Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003532.1 Hibiscus syriacus cultivar Beakdansim tig00007455_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: 135006
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10195 original size:62 final size:64
Alignment explanation
Indices: 10064--10201 Score: 172
Period size: 62 Copynumber: 2.2 Consensus size: 64
10054 TTATTCAAGG
* * * *
10064 TGTATTGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGACATCAA
1 TGTATCGATGCACAAGAAGTGCATCGATACACTCCCTTAAAATAAAAACATCGAATGACATCAA
* * ** **
10128 TGTATCGATGCACAAGTAGTGCATCGATACAC-CCCTT-AAATACAAACATCGAATGTGATTTA
1 TGTATCGATGCACAAGAAGTGCATCGATACACTCCCTTAAAATAAAAACATCGAATGACATCAA
10190 TGTATCGATGCA
1 TGTATCGATGCA
10202 TAGATAGAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 32 0.50
63 4 0.06
64 28 0.44
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
TGTATCGATGCACAAGAAGTGCATCGATACACTCCCTTAAAATAAAAACATCGAATGACATCAA
Found at i:10876 original size:23 final size:23
Alignment explanation
Indices: 10850--10901 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
10840 TATAGCACTA
10850 CGGTGCAATTCTACGTGGAACTT
1 CGGTGCAATTCTACGTGGAACTT
* * *
10873 CGGTGTAATTCTATGTGGCACTT
1 CGGTGCAATTCTACGTGGAACTT
10896 -GGTGCA
1 CGGTGCA
10902 TTTATACGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGAACTT
Found at i:12053 original size:21 final size:21
Alignment explanation
Indices: 12029--12074 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
12019 ATTCGACAAA
12029 TGAAGCATGAGTTTATGAACT
1 TGAAGCATGAGTTTATGAACT
12050 TGAAGCATGAGTTTATGAACT
1 TGAAGCATGAGTTTATGAACT
12071 TGAA
1 TGAA
12075 ACAAATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.33
Consensus pattern (21 bp):
TGAAGCATGAGTTTATGAACT
Found at i:12839 original size:2 final size:2
Alignment explanation
Indices: 12832--12930 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
12822 ATATCACAAA
12832 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12874 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12916 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
12931 TATATATATA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13293 original size:31 final size:30
Alignment explanation
Indices: 13253--13378 Score: 121
Period size: 31 Copynumber: 4.1 Consensus size: 30
13243 GAACCTCGAC
* *
13253 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
* **
13283 AAGCTGTCCATATATTCCTTAGAACATAGGT
1 AA-CTGTCCATATGTTCCGAAGAACATAGGT
*
13314 ATACTATCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
13345 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
13377 AA
1 AA
13379 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.08
31 44 0.57
32 24 0.31
33 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:17002 original size:2 final size:2
Alignment explanation
Indices: 16995--17027 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16985 ATATCACAAA
16995 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
17028 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17480 original size:32 final size:32
Alignment explanation
Indices: 17361--17484 Score: 123
Period size: 31 Copynumber: 3.9 Consensus size: 32
17351 AACCTCGACA
*
17361 ACTGTCCATA-GTTTCCGA-AGAACCTAGGTAA-
1 ACTGTCCATATG-TTCC-ATAGAACATAGGTAAT
*
17392 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* * *
17423 ACTATCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCATAGAACATAGGTAAT
* *
17455 TCTGTCTATATGTTCCATAGAACATAGGTA
1 ACTGTCCATATGTTCCATAGAACATAGGTA
17485 CACCCTCGAC
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.01
31 49 0.64
32 26 0.34
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (32 bp):
ACTGTCCATATGTTCCATAGAACATAGGTAAT
Found at i:19506 original size:26 final size:28
Alignment explanation
Indices: 19449--19506 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
