGTCTAA
1 CATGACTGACACCTCAAACCCAAGTCTAA
12871 CATGACTGACACCTCAAACCCAAGTCTAA
1 CATGACTGACACCTCAAACCCAAGTCTAA
12900 GTACAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (29 bp):
CATGACTGACACCTCAAACCCAAGTCTAA
Found at i:15978 original size:7 final size:7
Alignment explanation
Indices: 15946--16007 Score: 65
Period size: 7 Copynumber: 8.9 Consensus size: 7
15936 AAACAGGAGG
15946 CTTTTTC
1 CTTTTTC
*
15953 TTTCTTTC
1 CTT-TTTC
*
15961 TTTTCTTC
1 CTTT-TTC
15969 CTTTTTC
1 CTTTTTC
15976 CTTTTTC
1 CTTTTTC
15983 CTTTTT-
1 CTTTTTC
*
15989 CTTTTTT
1 CTTTTTC
15996 C-TTTTC
1 CTTTTTC
16002 CTTTTT
1 CTTTTT
16008 TCTCCTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 11 0.23
7 24 0.50
8 13 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
CTTTTTC
Found at i:15983 original size:14 final size:14
Alignment explanation
Indices: 15946--16007 Score: 65
Period size: 13 Copynumber: 4.4 Consensus size: 14
15936 AAACAGGAGG
*
15946 CTTTTTCTTTCTTTC
1 CTTTTTCCTT-TTTC
*
15961 TTTTCTTCCTTTTTC
1 CTTT-TTCCTTTTTC
15976 CTTTTTCCTTTTT-
1 CTTTTTCCTTTTTC
*
15989 CTTTTTTC-TTTTC
1 CTTTTTCCTTTTTC
16002 CTTTTT
1 CTTTTT
16008 TCTCCTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 4 0.10
13 13 0.32
14 9 0.22
15 10 0.24
16 5 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTTCCTTTTTC
Found at i:22019 original size:21 final size:20
Alignment explanation
Indices: 21981--22020 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21971 TCGCTCTTTC
**
21981 TTTCCTCCCTTTTTCTCTCG
1 TTTCCTCCCTTTCCCTCTCG
22001 TTTCTCTCCCTTTCCCTCTC
1 TTTC-CTCCCTTTCCCTCTC
22021 CCGACGACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTCCTCCCTTTCCCTCTCG
Found at i:30139 original size:20 final size:20
Alignment explanation
Indices: 30114--30152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30104 TTTTTGTTTG
*
30114 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
30134 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
30153 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:31802 original size:10 final size:10
Alignment explanation
Indices: 31787--31820 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31777 TTCATTTACC
31787 ATTTATTTTT
1 ATTTATTTTT
31797 ATTTATTTTT
1 ATTTATTTTT
* *
31807 ATCTATTTCT
1 ATTTATTTTT
31817 ATTT
1 ATTT
31821 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:42232 original size:106 final size:106
Alignment explanation
Indices: 42047--42506 Score: 778
Period size: 106 Copynumber: 4.3 Consensus size: 106
42037 AGGTTTTACC
* *
42047 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
*
42112 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
42153 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-
42218 AA-GAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
65 AACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
42259 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
42324 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
42365 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
* * * *
42430 ACGAATGGACCGCTGGTTGTCAACAAATAATTTCCAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
42471 CGGAGTCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
42507 CCTCGGAACA
Statistics
Matches: 339, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
105 2 0.01
106 336 0.99
107 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
Found at i:43899 original size:20 final size:20
Alignment explanation
Indices: 43874--43912 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43864 TTTTTGTTTG
43874 GCCGCCGATAAACGACGGCC
1 GCCGCCGATAAACGACGGCC
* *
43894 GCCGCCGATCAACGGCGGC
1 GCCGCCGATAAACGACGGC
43913 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.41, G:0.33, T:0.05
Consensus pattern (20 bp):
GCCGCCGATAAACGACGGCC
Found at i:46653 original size:232 final size:231
Alignment explanation
Indices: 46200--46667 Score: 830
Period size: 230 Copynumber: 2.0 Consensus size: 231
46190 TCGAGTTTTT
46200 TTATAAAAAAAATTGGGTTCGGGTCGGGTTTTTTTAAATGTGATATTCGAGTCGGGTTCGGTTTA
1 TTATAAAAAAAATTGGGTTCGGGTCGGGTTTTTTTAAATGTGATATTCGAGTCGGGTTCGGTTTA
46265 GGATGAAAATATCCAACCCGAACCGACCCAAAAAATAATTTTACATTATATATTTAAGAATAATT
66 GGATGAAAATATCCAACCCGAACCGACCCAAAAAATAATTTTACATTATATATTTAAGAATAATT
46330 ACAATAATACCCCTCTATATATTATTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAATA
131 ACAATAATACCCCTCTATATATTATTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAATA
*
46395 TTTTTATTATTATTTCGGGTCGGGTCGTATTTTAAG
196 TTTTTATTATTATTTCGAGTCGGGTCGTATTTTAAG
* *
46431 TTATAAAAAAAATTGGGTTTGGGTCGGGTTTTTTTAAATTTGATATTCGAGTC-GGTTCGGTTTA
1 TTATAAAAAAAATTGGGTTCGGGTCGGGTTTTTTTAAATGTGATATTCGAGTCGGGTTCGGTTTA
* *
46495 GGATGAAAATATCCAACTCGAACCGACCCAAAAAATAATTTTACATTATATATTTAGGAATAATT
66 GGATGAAAATATCCAACCCGAACCGACCCAAAAAATAATTTTACATTATATATTTAAGAATAATT
* * * *
46560 ATAATAATACCCCTCTATATATTATTTTTTTCAATTAAATCATTGTTTTTATTGAATAAACATAA
131 ACAATAATACCCCTCTATATATTA--TTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAA
46625 TATTTTTATTATTATTTCGAGTCGGGTCGTATTTTAAG
194 TATTTTTATTATTATTTCGAGTCGGGTCGTATTTTAAG
46663 TTATA
1 TTATA
46668 TATCGAGTCA
Statistics
Matches: 226, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
230 97 0.43
231 51 0.23
232 78 0.35
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (231 bp):
TTATAAAAAAAATTGGGTTCGGGTCGGGTTTTTTTAAATGTGATATTCGAGTCGGGTTCGGTTTA
GGATGAAAATATCCAACCCGAACCGACCCAAAAAATAATTTTACATTATATATTTAAGAATAATT
ACAATAATACCCCTCTATATATTATTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAATA
