Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002859.1 Hibiscus syriacus cultivar Beakdansim tig00005895_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: 75508
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4187 original size:19 final size:19
Alignment explanation
Indices: 4163--4210 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
4153 GTCTGAGTGT
* *
4163 ATCGATGCTTGGTCTGTGC
1 ATCGATGCATGGTCTGTAC
4182 ATCGATGCATGGTCTGTAC
1 ATCGATGCATGGTCTGTAC
4201 ATCGATGCAT
1 ATCGATGCAT
4211 AAAATGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (19 bp):
ATCGATGCATGGTCTGTAC
Found at i:4292 original size:36 final size:35
Alignment explanation
Indices: 4242--4319 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
4232 TAAAAACCTG
* * * *
4242 AGTGGATCGATGCATGGAATTGCATCGATGCATAGA
1 AGTGCATCAATGCATAGAAGTGCATCGATGCATA-A
4278 AGTGCATCAATGCATAGAAGTGCATCGATGCATAA
1 AGTGCATCAATGCATAGAAGTGCATCGATGCATAA
*
4313 AATGCAT
1 AGTGCAT
4320 TCGAAATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 7 0.19
36 30 0.81
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (35 bp):
AGTGCATCAATGCATAGAAGTGCATCGATGCATAA
Found at i:4323 original size:18 final size:18
Alignment explanation
Indices: 4242--4311 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
4232 TAAAAACCTG
* *
4242 AGTGGATCGATGCATGGA
1 AGTGCATCGATGCATAGA
*
4260 ATTGCATCGATGCATAGA
1 AGTGCATCGATGCATAGA
*
4278 AGTGCATCAATGCATAGA
1 AGTGCATCGATGCATAGA
4296 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
4312 AAATGCATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATAGA
Found at i:6978 original size:23 final size:23
Alignment explanation
Indices: 6948--7029 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
6938 GCATGGCATT
6948 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
6971 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
6993 -TGTATCGATGGACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
7015 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
7030 TATGCACAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 3 0.07
23 17 0.38
24 12 0.27
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:12307 original size:45 final size:46
Alignment explanation
Indices: 12243--12347 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 46
12233 TGCACTAAGG
*
12243 GTGCATCGATGCATAAAATGCATTCAATG-TTTCA-AACAAGCCTGA
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAA-AAACCTGA
* * *
12288 GTGCATCGTTGCATAAAATGCATTCGATGTTTTCATAAAAACTTGA
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAAACCTGA
12334 GTGCATCGATGCAT
1 GTGCATCGATGCAT
12348 GGAAGTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 27 0.51
46 24 0.45
47 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAAACCTGA
Found at i:12378 original size:18 final size:18
Alignment explanation
Indices: 12335--12374 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12325 AAAACTTGAG
* *
12335 TGCATCGATGCATGGAAG
1 TGCATCGATGCATGAAAA
12353 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
12370 TGCAT
1 TGCAT
12375 TCGAAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:16855 original size:41 final size:41
Alignment explanation
Indices: 16798--16905 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
16788 AAAAACTCTT
* * * *
16798 ACTTTAGTGGCCTTTGTATACAAATGCCGCTACAGACTCAG
1 ACTTTAGTGGCATTTGTATACAAACGACGCTACAAACTCAG
* * * *
16839 ACTTTAGTGGCGTTTGTATACAAACGACGCTATAAATTCAT
1 ACTTTAGTGGCATTTGTATACAAACGACGCTACAAACTCAG
* *
16880 ACGTTAGTGGCATTTTTATACAAACG
1 ACTTTAGTGGCATTTGTATACAAACG
16906 CTATTATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
ACTTTAGTGGCATTTGTATACAAACGACGCTACAAACTCAG