19439 GGTGACCATC
19449 ATGAATAAGTATCCCCTCCCGCGCATTG
1 ATGAATAAGTATCCCCTCCCGCGCATTG
19477 ATGAATAAGTATCCCCT-CC-CGCATTG
1 ATGAATAAGTATCCCCTCCCGCGCATTG
19503 ATGA
1 ATGA
19507 CTTGTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 11 0.37
27 2 0.07
28 17 0.57
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (28 bp):
ATGAATAAGTATCCCCTCCCGCGCATTG
Found at i:23002 original size:19 final size:19
Alignment explanation
Indices: 22978--23022 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
22968 ATTTATGTAA
22978 CGATGCATAGATAGTGCAT
1 CGATGCATAGATAGTGCAT
22997 CGATGCATAGATAGTGCAT
1 CGATGCATAGATAGTGCAT
23016 CGATGCA
1 CGATGCA
23023 CCCGTCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (19 bp):
CGATGCATAGATAGTGCAT
Found at i:31992 original size:22 final size:22
Alignment explanation
Indices: 31966--32018 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
31956 TAAGCTTAAC
31966 TTTTAAATC-AAGATTTTTTATT
1 TTTTAAATCTAA-ATTTTTTATT
*
31988 TTTTAAATCTTTAATTTTTTATT
1 TTTTAAATC-TAAATTTTTTATT
*
32011 TTTGAAAT
1 TTTTAAAT
32019 ATCAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 17 0.63
24 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTAAATCTAAATTTTTTATT
Found at i:32072 original size:18 final size:19
Alignment explanation
Indices: 32030--32076 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
32020 TCAAAATCAA
*
32030 TTTTCAAAAACTTCATTTGT
1 TTTTC-AAAACTTAATTTGT
*
32050 TTTTCAAAATTTAATTT-T
1 TTTTCAAAACTTAATTTGT
32068 TTTTCAAAA
1 TTTTCAAAA
32077 GAAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTCAAAACTTAATTTGT
Found at i:33971 original size:16 final size:15
Alignment explanation
Indices: 33946--33976 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
33936 ATTGTCAAAA
33946 AAATAAAAAATAATT
1 AAATAAAAAATAATT
33961 AAATGAAAAAATAATT
1 AAAT-AAAAAATAATT
33977 TGAAATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATAAAAAATAATT
Found at i:35037 original size:33 final size:33
Alignment explanation
Indices: 34995--35068 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
34985 GGCGATGGAG
34995 TTGGAGGTCTAGGCGGCAGAACTGGCAGCGGAC
1 TTGGAGGTCTAGGCGGCAGAACTGGCAGCGGAC
* ** * * *
35028 TTGGAGGTCTAGGTGGTTGAATTGGCGGCGGAG
1 TTGGAGGTCTAGGCGGCAGAACTGGCAGCGGAC
35061 TTGGAGGT
1 TTGGAGGT
35069 GGTCCAGGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.46, T:0.23
Consensus pattern (33 bp):
TTGGAGGTCTAGGCGGCAGAACTGGCAGCGGAC
Found at i:36880 original size:104 final size:104
Alignment explanation
Indices: 36697--36896 Score: 228
Period size: 104 Copynumber: 1.9 Consensus size: 104
36687 ATTTCATAAT
* * * *
36697 GAGAAGAACTTGTTCAATTTTGGCTCATCCATTGCAAAAGGAGTTGGATCAATATCACTATTTCG
1 GAGAAGAACTTGTTCAATTTTGACTCATCCATTGCAAAAGGAGTTGGACCAACATCACTATTCCG
* * *
36762 CTTGATTCAATCACAGAATGAGGTGAATCAGCATTTCTA
66 CTCGATTCAATCACAAAAGGAGGTGAATCAGCATTTCTA
* *
36801 GAGAAGAACTTGTTCAATCTTT-ACTCATCCA-T-CATAGAAGGAGTTGGACCAGCATCA-TCGT
1 GAGAAGAACTTGTTCAAT-TTTGACTCATCCATTGCA-A-AAGGAGTTGGACCAACATCACT-AT
** *
36862 TCCGCTCGATTCCCTCACAAAAGGAGGTGGATCAG
62 TCCGCTCGATTCAATCACAAAAGGAGGTGAATCAG
36897 TACGTTCAGT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
102 2 0.03
103 3 0.04
104 72 0.90
105 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.28
Consensus pattern (104 bp):
GAGAAGAACTTGTTCAATTTTGACTCATCCATTGCAAAAGGAGTTGGACCAACATCACTATTCCG
CTCGATTCAATCACAAAAGGAGGTGAATCAGCATTTCTA
Found at i:37881 original size:26 final size:27
Alignment explanation
Indices: 37851--37903 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
37841 TTATTTCTGT
37851 TTAATATCACATA-TAAAAATATATTA
1 TTAATATCACATACTAAAAATATATTA
* * *
37877 TTAATGTCACGTACTAAAATTATATTA
1 TTAATATCACATACTAAAAATATATTA
37904 CTAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (27 bp):
TTAATATCACATACTAAAAATATATTA