TTTTTATTATTATTTCGAGTCGGGTCGTATTTTAAG
Found at i:47693 original size:30 final size:29
Alignment explanation
Indices: 47651--47707 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
47641 ATCGGATTAA
*
47651 TTTTTTGTTTT-AAAAATTTATTACTAGT
1 TTTTTTGTTTTAAAAAAGTTATTACTAGT
47679 TTTTTATGATTTTAAAAAAGTTATTACTA
1 TTTTT-TG-TTTTAAAAAAGTTATTACTA
47708 ATTATGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 2 0.08
30 4 0.16
31 14 0.56
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTTTGTTTTAAAAAAGTTATTACTAGT
Found at i:47723 original size:31 final size:31
Alignment explanation
Indices: 47657--47723 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
47647 TTAATTTTTT
* * * **
47657 GTTTT-AAAAATTTATTACTAGTTTTTTATG
1 GTTTTAAAAAAGTTATTACTAATTATGGATG
*
47687 ATTTTAAAAAAGTTATTACTAATTATGGATG
1 GTTTTAAAAAAGTTATTACTAATTATGGATG
47718 GTTTTA
1 GTTTTA
47724 GATTAAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (31 bp):
GTTTTAAAAAAGTTATTACTAATTATGGATG
Found at i:49461 original size:21 final size:20
Alignment explanation
Indices: 49435--49532 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
49425 ATCAGTTTCC
49435 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
49456 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
49475 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
49498 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
49518 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
49533 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:49561 original size:20 final size:20
Alignment explanation
Indices: 49499--49728 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
49489 CGATTTTCAA
* ** *
49499 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
49519 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
49539 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
49559 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
49579 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
49599 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
49619 ATATCGCAACGCGTATCCAT
1 AAATCGCAACGCGTATCCGT
*
49639 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
49659 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
49679 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
49699 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
49719 AAATCACAAC
1 AAATCGCAAC
49729 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:52969 original size:33 final size:34
Alignment explanation
Indices: 52932--53115 Score: 144
Period size: 33 Copynumber: 5.2 Consensus size: 34
52922 GCAACGAGAG
52932 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * *
52965 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
52999 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
53037 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
*
53070 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
53108 AATCGCAA
1 AATCGCAA
53116 CGAGAGAATC
Statistics
Matches: 123, Mismatches: 12, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.01
32 6 0.05
33 47 0.38
34 29 0.24
35 2 0.02
37 1 0.01
38 30 0.24
39 6 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:52986 original size:34 final size:33
Alignment explanation
Indices: 52918--53021 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
52908 CGGAAATTAC
* *
52918 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
52951 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
52985 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
53018 AATC
1 AATC
53022 GCAATGCGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
32 1 0.02
33 33 0.52
34 29 0.45
35 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:53023 original size:19 final size:19
Alignment explanation
Indices: 52932--53115 Score: 227
Period size: 19 Copynumber: 10.4 Consensus size: 19
52922 GCAACGAGAG
52932 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52951 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
52965 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
52985 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
52999 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53018 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
53037 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
53051 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53070 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53089 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53108 AATCGCAA
1 AATCGCAA
53116 CGAGAGAATC
Statistics
Matches: 143, Mismatches: 6, Indels: 32
0.79 0.03 0.18
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 4 0.03
18 3 0.02
19 84 0.59
20 13 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:53045 original size:52 final size:52
Alignment explanation
Indices: 52960--53096 Score: 265
Period size: 52 Copynumber: 2.6 Consensus size: 52
52950 AAATCCCAAC
52960 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
53013 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
53065 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
53097 TGCGAAATGA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 68 0.81
53 16 0.19
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:53126 original size:52 final size:52
Alignment explanation
Indices: 52962--53137 Score: 232
Period size: 52 Copynumber: 3.4 Consensus size: 52
52952 ATCCCAACAT
* *
52962 GAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* *
