Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002669.1 Hibiscus syriacus cultivar Beakdansim tig00005484_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: 114860
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:9076 original size:47 final size:47
Alignment explanation
Indices: 9021--9118 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
9011 ATTAATACGA
* *
9021 AATATTACAAAATAATATCTATTTATAATTTTATTCATAATTTTTTT
1 AATATTACAAAATAATATCTATTTATAATTGTATTCATAATTATTTT
9068 AATATTACAAAATAATATCTATTTATAATTGTATTCATAATTATTTT
1 AATATTACAAAATAATATCTATTTATAATTGTATTCATAATTATTTT
9115 AATA
1 AATA
9119 GTGTGTAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (47 bp):
AATATTACAAAATAATATCTATTTATAATTGTATTCATAATTATTTT
Found at i:11221 original size:2 final size:2
Alignment explanation
Indices: 11214--11265 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
11204 CCGCCCCGAT
* *
11214 TA TA TA TA TA TA TA TA TA TA TT TA TA TA T- TT TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11253 T- TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
11266 TTTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
1 5 0.12
2 37 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:11259 original size:34 final size:34
Alignment explanation
Indices: 11220--11301 Score: 134
Period size: 32 Copynumber: 2.5 Consensus size: 34
11210 CGATTATATA
11220 TATATATATATATATTTATATATTTTATATTAAT
1 TATATATATATATATTTATATATTTTATATTAAT
*
11254 TATATATA-ATAT-TTTATATTTTTTATATTAAT
1 TATATATATATATATTTATATATTTTATATTAAT
11286 TATATATATA-ATATTT
1 TATATATATATATATTT
11302 TCGGGTTCGG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 29 0.64
33 8 0.18
34 8 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATATATATTTATATATTTTATATTAAT
Found at i:11302 original size:34 final size:33
Alignment explanation
Indices: 11212--11302 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 33
11202 TCCCGCCCCG
11212 ATTATATATATATATATATATATTTATATATTTTAT
1 ATTA-ATATATATATA-ATAT-TTTATATATTTTAT
*
11248 ATTAAT-TATATATAATATTTTATATTTTTTAT
1 ATTAATATATATATAATATTTTATATATTTTAT
11280 ATTAATTATATATATAATATTTT
1 ATTAA-TATATATATAATATTTT
11303 CGGGTTCGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
32 18 0.35
33 5 0.10
34 23 0.44
35 2 0.04
36 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
ATTAATATATATATAATATTTTATATATTTTAT
Found at i:13451 original size:78 final size:81
Alignment explanation
Indices: 13369--13530 Score: 174
Period size: 77 Copynumber: 2.0 Consensus size: 81
13359 TATATAAGAG
* * * *
13369 AAATACAATTGCGTCCAAT-AATGTCATGGTTCACTAAG-AAATATGTT-G-T-GAT-CTGTAAT
1 AAATA-AATTGC-ACCAATGAATGTCATGATTCACTAAGAAAATATATTAGATCGATAATGTAAT
13428 GTTAATATTTTTATTAATA
64 GTTAATATTTTT-TTAATA
* * * *
13447 AAATAAGTTGCACCTATGAATGTTATGATTCACTAAGAAAATATATTACGATCTATAATGTAATG
1 AAATAAATTGCACCAATGAATGTCATGATTCACTAAGAAAATATATTA-GATCGATAATGTAATG
13512 TTAATATTTTTTTAATA
65 TTAATATTTTTTTAATA
13529 AA
1 AA
13531 TTAGTTTGCG
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
76 4 0.06
77 22 0.32
78 13 0.19
80 1 0.01
81 1 0.01
82 10 0.14
83 18 0.26
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (81 bp):
AAATAAATTGCACCAATGAATGTCATGATTCACTAAGAAAATATATTAGATCGATAATGTAATGT
TAATATTTTTTTAATA
Found at i:14219 original size:100 final size:100
Alignment explanation
Indices: 13972--14358 Score: 363
Period size: 104 Copynumber: 3.9 Consensus size: 100
13962 TACCTATCAT
* * * * *
13972 GTTATCATGAAAAATATATTTTGTCTTACTTTTACATAAAATAAATGAATTT-ATACTTATAACT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTACATAATATAAACG-ATTTCATACTTATAACT
* * *
14036 TAAACGATTAACATTTAAGAAAAATGCGCTATCTAGTAC
65 TAAACGATTGACA-TTAA-AAAAA-ACGTTATCTAGTAC
* * * * * *
14075 GTTATCATAAGCAACATCTTTTTGTCTTACTTTTACATAATATAAATGGTTTCATACTTATAATT
1 GTTATCATGAGAAACAT-GTTTTGTCTTACTTTTACATAATATAAACGATTTCATACTTATAACT
* *
14140 TAAACGGTTGACACTAAAAAAAACGTTATCTAGTAC
65 TAAACGATTGACATTAAAAAAAACGTTATCTAGTAC
* ** * * * * *
14176 GTTATCATGAGCAGTATGTTTTGTCTTTCTCTTGCATAATATAAACAATTTCGTACTTATAACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTACATAATATAAACGATTTCATACTTATAACTT
* ** * *
14241 AAACGATTGATA-T-AAAAAAGTGTTACCTACTAC
66 AAACGATTGACATTAAAAAAAACGTTATCTAGTAC
* * ** * *
14274 GTTATCATGAGAAACATG--TTGTCATACTTTTGCAGCATATAAACGGTTTCATACTTATTACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTACATAATATAAACGATTTCATACTTATAACTT
14337 AAAC-AGTTGACATTAAAAAAAA
66 AAACGA-TTGACATTAAAAAAAA
14359 TGAGCTACCT
Statistics
Matches: 234, Mismatches: 45, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
95 1 0.00
96 45 0.19
97 1 0.00
98 37 0.16
99 1 0.00
100 49 0.21
101 26 0.11
102 5 0.02
103 19 0.08
104 50 0.21