Found at i:29858 original size:10 final size:10
Alignment explanation
Indices: 29845--29898 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
29835 ATGCAACTAT
29845 ATGCTCCTAA
1 ATGCTCCTAA
*
29855 ATGCAT-CTAT
1 ATGC-TCCTAA
29865 ATGCTCCTAA
1 ATGCTCCTAA
*
29875 ATGCAT-CTAT
1 ATGC-TCCTAA
29885 ATGCTCCTAA
1 ATGCTCCTAA
29895 ATGC
1 ATGC
29899 ATCTATATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (10 bp):
ATGCTCCTAA
Found at i:29864 original size:20 final size:20
Alignment explanation
Indices: 29835--29913 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
29825 ATTCTACCAC
*
29835 ATGCAACTATATGCTCCTAA
1 ATGCATCTATATGCTCCTAA
29855 ATGCATCTATATGCTCCTAA
1 ATGCATCTATATGCTCCTAA
29875 ATGCATCTATATGCTCCTAA
1 ATGCATCTATATGCTCCTAA
*
29895 ATGCATCTATATGATCCTA
1 ATGCATCTATATGCTCCTA
29914 TATGAGCTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (20 bp):
ATGCATCTATATGCTCCTAA
Found at i:29914 original size:10 final size:10
Alignment explanation
Indices: 29841--29918 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
29831 CCACATGCAA
*
29841 CTATATGCTC
1 CTATATGATC
*
29851 CTAAATGCAT-
1 CTATATG-ATC
*
29861 CTATATGCTC
1 CTATATGATC
*
29871 CTAAATGCAT-
1 CTATATG-ATC
*
29881 CTATATGCTC
1 CTATATGATC
*
29891 CTAAATGCAT-
1 CTATATG-ATC
29901 CTATATGATC
1 CTATATGATC
29911 CTATATGA
1 CTATATGA
29919 GCTTTTAGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
9 4 0.08
10 44 0.86
11 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (10 bp):
CTATATGATC
Found at i:37638 original size:23 final size:23
Alignment explanation
Indices: 37612--37666 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
37602 TACCAAAAGT
37612 AGAGAAAAACGTACCACAAAGGA
1 AGAGAAAAACGTACCACAAAGGA
* * ** * *
37635 AGAGATAAATGTGTCATAAAGGC
1 AGAGAAAAACGTACCACAAAGGA
37658 AGAGAAAAA
1 AGAGAAAAA
37667 GTCACAGAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.11, G:0.24, T:0.11
Consensus pattern (23 bp):
AGAGAAAAACGTACCACAAAGGA
Found at i:37923 original size:24 final size:23
Alignment explanation
Indices: 37887--37931 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
37877 TTACACAGTT
*
37887 ATATTAGTTTAAATTTTAAAAACA
1 ATATTAGTTTAAA-GTTAAAAACA
37911 ATATTA-TTATAAAGTTAAAAA
1 ATATTAGTT-TAAAGTTAAAAA
37932 TGATTTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATTAGTTTAAAGTTAAAAACA
Found at i:38535 original size:14 final size:14
Alignment explanation
Indices: 38511--38565 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
38501 AGTGAAATAG
*
38511 AATATGAATAAATGA
1 AATA-GAATAAATTA
38526 AATAGAATAAATTA
1 AATAGAATAAATTA
38540 AATAGAATAAATTA
1 AATAGAATAAATTA
38554 AATAGAATAAAT
1 AATAGAATAAAT
38566 ATGTATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
14 35 0.90
15 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (14 bp):
AATAGAATAAATTA
Found at i:38859 original size:16 final size:16
Alignment explanation
Indices: 38838--38879 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
38828 CCGAGTGACG
38838 TATTATTATTA-TATAA
1 TATTATTATTATTAT-A
*
38854 TATTATTAATATTATA
1 TATTATTATTATTATA
38870 TATTATTATT
1 TATTATTATT
38880 TACCAAGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTATTATTATA
Found at i:38866 original size:19 final size:19
Alignment explanation
Indices: 38838--38879 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
38828 CCGAGTGACG
*
38838 TATTATTATTATATAATAT
1 TATTAATATTATATAATAT
*
38857 TATTAATATTATATATTAT
1 TATTAATATTATATAATAT
38876 TATT
1 TATT
38880 TACCAAGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTAATATTATATAATAT
Found at i:47333 original size:87 final size:88
Alignment explanation
Indices: 47164--47356 Score: 212
Period size: 87 Copynumber: 2.2 Consensus size: 88
