Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002380.1 Hibiscus syriacus cultivar Beakdansim tig00004865_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: 87059
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2745 original size:20 final size:20
Alignment explanation
Indices: 2722--2788 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2712 GTTTTTAGAT
*
2722 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
2742 TCGCAATGCGAATGTGTA-AA
1 TCGCAACGCGATTCTG-ACTA
2762 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
2782 TCGCAAC
1 TCGCAAC
2789 ACTGAATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:2969 original size:17 final size:14
Alignment explanation
Indices: 2935--2961 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2925 CGACATCCGT
2935 TCCTATATCCAACA
1 TCCTATATCCAACA
2949 TCCTATATCCAAC
1 TCCTATATCCAAC
2962 GACATCCTTC
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:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (14 bp):
TCCTATATCCAACA
Found at i:3139 original size:20 final size:20
Alignment explanation
Indices: 3114--3158 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3104 TTACAATATA
*
3114 TGCGATTTTGACTTTCGCAT
1 TGCGATTTTGACTTTAGCAT
* *
3134 TGCGATTTTGAGTTTAGCGT
1 TGCGATTTTGACTTTAGCAT
3154 TGCGA
1 TGCGA
3159 ATGTGTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.42
Consensus pattern (20 bp):
TGCGATTTTGACTTTAGCAT
Found at i:4868 original size:21 final size:21
Alignment explanation
Indices: 4844--4918 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
4834 GTGACAGAAT
4844 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* * * *
4865 AGGTGTATAG-TATGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
4886 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
4904 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
4919 AAGTGGAGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:6650 original size:22 final size:21
Alignment explanation
Indices: 6616--6679 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
6606 TCTGAGAGAT
6616 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
6636 GGAGATGATGACGGATTTCGTC
1 GGAGATGA-GACGGATTTCGCC
* * *
6658 AGAGATGGGACGGATGTCGCC
1 GGAGATGAGACGGATTTCGCC
6679 G
1 G
6680 TAGAGAGTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.17
21 12 0.33
22 18 0.50
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:6900 original size:19 final size:19
Alignment explanation
Indices: 6876--6912 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6866 TACGATACTG
*
6876 GAGATCATATTGCGATTTA
1 GAGATCATATTACGATTTA
*
6895 GAGATCGTATTACGATTT
1 GAGATCATATTACGATTT
6913 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
GAGATCATATTACGATTTA
Found at i:7190 original size:19 final size:19
Alignment explanation
Indices: 7166--7202 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7156 TACGATACTG
*
7166 GAGATCATATTGCGATTTA
1 GAGATCATATTACGATTTA
*
7185 GAGATCGTATTACGATTT
1 GAGATCATATTACGATTT
7203 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
GAGATCATATTACGATTTA
Found at i:9713 original size:26 final size:26
Alignment explanation
Indices: 9684--9736 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9674 TTTCAAACAA
9684 AAGAAGACACAAGCAACCAAGGAAGC
1 AAGAAGACACAAGCAACCAAGGAAGC
9710 AAGAAGACACAAGCAACCAAGGAAGC
1 AAGAAGACACAAGCAACCAAGGAAGC
9736 A
1 A
9737 GGGAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.23, G:0.23, T:0.00
Consensus pattern (26 bp):
AAGAAGACACAAGCAACCAAGGAAGC
Found at i:9840 original size:30 final size:30
Alignment explanation
Indices: 9804--9860 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
9794 CCACCAAGAG
9804 CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
1 CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
9834 CTTTCTTCAGCTTCTTAATGAGAGGCA
1 CTTTCTTCAGCTTCTTAATGAGAGGCA
9861 TTGAGGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (30 bp):
CTTTCTTCAGCTTCTTAATGAGAGGCAGAA
Found at i:11726 original size:44 final size:44
Alignment explanation
Indices: 11660--11747 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
11650 AATTCATTTT
11660 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
1 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
*