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (100 bp):
GTTATCATGAGAAACATGTTTTGTCTTACTTTTACATAATATAAACGATTTCATACTTATAACTT
AAACGATTGACATTAAAAAAAACGTTATCTAGTAC
Found at i:14689 original size:112 final size:116
Alignment explanation
Indices: 14533--14776 Score: 361
Period size: 112 Copynumber: 2.1 Consensus size: 116
14523 ATTTTTGCTT
* * *
14533 AAAGTATCGATACTTTCGAATTTAAAATAAAGATGAAAAATGATATTTTAACTTTCTAATTTAAA
1 AAAGTATCGATACTTTAGAATTTAAAATAAAGATGAAAAATGATATTTTAAATTTCGAATTTAAA
* * *
14598 AGTATCGATACTTTGCAATATTCTTATTTTCCATGTTTTTCTTTAAATTCG
66 AGTATCGATACTTTGCAACATCCTCATTTTCCATGTTTTTCTTTAAATTCG
* *
14649 AAAGTATTGATACTTTAGAA-TTAAAA-AAATA-G-AAAATGATATTTTAAATTTCGAATTTAAA
1 AAAGTATCGATACTTTAGAATTTAAAATAAAGATGAAAAATGATATTTTAAATTTCGAATTTAAA
* * *
14710 AGTATCTATACTTTGCAGCGTCCTCATTTTCCATGTTTTTCTTTAAATTCG
66 AGTATCGATACTTTGCAACATCCTCATTTTCCATGTTTTTCTTTAAATTCG
14761 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
14777 TGGAATAGTT
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
112 87 0.75
113 1 0.01
114 4 0.03
115 6 0.05
116 18 0.16
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (116 bp):
AAAGTATCGATACTTTAGAATTTAAAATAAAGATGAAAAATGATATTTTAAATTTCGAATTTAAA
AGTATCGATACTTTGCAACATCCTCATTTTCCATGTTTTTCTTTAAATTCG
Found at i:14967 original size:77 final size:78
Alignment explanation
Indices: 14812--14969 Score: 187
Period size: 77 Copynumber: 2.0 Consensus size: 78
14802 AAAATATAAT
* * * *
14812 ATAAAAAAATTAACATTCCAAATTACAACTTACTTTCTTAGTGAACCATAACATTTTTGTGCGTA
1 ATAAAAAAATTAACATTCCAAATAACAACCTACTTTCTTAGTGAACCATAACATTCTTGTGCGAA
*
14877 ACCAATTTTATTA
66 ACCAATTTGATTA
* ** * *
14890 ATAAAAATATTAACATTTTATATAACAACCTA-TTTCTTAGTGAACCATGACATTCTTG-GACGA
1 ATAAAAAAATTAACATTCCAAATAACAACCTACTTTCTTAGTGAACCATAACATTCTTGTG-CGA
14953 AACTC-ATTTGATTA
65 AAC-CAATTTGATTA
14967 ATA
1 ATA
14970 TTCCATATCG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.01
77 40 0.59
78 27 0.40
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (78 bp):
ATAAAAAAATTAACATTCCAAATAACAACCTACTTTCTTAGTGAACCATAACATTCTTGTGCGAA
ACCAATTTGATTA
Found at i:15066 original size:105 final size:105
Alignment explanation
Indices: 14876--15074 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 105
14866 TTTTGTGCGT
* *
14876 AACCAATTTTATTAATAAAAATATTAACATTTTATATAACAACCTATTTCTTAGTGAACCATGAC
1 AACCAATTTTATTAATAAAAATATTAACATTTCATATAACAACATATTTCTTAGTGAACCATGAC
*
14941 ATTCTTGGACGAAACTCATTTGATTAATATTCCATATCGC
66 ATTCTTGGACGAAACCCATTTGATTAATATTCCATATCGC
* * * * * * *
14981 AACCTATTTTATTAATAAAAATATTAATATTTCATATCATAACATTTTTTTTAGTGAACCATGAT
1 AACCAATTTTATTAATAAAAATATTAACATTTCATATAACAACATATTTCTTAGTGAACCATGAC
* *
15046 ATTTTTGGAC-ACAACCCATTTTATTAATA
66 ATTCTTGGACGA-AACCCATTTGATTAATA
15075 AAAATATTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 1 0.01
105 80 0.99
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (105 bp):
AACCAATTTTATTAATAAAAATATTAACATTTCATATAACAACATATTTCTTAGTGAACCATGAC
ATTCTTGGACGAAACCCATTTGATTAATATTCCATATCGC
Found at i:15067 original size:77 final size:77
Alignment explanation
Indices: 14980--15205 Score: 310
Period size: 77 Copynumber: 2.9 Consensus size: 77
14970 TTCCATATCG
* * * *
14980 CAACCTATTTTATTAATAAAAATATTAATATTTCATATCATAACATTTTTTTTAGTGAACCATGA
1 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCATAACATATTTTTTAGTGAACCATGA
15045 TATTTTTGGACA
66 TATTTTTGGACA
* * *
15057 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTTTTAGTGAACCATTA
1 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCATAACATATTTTTTAGTGAACCATGA
* *
15122 AATTTTTGGACG
66 TATTTTTGGACA
* * ** *
15134 CAACCCATTTTATTAATAAAAATATTAACATTCCAAATCGTAACATGCTTCTTAGTGAACCATG-
1 CAACCCATTTTATTAATAAAAATATTAACATTCCATATCATAACATATTTTTTAGTGAACCATGA
15198 TCATTTTT
66 T-ATTTTT
15206 AGGTACAATC
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 130 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (77 bp):
CAACCCATTTTATTAATAAAAATATTAACATTCCATATCATAACATATTTTTTAGTGAACCATGA
TATTTTTGGACA
Found at i:15100 original size:40 final size:40
Alignment explanation
Indices: 15053--15168 Score: 107
Period size: 40 Copynumber: 3.0 Consensus size: 40
15043 GATATTTTTG
15053 GACACAACCCATTTTATTAATAAAAATATTAACATTCCAT
1 GACACAACCCATTTTATTAATAAAAATATTAACATTCCAT
* * * ** **
15093 -ATCACAACCTATTTT-TTAGT-GAACCATTAA-ATT-TTT
1 GA-CACAACCCATTTTATTAATAAAAATATTAACATTCCAT
*
15129 GGACGCAACCCATTTTATTAATAAAAATATTAACATTCCA
1 -GACACAACCCATTTTATTAATAAAAATATTAACATTCCA
15169 AATCGTAACA
Statistics
Matches: 54, Mismatches: 15, Indels: 13
0.66 0.18 0.16
Matches are distributed among these distances:
36 1 0.02
37 14 0.26
38 12 0.22
39 12 0.22
40 15 0.28
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (40 bp):