Found at i:37915 original size:17 final size:18
Alignment explanation
Indices: 37893--37926 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37883 TCACGTACTA
37893 AAATTA-TATTACTAAAT
1 AAATTACTATTACTAAAT
*
37910 AAATTACTCTTACTAAA
1 AAATTACTATTACTAAA
37927 AAAAATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTACTATTACTAAAT
Found at i:37956 original size:24 final size:24
Alignment explanation
Indices: 37925--37974 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
37915 ACTCTTACTA
*
37925 AAAAAAATTCATAGACCTTTGATT
1 AAAAAAATTCAAAGACCTTTGATT
37949 AAAAAAATTCAAAGACCTTTGATT
1 AAAAAAATTCAAAGACCTTTGATT
37973 AA
1 AA
37975 TTTCTTATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (24 bp):
AAAAAAATTCAAAGACCTTTGATT
Found at i:38060 original size:2 final size:2
Alignment explanation
Indices: 38053--38093 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38043 TAAAAGTCAT
38053 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
38094 TGGAACACTT
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:38838 original size:24 final size:24
Alignment explanation
Indices: 38791--38850 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
38781 AAACTGATTT
* *
38791 TTTTTATAATTTAATTTTTTAATA
1 TTTTTATAATTTAATTATTGAATA
38815 TTTTTAT-ATTTAATGTATTGAATA
1 TTTTTATAATTTAAT-TATTGAATA
* *
38839 TCTTAATAATTT
1 TTTTTATAATTT
38851 TTTATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 7 0.23
24 19 0.63
25 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTTTATAATTTAATTATTGAATA
Found at i:44457 original size:2 final size:2
Alignment explanation
Indices: 44450--44482 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44440 AATATCTAGA
44450 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
44483 ACTTAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48280 original size:19 final size:19
Alignment explanation
Indices: 48252--48293 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
48242 TAATATTTTA
48252 ATTTAATAAAATAAATAAT
1 ATTTAATAAAATAAATAAT
*
48271 ATTTATTAAAATAAATAAT
1 ATTTAATAAAATAAATAAT
48290 ATTT
1 ATTT
48294 TAATTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTAATAAAATAAATAAT
Found at i:48300 original size:24 final size:24
Alignment explanation
Indices: 48242--48301 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 24
48232 TTTAATCATT
*
48242 TAATATTTTAATTTAATAAAATAAA
1 TAATATTTTAA-TTATTAAAATAAA
48267 TAATA---T--TTATTAAAATAAA
1 TAATATTTTAATTATTAAAATAAA
48286 TAATATTTTAATTATT
1 TAATATTTTAATTATT
48302 TAATACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
19 17 0.59
22 2 0.07
24 5 0.17
25 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATATTTTAATTATTAAAATAAA
Found at i:48657 original size:39 final size:39
Alignment explanation
Indices: 48563--48650 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
48553 TAGGGTCGTG
* * *
48563 TATATAT-ATTTAAATTAAATATATAAATATTAAATATA
1 TATATATAATATAAATTAAATTTATTAATATTAAATATA
* * * *
48601 TATTTTTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATAATATAAATTAAATTTATTAATATTAAATATA
48640 TATATATAATA
1 TATATATAATA
48651 ATAATTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 5 0.12
39 36 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TATATATAATATAAATTAAATTTATTAATATTAAATATA
Found at i:50607 original size:35 final size:35
Alignment explanation
Indices: 50560--50636 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
50550 CAACAAGTCC
50560 TCAATTTCATTTTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTTTAAACCCTAAATTTCAAAATAAT
* *
50595 TCAATTAT-ATTTTAAACCCTAAATTTTAAAATACT
1 TCAATT-TCATTTTAAACCCTAAATTTCAAAATAAT
*
50630 TTAATTT
1 TCAATTT
50637 AGGGTTTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (35 bp):
TCAATTTCATTTTAAACCCTAAATTTCAAAATAAT
Found at i:50671 original size:35 final size:35
Alignment explanation