11704 AAGATGGAAATTGTTAGTCTGATTCAAAGTCATTATGGCATAAA
1 AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
11748 TTAATTAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (44 bp):
AAGATGGAAATTGTTAGCCTGATTCAAAGTCATTATGGCATAAA
Found at i:12335 original size:22 final size:22
Alignment explanation
Indices: 12308--12363 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
12298 TTTTAAAGTT
*
12308 TTTAAAGTTTAATTAATATTAG
1 TTTAAAGTTTAAATAATATTAG
* * *
12330 TTTAAATTTTTAAATCATATTCG
1 TTTAAA-GTTTAAATAATATTAG
*
12353 TTTAATGTTTA
1 TTTAAAGTTTA
12364 CAAACCAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTAAAGTTTAAATAATATTAG
Found at i:15699 original size:11 final size:11
Alignment explanation
Indices: 15685--15710 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15675 TTAAATAATA
15685 TTATTTTATAT
1 TTATTTTATAT
15696 TTATTTTATAT
1 TTATTTTATAT
15707 TTAT
1 TTAT
15711 CCAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTATAT
Found at i:35968 original size:31 final size:31
Alignment explanation
Indices: 35926--35984 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35916 AATTTAAAAG
* *
35926 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
35957 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
35985 CCATACAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:36035 original size:22 final size:22
Alignment explanation
Indices: 36009--36051 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35999 TAATAAATTA
36009 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
36031 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
36052 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:36060 original size:22 final size:22
Alignment explanation
Indices: 36011--36059 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
36001 ATAAATTATT
**
36011 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
36033 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
36056 TAAA
1 TAAA
36060 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:36136 original size:18 final size:16
Alignment explanation
Indices: 36112--36191 Score: 51
Period size: 14 Copynumber: 5.0 Consensus size: 16
36102 AATCCAAATT
36112 TTAAAATAAATCAATC
1 TTAAAATAAATCAATC
*
36128 TATACAAATAAAT-TAT-
1 T-TA-AAATAAATCAATC
*
36144 TTAAAATAAATCAGTCC
1 TTAAAATAAATCAAT-C
* * *
36161 ATACTAATAAAT-TAT-
1 TTA-AAATAAATCAATC
36176 TTAAAATAAATCAATC
1 TTAAAATAAATCAATC
36192 CATATTTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
14 15 0.33
15 7 0.15
16 2 0.04
17 7 0.15
18 15 0.33
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (16 bp):
TTAAAATAAATCAATC
Found at i:36147 original size:32 final size:32
Alignment explanation
Indices: 36111--36485 Score: 248
Period size: 32 Copynumber: 13.4 Consensus size: 32
36101 CAATCCAAAT
*
36111 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
36143 TTTAAAATAAATCAGTCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36175 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36197 TTTAAAATAAATCAATCCATAC---TAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* * *
36226 TTAAAATAATAAATCAATCCATACAACTACA--A
1 TT-TAA-AATAAATCAATCCATACAAATAAATTA
36258 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36276 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
36308 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
36340 TTTAAAATAAATCAATCCATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36370 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
36388 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36420 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
36442 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
36474 TTTAAAATAAAT
1 TTTAAAATAAAT
36486 TATTTTAAAA
Statistics
Matches: 279, Mismatches: 13, Indels: 102
0.71 0.03 0.26
Matches are distributed among these distances:
20 2 0.01
22 64 0.23
23 4 0.01
24 2 0.01
25 1 0.00
26 40 0.14
27 1 0.00
28 6 0.02
29 2 0.01
30 4 0.01
31 20 0.07
32 130 0.47
34 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:36201 original size:22 final size:22
Alignment explanation
Indices: 36175--36296 Score: 100
Period size: 22 Copynumber: 5.0 Consensus size: 22
36165 TAATAAATTA
36175 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