GACACAACCCATTTTATTAATAAAAATATTAACATTCCAT
Found at i:18500 original size:12 final size:12
Alignment explanation
Indices: 18483--18512 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
18473 ATACAATTAG
18483 GTTTAAATCCCA
1 GTTTAAATCCCA
18495 GTTTAAATCCCA
1 GTTTAAATCCCA
18507 GTTTAA
1 GTTTAA
18513 GACTGTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (12 bp):
GTTTAAATCCCA
Found at i:20037 original size:36 final size:36
Alignment explanation
Indices: 19966--20038 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
19956 GTTGGAAAAT
** *
19966 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATAAAAAATCATAAA
20002 ATTTATATAATTTT-TTTATAAAATAAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATAAAAAATCATAAA
20038 A
1 A
20039 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATAAAAAATCATAAA
Found at i:21344 original size:32 final size:32
Alignment explanation
Indices: 21280--21357 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
21270 AACTGCTACA
* *
21280 CATTATCTAAATGCTACATTGATACTCCTGTG
1 CATTATCTGAATGCAACATTGATACTCCTGTG
**
21312 CATTATCTGAATGCAACATTGACT-CTTTTGTG
1 CATTATCTGAATGCAACATTGA-TACTCCTGTG
*
21344 CATAATCTGAATGC
1 CATTATCTGAATGC
21358 GACACTACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 39 0.98
33 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (32 bp):
CATTATCTGAATGCAACATTGATACTCCTGTG
Found at i:23674 original size:117 final size:116
Alignment explanation
Indices: 23458--23690 Score: 303
Period size: 117 Copynumber: 2.0 Consensus size: 116
23448 TTAGTTCCTT
* * * * * *
23458 GGGCCGTGTAATATTGGTTTGATTGAATCTCGGTCTTGCTTGTAATTTTACATGAATAATAAAAG
1 GGGCCCTGTAATATTGGTTTGATTGAACCTCGATCTTGCTTGTAATTTGACATGAAAAATAAAAA
23523 AACAAAATTATTTAATATTTAATATATATAATATATAATAAAAAAACGACAA
66 AACAAAATTATTTAATATTTAATATATATAATATAT-ATAAAAAAACGACAA
* * * *
23575 GGGCCCTGTACTATTGGTTTGATTGAACCTTGATCTTGCTTGTAATTTGGGCTTGAAAAATAAAA
1 GGGCCCTGTAATATTGGTTTGATTGAACCTCGATCTTGCTTGTAATTT-GACATGAAAAAT-AAA
23640 TAAAACAAAA-TATTTAATTATTT-A-ATATAT-ATATATATAAAAAAACGACAA
64 -AAAACAAAATTATTTAA-TATTTAATATATATAATATATATAAAAAAACGACAA
23691 CCCAGACAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
116 15 0.15
117 49 0.48
118 14 0.14
119 11 0.11
120 13 0.13
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (116 bp):
GGGCCCTGTAATATTGGTTTGATTGAACCTCGATCTTGCTTGTAATTTGACATGAAAAATAAAAA
AACAAAATTATTTAATATTTAATATATATAATATATATAAAAAAACGACAA
Found at i:33817 original size:13 final size:13
Alignment explanation
Indices: 33799--33825 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33789 ATTATGTTAA
33799 TATTTTTATTTTT
1 TATTTTTATTTTT
33812 TATTTTTATTTTT
1 TATTTTTATTTTT
33825 T
1 T
33826 TCGTTCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:39913 original size:17 final size:17
Alignment explanation
Indices: 39893--40015 Score: 51
Period size: 17 Copynumber: 7.2 Consensus size: 17
39883 ATAAAAGAGA
*
39893 AAAAATGAGAAAATGAG
1 AAAAATGAAAAAATGAG
*
39910 AAAAAAG-AAAAATGATGG
1 AAAAATGAAAAAATGA--G
* * *
39928 AAAAA--ACGAAAAGGAA
1 AAAAATGA-AAAAATGAG
*
39944 AAAAGAAGAAAAAATG-G
1 AAAA-ATGAAAAAATGAG
**
39961 AAAAGGGAAGAAAAAATGA-
1 AAAAATG-A-AAA-AATGAG
*
39980 AA-AATGAAAAAAAGAG
1 AAAAATGAAAAAATGAG
*
39996 AAAAATGAAAAAAAGAG
1 AAAAATGAAAAAATGAG
40013 AAA
1 AAA
40016 TAAAAGGAGG
Statistics
Matches: 80, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
15 4 0.05
16 17 0.21
17 30 0.38
18 22 0.28
19 7 0.09
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.07
Consensus pattern (17 bp):
AAAAATGAAAAAATGAG
Found at i:39913 original size:25 final size:25
Alignment explanation
Indices: 39885--40015 Score: 78
Period size: 26 Copynumber: 5.1 Consensus size: 25
39875 AAGAAGAAAT
39885 AAAAGAGAAAAAATGAGAAAATGAG
1 AAAAGAGAAAAAATGAGAAAATGAG
* *
39910 AAAAAAG-AAAAATGATGGAAAA-AACG
1 AAAAGAGAAAAAATGA--GAAAATGA-G
39936 AAAAG-GAAAAAA-GAAGAAAAAATG-G
1 AAAAGAGAAAAAATG-AG--AAAATGAG
39961 AAAAGGGAAGAAAAAATGA-AAAATGA-
1 AAAA--G-AGAAAAAATGAGAAAATGAG
* * *
39987 AAAAAAGAGAAAAATGAAAAAAAGAG
1 AAAAGAGA-AAAAATGAGAAAATGAG
40013 AAA
1 AAA
40016 TAAAAGGAGG
Statistics
Matches: 83, Mismatches: 6, Indels: 33
0.68 0.05 0.27
Matches are distributed among these distances:
23 3 0.04
24 17 0.20
25 20 0.24
26 33 0.40
27 1 0.01
29 8 0.10
30 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAAGAGAAAAAATGAGAAAATGAG
Found at i:39964 original size:19 final size:19
Alignment explanation
Indices: 39936--39992 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
39926 GGAAAAAACG
39936 AAAA-GGAAAAAAGAAGAA
1 AAAATGGAAAAAAGAAGAA
**
39954 AAAATGGAAAAGGGAAGAA
1 AAAATGGAAAAAAGAAGAA
*
39973 AAAAT-GAAAAATGAA-AA
1 AAAATGGAAAAAAGAAGAA
39990 AAA
1 AAA