47154 AAAATTCGCT
* * * *
47164 CTCCACAGAAGAGTAGTGGAATAAATGTTTCAACAAAGTATGAGAACTTCACGGAAGAGTAGTGG
1 CTCCACGGAAGAGTAGTGGAACAAATGTTTCAACAAAGTATGAGAACTTCACGGAAGACTAGTGA
*
47229 AGTAATCCAAGTTTGAGTCTGAA
66 AGTAATCCAAGTGTGAGTCTGAA
* * * * * *
47252 CTCCACGGAATAGTAGTGGAACGAAT-TTTTAGCAAAGTATGA-AATCTTCACGGAATACTAGTT
1 CTCCACGGAAGAGTAGTGGAACAAATGTTTCAACAAAGTATGAGAA-CTTCACGGAAGACTAGTG
* *
47315 AAGTAATCCAACG-GTGAGTTTGAT
65 AAGTAATCCAA-GTGTGAGTCTGAA
* *
47339 CTTCACGGAAGAGCAGTG
1 CTCCACGGAAGAGTAGTG
47357 AAATTAGATT
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
86 2 0.02
87 62 0.71
88 23 0.26
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (88 bp):
CTCCACGGAAGAGTAGTGGAACAAATGTTTCAACAAAGTATGAGAACTTCACGGAAGACTAGTGA
AGTAATCCAAGTGTGAGTCTGAA
Found at i:47690 original size:3 final size:3
Alignment explanation
Indices: 47682--47724 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
47672 ACGAGTGATG
*
47682 TAT TAT TAT TAT ATAA TAT TAT ATAT TAT TAT ATAT TAT TAT T
1 TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT -TAT TAT TAT T
47725 TACAAAGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 27 0.77
4 8 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:47703 original size:10 final size:10
Alignment explanation
Indices: 47685--47723 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
47675 AGTGATGTAT
47685 TATTATTATA
1 TATTATTATA
*
47695 TAATATTATA
1 TATTATTATA
47705 TATTATTATA
1 TATTATTATA
47715 TATTATTAT
1 TATTATTAT
47724 TTACAAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTATTATA
Found at i:50177 original size:3 final size:3
Alignment explanation
Indices: 50169--50212 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
50159 CATCCCAAAA
*
50169 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
50213 GTAATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:50222 original size:15 final size:15
Alignment explanation
Indices: 50170--50227 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
50160 ATCCCAAAAT
* *
50170 ATTATTATTATTATT
1 ATTATAATTATTATA
* *
50185 ATTATTATTATTATT
1 ATTATAATTATTATA
50200 ATTATAATTATTAGTA
1 ATTATAATTATTA-TA
50216 ATT-TAATT-TTAT
1 ATTATAATTATTAT
50228 TTTTTACAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 32 0.80
16 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTATAATTATTATA
Found at i:51944 original size:4 final size:4
Alignment explanation
Indices: 51935--51961 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
51925 CTGAATCTCT
51935 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
51962 TAATTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:56750 original size:19 final size:18
Alignment explanation
Indices: 56693--56755 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
56683 TGGAAATCAT
*
56693 TTTATACATTTTCATATTC
1 TTTAT-CATTTTTATATTC
* * *
56712 TTTGTCATCCTTTAGATTC
1 TTTATCAT-TTTTATATTC
56731 TTTATCATTTTTATACTTC
1 TTTATCATTTTTATA-TTC
56750 TATTAT
1 T-TTAT
56756 TATTAGTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 8 0.24
19 22 0.65
20 4 0.12
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTATCATTTTTATATTC
Found at i:58298 original size:13 final size:13
Alignment explanation
Indices: 58279--58319 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
58269 TACCACACTC
58279 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
*
58292 GAAAAAAAG-AGA
1 AAAAAAAAGAAGA
58304 AAAATAAAAGAA-A
1 AAAA-AAAAGAAGA
58317 AAA
1 AAA
58320 GAAAGAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 6 0.25
13 17 0.71
14 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:58301 original size:10 final size:11
Alignment explanation