36197 TTTAAAATAAATCAATCCATACTAAAT
1 TTTAAAATAAATCAATCC--A-T--AT
*
36224 TATTAAAATAATAAATCAATCCATACAAC
1 T-TTAAAAT-A--AATCAATCCAT---AT
**
36253 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
36276 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
36297 CAAATAAATT
Statistics
Matches: 82, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
22 34 0.41
23 4 0.05
24 1 0.01
25 1 0.01
26 11 0.13
27 3 0.04
28 11 0.13
29 8 0.10
31 9 0.11
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:36305 original size:22 final size:22
Alignment explanation
Indices: 36229--36305 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 22
36219 TAAATTATTA
36229 AAAT-AATAAATCAATCCATAC
1 AAATAAATAAATCAATCCATAC
*
36250 AACTACAATAATAAATCAATCCATA-
1 AA--A-TA-AATAAATCAATCCATAC
***
36275 TTTTAAAATAAATCAATCCATAC
1 AAAT-AAATAAATCAATCCATAC
36298 AAATAAAT
1 AAATAAAT
36306 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 13
0.66 0.13 0.21
Matches are distributed among these distances:
21 2 0.05
22 20 0.49
23 3 0.07
26 16 0.39
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATAAATCAATCCATAC
Found at i:36378 original size:112 final size:111
Alignment explanation
Indices: 36197--36440 Score: 429
Period size: 112 Copynumber: 2.2 Consensus size: 111
36187 CAATCCATAT
36197 TTTAAAATAAATCAATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAATAAT
1 TTTAAAATAAATCAATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAATAAT
36262 AAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
66 AAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
*
36308 TTTAAAATAAATCAATCCATACTAATAAATTATT-TAA-AATAAATCAATCCATACAACTACAAT
1 TTTAAAATAAATCAATCCATAC---TAAATTATTAAAATAATAAATCAATCCATACAACTACAAT
*
36371 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
63 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
36420 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
36441 TTTTAAAATA
Statistics
Matches: 128, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
111 22 0.17
112 95 0.74
113 2 0.02
114 9 0.07
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (111 bp):
TTTAAAATAAATCAATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAATAAT
AAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:36417 original size:22 final size:23
Alignment explanation
Indices: 36342--36416 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
36332 ATAAATTATT
36342 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
36364 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
36390 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
36413 TAAA
1 TAAA
36417 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:36440 original size:54 final size:54
Alignment explanation
Indices: 36259--36485 Score: 288
Period size: 54 Copynumber: 4.1 Consensus size: 54
36249 CAACTACAAT
*
36259 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
36313 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
36371 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
36425 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
36479 AATAAAT
1 AATAAAT
36486 TATTTTAAAA
Statistics
Matches: 153, Mismatches: 2, Indels: 36
0.80 0.01 0.19
Matches are distributed among these distances:
48 25 0.16
49 3 0.02
50 2 0.01
52 3 0.02
54 73 0.48
55 1 0.01
57 1 0.01
58 12 0.08
60 3 0.02
62 2 0.01
63 3 0.02
64 25 0.16
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:36444 original size:245 final size:244
Alignment explanation
Indices: 36014--36466 Score: 661
Period size: 245 Copynumber: 1.8 Consensus size: 244
36004 AATTATTTAA
* * *
36014 AATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
* ** * *
36079 CCATACAACTACAATAATAAATCAATCCAAATTTTAAAATAAATCAATCTATACAAATAAATTAT
66 CCATACAACTAAAATAATAAATCAATCCAAATACTAAAATAAATAAATCAATACAAAT-AATTAT
*
36144 TTAAAATAAATCAGTCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
130 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
36209 CAATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAAT
195 CAATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAAT
36259 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
* *
36324 CCATACTAA-TAAATTATTTAAAATAAATCAATCCATACA-ACTACAAT-AATAAATCAAT-C-C
66 CCATAC-AACTAAA--A--T--AATAAATCAATCCA-A-ATACTAAAATAAATAAATCAATACAA