39993 GAGAAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.15
18 12 0.35
19 17 0.50
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (19 bp):
AAAATGGAAAAAAGAAGAA
Found at i:40016 original size:15 final size:15
Alignment explanation
Indices: 39970--40020 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
39960 GAAAAGGGAA
* *
39970 GAAAAAATGAAAAAT
1 GAAAAAAAGAGAAAT
39985 GAAAAAAAGAGAAAAAT
1 GAAAAAAAGAG--AAAT
40002 GAAAAAAAGAGAAAT
1 GAAAAAAAGAGAAAT
40017 -AAAA
1 GAAAA
40021 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 4 0.12
15 13 0.41
17 15 0.47
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAGAAAT
Found at i:41258 original size:15 final size:15
Alignment explanation
Indices: 41238--41268 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41228 AATATTTTTC
41238 AAATATACATTCATG
1 AAATATACATTCATG
41253 AAATATACATTCATG
1 AAATATACATTCATG
41268 A
1 A
41269 TGAATAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
AAATATACATTCATG
Found at i:41414 original size:51 final size:51
Alignment explanation
Indices: 41353--41923 Score: 594
Period size: 51 Copynumber: 10.8 Consensus size: 51
41343 AAATTCGTTC
*
41353 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
* *
41404 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
*
41455 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
*
41506 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
*
41557 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
* * * **
41608 ATTGAAGATCGAGTTCTATACTC-CTTGAACGG-ATAGGGAGCGGACCCGTTT
1 GTTGAAGATTGAGTCCTATACTCTC-TGAA-GGAATAGGGAGCGGACAAGTTT
* * **
41659 -TATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT
1 GT-TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
** * *
41714 CATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-AACGTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA-GTTT
* * **
41769 GTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
* * * * *
41824 -TATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCAGACACGTTT
1 GT-TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
* * * *
41879 GCTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGC
41924 AGACTCGTCA
Statistics
Matches: 480, Mismatches: 26, Indels: 24
0.91 0.05 0.05
Matches are distributed among these distances:
50 2 0.00
51 248 0.52
52 2 0.00
54 4 0.01
55 223 0.46
56 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
Found at i:41941 original size:110 final size:107
Alignment explanation
Indices: 41363--41945 Score: 553
Period size: 110 Copynumber: 5.5 Consensus size: 107
41353 GTTGAAGATT
* * * * *
41363 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGTTGAAGA--TT-GAGTCCTATAC
1 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG--TATTGAAGATTTTCGAGTTCTATAC
* * *
41425 TCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
64 TCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTC
* * * *
41465 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-GAGTCCTATAC
1 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG-T-ATTGAAGATTTTCGAGTTCTATAC
* *
41527 TCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
64 TCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTC
*
41567 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA---TCGAGTTCTATAC
1 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG--TATTGAAGATTTTCGAGTTCTATAC
*
41629 TC-CTTGAACGG-ATAGGGAGCGGACCCGTTT-TATGAAGATTGTTC
64 TCTC-TGAA-GGAATAGGGAGCGGACACGTTTGT-TGAAGATTGTTC
* * *
41673 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTAT
1 GAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACACGTAT--TGAAGATT-TTCGAGTTCTAT
* *
41737 ACTCTCTGAAGGAATAGAGAGCGGAAACGTTTGTTGAAGATTGTTC
62 ACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTC
* * *
41783 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTAT
1 GAGTCT-TATACTCTCTGAAGGAATAGGGAGCGGACACG-TAT-TGAAGATT-TTCGAGTTCTAT
* * * *
41847 ACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTC
62 ACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTC
* * * *
41893 GAGTCTTATACTCCCTGAACGAATAGGGAGCAGACTCGTCATTCGAAGATTTT
1 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGT-ATT-GAAGATTTT
41946 TCAAGTCTTG
Statistics
Matches: 430, Mismatches: 27, Indels: 41
0.86 0.05 0.08
Matches are distributed among these distances:
101 5 0.01
102 179 0.42
103 4 0.01
104 2 0.00
105 2 0.00
106 40 0.09
109 6 0.01
110 186 0.43
111 6 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (107 bp):
GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTATTGAAGATTTTCGAGTTCTATACTC
TCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGATTGTTC
Found at i:41966 original size:55 final size:55