Indices: 58282--58327 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
58272 CACACTCAAA
58282 AAAAAGAAGAG
1 AAAAAGAAGAG
58293 AAAAA-AAGAG
1 AAAAAGAAGAG
* *
58303 AAAAATAAAAG
1 AAAAAGAAGAG
58314 AAAAAAGAA-AG
1 -AAAAAGAAGAG
58325 AAA
1 AAA
58328 TGATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 13 0.42
11 11 0.35
12 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAGAAGAG
Found at i:58324 original size:11 final size:10
Alignment explanation
Indices: 58280--58327 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 10
58270 ACCACACTCA
58280 AAAAAAAGAAG
1 AAAAAAA-AAG
58291 AGAAAAAAAGAG
1 A-AAAAAAA-AG
58303 AAAAATAAAAG
1 AAAAA-AAAAG
58314 AAAAAAGAAAG
1 AAAAAA-AAAG
58325 AAA
1 AAA
58328 TGATAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.03
11 20 0.61
12 12 0.36
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:60444 original size:233 final size:233
Alignment explanation
Indices: 60029--61162 Score: 1273
Period size: 233 Copynumber: 5.0 Consensus size: 233
60019 TTTATAAGTT
** *
60029 AAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAATGAGAAAGACTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
* * * * * *
60094 TTTACCTAGTAAACTTTTTCCAAAGTTGGTAAGTCCTTCGGGCCATTAGTAAGTCTATCGAGCAT
66 CTTACCTAGTAAACTATTTCCAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
60159 AATGTTTAAA-TCTTTCGGGTCATCTGTAACTCTTTTGAGCAAGATGATAAGTCCTTCGGGCCAT
131 GATGCTTAAATTC-TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT
*
60223 CCATAAGACCTTCGGCCAGGATGTTTTCACATGTCTCTC
195 CCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC
* *
60262 GAAAAATGAGAAAGACTTCTCTTTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAATGAGAAAGACTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
* * * * * *
60327 CTTATCTAGTAAACTATTTCCAAAGTTGGTGATTCATTTGAGCCATCAGTAAGTCTTTCGAGCAT
66 CTTACCTAGTAAACTATTTCCAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
60392 GATGCCTAAATTCTTCGGGTCATTTGTAATTCTTT----C--GA-G-TAA---------G--AT-
131 GATGCTTAAATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* * *
60437 AATAAGTCCTTCGGGCAGGATGTTTTCGCATGTCTCTC
196 CATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC
* * * * *
60475 AAAAAATGA-AAA-AGTTCCTAATTTAAATCTGAAAATTAAAATTTTTGAAAAGAAAGAAAGGTT
1 AAAAAATGAGAAAGACTT-CTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTT
* ** *
60538 TCTTACCTAGTAAACTATTTCAAAATTTTATAAGTCCTTTGGGACATCAGTAAGTCTTTCGAGCA
65 TCTTACCTAGTAAACTATTTCCAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCA
* * ** *
60603 TGATGATTAACA-CCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTTATTCGAGCCA
130 TGATGCTTAA-ATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCA
* * **
60667 TCCATATGACCTTTGGGCATAATGTTTTCACATGTCTCTC
194 TCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC
* * * * **
60707 GAAAAATAAGAAAGGCTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAAATT
1 AAAAAATGAGAAAGACTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
* ** *
60772 ATTACCTAGTAAACTA-TTCTTGAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGACCA
66 CTTACCTAGTAAACTATTTC-CAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCA
* * * *
60836 TGATGCTTAAATAT-TTCAGGTTATCTGTAAGTCATTCGAGCAAGATGATAAGTCCTTCGGGTCA
130 TGATGCTTAAAT-TCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCA
* * *
60900 TCCATAAGACCTTCGGGCAGGATGTCTTCACATGTTTTTC
194 TCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC
* *
60940 AAAAAAATTGAGAAA-AGTTTCTCATTTAAATCTG-AAATTGAATTTTTTGAAAAGTAAGAAAAG
1 -AAAAAA-TGAGAAAGA-CTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAG
* * * * * *
61003 TTTCTTACCAAGTAAACTA-TTCTCAAATTTGGTAAGTCCTTCGAGCCATAAGTAAGCCTTTTGA