53015 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* * *
53067 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAAC
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-AAATGCGAAAC
53117 GAGAGAATCGCAATGCGAAAT
1 GA-A-AATCGCAATGCGAAAT
53138 TATAAACGCA
Statistics
Matches: 115, Mismatches: 5, Indels: 7
0.91 0.04 0.06
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 87 0.76
53 14 0.12
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
Found at i:53131 original size:33 final size:33
Alignment explanation
Indices: 53018--53137 Score: 186
Period size: 33 Copynumber: 3.5 Consensus size: 33
53008 GCGAAATGAA
53018 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
53051 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
53089 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
53122 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
53138 TATAAACGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 45 0.56
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 29 0.36
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:53153 original size:71 final size:71
Alignment explanation
Indices: 52999--53137 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 71
52989 GCAACGAGAG
52999 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
53064 AATGAA
66 AATGAA
53070 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
53135 AAT
66 AAT
53138 TATAAACGCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:53256 original size:52 final size:53
Alignment explanation
Indices: 53144--53259 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
53134 AAATTATAAA
53144 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
*
53197 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTTATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
53249 CGCATTGCGAT
1 CGCATTGCGAT
53260 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:53267 original size:19 final size:19
Alignment explanation
Indices: 53162--53259 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
53152 GATTCTCTCG
53162 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
53182 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
53201 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
53215 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
53234 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
53253 TTGCGAT
1 TTGCGAT
53260 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:53386 original size:14 final size:14
Alignment explanation
Indices: 53367--53402 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53357 ATCAATTACT
53367 CAAATCAACTTTTA
1 CAAATCAACTTTTA
*
53381 CAAATCATCTTTTA
1 CAAATCAACTTTTA
53395 CAAATCAA
1 CAAATCAA
53403 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
CAAATCAACTTTTA
Found at i:55405 original size:33 final size:33
Alignment explanation
Indices: 55359--55451 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
55349 GCGAAACCAA
*
55359 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
55392 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
55425 AATTGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
55452 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:55416 original size:19 final size:19
Alignment explanation
Indices: 55322--55456 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
55312 TAGTTTACTT
* *
55322 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
55342 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
55361 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55380 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
55394 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
55413 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
55427 TTGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55446 TCGCAATGCGA
1 TCGCAACGCGA
55457 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:55474 original size:19 final size:19
Alignment explanation
Indices: 55452--55580 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
55442 AAAATCGCAA
55452 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
55471 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
55485 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
55504 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
55518 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
55537 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
55556 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
55576 TGCGA
1 TGCGA
55581 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:55494 original size:33 final size:33
Alignment explanation
Indices: 55452--55543 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
55442 AAAATCGCAA
55452 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
55485 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
55518 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
55544 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:55744 original size:93 final size:93
Alignment explanation
Indices: 55628--56188 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
55618 ATGGATTGCA
55628 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55692 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55720 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55785 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55813 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55878 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55906 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55970 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55998 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