Indices: 50632--50706 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
50622 AAAATACTTT
50632 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* * * *
50667 AATTTGGGGTTTAGAATGTAATTTAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
50702 AATTT
1 AATTT
50707 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:56111 original size:11 final size:11
Alignment explanation
Indices: 56097--56131 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
56087 ATTTTACGGA
56097 AGTACTATAGC
1 AGTACTATAGC
*
56108 AGTACTGTAGC
1 AGTACTATAGC
56119 AGTACTATAGC
1 AGTACTATAGC
56130 AG
1 AG
56132 GGGAATCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (11 bp):
AGTACTATAGC
Found at i:56148 original size:22 final size:22
Alignment explanation
Indices: 56123--56170 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
56113 TGTAGCAGTA
56123 CTATAGCAGGGGAATCAGTTCC
1 CTATAGCAGGGGAATCAGTTCC
*
56145 CTATAGCAGGGGAATCGGTTCC
1 CTATAGCAGGGGAATCAGTTCC
56167 CTAT
1 CTAT
56171 TTGTAATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (22 bp):
CTATAGCAGGGGAATCAGTTCC
Found at i:57804 original size:23 final size:23
Alignment explanation
Indices: 57773--57841 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
57763 GACATATATG
*
57773 TGGTTATTCGGGACAATTCTATA
1 TGGTCATTCGGGACAATTCTATA
* * **
57796 TGGTCATTCAGGATAATTCTACG
1 TGGTCATTCGGGACAATTCTATA
* *
57819 CGGTCATTCGGGAC-ATTTTATA
1 TGGTCATTCGGGACAATTCTATA
57841 T
1 T
57842 AGCACTTAGT
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (23 bp):
TGGTCATTCGGGACAATTCTATA
Found at i:61990 original size:23 final size:23
Alignment explanation
Indices: 61961--62045 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
61951 GGATATATAT
*
61961 ATGGTCCTTTGGGATAATTCTAC
1 ATGGTCCTTTGGGACAATTCTAC
61984 ATGGTCCTTTGGGACAATTCTAC
1 ATGGTCCTTTGGGACAATTCTAC
62007 ATGGTCCTTTGGGACAATTCTAC
1 ATGGTCCTTTGGGACAATTCTAC
* *
62030 GTGGTCCTTCGGGACA
1 ATGGTCCTTTGGGACA
62046 TTTTATATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (23 bp):
ATGGTCCTTTGGGACAATTCTAC
Found at i:62258 original size:19 final size:20
Alignment explanation
Indices: 62234--62284 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
62224 GTTCTTGTCT
62234 GTGTGAGATATGATGATTC-
1 GTGTGAGATATGATGATTCA
62253 GTGTGAGATATGATGATTCA
1 GTGTGAGATATGATGATTCA
*
62273 G-GTAAGATATGA
1 GTGTGAGATATGA
62285 AAGTATGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 29 0.97
20 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (20 bp):
GTGTGAGATATGATGATTCA
Found at i:64224 original size:2 final size:2
Alignment explanation
Indices: 64217--64245 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64207 TTACCTGTTA
64217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64246 ATTTGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65248 original size:2 final size:2
Alignment explanation
Indices: 65241--65300 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
65231 AATGGTTTTA
65241 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
65283 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
65301 TAGTTTCAAT
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:65646 original size:2 final size:2
Alignment explanation
Indices: 65641--65665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65631 AAAAAAAAGA
65641 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
65666 GATCAGGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66369 original size:199 final size:200
Alignment explanation
Indices: 66018--66525 Score: 492
Period size: 199 Copynumber: 2.5 Consensus size: 200
66008 AACATTTTTG
* * * * * * * *
66018 TAATTTATAAGATTAGAGGTGTAGTATTGGA-ATTTATCTTTCAGTTGAGGCCAATATCGAGACA
1 TAATTAATAAGATTAGAGGCGTAGTATT-GATACTTATCTTTCAATTAAGGCTAATACCGACACA
* * * ** * * * *
66082 TA-AGAGATATTATAAGCGGATTAAAAATCTCATTAAAAATGGTTCCAAAGCTTGTTTTGTACAT
