Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008749.1 Hibiscus syriacus cultivar Beakdansim tig00111840_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: 379273
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 1 of 3
Found at i:4647 original size:3 final size:3
Alignment explanation
Indices: 4633--4670 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
4623 CCAAATGTAA
*
4633 AAT AAT ATT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
4671 GAACGAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4713 original size:5 final size:5
Alignment explanation
Indices: 4703--4746 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
4693 TCGACACAAG
4703 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAG
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAG
4747 TAGGATTCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:6386 original size:25 final size:27
Alignment explanation
Indices: 6358--6410 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
6348 AAAGAAACAA
6358 AGAAAA-ATGAAGGT-A-AGCATGACTG
1 AGAAAAGA-GAAGGTAAGAGCATGACTG
6383 AGAAAAGAGAAGGTAAGAGCATGACTG
1 AGAAAAGAGAAGGTAAGAGCATGACTG
6410 A
1 A
6411 ATCTTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 12 0.48
26 2 0.08
27 11 0.44
ACGTcount: A:0.49, C:0.08, G:0.30, T:0.13
Consensus pattern (27 bp):
AGAAAAGAGAAGGTAAGAGCATGACTG
Found at i:8308 original size:2 final size:2
Alignment explanation
Indices: 8303--8355 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
8293 CCCCCTCCCA
8303 TC TC TC TC TC TC TC TC -C TC TC TC TC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8343 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
8356 ACTTTTTGCT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:13386 original size:184 final size:182
Alignment explanation
Indices: 13164--13525 Score: 595
Period size: 184 Copynumber: 2.0 Consensus size: 182
13154 TAAATTTTAA
*
13164 ATATATTATATATATAACATATGGGCTCAACCCAAACCATTTGAAACCCAATTAATAATTTAAGA
1 ATATATTATATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTTAAGA
*
13229 TCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTT
66 TCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTT
*
13294 ATAATTATATATTATTTAAATTAATTTTAAACTGTTTTTTTAATTAAAAAATATT
131 ATAATTATATATTATTTAAATTAATTAT-AAC--TTTTTTTAATTAAAAAATATT
*
13349 ATATA-TATTATATATAACATAT-GGCT-AAGCCCAAACCATTTAAAACCTAATTAATAATTTAA
1 ATATATTA-TATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATAATTTAA
* * *
13411 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTTTTATT
64 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATT
13476 TTATAATTATATATTATTTAAATTAATTATAACTTTTTTTAATTAAAAAA
129 TTATAATTATATATTATTTAAATTAATTATAACTTTTTTTAATTAAAAAA
13526 CATTTAATTT
Statistics
Matches: 168, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
181 17 0.10
183 5 0.03
184 127 0.76
185 19 0.11
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (182 bp):
ATATATTATATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTTAAGA
TCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTT
ATAATTATATATTATTTAAATTAATTATAACTTTTTTTAATTAAAAAATATT
Found at i:13558 original size:26 final size:25
Alignment explanation
Indices: 13509--13558 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
13499 TAATTATAAC
*
13509 TTTTTTTAATTAAAAAACATTTAAT
1 TTTTTTTAATTAAAAAACAATTAAT
13534 TTTTATTTAAATTAAAAAA-AATTAA
1 TTTT-TTT-AATTAAAAAACAATTAA
13559 AAAAAATCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTTTAATTAAAAAACAATTAAT
Found at i:16939 original size:106 final size:106
Alignment explanation
Indices: 16754--18054 Score: 1943
Period size: 106 Copynumber: 12.3 Consensus size: 106