56063 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
56091 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
56156 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
56184 TTACT
1 TTACT
56189 AAGCAATCTA
Statistics
Matches: 465, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 96 0.21
93 369 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:56034 original size:185 final size:185
Alignment explanation
Indices: 55628--56188 Score: 1079
Period size: 185 Copynumber: 3.0 Consensus size: 185
55618 ATGGATTGCA
55628 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55692 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACT
55757 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
55813 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55878 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
55943 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
55998 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
56063 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGA-CAAACAAAGACAAATACT
*
56128 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
56184 TTACT
1 TTACT
56189 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
185 188 0.51
186 184 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTA
TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:56144 original size:278 final size:279
Alignment explanation
Indices: 55628--56188 Score: 1090
Period size: 278 Copynumber: 2.0 Consensus size: 279
55618 ATGGATTGCA
55628 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55692 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
55757 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
55822 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
55887 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
55906 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55970 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
56035 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
*
56100 ACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
*
56165 TGGCAGCAACCGAATAAAT
261 TGGCAGCAACCGAACAAAT
56184 TTACT
1 TTACT
56189 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
278 266 0.95
279 14 0.05
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:57912 original size:14 final size:14
Alignment explanation
Indices: 57893--57982 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
57883 TTGAAATGAA
57893 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
57907 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
57926 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
57940 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
57959 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57973 AATCGCAACG
1 AATCGCAACG
57983 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:57930 original size:33 final size:33
Alignment explanation
Indices: 57885--57999 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
57875 TCTTTTGGTT
57885 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
57918 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57951 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57984 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
58000 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:57931 original size:19 final size:19
Alignment explanation
Indices: 57907--58004 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
57897 GCAACGAGAG
*
57907 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
57926 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
57940 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
57959 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
57973 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
57992 AATCGCAATGCGA
1 AATCGCAACGCGA
58005 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:58035 original size:14 final size:14
Alignment explanation
Indices: 58016--58072 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
58006 TTTGGTTTCG
58016 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
58030 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
58049 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
58063 CGTTGCGATT
1 CGTTGCGATT
58073 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:58048 original size:33 final size:33
Alignment explanation
Indices: 58000--58080 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
57990 AAAATCGCAA
**
58000 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
58033 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
58066 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
58081 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:58083 original size:21 final size:21
Alignment explanation
Indices: 58057--58132 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
58047 CGCGTTGCGA
58057 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
58078 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
58098 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
58119 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
58133 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
Found at i:58113 original size:41 final size:41
Alignment explanation
Indices: 58056--58133 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