65 TACA-AGACATTCTAAGTGGGGTAAAAATCACGTTCAAAATGGTTCCAAAGCTTGTTTTCTACAT
* * * *
66146 GAAGAAAATGCTAAAATAGTTTGATAGTCATATTTGAAGG-GT-TTTTCGGGTAGTTAATCTGAA
129 GAAGAAAAAGCTAAAATAGTTTGATAGGCATATTCG-AGGAGTATTTTCGGGAAGTTAATCTGAA
*
66209 AAAAATCG
193 AAAAATCA
66217 TAATTAATAAGATTAGAGGCGTAGTATTG-TAACTT-TCTTTCAATTAAGAG-TAATACCGACAC
1 TAATTAATAAGATTAGAGGCGTAGTATTGAT-ACTTATCTTTCAATTAAG-GCTAATACCGACAC
* * *
66279 ATACAAGACATTGTAAGTGGGGTAAAAATCATGTTCAAAATGGTTCTAAAGCTTGGTTTTCTACA
64 ATACAAGACATTCTAAGTGGGGTAAAAATCACGTTCAAAATGGTTCCAAAGCTT-GTTTTCTACA
* * * * * *
66344 TGAA-AAAGAAGCTAACATGGTTTGATAGGCATGTTCGGGGAGTATTTTTGGGAAGTTAGTCTGA
128 TGAAGAAA-AAGCTAAAATAGTTTGATAGGCATATTCGAGGAGTATTTTCGGGAAGTTAATCTGA
***
66408 AAATTTTCA
192 AAAAAATCA
* * * * * * *
66417 TCATTTATAATATTAGAGGCGTAGTATTGATACTTATGTTTCAATTGAGGCTAGTATCGACACAT
1 TAATTAATAAGATTAGAGGCGTAGTATTGATACTTATCTTTCAATTAAGGCTAATACCGACACAT
* * * *
66482 ACGAGACATTCTAAGTGGTGTAAAAATTACGTTCAAACTGGTTC
66 ACAAGACATTCTAAGTGGGGTAAAAATCACGTTCAAAATGGTTC
66526 AAAACCAAAC
Statistics
Matches: 252, Mismatches: 46, Indels: 20
0.79 0.14 0.06
Matches are distributed among these distances:
198 68 0.27
199 69 0.27
200 53 0.21
201 62 0.25
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (200 bp):
TAATTAATAAGATTAGAGGCGTAGTATTGATACTTATCTTTCAATTAAGGCTAATACCGACACAT
ACAAGACATTCTAAGTGGGGTAAAAATCACGTTCAAAATGGTTCCAAAGCTTGTTTTCTACATGA
AGAAAAAGCTAAAATAGTTTGATAGGCATATTCGAGGAGTATTTTCGGGAAGTTAATCTGAAAAA
AATCA
Found at i:67089 original size:44 final size:42
Alignment explanation
Indices: 67041--67142 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
67031 GAAAGGAAAG
*
67041 ATCTATAGCTGCATTTTTTGAACAAACGTCTCA-AAAAAGTCAAT
1 ATCTATAGC-GCATTTTTGGAACAAACG-C-CATAAAAAGTCAAT
* *
67085 ATCTATAGCG-GTGTTTTGGAACAAACGCCATAAAAGGTCAAT
1 ATCTATAGCGCAT-TTTTGGAACAAACGCCATAAAAAGTCAAT
67127 ATCTATAGCGGCATTT
1 ATCTATAGC-GCATTT
67143 GTATCCACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
41 2 0.04
42 21 0.42
43 17 0.34
44 10 0.20
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (42 bp):
ATCTATAGCGCATTTTTGGAACAAACGCCATAAAAAGTCAAT
Found at i:67111 original size:43 final size:42
Alignment explanation
Indices: 67055--67137 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
67045 ATAGCTGCAT
*
67055 TTTTTGAACAAACGTCTCA-AAAAAGTCAATATCTATAGCGGTG
1 TTTTGGAACAAACG-C-CATAAAAAGTCAATATCTATAGCGGTG
*
67098 TTTTGGAACAAACGCCATAAAAGGTCAATATCTATAGCGG
1 TTTTGGAACAAACGCCATAAAAAGTCAATATCTATAGCGG
67138 CATTTGTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 2 0.05
42 22 0.59
43 13 0.35
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (42 bp):
TTTTGGAACAAACGCCATAAAAAGTCAATATCTATAGCGGTG
Found at i:69991 original size:41 final size:41
Alignment explanation
Indices: 69946--70404 Score: 363
Period size: 41 Copynumber: 11.2 Consensus size: 41
69936 GTTTACAAAT
* * *
69946 GCCACTAAAGTACAAGTCTTTAGCGACGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* *
69987 GCCACTGAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * * *
70028 GACACTGAAGTATGAGTCTATAGCGGCGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * * *
70069 GCCACTGAATTACGAGTCTTTAGCAGTGTTTGTAAACACAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A-AAAC
* * *
70112 ACCACTAAAGTACGAGTCGTTAGCGGCGTTTGTATAAAACC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * * * *
70153 ACCACTAAA-TAACTAGTTTTTAGCGGCATTTGTACAAAAAT
1 GCCACTAAAGT-ACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * ** * * * *
70194 GCCACTAATGAACTCGTTTTTTGCGGCGTTTGTACAAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTA-TAAAAAC
* * * *
70236 GCCATTAAAGTACGAGTCTTTCGTGGCGTTTGTATAAAACCC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAA-AC
* * * * *
70278 CCCACTAAATTAC-AATCTTTAGCGGAGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * *
70318 GCCACTAAAATATGAGTATTTAGCGGCGTTT-TA-AAAAAA