36384 AT-A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
122 ATAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
36446 AAATAAATCAATCCATACTAA
187 AAATAAATCAATCCATACTAA
36467 TAAATTATTT
Statistics
Matches: 188, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
245 149 0.79
246 3 0.02
247 2 0.01
249 3 0.02
250 1 0.01
251 23 0.12
252 6 0.03
253 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (244 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTAAAATAATAAATCAATCCAAATACTAAAATAAATAAATCAATACAAATAATTATT
TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATC
AATCCATACTAAATTATTAAAATAATAAATCAATCCATACAACTACAAT
Found at i:36446 original size:22 final size:22
Alignment explanation
Indices: 36420--36462 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
36410 TAATAAATTA
36420 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
36442 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
36463 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:36471 original size:22 final size:22
Alignment explanation
Indices: 36422--36470 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
36412 ATAAATTATT
**
36422 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
36444 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
36467 TAAA
1 TAAA
36471 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:36484 original size:14 final size:15
Alignment explanation
Indices: 36465--36553 Score: 113
Period size: 15 Copynumber: 6.5 Consensus size: 15
36455 AATCCATACT
36465 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
36479 AATAAATTATTTTAA
1 AATAAATTATTTTAA
36494 AAT--A--A--TTAA
1 AATAAATTATTTTAA
*
36503 AATAAATTATTTTAT
1 AATAAATTATTTTAA
36518 AATAAATTATTTTAA
1 AATAAATTATTTTAA
36533 AAT-AATTATTTTAA
1 AATAAATTATTTTAA
36547 AATAAAT
1 AATAAAT
36554 AACCTTATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
9 7 0.11
11 2 0.03
13 2 0.03
14 23 0.35
15 31 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:36498 original size:29 final size:29
Alignment explanation
Indices: 36465--36553 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 29
36455 AATCCATACT
36465 AATAAATTATTTAAAATAAATTATTTTAA
1 AATAAATTATTTAAAATAAATTATTTTAA
*
36494 AAT--A--A-TTAAAATAAATTATTTTAT
1 AATAAATTATTTAAAATAAATTATTTTAA
36518 AATAAATTATTTTAAAAT-AATTATTTTAA
1 AATAAATTA-TTTAAAATAAATTATTTTAA
36547 AATAAAT
1 AATAAAT
36554 AACCTTATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
24 21 0.40
25 1 0.02
26 1 0.02
27 1 0.02
28 1 0.02
29 20 0.38
30 7 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAAATTATTTAAAATAAATTATTTTAA
Found at i:36529 original size:39 final size:38
Alignment explanation
Indices: 36465--36540 Score: 134
Period size: 39 Copynumber: 2.0 Consensus size: 38
36455 AATCCATACT
36465 AATAAATTATTTAAAATAAATTATTTTAAAATAATTAA
1 AATAAATTATTTAAAATAAATTATTTTAAAATAATTAA
*
36503 AATAAATTATTTTATAATAAATTATTTTAAAATAATTA
1 AATAAATTA-TTTAAAATAAATTATTTTAAAATAATTA
36541 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 9 0.25
39 27 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (38 bp):
AATAAATTATTTAAAATAAATTATTTTAAAATAATTAA
Found at i:39469 original size:16 final size:16
Alignment explanation
Indices: 39448--39480 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39438 TGCATATTGT
39448 TTTTTAAAAAAATAAA
1 TTTTTAAAAAAATAAA
*
39464 TTTTTAAAATAATAAA
1 TTTTTAAAAAAATAAA
39480 T
1 T
39481 ATTAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTTAAAAAAATAAA
Found at i:40591 original size:6 final size:6
Alignment explanation
Indices: 40580--40645 Score: 114
Period size: 6 Copynumber: 10.7 Consensus size: 6
40570 GTCATTGGCT
40580 CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC
1 CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC CATTGC
40628 CATTTGC CATTTGC CATT
1 CA-TTGC CA-TTGC CATT
40646 TGTGCTATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
6 46 0.78
7 13 0.22
ACGTcount: A:0.17, C:0.32, G:0.15, T:0.36
Consensus pattern (6 bp):
CATTGC
Found at i:42201 original size:21 final size:21
Alignment explanation
Indices: 42177--42244 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
42167 ACTTTGACTA
*
42177 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATATTCCAAGT
* * *