16744 TATTGTTCCA
* * * * * *
16754 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTATTGAAAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * *
16819 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
16860 AGTCCAATATCCTTCGCAGTGAAGTTGAAATTGGCTCTGAGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
16925 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
16966 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
17031 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17072 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
17137 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
17178 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
17243 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17284 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
17349 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
17390 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
17455 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17496 AGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAAGTGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTGTTTATTGACAA
17560 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17602 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAATTTTTTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTTATTGACAA
*
17667 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * * *
17709 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTATGAAATT-ATTGTTGACAAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
17773 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
17814 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAA--ATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* *
17877 CAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
17918 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAGTGTTTGTTGACAAT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * * *
17982 CAGTC-GCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTGG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
* * ** *
18024 A-TTCAAGATCCTTCATTGAGAAGTTGAAATT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATT
18055 TACTCTCAAG
Statistics
Matches: 1111, Mismatches: 75, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
103 2 0.00
104 93 0.08
105 163 0.15
106 752 0.68
107 101 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:21825 original size:2 final size:2
Alignment explanation
Indices: 21818--21842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21808 AACATGCATA
21818 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
21843 ATGCACGCAC
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:29525 original size:2 final size:2
Alignment explanation
Indices: 29514--29566 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
29504 GCAGACATTC
*
29514 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
29555 TA GA TA TA TA TA
1 TA TA TA TA TA TA
29567 ATTGGAGGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:33289 original size:16 final size:16
Alignment explanation
Indices: 33268--33306 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
33258 GGTATTACCC
*
33268 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
33284 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
33300 GACCTGT
1 GACCTGT
33307 AATTGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:33426 original size:27 final size:26
Alignment explanation
Indices: 33388--33440 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
33378 AAATTACAAT
* *
33388 TAATATAATTATGGTATTTTAAATTTA
1 TAATATAATTATGATA-ATTAAATTTA
33415 TAATA-AACTTATGATAATTAAATTTA
1 TAATATAA-TTATGATAATTAAATTTA