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
* * * * *
70357 GCCACTATAGCAC-ATGT-TTTTGCGGCGTTTTTATAACAAAT
1 GCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA-AAAC
70398 GCCACTA
1 GCCACTA
70405 TTGATGAACC
Statistics
Matches: 336, Mismatches: 71, Indels: 22
0.78 0.17 0.05
Matches are distributed among these distances:
38 13 0.04
39 18 0.05
40 16 0.05
41 212 0.63
42 44 0.13
43 33 0.10
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAC
Found at i:70177 original size:125 final size:122
Alignment explanation
Indices: 69981--70363 Score: 348
Period size: 125 Copynumber: 3.1 Consensus size: 122
69971 ACGTTTATAT
* * * *
69981 AAAAACGCCACTGAAGTACGAGTCTTTAGCGACGTTTGTATAAAAACGA-CACTGAAGTA-TGAG
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT-AAAACCACCACT-AAATACT-AG
* * *
70044 TCTATAGCGGCGTTTATATAAAAACGCCACTGAATTACGAGTCTTTAGCAGTGTTTGTA-A
63 TCTTTAGCGGCGTTTATATAAAAACGCCACT-AATTACGAGTATTTAGCAGCGTTTGTACA
* *
70104 ACACAAACACCACTAAAGTACGAGTCGTTAGCGGCGTTTGTATAAAACCACCACTAAATAACTAG
1 A-A-AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAACCACCACTAAAT-ACTAG
* * * * * * ** * * *
70169 TTTTTAGCGGCATTTGTACAAAAATGCCACTAATGAACTCGTTTTTTGCGGCGTTTGTACA
63 TCTTTAGCGGCGTTTATATAAAAACGCCACTAAT-TACGAGTATTTAGCAGCGTTTGTACA
* * * * * *
70230 AAAAATGCCATTAAAGTACGAGTCTTTCGTGGCGTTTGTATAAAACCCCCCACTAAATTAC-AAT
1 AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAA-CCACCACTAAA-TACTAGT
* * * *
70294 CTTTAGCGGAGTTTATATAAAAACGCCACTAAAATATGAGTATTTAGCGGCGTTT-TA-A
64 CTTTAGCGGCGTTTATATAAAAACGCCACT-AATTACGAGTATTTAGCAGCGTTTGTACA
70352 AAAAA-GCCACTA
1 AAAAACGCCACTA
70364 TAGCACATGT
Statistics
Matches: 209, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
121 6 0.03
122 6 0.03
123 3 0.01
124 91 0.44
125 99 0.47
126 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (122 bp):
AAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAACCACCACTAAATACTAGTCT
TTAGCGGCGTTTATATAAAAACGCCACTAATTACGAGTATTTAGCAGCGTTTGTACA
Found at i:79395 original size:18 final size:18
Alignment explanation
Indices: 79372--79406 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
79362 TTGTTTTTAA
79372 ATTCTTCTAAGAACAAAG
1 ATTCTTCTAAGAACAAAG
79390 ATTCTTCTAAGAACAAA
1 ATTCTTCTAAGAACAAA
79407 CACCAAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (18 bp):
ATTCTTCTAAGAACAAAG
Found at i:80632 original size:23 final size:23
Alignment explanation
Indices: 80572--80638 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
80562 CACCACAGCT
* *
80572 CGTATAAATGCACCAAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
*
80595 CGTAGAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
80618 CGTATAATTGTACCGTAGTGC
1 CGTATAATTGCACCGAAGTGC
80639 TATATAAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:87509 original size:23 final size:23
Alignment explanation
Indices: 87483--87526 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
87473 CACCACAGCT
*
87483 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
87506 CGTAGAATTGCACCGTAGTGC
1 CGTAGAAATGCACCGAAGTGC
87527 TATATAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:93393 original size:23 final size:23
Alignment explanation
Indices: 93339--93394 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
93329 CACCACAGCT
*
93339 CGTATAAATGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
*
93362 CGTAGAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
93385 CGTATAATTG
1 CGTATAATTG
93395 TATCGTAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:99910 original size:23 final size:23
Alignment explanation
Indices: 99892--99950 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
99882 TTCGTATAAA
99892 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
99915 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
99938 TGCACCGTAGTGC
1 TGCACCGAAGTGC