63 TTTCTTACCTAGTAAACTATTTC-CAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGA
* * * * * * *
61067 GCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTCTCGAGTAAGATTATAAGTTCTTCGGGC
127 GCATGATGCTTAAATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGC
*
61132 CATCCATAAGTCCTTCGGGCAGGATGTTTTC
192 CATCCATAAGACCTTCGGGCAGGATGTTTTC
61163 GCATTATTTT
Statistics
Matches: 751, Mismatches: 118, Indels: 63
0.81 0.13 0.07
Matches are distributed among these distances:
211 3 0.00
212 128 0.17
213 43 0.06
214 2 0.00
216 2 0.00
218 2 0.00
219 1 0.00
220 3 0.00
225 3 0.00
226 1 0.00
227 2 0.00
229 2 0.00
231 2 0.00
232 42 0.06
233 323 0.43
234 171 0.23
235 21 0.03
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (233 bp):
AAAAAATGAGAAAGACTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
CTTACCTAGTAAACTATTTCCAAATTTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCAT
GATGCTTAAATTCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
CATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTC
Found at i:60889 original size:445 final size:446
Alignment explanation
Indices: 60029--61162 Score: 1213
Period size: 445 Copynumber: 2.5 Consensus size: 446
60019 TTTATAAGTT
* * * * *
60029 AAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAATGAGAAAAGTTCCTAATTTAAATATGAAAATTAAAATTTTTGAAAAGAAAGAAAAGTTT
* * * * * *
60094 TTTACCTAGTAAACTTTTTCCAAAGTTGGTAAGTCCTTCGGGCCATTAGTAAGTCTATCGAGCAT
66 CTTACCTAGTAAACTATTTCAAAAGTTGATAAGTCCTTCGGGACATCAGTAAGTCTATCGAGCAT
* * * * *
60159 AATGTTTAAATCTTTCGGGTCATCTGTAACTCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATC
131 AATGATTAAATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATC
* * *
60224 CATAAGACCTTCGGCCAGGATGTTTTCACATGTCTCTCGAAAAATGAGAAAGACTTCTCTTTTAA
196 CATAAGACCTTCGGCCAGAATGTTTTCACATGTCTCTCGAAAAATAAGAAAGACTTCTCATTTAA
* ** * *
60289 ATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTATCTAGTAAACTATTTCCAAAGTT
261 ATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAAATTATTACCTAGTAAACTATTTCCAAAGTT
* * * * *
60354 GGTGATTCATTTGAGCCATCAGTAAGTCTTTCGAGCATGATGCCTAAATTCTTCGGGTCATTTGT
326 GGTAAGTCATTTGAGCCATCAGTAAGTCTTTCGACCATGATGCCTAAATTCTTCAGGTCATCTGT
* * *
60419 AATTCTTTCGAGTAAGATAATAAGTCCTTCGGGCAGGATGTTTTCGCATGTCTCTC
391 AAGTCATTCGAGCAAGATAATAAGTCCTTCGGGCAGGATGTTTTCGCATGTCTCTC
* *
60475 AAAAAATGA-AAAAGTTCCTAATTTAAATCTGAAAATTAAAATTTTTGAAAAGAAAGAAAGGTTT
1 AAAAAATGAGAAAAGTTCCTAATTTAAATATGAAAATTAAAATTTTTGAAAAGAAAGAAAAGTTT
* * * *
60539 CTTACCTAGTAAACTATTTCAAAATTTTATAAGTCCTTTGGGACATCAGTAAGTCTTTCGAGCAT
66 CTTACCTAGTAAACTATTTCAAAAGTTGATAAGTCCTTCGGGACATCAGTAAGTCTATCGAGCAT
* * *
60604 GATGATTAACA-CCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTTATTCGAGCCAT
131 AATGATTAA-ATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAGATGATAAGTCATTCGAGCCAT
* * * * *
60668 CCATATGACCTTTGGGCATAATGTTTTCACATGTCTCTCGAAAAATAAGAAAGGCTTCTCATTTA
195 CCATAAGACCTTCGGCCAGAATGTTTTCACATGTCTCTCGAAAAATAAGAAAGACTTCTCATTTA
** *
60733 AATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAAATTATTACCTAGTAAACTA-TTCTTGAAT
260 AATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAAATTATTACCTAGTAAACTATTTC-CAAAG
* * * *
60797 TTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGACCATGATGCTTAAATAT-TTCAGGTTATC
324 TTGGTAAGTCATTTGAGCCATCAGTAAGTCTTTCGACCATGATGCCTAAAT-TCTTCAGGTCATC
* *
60861 TGTAAGTCATTCGAGCAAGATGATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTC
388 TGTAAGTCATTCGAGC-A-A-G---A----------T-A---ATAAGTCCTTCGGGCAGGATGTT
* * *
60926 TTCACATGTTTTTC
433 TTCGCATGTCTCTC
* * * * * *
60940 AAAAAAATTGAGAAAAGTTTCTCATTTAAATCTG-AAATTGAATTTTTTGAAAAGTAAGAAAAGT
1 -AAAAAA-TGAGAAAAGTTCCTAATTTAAATATGAAAATTAAAATTTTTGAAAAGAAAGAAAAGT
* * * * * * * * *