33441 GTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (26 bp):
TAATATAATTATGATAATTAAATTTA
Found at i:33468 original size:19 final size:19
Alignment explanation
Indices: 33444--33489 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
33434 AAATTTAGTT
33444 TTTATATTAATTACAATTC
1 TTTATATTAATTACAATTC
** *
33463 TTTATATTTTTTATAATTC
1 TTTATATTAATTACAATTC
33482 -TTATATTA
1 TTTATATTA
33490 TAATTTGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:33511 original size:15 final size:14
Alignment explanation
Indices: 33473--33511 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
33463 TTTATATTTT
33473 TTATAATTCT-TATA
1 TTATAATT-TGTATA
33487 TTATAATTTGTATA
1 TTATAATTTGTATA
33501 TTATAAATTTG
1 TTAT-AATTTG
33512 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:33566 original size:12 final size:13
Alignment explanation
Indices: 33534--33567 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
33524 ATTCAAATTC
33534 TTTATAATTCTTA
1 TTTATAATTCTTA
33547 TATTATAATT-TTA
1 T-TTATAATTCTTA
33560 TTTATAAT
1 TTTATAAT
33568 CACTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 5 0.25
14 8 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATAATTCTTA
Found at i:34147 original size:23 final size:23
Alignment explanation
Indices: 34117--34171 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
34107 ACAGCAACCG
*
34117 GCAAGCATCAATGTACCAATTCA
1 GCAAGCATCAATGCACCAATTCA
* * *
34140 GCAAGCATCATTGCATCACTTCA
1 GCAAGCATCAATGCACCAATTCA
34163 GCAAGCATC
1 GCAAGCATC
34172 CTGCATTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (23 bp):
GCAAGCATCAATGCACCAATTCA
Found at i:34968 original size:7 final size:7
Alignment explanation
Indices: 34956--34982 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34946 ATCGATAACT
34956 AACAAGG
1 AACAAGG
34963 AACAAGG
1 AACAAGG
34970 AACAAGG
1 AACAAGG
34977 AACAAG
1 AACAAG
34983 TCGGTCCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (7 bp):
AACAAGG
Found at i:36777 original size:19 final size:18
Alignment explanation
Indices: 36753--36932 Score: 90
Period size: 19 Copynumber: 9.6 Consensus size: 18
36743 CCTATAAATT
36753 TATATTAATAAACTAATAA
1 TATATTAATAAA-TAATAA
*
36772 TATATTAAAATTAATATTATAA
1 TATATT--AA-TAA-ATAATAA
* *
36794 AATATT-ATAAATAATAT
1 TATATTAATAAATAATAA
36811 TAATATTATATAAATATATTAA
1 T-ATATTA-ATAAATA-A-TAA
*
36833 TATTAATTAATATAAT-ATAG
1 TA-T-ATTAATA-AATAATAA
* *
36853 TATAGTTTATAAAAAATATA
1 TATA-TTAATAAATAATA-A
36873 TATATTAAT--ATAA-AA
1 TATATTAATAAATAATAA
36888 TATAGTTAATAAAT--TAA
1 TATA-TTAATAAATAATAA
36905 TATA-TAATAAACT-ATATA
1 TATATTAATAAA-TAATA-A
36923 TATATTAATA
1 TATATTAATA
36933 TAAATAGTAG
Statistics
Matches: 126, Mismatches: 12, Indels: 46
0.68 0.07 0.25
Matches are distributed among these distances:
15 12 0.10
16 7 0.06
17 16 0.13
18 18 0.14
19 25 0.20
20 15 0.12
21 5 0.04
22 20 0.16
23 8 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (18 bp):
TATATTAATAAATAATAA
Found at i:36798 original size:22 final size:22
Alignment explanation
Indices: 36768--36812 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
36758 TAATAAACTA
*
36768 ATAATATATTA-AAATTAATATT
1 ATAAAATATTATAAA-TAATATT
36790 ATAAAATATTATAAATAATATT
1 ATAAAATATTATAAATAATATT
36812 A
1 A
36813 ATATTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAATATTATAAATAATATT
Found at i:36816 original size:28 final size:29
Alignment explanation
Indices: 36780--36851 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
36770 AATATATTAA
36780 AATTAATATTATA-AAATATTATAAATAAT
1 AATTAATATTATATAAATA-TATAAATAAT
* *
36809 -ATTAATATTATATAAATATATTAATATT
1 AATTAATATTATATAAATATATAAATAAT
*
36837 AATTAATATAATATA