99951 TATATAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:100609 original size:24 final size:24
Alignment explanation
Indices: 100577--100656 Score: 151
Period size: 24 Copynumber: 3.3 Consensus size: 24
100567 ATAGTGTATT
100577 GATGCACTCCTTAATGTGCGCATC
1 GATGCACTCCTTAATGTGCGCATC
100601 GATGCACTCCTTAATGTGCGCATC
1 GATGCACTCCTTAATGTGCGCATC
*
100625 AATGCACTCCTTAATGTGCGCATC
1 GATGCACTCCTTAATGTGCGCATC
100649 GATGCACT
1 GATGCACT
100657 ACCCGTGCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (24 bp):
GATGCACTCCTTAATGTGCGCATC
Found at i:103975 original size:143 final size:139
Alignment explanation
Indices: 103731--103990 Score: 358
Period size: 143 Copynumber: 1.8 Consensus size: 139
103721 TTGCCCTTCT
* * * ***
103731 GTTTTATTGAATCTGTTGTTAATTTTGCTTAATTTTCCTTATTTGTTTTTGAGTGATGATAAACA
1 GTTTCATTGAATCTGTTGTTAATTTTGCTTAATTTTCCGTATATGTTAACGAGTGATGATAAACA
*
103796 CTGAATTTAGTATTAGGATAGCTTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTT
66 CTGAATTTAGTATTAGGATACCTTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTT
103861 TCTTCTCCC
131 TCTTCTCCC
* * *
103870 GTTTCATTGAATCTTTTGTTAATTTTGCTTAATATTCCTTCCGTATATGTTAACGAGTTATTATA
1 GTTTCATTGAATCTGTTGTTAATTTTGCTT-A-ATT--TTCCGTATATGTTAACGAGTGATGATA
* * * *
103935 AACACTGGATTTAGTGTTAGGATACCTTTGGTTTTGATGGGTTTGATTTATTTTGA
62 AACACTGAATTTAGTATTAGGATACCTTTGATTTTAATGGGTTTGATTTATTTTGA
103991 ATTTTTCTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
139 28 0.27
140 1 0.01
141 3 0.03
143 71 0.69
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (139 bp):
GTTTCATTGAATCTGTTGTTAATTTTGCTTAATTTTCCGTATATGTTAACGAGTGATGATAAACA
CTGAATTTAGTATTAGGATACCTTTGATTTTAATGGGTTTGATTTATTTTGACTGTTCCTTTTTT
TCTTCTCCC
Found at i:108341 original size:44 final size:44
Alignment explanation
Indices: 108291--108381 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
108281 AATGAATTCC
*
108291 TAGCTAACTGTGATCTTCATCACTAAGGGTTCAAAATGAGTTTT
1 TAGCTAACTGTGATCTTCATCACTAAGGATTCAAAATGAGTTTT
108335 TAGCTAACTGTGATCTTCATCACTAAGGATTCAAAATGAGTTTT
1 TAGCTAACTGTGATCTTCATCACTAAGGATTCAAAATGAGTTTT
108379 TAG
1 TAG
108382 AGACTACTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (44 bp):
TAGCTAACTGTGATCTTCATCACTAAGGATTCAAAATGAGTTTT
Found at i:112411 original size:25 final size:25
Alignment explanation
Indices: 112382--112477 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
112372 GGTTAAAGAA
*
112382 TAGTAATTGTTAATATTAGTTGTGG
1 TAGTAATTGTTAATATTAATTGTGG
*
112407 TAGTAATTATTAATATTAATTGTGG
1 TAGTAATTGTTAATATTAATTGTGG
** * *
112432 TAGTAATTGTTAGCATTAAATGTGT
1 TAGTAATTGTTAATATTAATTGTGG
* * *
112457 TAATGATTGTTAATACTAATT
1 TAGTAATTGTTAATATTAATT
112478 ATGTTACCCT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (25 bp):
TAGTAATTGTTAATATTAATTGTGG
Found at i:112531 original size:18 final size:18
Alignment explanation
Indices: 112505--112544 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
112495 ATATTAAGTG
* *
112505 TGTTTTAGTAATTGTTGA
1 TGTTCTAGTAATTGTTAA
112523 TGTTCTAGTAATTGTTAA
1 TGTTCTAGTAATTGTTAA
112541 TGTT
1 TGTT
112545 AATTGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.55
Consensus pattern (18 bp):
TGTTCTAGTAATTGTTAA
Found at i:114119 original size:14 final size:14
Alignment explanation
Indices: 114100--114126 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
114090 ATATTTTTAA
114100 TATTTATGTATATG
1 TATTTATGTATATG
114114 TATTTATGTATAT
1 TATTTATGTATAT
114127 AATTTTTTTA
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TATTTATGTATATG
Found at i:115307 original size:28 final size:28
Alignment explanation
Indices: 115273--115336 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
115263 ATTTATTGTC
*
115273 AAAGCAAAGCGGATCAATGATCTGTAAG
1 AAAGCAAAGCGAATCAATGATCTGTAAG
115301 AAAGCAAAGCGAATCAATGATCTGTAAG
1 AAAGCAAAGCGAATCAATGATCTGTAAG
115329 AAAGCAAA
1 AAAGCAAA