61004 TTCTTACCAAGTAAACTATTCTC-AAATTTGGTAAGTCCTTCGAGCCATAAGTAAGCCTTTTGAG
64 TTCTTACCTAGTAAACTATT-TCAAAAGTTGATAAGTCCTTCGGGACATCAGTAAGTCTATCGAG
* * * * * * *
61068 CATGATGCTTAAATCCTTCGGGTCATCTATAAGC-CTCTCGAGTAAGATTATAAGTTC-TTCGGG
128 CATAATGATTAAATCCTTCGGGTCATCTGTAA-CTCTTTCGAGCAAGATGATAAG-TCATTCGAG
* * *
61131 CCATCCATAAGTCCTTCGGGCAGGATGTTTTC
191 CCATCCATAAGACCTTCGGCCAGAATGTTTTC
61163 GCATTATTTT
Statistics
Matches: 572, Mismatches: 86, Indels: 39
0.82 0.12 0.06
Matches are distributed among these distances:
444 3 0.01
445 332 0.58
446 12 0.02
447 1 0.00
448 1 0.00
451 1 0.00
461 1 0.00
462 1 0.00
465 32 0.06
466 7 0.01
467 158 0.28
468 23 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (446 bp):
AAAAAATGAGAAAAGTTCCTAATTTAAATATGAAAATTAAAATTTTTGAAAAGAAAGAAAAGTTT
CTTACCTAGTAAACTATTTCAAAAGTTGATAAGTCCTTCGGGACATCAGTAAGTCTATCGAGCAT
AATGATTAAATCCTTCGGGTCATCTGTAACTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATC
CATAAGACCTTCGGCCAGAATGTTTTCACATGTCTCTCGAAAAATAAGAAAGACTTCTCATTTAA
ATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAAATTATTACCTAGTAAACTATTTCCAAAGTT
GGTAAGTCATTTGAGCCATCAGTAAGTCTTTCGACCATGATGCCTAAATTCTTCAGGTCATCTGT
AAGTCATTCGAGCAAGATAATAAGTCCTTCGGGCAGGATGTTTTCGCATGTCTCTC
Found at i:61679 original size:134 final size:134
Alignment explanation
Indices: 61480--61827 Score: 385
Period size: 134 Copynumber: 2.6 Consensus size: 134
61470 ATTGAACTCA
* * * * * *
61480 ATTCAATCTTCCCTG-AGTAATAGTGGAACGAATTAACATCCCCAGATCTAATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAG-AACAATGAAATGAATAAACGTCCCCAGATCTAATTTTCCCTCAAGA
* * * * **
61544 AGAAGCGGAACAGATTCATCTATTTCAATATTTGATATTCTCTAAATAATAGTGGAACAAATCTA
65 AGAAGCGGAACAGATCCATCTATTTCAAAATTTGATATTCCCTAAATAACAGTAAAACAAATCTA
*
61609 CCTTG
130 CCTCG
* * * *
61614 ATTCAGTTTTCCCTGAAGAACAAT-AGAATGAATAAATGTCCCCAGATCTGATTTTCCCTCAAGA
1 ATTCAATCTTCCCTGAAGAACAATGA-AATGAATAAACGTCCCCAGATCTAATTTTCCCTCAAGA
* * * * * * *
61678 AGAAGCGGAACAGATCCCTCTCTTTCAAAATTTGGTATTCCCTGAGTAACAGTAAAACAAGTCTG
65 AGAAGCGGAACAGATCCATCTATTTCAAAATTTGATATTCCCTAAATAACAGTAAAACAAATCTA
61743 CCTCG
130 CCTCG
* * * * *
61748 ATTCAATCTTCCCTGAAGAATAGTGAAATGAATCAACGTCCCTAGATCTTATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTGAAGAACAATGAAATGAATAAACGTCCCCAGATCTAATTTTCCCTCAAGAA
* *
61813 GAAGCGAAACGGATC
66 GAAGCGGAACAGATC
61828 TCTCCTTTCG
Statistics
Matches: 177, Mismatches: 34, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
134 174 0.98
135 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (134 bp):
ATTCAATCTTCCCTGAAGAACAATGAAATGAATAAACGTCCCCAGATCTAATTTTCCCTCAAGAA
GAAGCGGAACAGATCCATCTATTTCAAAATTTGATATTCCCTAAATAACAGTAAAACAAATCTAC
CTCG
Found at i:62789 original size:97 final size:95
Alignment explanation
Indices: 62686--62860 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 95
62676 CAGTGAGACG
* ** * *
62686 GTATCGATACCATGGTAAGGGGGCATCGATACCAGTGAACATCAAATATAATTTTGGTATCGATA
1 GTATCGATACAATGGTAA--GGGCATCGATACCAGACAACATCAAAGATAATTTTGGCATCGATA
62751 CCAGAAAGGGGTATCGATGTCATAATATAGTA
64 CCAGAAAGGGGTATCGATGTCATAATATAGTA
* * * * * *
62783 GTATCGATACAATGGTAAGGGTATTGATGCCAGACAACATCGAAGCTAATTTTGGCATCTATACC
1 GTATCGATACAATGGTAAGGGCATCGATACCAGACAACATCAAAGATAATTTTGGCATCGATACC
*
62848 AGAAGGGGGTATC
66 AGAAAGGGGTATC
62861 ATTACCATAG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
95 49 0.74
97 17 0.26
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (95 bp):
GTATCGATACAATGGTAAGGGCATCGATACCAGACAACATCAAAGATAATTTTGGCATCGATACC
AGAAAGGGGTATCGATGTCATAATATAGTA
Found at i:63335 original size:20 final size:20
Alignment explanation
Indices: 63310--63383 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 20
63300 AATTAAAAAT