58046 TCGCGTTGCG
*
58056 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
58097 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
58134 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:58254 original size:33 final size:33
Alignment explanation
Indices: 58212--58282 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
58202 AATACTAACT
*
58212 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
58245 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
58278 TGAAA
1 TGAAA
58283 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:58516 original size:22 final size:22
Alignment explanation
Indices: 58464--58518 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
58454 TGGTTGTGAG
**
58464 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
58486 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
58508 GGATTTCTTCG
1 GGATTTCTTCG
58519 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:58690 original size:20 final size:20
Alignment explanation
Indices: 58665--58858 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
58655 CTTTAAATAT
58665 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58685 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
58707 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58726 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
58746 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
58766 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58786 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58806 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
58826 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
58846 CGCGTTGCGATTT
1 CGCGTTGCGATTT
58859 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:58852 original size:60 final size:60
Alignment explanation
Indices: 58665--58858 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
58655 CTTTAAATAT
**
58665 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
58726 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
58786 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
58846 CGCGTTGCGATTT
1 CGCGTTGCGATTT
58859 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:58875 original size:21 final size:21
Alignment explanation
Indices: 58845--58927 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
58835 ATTTTCATAT
*
58845 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
58866 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
58887 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
58908 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
58928 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:58918 original size:42 final size:43
Alignment explanation
Indices: 58825--58923 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
58815 ATTTATGTGT
* *
58825 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
58866 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
58908 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
58924 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:59147 original size:16 final size:16
Alignment explanation
Indices: 59126--59158 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
59116 TAATAAATAA
59126 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
59142 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
59158 A
1 A
59159 ATTTTTTTTG
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:59569 original size:24 final size:26
Alignment explanation
Indices: 59540--59591 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
59530 GCCCCCTGTT
**
59540 CGAACATAAATTAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
59564 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
59590 CG
1 CG
59592 TTCACGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:67323 original size:6 final size:6
Alignment explanation
Indices: 67312--67342 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
67302 TTTTTAACAA
67312 TATATG TATATG TATATG TATATG ATATATG
1 TATATG TATATG TATATG TATATG -TATATG
67343 ATTATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:67643 original size:2 final size:2
Alignment explanation
Indices: 67636--67695 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
67626 GATGTAAACA
67636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67678 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
67696 GGTTTAAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68151 original size:28 final size:28
Alignment explanation
Indices: 68111--68168 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
68101 ATTATATCAA
68111 CAAGTGGTGGCTCGATCCACTACTGAAG
1 CAAGTGGTGGCTCGATCCACTACTGAAG
68139 CAAGTGGTGGCTCGATCCACTACTGAAG
1 CAAGTGGTGGCTCGATCCACTACTGAAG
68167 CA
1 CA
68169 GAGTATCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (28 bp):
CAAGTGGTGGCTCGATCCACTACTGAAG
Found at i:68747 original size:2 final size:2
Alignment explanation
Indices: 68740--68777 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
68730 CCGTTAAGAT
68740 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68778 TACAGCTGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:70852 original size:17 final size:17
Alignment explanation
Indices: 70830--70868 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
70820 TGAATCAAAT
*
70830 TAATTATATATTATTTA
1 TAATTAGATATTATTTA
70847 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
70864 -AATTA
1 TAATTA