1 AATTAATATTATATA
36852 GTATAGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 20 0.53
29 18 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTAATATTATATAAATATATAAATAAT
Found at i:36843 original size:10 final size:9
Alignment explanation
Indices: 36781--36845 Score: 60
Period size: 10 Copynumber: 6.9 Consensus size: 9
36771 ATATATTAAA
36781 ATTAATATT
1 ATTAATATT
*
36790 ATAAAATATT
1 AT-TAATATT
* *
36800 ATAAATAAT
1 ATTAATATT
36809 ATTAATATT
1 ATTAATATT
36818 ATATAA-ATAT
1 AT-TAATAT-T
36828 ATTAATATT
1 ATTAATATT
36837 AATTAATAT
1 -ATTAATAT
36846 AATATAGTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 23 0.49
10 24 0.51
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTAATATT
Found at i:36883 original size:38 final size:35
Alignment explanation
Indices: 36831--36912 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
36821 TAAATATATT
*
36831 AATAT-TAATTAATATAATATAGTATAGTTTATAAA-A
1 AATATATAATTAATATAA-A-A-TATAGTTAATAAATA
*
36867 AATATATATATTAATATAAAATATAGTTAATAAATT
1 AATATATA-ATTAATATAAAATATAGTTAATAAATA
36903 AATATATAAT
1 AATATATAAT
36913 AAACTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 14 0.34
36 14 0.34
37 3 0.07
38 10 0.24
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (35 bp):
AATATATAATTAATATAAAATATAGTTAATAAATA
Found at i:36906 original size:24 final size:23
Alignment explanation
Indices: 36876--36973 Score: 99
Period size: 24 Copynumber: 4.1 Consensus size: 23
36866 AAATATATAT
36876 ATTAATATAAAATATAGTTAATAA
1 ATTAATAT-AAATATAGTTAATAA
* * *
36900 ATTAATATATAATAAACTATATATAT
1 ATTAATATA-AATATAGT-TA-ATAA
*
36926 ATTAATATAAATAGTAGTTTATAA
1 ATTAATATAAATA-TAGTTAATAA
*
36950 ATT-ATATATATATAGTTAATAA
1 ATTAATATAAATATAGTTAATAA
36972 AT
1 AT
36974 ATAAACTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
22 11 0.18
23 9 0.15
24 20 0.33
25 7 0.11
26 14 0.23
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (23 bp):
ATTAATATAAATATAGTTAATAA
Found at i:36926 original size:35 final size:34
Alignment explanation
Indices: 36823--36996 Score: 95
Period size: 36 Copynumber: 4.8 Consensus size: 34
36813 ATATTATATA
*
36823 AATATATTAATAT-TAATTAATATAATATAGTATAGTT
1 AATAAATTAATATATAA-TAA-AT-ATATA-TATAGTT
* * * *
36860 TATAAA-AAATATATATATTAATATAAAATATAGTT
1 AATAAATTAATATATA-ATAAATAT-ATATATAGTT
36895 AATAAATTAATATATAATAAACTATATATATA-TT
1 AATAAATTAATATATAATAAA-TATATATATAGTT
* * *
36929 AATATAAATAGTAGTTTATAA-ATTATATATATATAGTT
1 -A-ATAAAT--TAATATATAATA-AATATATATATAGTT
* *
36967 AATAAATATAAACTATATAGTAATTATATA
1 AATAAAT-T-AA-TATATAATAAATATATA
36997 AACTATAGTT
Statistics
Matches: 105, Mismatches: 18, Indels: 28
0.70 0.12 0.19
Matches are distributed among these distances:
34 2 0.02
35 26 0.25
36 33 0.31
37 31 0.30
38 13 0.12
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (34 bp):
AATAAATTAATATATAATAAATATATATATAGTT
Found at i:36931 original size:34 final size:33
Alignment explanation
Indices: 36753--36932 Score: 97
Period size: 36 Copynumber: 5.3 Consensus size: 33
36743 CCTATAAATT
* *
36753 TATATTAATAAACTAATAATATATTAAA-AT-TA
1 TATATTAATAAATTAAT-ATATAATAAATATATA
* *
36785 -ATATT-ATAAAATATTATA-AAT-AATATTAATA
1 TATATTAATAAATTAATATATAATAAATA-T-ATA
* *
36816 TTATATAAATATATTAATAT-TAATTAATATAATATA
1 -TATATTAATAAATTAATATATAA-TAA-AT-ATATA
* * * *
36852 GTATAGTTTATAAA-AAATATATATATTAATATAAAA
1 -TATA-TTAATAAATTAATATATA-ATAAATAT-ATA
36888 TATAGTTAATAAATTAATATATAATAAACTATATA
1 TATA-TTAATAAATTAATATATAATAAA-TATATA
36923 TATATTAATA
1 TATATTAATA
36933 TAAATAGTAG
Statistics
Matches: 112, Mismatches: 18, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
27 2 0.02
28 3 0.03
29 4 0.04
30 8 0.07
31 7 0.06
33 4 0.04
34 17 0.15