42198 TCGCATTACGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAGT
*
42219 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA--TATTCCAAGT
42242 TCG
1 TCG
42245 TTGCGTTGCG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 26 0.70
23 11 0.30
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAGT
Found at i:42256 original size:26 final size:26
Alignment explanation
Indices: 42221--42299 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
42211 TTCCAAATTC
42221 GCGTTGCGATTTATTCCAAGTTCGTT
1 GCGTTGCGATTTATTCCAAGTTCGTT
42247 GCGTTGCGATTTATTCCAAGTTCGTT
1 GCGTTGCGATTTATTCCAAGTTCGTT
* *
42273 GCGTTGCAATTTATTCTAAGTTCGTT
1 GCGTTGCGATTTATTCCAAGTTCGTT
42299 G
1 G
42300 AGATAGTCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (26 bp):
GCGTTGCGATTTATTCCAAGTTCGTT
Found at i:43224 original size:21 final size:21
Alignment explanation
Indices: 43199--43288 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
43189 TTTGGAATAA
43199 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
43220 ATCGCAA--C-AAATT----T
1 ATCGCAACGCGAACTTGGACT
*
43234 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
43255 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
43276 ATCGCAATGCGAA
1 ATCGCAACGCGAA
43289 TATGTAAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
14 8 0.14
16 1 0.02
17 4 0.07
18 4 0.07
19 1 0.02
21 40 0.69
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:43966 original size:14 final size:15
Alignment explanation
Indices: 43941--43971 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43931 CACCAGCTCG
43941 AATAACAATAAATAA
1 AATAACAATAAATAA
43956 AATAA-AATAAATAA
1 AATAACAATAAATAA
43970 AA
1 AA
43972 AGGAAACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAACAATAAATAA
Found at i:44094 original size:2 final size:2
Alignment explanation
Indices: 44087--44139 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
44077 AATCTCCATC
* *
44087 CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT AT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44129 CT CT CT CT CT C
1 CT CT CT CT CT C
44140 AATTCAGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:46595 original size:68 final size:69
Alignment explanation
Indices: 46484--46614 Score: 158
Period size: 68 Copynumber: 1.9 Consensus size: 69
46474 AAAACCGGTA
** ** * * *
46484 AAAAATGACCTTAAATATTATTAGTTGCTACTGGTTTTGTTATTATTTGACA-TTTTACCGGATT
1 AAAAATGACCAGAAATATTATTAGACGCTACTGATTTTATTATTATTGGACATTTTTACCGGATT
46548 TGAT
66 TGAT
* *
46552 AAAAATGACCAGAAATATTATTAGACGCTA-TCGATTTTATTATTGTTGGATATTTTTACCGGA
1 AAAAATGACCAGAAATATTATTAGACGCTACT-GATTTTATTATTATTGGACATTTTTACCGGA
46615 AATGTTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
67 1 0.02
68 41 0.79
69 10 0.19
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (69 bp):
AAAAATGACCAGAAATATTATTAGACGCTACTGATTTTATTATTATTGGACATTTTTACCGGATT
TGAT
Found at i:49323 original size:11 final size:11
Alignment explanation
Indices: 49307--49333 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
49297 AAAAATACAA
49307 AAATACAAAAT
1 AAATACAAAAT
49318 AAATACAAAAT
1 AAATACAAAAT
49329 AAATA
1 AAATA
49334 TTAAAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATACAAAAT
Found at i:53075 original size:3 final size:3
Alignment explanation
Indices: 53067--53164 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
53057 AATATATATT
* *
53067 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
53115 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53163 TA
1 TA
53165 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54037 original size:112 final size:113
Alignment explanation
Indices: 53479--54031 Score: 871
Period size: 113 Copynumber: 4.9 Consensus size: 113
53469 TGTGATAGTA
*
53479 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
53543 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
66 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
*** *
53591 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
53656 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
66 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
* * *
53704 TCAATCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCCTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