Alignment explanation
Indices: 41364--41954 Score: 320
Period size: 55 Copynumber: 11.1 Consensus size: 55
41354 TTGAAGATTG
* * * * * *
41364 AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTTGTTGAAGATTG----
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * * * *
41415 AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTG----
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * * * *
41466 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTG----
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * * * *
41517 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTG----
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * ** *
41568 AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA----TCG
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * ** *
41619 AGT-TCTATACTCCTTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * * *
41674 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-CATGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGC-TGAAGATTGTTCA
* * * * * * *
41729 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGAAACGTTTGTTGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* * * * * ** *
41784 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* *
41839 AGT-TCTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
* *
41894 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACTCGTCATT-C-GAAGATTTTTCA
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGT--TTGCTGAAGATTGTTCA
41949 AGTCTT
1 AGTCTT
41955 GCTTATCCTG
Statistics
Matches: 490, Mismatches: 37, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
51 235 0.48
55 251 0.51
56 2 0.00
57 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
AGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCA
Found at i:50909 original size:18 final size:17
Alignment explanation
Indices: 50835--50910 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 17
50825 AAATAAAAGA
*
50835 GAAAAAATGAAAAAAT-
1 GAAAAAAAGAAAAAATG
50851 GAGAAAAAAGAAAAATGATG
1 GA-AAAAAAGAAAAA--ATG
*
50871 GAAAAAACA-AAAAGAA-A
1 GAAAAAA-AGAAAA-AATG
50888 GAAAAAGAAGAAAAAATG
1 GAAAAA-AAGAAAAAATG
50906 GAAAA
1 GAAAA
50911 GGGAAGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
16 2 0.04
17 20 0.42
18 11 0.23
19 11 0.23
20 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (17 bp):
GAAAAAAAGAAAAAATG
Found at i:50910 original size:53 final size:53
Alignment explanation
Indices: 50834--50949 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 53
50824 GAAATAAAAG
* *
50834 AGAAAAA-ATGAAAAAATGAGAAAA-AAGAAAA-ATGATGGAAAAAACAAAAAGAA
1 AGAAAAAGAAGAAAAAATGAGAAAAGAAGAAAACGT-AT-G-AAAAACAAAAAGAA
50887 AGAAAAAGAAGAAAAAATG-GAAAAGGGAAGAAAACGTATGAAAAACAAAAAGAA
1 AGAAAAAGAAGAAAAAATGAGAAAA--GAAGAAAACGTATGAAAAACAAAAAGAA
50941 A-AAAAAGAA
1 AGAAAAAGAA
50950 ATAAAAAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
53 20 0.36
54 25 0.45
55 1 0.02
56 9 0.16
57 1 0.02
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (53 bp):
AGAAAAAGAAGAAAAAATGAGAAAAGAAGAAAACGTATGAAAAACAAAAAGAA
Found at i:50911 original size:17 final size:16
Alignment explanation
Indices: 50835--50910 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 16
50825 AAATAAAAGA
50835 GAAAAAATGAAAAAATG
1 GAAAAAA-GAAAAAATG
50852 AGAAAAAAGAAAAATGATG
1 -GAAAAAAGAAAAA--ATG
* *
50871 GAAAAAACAAAAAGAAAG
1 GAAAAAA-GAAAA-AATG
*
50889 AAAAAGAAGAAAAAATG
1 GAAAA-AAGAAAAAATG
50906 GAAAA
1 GAAAA
50911 GGGAAGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
17 13 0.28
18 24 0.51
19 9 0.19
20 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (16 bp):
GAAAAAAGAAAAAATG
Found at i:50947 original size:9 final size:9
Alignment explanation
Indices: 50933--50966 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
50923 TATGAAAAAC
50933 AAAAAGAAA
1 AAAAAGAAA
50942 AAAAAGAAA
1 AAAAAGAAA
50951 TAAAAAGAAA
1 -AAAAAGAAA
*
50961 TAAAAG
1 AAAAAG
50967 GAGGGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:52339 original size:51 final size:51
Alignment explanation
Indices: 52274--52698 Score: 571
Period size: 51 Copynumber: 8.1 Consensus size: 51
52264 AAGCAAATTC
52274 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
52325 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* *
52376 GTTTGTTGAAGATTGAGTCATATACTCTCTGAAGGAATAGGGAACGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
52427 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
*
52478 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * **
52529 GTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * *
52584 GTTTGTTGAAGATTATTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACAC
1 GTTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