63310 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
63330 GCATGAAA-GATATCATAATTGAAAAT
1 GCATGAAAGGAT-GC---ATT---AAG
63356 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
63376 GCATGAAA
1 GCATGAAA
63384 TGACGCCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
19 3 0.07
20 19 0.45
23 6 0.14
26 11 0.26
27 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:63349 original size:46 final size:47
Alignment explanation
Indices: 63296--63465 Score: 234
Period size: 46 Copynumber: 3.6 Consensus size: 47
63286 TAAATCGAAT
63296 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAA-GATA
1 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
* * **
63342 TCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAATGACG
1 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
* * *
63389 CCATGATTAAAAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATA
1 TCATAATT--AAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
* *
63438 TCATAATTGAAAATGCATGAAATGATGC
1 TCATAATTAAAAATGCATGAAAGGATGC
63466 CAGATATATC
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
46 41 0.38
47 27 0.25
49 40 0.37
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (47 bp):
TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
Found at i:64305 original size:20 final size:20
Alignment explanation
Indices: 64280--64379 Score: 119
Period size: 20 Copynumber: 4.7 Consensus size: 20
64270 GATTAAAAAT
64280 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
64300 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
64320 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
64347 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
64367 GCATGAAATGATG
1 GCATGAAAGGATG
64380 TCAGATATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
20 47 0.67
21 1 0.01
23 3 0.04
24 3 0.04
26 1 0.01
27 15 0.21
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:64355 original size:67 final size:67
Alignment explanation
Indices: 64242--64379 Score: 240
Period size: 67 Copynumber: 2.1 Consensus size: 67
64232 TGTTATTATA
* *
64242 GATGTATTAAGGCATGAAAGGATGCCATGATTAAAAATGCATGAAAGGATGCATTAAGGCATGAA
1 GATGCATTAAGGCATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAA
64307 AG
66 AG
*
64309 GATGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAA
1 GATGCATTAAGGCATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAA
*
64374 AT
66 AG
64376 GATG
1 GATG
64380 TCAGATATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.41, C:0.09, G:0.27, T:0.22
Consensus pattern (67 bp):
GATGCATTAAGGCATGAAAGGATGCCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAA
AG
Found at i:65171 original size:3 final size:3
Alignment explanation
Indices: 65163--65258 Score: 174
Period size: 3 Copynumber: 32.0 Consensus size: 3
65153 TCCCAAAATT
65163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
65211 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65259 GTAGTAGTAG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:65263 original size:3 final size:3
Alignment explanation
Indices: 65257--65284 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
65247 TCATTATTAT
65257 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
65285 GGTAATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:65382 original size:22 final size:22
Alignment explanation
Indices: 65357--65400 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
65347 CAAATCATTC
65357 GGCCCAAACCC-AGAGCCCAACA
1 GGCCCAAACCCGA-AGCCCAACA
*
65379 GGCCCATACCCGAAGCCCAACA
1 GGCCCAAACCCGAAGCCCAACA
65401 AGCAATCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.34, C:0.45, G:0.18, T:0.02
Consensus pattern (22 bp):
GGCCCAAACCCGAAGCCCAACA
Done.