53769 TCTCATTATGAACTTTTTCTGGAAAAGCTAATCCATCAATTGACGAAT
66 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
*** *
53817 TCATGTAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * *
53882 TCTCATTATGAAC-TTCTCTGGCAATGTTGATCCATTCAA-TGATGAAT
66 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCA-TCAATTGACGAAT
53929 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
53994 TCTCATTATGAAC-TTATCTGGCAATGTTGATCCATCAA
66 TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAA
54032 GTGATGGATT
Statistics
Matches: 412, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
111 4 0.01
112 120 0.29
113 288 0.70
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAATTGACGAAT
Found at i:54815 original size:83 final size:83
Alignment explanation
Indices: 54670--55160 Score: 930
Period size: 83 Copynumber: 5.9 Consensus size: 83
54660 CCTACTGAAT
* * *
54670 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAATTCA
54734 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
54753 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
54818 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
54836 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
54901 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
54919 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
54984 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
55002 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
55067 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
55085 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
55150 TGATTGGTTCT
66 TGATTGGTTCT
55161 AAGATATCAC
Statistics
Matches: 402, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
83 400 1.00
84 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGCCAAAC
Found at i:67640 original size:23 final size:24
Alignment explanation
Indices: 67603--67648 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
67593 TTCGATATTG
67603 AAAAAATATTAAAATAATTTATTTT
1 AAAAAATATTAAAATAA-TTATTTT
*
67628 AAAAAATA-T-AAATTATTATTT
1 AAAAAATATTAAAATAATTATTT
67649 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 1 0.05
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATATTAAAATAATTATTTT
Found at i:69128 original size:3 final size:3
Alignment explanation
Indices: 69120--69208 Score: 133
Period size: 3 Copynumber: 29.7 Consensus size: 3
69110 AATATATATT
* * * *
69120 TAA TAA TAA TAA TAA TAA TGA TGA TGA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
69168 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
69209 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:69664 original size:27 final size:27
Alignment explanation
Indices: 69634--69690 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
69624 TTTTGGTGTA
69634 ATTAATTGATCTCCCTATTGATTTAGT
1 ATTAATTGATCTCCCTATTGATTTAGT
69661 ATTAATTGATCTCCCTATTGATTTAGT
1 ATTAATTGATCTCCCTATTGATTTAGT
69688 ATT
1 ATT
69691 TGTGAACACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (27 bp):
ATTAATTGATCTCCCTATTGATTTAGT
Found at i:74515 original size:11 final size:11
Alignment explanation
Indices: 74499--74528 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
74489 TGTCATTGTC
74499 CATGAAAAAAA
1 CATGAAAAAAA
74510 CATGAAAAAAA
1 CATGAAAAAAA
74521 CATGAAAA
1 CATGAAAA
74529 GATGAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.70, C:0.10, G:0.10, T:0.10
Consensus pattern (11 bp):
CATGAAAAAAA
Found at i:75903 original size:23 final size:23
Alignment explanation
Indices: 75877--75920 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
75867 AGTAAACTGT
*
75877 TACAGTACAGACATCAGAACAAA
1 TACAGTACAGACATCAAAACAAA
*
75900 TACAGTATAGACATCAAAACA
1 TACAGTACAGACATCAAAACA
75921 GTTTCAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (23 bp):
TACAGTACAGACATCAAAACAAA
Found at i:75928 original size:23 final size:23
Alignment explanation
Indices: 75870--75928 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
75860 TGAGAGCAGT
*
75870 AAACTGTTACAGTACAGACATCA
1 AAACAGTTACAGTACAGACATCA
* ** *
75893 GAACAAATACAGTATAGACATCA
1 AAACAGTTACAGTACAGACATCA
*
75916 AAACAGTTTCAGT
1 AAACAGTTACAGT
75929 CATCAAAACA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (23 bp):
AAACAGTTACAGTACAGACATCA
Found at i:80810 original size:76 final size:76
Alignment explanation