70869 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:71727 original size:29 final size:29
Alignment explanation
Indices: 71679--71764 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
71669 AGTGTTGGCC
** *
71679 GTAGGTCGCCATATATTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
71708 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
71737 GTAGGTCGCCATGCACTCCGGGCAACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
71765 ACCCTTACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.16, C:0.33, G:0.29, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:71856 original size:29 final size:29
Alignment explanation
Indices: 71823--71878 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
71813 TCCCAACACA
* *
71823 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
71852 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
71879 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:71923 original size:33 final size:33
Alignment explanation
Indices: 71882--71951 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
71872 GCGACCTACC
*
71882 CTCGCTCGGCTTCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGCTTCCCTCGGATGCCCTCGCATAG
*
71915 CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGCTTCCCTCGGATGCCCTCGCATAG
71948 CTCG
1 CTCG
71952 TTCAGATGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.09, C:0.41, G:0.23, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGCTTCCCTCGGATGCCCTCGCATAG
Found at i:71982 original size:10 final size:10
Alignment explanation
Indices: 71967--72013 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
71957 ATGGTATCGG
71967 TCGGATGGCC
1 TCGGATGGCC
71977 TCGGAT-GCTC
1 TCGGATGGC-C
71987 TCGGATGGCC
1 TCGGATGGCC
71997 TCGGATGGCC
1 TCGGATGGCC
72007 TCGGATG
1 TCGGATG
72014 CCCAGCGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.11, C:0.28, G:0.38, T:0.23
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:72090 original size:29 final size:29
Alignment explanation
Indices: 72053--72110 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
72043 GCAATCTCTT
*
72053 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
72082 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
72111 CAACCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:81338 original size:50 final size:51
Alignment explanation
Indices: 81284--81389 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 51
81274 TTTTATAATG
* * *
81284 TTATTGAAATTCGTCATATCAAGAA-GACGAGTTCTAATAAAA-ATTATTTT
1 TTATTGAAATTCGTCATATCAA-AATGACAAATTCTAATAAAATATAATTTT
*
81334 TTATTGAAATTCGTCATCTCAAAATGACAAATTCTAATAAAATATAATTTT
1 TTATTGAAATTCGTCATATCAAAATGACAAATTCTAATAAAATATAATTTT
81385 TTATT
1 TTATT
81390 AACATATATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 2 0.04
50 36 0.72
51 12 0.24
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (51 bp):
TTATTGAAATTCGTCATATCAAAATGACAAATTCTAATAAAATATAATTTT
Found at i:85796 original size:21 final size:21
Alignment explanation
Indices: 85772--85813 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
85762 ACTAGTATTT
*
85772 AATTT-TTTAATTTATTCATTA
1 AATTTATTT-ATTTATTAATTA
85793 AATTTATTTATTTATTAATTA
1 AATTTATTTATTTATTAATTA
85814 GTTTTGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTATTTATTTATTAATTA
Found at i:90968 original size:12 final size:12
Alignment explanation
Indices: 90951--90983 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
90941 AGTTTCATTA
90951 TTTTTATATTCG
1 TTTTTATATTCG
*
90963 TTTTTATATCCG
1 TTTTTATATTCG
90975 -TTTTATATT
1 TTTTTATATT
90984 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (12 bp):
TTTTTATATTCG
Found at i:95778 original size:17 final size:17
Alignment explanation
Indices: 95758--95796 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
95748 TTTTCATGGT
95758 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
95775 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
95792 GTTAT
1 GTTAT
95797 GGATATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (17 bp):
GTTATTGGTTCATTAGA
Found at i:95879 original size:2 final size:2
Alignment explanation
Indices: 95872--95906 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
95862 TATGAGTTGC
95872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95907 TGAAAATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96222 original size:17 final size:17
Alignment explanation
Indices: 96200--96238 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
96190 TTTTCATGGT
96200 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
96217 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
96234 GTTAT
1 GTTAT
96239 GGATATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (17 bp):
GTTATTGGTTCATTAGA
Found at i:96321 original size:2 final size:2
Alignment explanation
Indices: 96314--96360 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
96304 TATGAGTTGC
96314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96356 TA TA T
1 TA TA T
96361 TGAAAATTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96518 original size:454 final size:449
Alignment explanation
Indices: 95682--97035 Score: 2598
Period size: 454 Copynumber: 3.0 Consensus size: 449
95672 CTGCCACCTA
95682 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
1 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
95747 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
66 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
95812 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGC-----