* * * * *
52639 GTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACAC
1 GTTTGTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
52694 GTTTG
1 GTTTG
52699 CCAAAAATTG
Statistics
Matches: 341, Mismatches: 22, Indels: 18
0.90 0.06 0.05
Matches are distributed among these distances:
51 206 0.60
52 1 0.00
54 2 0.01
55 129 0.38
56 2 0.01
58 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
Found at i:52709 original size:55 final size:55
Alignment explanation
Indices: 52273--52762 Score: 477
Period size: 51 Copynumber: 9.3 Consensus size: 55
52263 GAAGCAAATT
* *
52273 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * * *
52324 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
52375 AGTTTGTTGAAGA---TT-GAGTCATATACTCTCTGAAGGAATAGGGAACGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
52426 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
52477 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
52528 AGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACA
* *
52583 CGTTTGTTGAAGATTATTCGAGTCTTATACTCTCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
52638 CGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
*** * * * *
52693 CGTTTGCCAAAAATTGTTCGAGTCTTATACTC-CTTGAAAGAAAAGGGAGCAGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTC-TGAAGGAATAGGGAGCAGACA
52748 CGTTAT-TTGAAGATT
1 CGTT-TGTTGAAGATT
52763 TTTCAAGTAT
Statistics
Matches: 395, Mismatches: 36, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
51 206 0.52
54 3 0.01
55 184 0.47
56 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:53737 original size:23 final size:22
Alignment explanation
Indices: 53707--53752 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
53697 AGAGAGCAGA
* *
53707 TAAATAAGGTTTAGGTTAGGTT
1 TAAATAAGCTTTAGATTAGGTT
*
53729 TAAAGTAAGCTTTATATTAGGTT
1 TAAA-TAAGCTTTAGATTAGGTT
53752 T
1 T
53753 TTAGGGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (22 bp):
TAAATAAGCTTTAGATTAGGTT
Found at i:54438 original size:13 final size:13
Alignment explanation
Indices: 54420--54446 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54410 ATTATGTTAA
54420 TATTTTTATTTTT
1 TATTTTTATTTTT
54433 TATTTTTATTTTT
1 TATTTTTATTTTT
54446 T
1 T
54447 TTCGTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:56544 original size:18 final size:18
Alignment explanation
Indices: 56516--56558 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
56506 TCTTCTTATT
*
56516 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
56535 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
56553 -TTATTT
1 TTTATTT
56559 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:60407 original size:16 final size:16
Alignment explanation
Indices: 60358--60413 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
60348 GCTCCATTGA
*
60358 AAAAAAATGTTGAATGCG
1 AAAAAAATGTTG--TTCG
**
60376 AAAAAAATAGCAGTTCG
1 AAAAAAAT-GTTGTTCG
60393 AAAAAAATGTTGTTCG
1 AAAAAAATGTTGTTCG
60409 AAAAA
1 AAAAA
60414 TAGAGAGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 11 0.34
17 11 0.34
18 8 0.25
19 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (16 bp):
AAAAAAATGTTGTTCG
Found at i:62174 original size:18 final size:18
Alignment explanation
Indices: 62121--62163 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
62111 TCTTCTTATT
*
62121 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
62140 TTTATTTAATCACTTTTA
1 TTTATTTAATCACTTTTA
62158 -TTATTT
1 TTTATTT
62164 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:69992 original size:18 final size:19
Alignment explanation
Indices: 69952--69998 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
69942 GACATAAATA
*
69952 ATAAATAGTA-ATAGTAATG
1 ATAAATA-TATATAGTAATC
69971 ATAAATATATATA-TAATC
1 ATAAATATATATAGTAATC
69989 ATAAATATAT
1 ATAAATATAT
69999 GAAAGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (19 bp):
ATAAATATATATAGTAATC
Found at i:71602 original size:3 final size:3
Alignment explanation
Indices: 71585--71638 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
71575 TTATAATATT
**
71585 TAA TAAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
71630 TAA TAA TAA
1 TAA TAA TAA
71639 ATTTAAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:75943 original size:21 final size:21
Alignment explanation
Indices: 75906--75946 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
75896 GAAAAGTAAT
*
75906 TTTATAATTATCTTATAAATA
1 TTTATAATTATATTATAAATA
75927 TTTA-AATTATATATATAAAT
1 TTTATAATTATAT-TATAAAT
75947 TAAATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATAATTATATTATAAATA
Found at i:76063 original size:18 final size:19
Alignment explanation