Indices: 80717--80956 Score: 288
Period size: 76 Copynumber: 3.1 Consensus size: 76
80707 TACAACTTAG
* * *
80717 ACGGTTAAAATAAAATAGTCACAACATACTACGTTAAACTAGCTACCGATTTGTTTAAAGGTATA
1 ACGG-TAAAATAAAATAGACGCAACATATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTATA
80782 ATAATAATGTAA
65 ATAATAATGTAA
* * *
80794 ACGGTATAATAAAATAGACGCAACCTATTACATTAAACTAGCT-CC-ATGTTTGTTTAAAGGTAT
1 ACGGTAAAATAAAATAGACGCAACATATTACGTTAAACTAGCTACCGA--TTTGTTTAAAGGTAT
80857 AATAATAATGTAA
64 AATAATAATGTAA
* * * * *
80870 ACGGTAAAATAAAATAGACGCTAA-TTATTACGTTAAACTACCTACTGGTTTATTTAAAGGTATA
1 ACGGTAAAATAAAATAGACGC-AACATATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTATA
* *
80934 GTAATAATGCAA
65 ATAATAATGTAA
* *
80946 TCGATAAAATA
1 ACGGTAAAATA
80957 TTTACAACTT
Statistics
Matches: 141, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
74 1 0.01
75 2 0.01
76 131 0.93
77 7 0.05
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (76 bp):
ACGGTAAAATAAAATAGACGCAACATATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTATAA
TAATAATGTAA
Found at i:81131 original size:76 final size:75
Alignment explanation
Indices: 80972--81208 Score: 267
Period size: 76 Copynumber: 3.1 Consensus size: 75
80962 AACTTAACTG
* * * *
80972 GTTAAAATAAAATAGGTGTTACCTATTACGCTAAACTACCTACCGGTTTGTTTAAAGGTATAATA
1 GTTAAAATAAAATAGGAGCTACCTATTACGTTAAACTACCTA-CTGTTTGTTTAAAGGTATAATA
*
81037 ATCATGTAAAC
65 ATAATGTAAAC
** * * * *
81048 GGCAAAATAAAATAGGCGCTACCTATTATGTTAAACTACATACTGATTGTTTAAAGGTATAATAA
1 GTTAAAATAAAATAGGAGCTACCTATTACGTTAAACTACCTACTGTTTGTTTAAAGGTATAATAA
*
81113 TAATGTAACC
66 TAATGTAAAC
* * * * * *
81123 GATTAAAATAAAATAGAAGCTACCTATTACATTAGACCACCTATTAGTTTGTTTAAATGTATAAT
1 G-TTAAAATAAAATAGGAGCTACCTATTACGTTAAACTACCTACT-GTTTGTTTAAAGGTATAAT
*
81188 ATTAATGTAAAC
64 AATAATGTAAAC
*
81200 GGTAAAATA
1 GTTAAAATA
81209 TTTACAACTT
Statistics
Matches: 133, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
75 30 0.23
76 75 0.56
77 28 0.21
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (75 bp):
GTTAAAATAAAATAGGAGCTACCTATTACGTTAAACTACCTACTGTTTGTTTAAAGGTATAATAA
TAATGTAAAC
Found at i:81208 original size:252 final size:250
Alignment explanation
Indices: 80705--81559 Score: 1083
Period size: 252 Copynumber: 3.4 Consensus size: 250
80695 CTCCCTTTAT
* * * * *
80705 TTTACAACTTAGA-CGGTTAAAATAAAATA-GTCACAACATACTACGTTAAACTAGCTACCGATT
1 TTTACAACTTA-ACCGGTTAAAATAAAATAGGT-GCTACCTATTACGTTAAACTACCTACCGATT
* * * * *
80768 TGTTTAAAGGTATAATAATAATGTAAACGGTATAATAAAATAGACGCAACCTATTACATTAAACT
64 TGTTTAAAGGTATAATAATAATGTAAACGGCAAAATAAAATAGGCGCTACCTATTACGTTAAACT
* * * **
80833 AGCTCCATGTTTGTTTAAAGGTATAATAATAATGTAAACG-GTAAAATAAAATAGACGCTAATTA
129 A-CTAC-TGATTGTTTAAAGGTATAATAATAATGT-AACGATTAAAATAAAATAGACGCTACCTA
* * * * * *
80897 TTACGTTAAACTACCTACTGGTTTATTTAAAGGTATAGTAATAATGCAATCGATAAAATA
191 TTACGTTAAACTACCTACTGGTTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATA
* * * *
80957 TTTACAACTTAACTGGTTAAAATAAAATAGGTGTTACCTATTACGCTAAACTACCTACCGGTTTG
1 TTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCGATTTG
* *
81022 TTTAAAGGTATAATAATCATGTAAACGGCAAAATAAAATAGGCGCTACCTATTATGTTAAACTAC
66 TTTAAAGGTATAATAATAATGTAAACGGCAAAATAAAATAGGCGCTACCTATTACGTTAAACTAC
*
81087 ATACTGATTGTTTAAAGGTATAATAATAATGTAACCGATTAAAATAAAATAGAAGCTACCTATTA
131 -TACTGATTGTTTAAAGGTATAATAATAATGTAA-CGATTAAAATAAAATAGACGCTACCTATTA
* * * * * *
81152 CATTAGACCACCTATTAGTTTGTTTAAATGTATAATATTAATGTAAACGGTAAAATA
194 CGTTAAACTACCTACTGGTTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATA
* * * * * *
81209 TTTACAACTTAACCGATTAAAAT-AAATAGGGGCTAACTATTATGTTAAACTAGCTATCGATTTG
1 TTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCGATTTG
** *
81273 TTTAAAGGTATAATAATAATGTAAACGATAAAATAAAATAGGCGCTATCTATTACGTTAAACTAC
66 TTTAAAGGTATAATAATAATGTAAACGGCAAAATAAAATAGGCGCTACCTATTACGTTAAACTA-
**
81338 CTACTGATTTGTTTAAAGGTATAATAATAATGTAATAAGTTAAAATAAAATAGACGCTACCTATT
130 CTACTGA-TTGTTTAAAGGTATAATAATAATGTAACGA-TTAAAATAAAATAGACGCTACCTATT
* * * * *
81403 ACGTTAAATTAACTACCGGTTTGTTTAAAGGTACAAAATTAATGTAAACGGTAAAATA
193 ACGTTAAACTACCTACTGGTTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATA
* * * *
81461 TTTAAAACTTAACCGGTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACTTACCAATTTG
1 TTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCGATTTG
81526 TTTAAAGGTAT-ATAATAATGTAAAC-GCTAAAATA
66 TTTAAAGGTATAATAATAATGTAAACGGC-AAAATA
81560 TTTACAACTT
Statistics
Matches: 519, Mismatches: 74, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
250 2 0.00
251 130 0.25
252 340 0.66
253 47 0.09
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (250 bp):
TTTACAACTTAACCGGTTAAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCGATTTG
TTTAAAGGTATAATAATAATGTAAACGGCAAAATAAAATAGGCGCTACCTATTACGTTAAACTAC
TACTGATTGTTTAAAGGTATAATAATAATGTAACGATTAAAATAAAATAGACGCTACCTATTACG
TTAAACTACCTACTGGTTTGTTTAAAGGTATAATATTAATGTAAACGGTAAAATA
Found at i:81238 original size:175 final size:176
Alignment explanation
Indices: 81051--81372 Score: 465
Period size: 175 Copynumber: 1.8 Consensus size: 176
81041 TGTAAACGGC
*
81051 AAAATAAAATAGGCGCTACCTATTATGTTAAACTA-C-ATACTGA-TTGTTTAAAGGTATAATAA
1 AAAATAAAATAGGCGCTAACTATTATGTTAAACTAGCTAT-C-GATTTGTTTAAAGGTATAATAA
* * *
81113 TAATGTAACCGATTAAAATAAAATAGAAGCTACCTATTACATTAGACCACCTA-TTAGTTTGTTT
64 TAATGTAAACGA-TAAAATAAAATAGAAGCTACCTATTACATTAAACCACCTACTGA-TTTGTTT
* *
81177 AAATGTATAATATTAATGTAAACGGTAAAATATTTACAACTTAACCGATT
127 AAAGGTATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCGATT
*
81227 AAAAT-AAATAGGGGCTAACTATTATGTTAAACTAGCTATCGATTTGTTTAAAGGTATAATAATA
1 AAAATAAAATAGGCGCTAACTATTATGTTAAACTAGCTATCGATTTGTTTAAAGGTATAATAATA
** * * *
81291 ATGTAAACGATAAAATAAAATAGGCGCTATCTATTACGTTAAACTACCTACTGATTTGTTTAAAG
66 ATGTAAACGATAAAATAAAATAGAAGCTACCTATTACATTAAACCACCTACTGATTTGTTTAAAG
81356 GTATAATAATAATGTAA
131 GTATAATAATAATGTAA
81373 TAAGTTAAAA
Statistics
Matches: 130, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
175 89 0.68
176 39 0.30
177 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (176 bp):
AAAATAAAATAGGCGCTAACTATTATGTTAAACTAGCTATCGATTTGTTTAAAGGTATAATAATA
ATGTAAACGATAAAATAAAATAGAAGCTACCTATTACATTAAACCACCTACTGATTTGTTTAAAG
GTATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCGATT
Found at i:81426 original size:77 final size:76
Alignment explanation
Indices: 81225--81460 Score: 296
Period size: 76 Copynumber: 3.1 Consensus size: 76
81215 ACTTAACCGA
* * * *
81225 TTAAAAT-AAATAGGGGCTAACTATTATGTTAAACTAGCTATCGATTTGTTTAAAGGTATAATAA
1 TTAAAATAAAATAGGCGCTAACTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAA
*
81289 TAATGTAAACG
66 TAATGTAAAAG
* * * *
81300 ATAAAATAAAATAGGCGCTATCTATTACGTTAAACTACCTACTGATTTGTTTAAAGGTATAATAA
1 TTAAAATAAAATAGGCGCTAACTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAA
81365 TAATGTAATAAG
66 TAATGTAA-AAG
* * * * *
81377 TTAAAATAAAATAGACGCTACCTATTACGTTAAATTAACTACCGGTTTGTTTAAAGGTACAA-AA
1 TTAAAATAAAATAGGCGCTAACTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAA
*
81441 TTAATGTAAACG
66 -TAATGTAAAAG
*
81453 GTAAAATA
1 TTAAAATA
81461 TTTAAAACTT
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
75 6 0.04
76 70 0.50
77 64 0.46
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (76 bp):
TTAAAATAAAATAGGCGCTAACTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAA
TAATGTAAAAG
Found at i:82384 original size:108 final size:108
Alignment explanation
Indices: 82191--82495 Score: 357
Period size: 108 Copynumber: 2.8 Consensus size: 108
82181 TATTGGGCTT
* * * * *
82191 AACCTAGTATGTTAATATTATTTATAACAAAATAAATATTTAACCTATTTTGTTGTCGTG-GTAT
1 AACCTAATATGTTGATAATATTTATAACAAAATAAATAATTAACCTATTTTGTTATCGTGAG-AT
* * * *
82255 TTCGAATGCCTC-ATCATCTTAAACTTTGGTAACATATTATG-CAC
65 TTCTAAGGCC-CAATCAACTTAAACTTTGATAACATATTA-GACAC
* *
82299 AACCTAATATGTTGATAATATTTATAGCAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATT
1 AACCTAATATGTTGATAATATTTATAACAAAATAAATAATTAACCTATTTTGTTATCGTGAGATT
* *
82364 TCTAAGGCCCAATCAACTTAAACTTTGATAACATTTTAGACGC
66 TCTAAGGCCCAATCAACTTAAACTTTGATAACATATTAGACAC
* * * * *
82407 TACCTAATATGTTGATAATATTAATAACAAAATAAATAATTAATCTATTTTGTTATCTTCAGATT
1 AACCTAATATGTTGATAATATTTATAACAAAATAAATAATTAACCTATTTTGTTATCGTGAGATT
* *
82472 TTTAAGG-TCACATCAACTTTAAAC
66 TCTAAGGCCCA-ATCAAC-TTAAAC
82496 AAATACAATC
Statistics
Matches: 170, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
107 4 0.02
108 159 0.94
109 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (108 bp):
AACCTAATATGTTGATAATATTTATAACAAAATAAATAATTAACCTATTTTGTTATCGTGAGATT
TCTAAGGCCCAATCAACTTAAACTTTGATAACATATTAGACAC
Done.