115337 ACCACCATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.16
Consensus pattern (28 bp):
AAAGCAAAGCGAATCAATGATCTGTAAG
Found at i:125032 original size:6 final size:6
Alignment explanation
Indices: 125021--125077 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
125011 TTTCATGGTC
* *
125021 TGAAGA TGAAGA TGAAGA TAAAGA TGAATGG T-ACAGA TCTGAAGA TGAAGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAA-GA TGA-AGA --TGAAGA TGAAGA
125072 TGAAGA
1 TGAAGA
125078 GATGACTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 34 0.81
7 3 0.07
8 4 0.10
9 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.30, T:0.19
Consensus pattern (6 bp):
TGAAGA
Found at i:133204 original size:38 final size:37
Alignment explanation
Indices: 133154--133242 Score: 142
Period size: 38 Copynumber: 2.4 Consensus size: 37
133144 TTTTCACCCC
133154 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
* *
133191 AAACCCCGACCCGATTTGACCCGAATATCACACTTAAA
1 AAA-CCCGACCCGACTCGACCCGAATATCACACTTAAA
*
133229 AAACCCAACCCGAC
1 AAACCCGACCCGAC
133243 CCGAACAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
37 12 0.26
38 35 0.74
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.13
Consensus pattern (37 bp):
AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
Found at i:133495 original size:31 final size:31
Alignment explanation
Indices: 133457--133536 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
133447 CACTTAAAAA
*
133457 ACCCGACCCGACCCGACCAAAATAAAGTTTC
1 ACCCGACCCAACCCGACCAAAATAAAGTTTC
133488 ACCCGACCCAACCCGACCAAAATAAAGTTTC
1 ACCCGACCCAACCCGACCAAAATAAAGTTTC
133519 ACCCGACCCAACCCGACC
1 ACCCGACCCAACCCGACC
133537 CGAATATATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.35, C:0.44, G:0.11, T:0.10
Consensus pattern (31 bp):
ACCCGACCCAACCCGACCAAAATAAAGTTTC
Found at i:133527 original size:257 final size:252
Alignment explanation
Indices: 133066--133598 Score: 650
Period size: 257 Copynumber: 2.1 Consensus size: 252
133056 ACCCGACCCG
* * *
133066 AATTATTTTTATTTAATAAAAATATTGACTTAATCCGACCCGACTCGAATTATATATATTTTCGT
1 AATTATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGT
* *
133131 GTCGGTCCGATTTTTTTCACCCCAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACC
66 GTCGGTCCGATTTTTTTCACCCCAAACCCGACCCAACCCGACCCGAATATCACACTTAAAAAACC
*** * * *
133196 CCGACCCGATTTGACCCGAATATCACACTTAAAAAACCCAACCCGACCCGAACAAAATAAAGTTT
131 CCGACCCGACCCGACCCGAAAATCAAACTT--AAAACCCAACCCAACCCGAACAAAATAAAGTTT
*
133261 CATCCG-ACCCGACCCGAATATATGAATTAGAAATCCGACCGACCCGACCCGAAATAA-TAAAA
194 CACCCGCACCCGACCCGAATATATGAATTAGAAA-CC-A--GA-CCGACCCGAAATAATTAAAA
133323 AATTATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCAG
1 AATTATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTC-G
* *
133388 -GTCGGTCCGGTTTTTTTTCACCCTAAACCTGAACTCGACCCAACCCGACCCGAATATCACACTT
65 TGTCGGTCC-GATTTTTTTCACCCCAAA-C----C-CGACCCAACCCGACCCGAATATCACACTT
* ** * *
133452 AAAAAA-CCCGACCCGACCCGA-CC-AAAAT-AAAGTT-TCACCCGACCCAACCCGACCAAAATA
123 AAAAAACCCCGACCCGACCCGACCCGAAAATCAAACTTAAAACCCAACCCAACCCGAACAAAATA
133512 AAGTTTCACCCGACCCAACCCGACCCGAATATATGAATTAGAAACCAGACCGACCCGAAATAATT
188 AAGTTTCACCCG---C-ACCCGACCCGAATATATGAATTAGAAACCAGACCGACCCGAAATAATT
133577 AAAA
249 AAAA
* *
133581 AAATATTTTTATTCAATA
1 AATTATTTTTATTTAATA
133599 TATGAATAAG
Statistics
Matches: 241, Mismatches: 21, Indels: 27
0.83 0.07 0.09
Matches are distributed among these distances:
257 114 0.47
258 40 0.17
259 1 0.00
260 5 0.02
261 6 0.02
262 29 0.12
263 13 0.05
264 33 0.14
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (252 bp):
AATTATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGT
GTCGGTCCGATTTTTTTCACCCCAAACCCGACCCAACCCGACCCGAATATCACACTTAAAAAACC
CCGACCCGACCCGACCCGAAAATCAAACTTAAAACCCAACCCAACCCGAACAAAATAAAGTTTCA
CCCGCACCCGACCCGAATATATGAATTAGAAACCAGACCGACCCGAAATAATTAAAA
Done.