Indices: 76028--76064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
76018 CACGGAATGT
76028 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
76048 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
76065 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:76234 original size:15 final size:15
Alignment explanation
Indices: 76216--76248 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
76206 AAATTCTAAA
76216 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
76231 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
76246 TAT
1 TAT
76249 ATCTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:80079 original size:13 final size:13
Alignment explanation
Indices: 80061--80109 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
80051 AAAATTAATG
*
80061 AAAATAAATGAAT
1 AAAATAAATAAAT
80074 AAAATAAATAAAT
1 AAAATAAATAAAT
*
80087 AAATATTTAATAAAT
1 AAA-A-TAAATAAAT
80102 AATAATAA
1 AA-AATAA
80110 TGAGAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 15 0.50
14 3 0.10
15 11 0.37
16 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:80101 original size:32 final size:32
Alignment explanation
Indices: 80063--80123 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
80053 AATTAATGAA
80063 AATAAATGAATAA-AAT-AAATAAATAAATATTT
1 AATAAAT-AATAATAATGAAA-AAATAAATATTT
*
80095 AATAAATAATAATAATGAGAAAATAAATA
1 AATAAATAATAATAATGAAAAAATAAATA
80124 AAGTAGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.19
32 19 0.73
33 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (32 bp):
AATAAATAATAATAATGAAAAAATAAATATTT
Found at i:80749 original size:13 final size:13
Alignment explanation
Indices: 80716--80749 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
80706 AGCATTGTGA
* *
80716 AAAGAAAATAATG
1 AAAGAAAGTAAAG
80729 AAAGAAAGTAAAG
1 AAAGAAAGTAAAG
80742 AAAGAAAG
1 AAAGAAAG
80750 ATGTAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (13 bp):
AAAGAAAGTAAAG
Found at i:80930 original size:19 final size:21
Alignment explanation
Indices: 80901--80939 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
80891 AAAATCGTAA
80901 TAAGATTTT-AATAAAATAAC
1 TAAGATTTTAAATAAAATAAC
80921 TAAG-TTTTAAATAAAATAA
1 TAAGATTTTAAATAAAATAA
80940 TAATAGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAGATTTTAAATAAAATAAC
Found at i:86934 original size:24 final size:24
Alignment explanation
Indices: 86905--86971 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
86895 AAAAATTCAG
86905 GAGCTCGATTAAAGCTCGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
* *
86929 GAGCTCGATTGAAGCTTGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
86953 GAGCTCGATTGAAA-CTCGA
1 GAGCTCGATT-AAAGCTCGA
86972 TTCAAACTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 36 0.95
25 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAGACTC
Found at i:89589 original size:11 final size:11
Alignment explanation
Indices: 89573--89635 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
89563 GTATTATAGA
89573 ATTTTTAATAT
1 ATTTTTAATAT
89584 ATTTTTAA-A-
1 ATTTTTAATAT
89593 ATTTTATAAT-T
1 ATTTT-TAATAT
* * *
89604 ATCTATAATTT
1 ATTTTTAATAT
89615 ATTTTTAATAT
1 ATTTTTAATAT
*
89626 AATTTTAATA
1 ATTTTTAATA
89636 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:97265 original size:35 final size:35
Alignment explanation
Indices: 97191--97300 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 35
97181 AATAGTCCTT
* * *
97191 AATTTCATTCTAAACCCTAAATTCAAAAATAATTT--
1 AATTTCATTCTAAACCTTAAATT--GAAATATTTTAG
*
97226 AATTTCATTCTAAACCTTAAATTGAAGTATTTTAG
1 AATTTCATTCTAAACCTTAAATTGAAATATTTTAG
* * * *
97261 AATTTGGAGTT-TAAA-ATGAAATTGAATTATTTTAG
1 AATTT-CA-TTCTAAACCTTAAATTGAAATATTTTAG
97296 AATTT
1 AATTT
97301 GGGGTTTAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
33 7 0.11
35 49 0.78
36 5 0.08
37 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (35 bp):
AATTTCATTCTAAACCTTAAATTGAAATATTTTAG
Found at i:97301 original size:35 final size:35
Alignment explanation
Indices: 97244--97320 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
97234 TCTAAACCTT
97244 AAATTGAAGTATTTTAGAATTTGGAGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTGGAGTTTAAAATG
* * *
97279 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTGGAGTTTAAAATG
97314 AAATTGA
1 AAATTGA
97321 TGACTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.40
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTGGAGTTTAAAATG
Found at i:99573 original size:3 final size:3
Alignment explanation
Indices: 99565--99675 Score: 222
Period size: 3 Copynumber: 37.0 Consensus size: 3
99555 TAGTTCTCTG
99565 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
99613 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