131 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGCTATAT
95872 -TATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCGCACACT
196 ATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCGCACACT
95936 GCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAAGAATAA
261 GCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAAGAATAA
96001 ATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAAAAAATA
326 ATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAAAAAATA
96066 TTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
391 TTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
96125 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTA-T
1 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
96189 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
66 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
96254 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGCTATAT
131 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGC-----
96319 ATATATATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCG
191 -TATATATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCG
96384 CACACTGCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAA
255 CACACTGCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAA
96449 GAATAAATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAA
320 GAATAAATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAA
96514 AAAATATTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTA-TTTTAATTACCGATCAC
385 AAAATATTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
96578 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
1 TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
96643 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
66 TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
96708 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGCTATAT
131 CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGCTATAT
96773 ATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCGCACACT
196 ATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCGCACACT
96838 GCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAAGAATAA
261 GCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAAGAATAA
96903 ATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAAAAAATA
326 ATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAAAAAATA
96968 TTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
391 TTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
97027 TTTTTTCTT
1 TTTTTTCTT
97036 TATTCGTCAA
Statistics
Matches: 897, Mismatches: 0, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
442 126 0.14
443 63 0.07
448 241 0.27
449 26 0.03
453 80 0.09
454 361 0.40
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (449 bp):
TTTTTTCTTGGTTAGTTTTGCCATTATCATCTTGGTTTTTGCTTGACATCTACTTGTCTTTTATT
TTTTTCATGGTGTTATTGGTTCATTAGAGTTATTGGTTCATTAGAGTTATGGATATCAAAATTGT
CTCTCTCAAACTCATTTTTGTGAATAAATAATTCCTTTTAAACTTAATTTTATGAGTTGCTATAT
ATATATATATATATATATATATATATATATATATATTGAAAATTCTAATACAAACGTCGCACACT
GCAACACACCACGCAAAACACGCCACTAATTAAAATGTCCTTATTAAGCGAATATTAAAGAATAA
ATTACATGTTTTGTACTTAAATTGTCACTTTTTTCGTTTTATTATTTATTTATTTAAAAAAAATA
TTAATGACAATGTTTATGTGGCATGACATATCAATTTTTTATTTTTAATTACCGATCAC
Found at i:96674 original size:17 final size:17
Alignment explanation
Indices: 96654--96692 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
96644 TTTTCATGGT
96654 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
96671 GTTATTGGTTCATTAGA
1 GTTATTGGTTCATTAGA
96688 GTTAT
1 GTTAT
96693 GGATATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (17 bp):
GTTATTGGTTCATTAGA
Found at i:96775 original size:2 final size:2
Alignment explanation
Indices: 96768--96808 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
96758 TATGAGTTGC
96768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96809 TGAAAATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:97953 original size:60 final size:59
Alignment explanation
Indices: 97860--97979 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 59
97850 GAATTACGTT
97860 ATTTAATCATTAGGGAAGAATTGAGAAACATAGGCCTTAAGACTATTCATGTTAAAACTG
1 ATTTAATCATTAGGGAAGAATTGAGAAACATAGG-CTTAAGACTATTCATGTTAAAACTG
*
97920 ATTTAATTATTAGGGAAGAATTGAGAAACATAGGCTTAAGACTATTCATGTTAAAACTG
1 ATTTAATCATTAGGGAAGAATTGAGAAACATAGGCTTAAGACTATTCATGTTAAAACTG
97979 A
1 A
97980 CACAAGCCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 26 0.44
60 33 0.56
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (59 bp):
ATTTAATCATTAGGGAAGAATTGAGAAACATAGGCTTAAGACTATTCATGTTAAAACTG
Found at i:108339 original size:35 final size:35
Alignment explanation
Indices: 108298--108393 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
108288 AACACAATCA
* *
108298 TCAATTATATTTTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
**
108333 TCAATTACATTCTAAACCTTAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* * *
108368 TTAATTACATGCTCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
108394 ATAATCCCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.41, C:0.25, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:124211 original size:20 final size:20
Alignment explanation
Indices: 124173--124211 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
124163 TGTTCCTTAT
*
124173 TAATTTAAAAAATTGAAAAA
1 TAATTTAAAAAATTAAAAAA
124193 TAATTTAAAATAA-TAAAAA
1 TAATTTAAAA-AATTAAAAA
124212 CAGAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TAATTTAAAAAATTAAAAAA
Found at i:133412 original size:42 final size:42
Alignment explanation
Indices: 133352--133519 Score: 180
Period size: 42 Copynumber: 4.0 Consensus size: 42
133342 ATCTGCACCA
* *
133352 AAAGATGAATTTCCGGGAAATGAT-TCTGATAATGGAAGTAAC
1 AAAGACGAATTTCCGGGAAATGATATC-AATAATGGAAGTAAC
*
133394 AAAGACGAATTTCTGGGAAATGATATCAATAATGGAAGTAAC
1 AAAGACGAATTTCCGGGAAATGATATCAATAATGGAAGTAAC
** ** * *
133436 AAAGGTGAATTTCCGGTTACTGATATCCAA-AATGGAAGTAGC
1 AAAGACGAATTTCCGGGAAATGATAT-CAATAATGGAAGTAAC
* * *
133478 AAAGACGAATTTCCGGTAACTGATATCCAA-AATGGAAATAAC
1 AAAGACGAATTTCCGGGAAATGATAT-CAATAATGGAAGTAAC
133520 GATTGTCCTT
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 104 0.95
43 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAGACGAATTTCCGGGAAATGATATCAATAATGGAAGTAAC
Found at i:134338 original size:18 final size:18
Alignment explanation
Indices: 134315--134374 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
134305 AATGCTGAAG
134315 AAACCTAAAGGATCAACC
1 AAACCTAAAGGATCAACC
*
134333 AAACCTGAAGGATCAGA-C
1 AAACCTAAAGGATCA-ACC
* *
134351 AAATCTAAAAGATCAACC
1 AAACCTAAAGGATCAACC
134369 AAACCT
1 AAACCT
134375 TCAACCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.94
19 1 0.03
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.13
Consensus pattern (18 bp):
AAACCTAAAGGATCAACC
Found at i:136828 original size:15 final size:15
Alignment explanation
Indices: 136808--136848 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
136798 TGTTCTTCTA
136808 GTTGCTCAGGTGTAT
1 GTTGCTCAGGTGTAT
*
136823 GTTGCTCAGATGTAT
1 GTTGCTCAGGTGTAT
136838 GTTGCTCAGGT
1 GTTGCTCAGGT
136849 TTTTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.39
Consensus pattern (15 bp):
GTTGCTCAGGTGTAT
Found at i:143649 original size:2 final size:2
Alignment explanation
Indices: 143642--143666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143632 AAAATAAAAC
143642 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
143667 GTTTTATATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:145949 original size:40 final size:40
Alignment explanation
Indices: 145894--145984 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
145884 GAAGTTGTTA
145894 GTATCGATACCCGGCCATCGATATTGCTATCAGATGTACG
1 GTATCGATACCCGGCCATCGATATTGCTATCAGATGTACG
*
145934 GTATCGATACCCGGCCATCGATATTGGTATCAGATGTACG
1 GTATCGATACCCGGCCATCGATATTGCTATCAGATGTACG
*
145974 GTACCGATACC
1 GTATCGATACC
145985 ACATGATCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
GTATCGATACCCGGCCATCGATATTGCTATCAGATGTACG
Found at i:148411 original size:16 final size:16
Alignment explanation
Indices: 148390--148427 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
148380 GATGTTGATG
*
148390 CGTCACCATAAGGTAA
1 CGTCACCATAAGATAA
148406 CGTCACCATAAGATAA
1 CGTCACCATAAGATAA
148422 CGTCAC
1 CGTCAC
148428 ATCATCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (16 bp):
CGTCACCATAAGATAA
Found at i:149405 original size:16 final size:17
Alignment explanation
Indices: 149384--149418 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
149374 TTATCGGTGG
149384 AAATATAA-AAAATTTA
1 AAATATAAGAAAATTTA
149400 AAATATAAGAAAATTTA
1 AAATATAAGAAAATTTA
149417 AA
1 AA
149419 GGGGCAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATATAAGAAAATTTA
Found at i:151817 original size:21 final size:21
Alignment explanation
Indices: 151791--151853 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
151781 CTTGCATACC
*
151791 ATCTAAATTTTAAATCTTAAA
1 ATCTAAATTTTAAATCATAAA
* * *
151812 ATCTAAACTCT-AATCATAACG
1 ATCTAAATTTTAAATCATAA-A
* *
151833 ATCTAAATCTTAAATCCTAAA
1 ATCTAAATTTTAAATCATAAA
151854 CTTTAATAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (21 bp):
ATCTAAATTTTAAATCATAAA
Found at i:151853 original size:35 final size:34
Alignment explanation
Indices: 151801--151871 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
151791 ATCTAAATTT
*
151801 TAAATCTTAAAATCTAAACTCTAATCATAACGATC
1 TAAATCTTAAAATCTAAACTCTAATAATAAC-ATC
*
151836 TAAATCTT-AAATCCTAAACTTTAATAATAACATC
1 TAAATCTTAAAAT-CTAAACTCTAATAATAACATC
151870 TA
1 TA
151872 TACCTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.34
Consensus pattern (34 bp):
TAAATCTTAAAATCTAAACTCTAATAATAACATC
Found at i:162671 original size:25 final size:24
Alignment explanation
Indices: 162625--162672 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
162615 GACTCAAACT
*
162625 CGAAATAAAAATTAAGGCTCGACA
1 CGAAATAAAAATTAAGGATCGACA
162649 CGAAATAAACAATTCAA-GATCGAC
1 CGAAATAAA-AATT-AAGGATCGAC
162673 TCGAGCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 10 0.48
26 2 0.10
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (24 bp):
CGAAATAAAAATTAAGGATCGACA
Found at i:162910 original size:30 final size:30
Alignment explanation
Indices: 162876--162936 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
162866 AATTCCGGCT
162876 CGAGTTGAGTCTATTCAATTTAAGAATTAA
1 CGAGTTGAGTCTATTCAATTTAAGAATTAA
*
162906 CGAGTTGAGTCTATTCGATTTAAGAATTAA
1 CGAGTTGAGTCTATTCAATTTAAGAATTAA
162936 C
1 C
162937 CGAACTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (30 bp):
CGAGTTGAGTCTATTCAATTTAAGAATTAA
Found at i:163089 original size:14 final size:14
Alignment explanation
Indices: 163070--163096 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
163060 TTTTCATTTC
163070 ATTGGGTCGTCTTA
1 ATTGGGTCGTCTTA
163084 ATTGGGTCGTCTT
1 ATTGGGTCGTCTT
163097 GAACATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (14 bp):
ATTGGGTCGTCTTA
Done.