99661 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
99676 GTAATAGAAT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:100936 original size:29 final size:28
Alignment explanation
Indices: 100874--100950 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
100864 TATAATAAGA
*
100874 TAAATGTATAAATATATAACTAAAGGAT
1 TAAATGTATAAATATATAAATAAAGGAT
**
100902 TAAAATG-ATAAATATAATAAATTTAGTGAT
1 T-AAATGTATAAATAT-ATAAATAAAG-GAT
100932 TAAAT-TATCAAA-ATATAAA
1 TAAATGTAT-AAATATATAAA
100951 AGATTAAGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
28 14 0.34
29 20 0.49
30 7 0.17
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.34
Consensus pattern (28 bp):
TAAATGTATAAATATATAAATAAAGGAT
Found at i:102058 original size:3 final size:3
Alignment explanation
Indices: 102045--102095 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
102035 TATTTATTTG
102045 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
102091 TAA TA
1 TAA TA
102096 CTAGGTAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:102339 original size:20 final size:21
Alignment explanation
Indices: 102311--102367 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
102301 TTACAATAAA
*
102311 TTAAAATTTAAAAATA-TATT
1 TTAATATTTAAAAATATTATT
*
102331 TTAATATTTCAAAACTATTATT
1 TTAATATTT-AAAAATATTATT
* *
102353 ATAATTTATTAAAAA
1 TTAATAT-TTAAAAA
102368 CTAAGTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 8 0.28
21 6 0.21
22 13 0.45
23 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATATTTAAAAATATTATT
Found at i:104103 original size:24 final size:23
Alignment explanation
Indices: 104042--104103 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
104032 CTCTAAATTA
* *
104042 GAATGAATTTAT-TATAAATTAT
1 GAATGAATTTATAAATAAAATAT
** *
104064 GAATGAAAATAAAAATAAAAATAT
1 GAATGAATTTATAAAT-AAAATAT
104088 GAATGAATTTATAAAT
1 GAATGAATTTATAAAT
104104 TATGTCATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 9 0.30
23 2 0.07
24 19 0.63
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (23 bp):
GAATGAATTTATAAATAAAATAT
Found at i:104183 original size:44 final size:43
Alignment explanation
Indices: 104096--104184 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
104086 ATGAATGAAT
* *
104096 TTATAAATTATGTCATTACAAGAAAATATGAATGGATTTATAAA
1 TTATAAATTATGTCATTACAAGAAAATATGAATCGA-TAATAAA
*
104140 TTATAAATTATGTCATTATAAGAAAATAATGAAATCGA-AATAAA
1 TTATAAATTATGTCATTACAAGAAAAT-ATG-AATCGATAATAAA
104184 T
1 T
104185 AAAATTGCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 32 0.80
45 3 0.08
46 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (43 bp):
TTATAAATTATGTCATTACAAGAAAATATGAATCGATAATAAA
Found at i:104737 original size:21 final size:22
Alignment explanation
Indices: 104712--104769 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
104702 TATAAAAATC
104712 GAAAACATGTCA-AAAGACATA
1 GAAAACATGTCATAAAGACATA
**
104733 GAAAATGTGTCATAAAGACATA
1 GAAAACATGTCATAAAGACATA
*
104755 GAAATCATGTCATAA
1 GAAAACATGTCATAA
104770 TAAAGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.21
Consensus pattern (22 bp):
GAAAACATGTCATAAAGACATA
Found at i:109470 original size:45 final size:45
Alignment explanation
Indices: 109382--109471 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
109372 AGAACTTTTT
*
109382 TTATTAATTTATTACAAAAATAATCTTCATCCAAAACTGTTTGAA
1 TTATTAATTTATTACAAAAATAATCTTCATCCAAAACTATTTGAA
*
109427 TTATTAATTTATCATA-AAAAATAATCTTCATCC-AAATTATTTGAA
1 TTATTAATTTAT--TACAAAAATAATCTTCATCCAAAACTATTTGAA
109472 AAATTGACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 22 0.54
46 17 0.41
47 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (45 bp):
TTATTAATTTATTACAAAAATAATCTTCATCCAAAACTATTTGAA
Found at i:110630 original size:20 final size:20
Alignment explanation
Indices: 110605--110652 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
110595 AAACATTAAG
110605 GTATTGATATCACCTATA-AA
1 GTATTGATA-CACCTATATAA
110625 GTATTG--ACACCTATATAA
1 GTATTGATACACCTATATAA
*
110643 GTATCGATAC
1 GTATTGATAC
110653 TCTTATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
20 8 0.33
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATTGATACACCTATATAA
Found at i:112480 original size:2 final size:2
Alignment explanation
Indices: 112475--112551 Score: 122
Period size: 2 Copynumber: 39.0 Consensus size: 2
112465 ACACACACAC
*
112475 AT AT AT AC A- AT AT AT AT AT AT AT AT A- 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
112515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
112552 GGGCCTGGGT
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
1 2 0.03
2 67 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Done.