35 25 0.22
36 28 0.25
37 12 0.11
38 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (33 bp):
TATATTAATAAATTAATATATAATAAATATATA
Found at i:36955 original size:21 final size:19
Alignment explanation
Indices: 36820--36983 Score: 68
Period size: 15 Copynumber: 8.8 Consensus size: 19
36810 TTAATATTAT
*
36820 ATAAATATATTAATATTAATTA
1 ATAAATATA--AATA-TAGTTA
* *
36842 ATATAATAT-AGTATAGTTT
1 ATA-AATATAAATATAGTTA
* *
36861 ATAAAAAATATATATA-TTA
1 AT-AAATATAAATATAGTTA
36880 AT--ATA-AAATATAGTTA
1 ATAAATATAAATATAGTTA
36896 ATAAAT-T-AATATA--TA
1 ATAAATATAAATATAGTTA
36911 ATAAACTAT--ATATA--T-
1 ATAAA-TATAAATATAGTTA
* *
36926 ATTAATATAAATAGTAGTTT
1 ATAAATATAAATA-TAGTTA
36946 ATAAATTATATATATATAGTTA
1 ATAAA-TATA-A-ATATAGTTA
36968 ATAAATATAAACTATA
1 ATAAATATAAA-TATA
36984 TAGTAATTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 40
0.68 0.07 0.25
Matches are distributed among these distances:
14 3 0.03
15 17 0.15
16 17 0.15
17 9 0.08
18 2 0.02
19 16 0.14
20 17 0.15
21 8 0.07
22 14 0.13
23 8 0.07
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (19 bp):
ATAAATATAAATATAGTTA
Found at i:36976 original size:50 final size:47
Alignment explanation
Indices: 36860--36976 Score: 128
Period size: 50 Copynumber: 2.4 Consensus size: 47
36850 TAGTATAGTT
* *
36860 TATAAAAAATATATATATTAATATAAAATATAGTTAATAAATTAATA
1 TATAATAAATAAATATATTAATATAAAATATAGTTAATAAATTAATA
*
36907 TATAATAAACTATATATATATTAATAT-AAATAGTAGTTTATAAATTATATA
1 TATAATAAA-TA-A-ATATATTAATATAAAATA-TAGTTAATAAATTA-ATA
*
36958 TATATAGTTAATAAATATA
1 TATA-A-TAAATAAATATA
36977 AACTATATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
47 8 0.14
48 2 0.03
49 5 0.08
50 30 0.51
51 8 0.14
52 3 0.05
53 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (47 bp):
TATAATAAATAAATATATTAATATAAAATATAGTTAATAAATTAATA
Found at i:36995 original size:20 final size:22
Alignment explanation
Indices: 36901--37003 Score: 76
Period size: 21 Copynumber: 4.9 Consensus size: 22
36891 AGTTAATAAA
*
36901 TTAATATATAATAAACTATATA-
1 TTAATAAAT-ATAAACTATATAG
* *
36923 -TATATTAATATAAA-TA-GTAG
1 TTA-ATAAATATAAACTATATAG
* *
36943 TTTATAAATTATATA-TATATAG
1 TTAATAAA-TATAAACTATATAG
36965 TTAATAAATATAAACTATATAG
1 TTAATAAATATAAACTATATAG
*
36987 -TAAT-TATATAAACTATA
1 TTAATAAATATAAACTATA
37004 GTTTATAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.03
20 18 0.28
21 24 0.37
22 21 0.32
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (22 bp):
TTAATAAATATAAACTATATAG
Found at i:37006 original size:62 final size:64
Alignment explanation
Indices: 36901--37080 Score: 179
Period size: 62 Copynumber: 3.0 Consensus size: 64
36891 AGTTAATAAA
* * *
36901 TTAATATATAATAAACTATATATATATTAATATAAATAGTAGTTTATAAATTATATATATATAG
1 TTAATAAATAATAAACTATATATATATTAATATAAATAGTAGTTTATAAACTATATACATATAG
36965 TTAATAAAT-ATAAACTATATAGTA-ATT-ATATAAACTA-TAGTTTATAAACTATATACATATA
1 TTAATAAATAATAAACTATATA-TATATTAATATAAA-TAGTAGTTTATAAACTATATACATATA
37026 -
64 G
* * * * *
37026 -T-A-AAGT-ATAAACTATATA-ACACTAATAT-AATA-TTG-TTATAAACTATCTACATATA
1 TTAATAAATAATAAACTATATATATATTAATATAAATAGTAGTTTATAAACTATATACATATA
37081 TAGTTATATA
Statistics
Matches: 105, Mismatches: 7, Indels: 17
0.81 0.05 0.13
Matches are distributed among these distances:
55 19 0.18
56 5 0.05
57 4 0.04
58 19 0.18
59 1 0.01
60 1 0.01
62 29 0.28
63 17 0.16
64 10 0.10
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (64 bp):
TTAATAAATAATAAACTATATATATATTAATATAAATAGTAGTTTATAAACTATATACATATAG
Found at i:37034 original size:24 final size:27
Alignment explanation
Indices: 37006--37082 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 27
36996 AAACTATAGT
37006 TTATAAACTATATACATATATAA-A-G
1 TTATAAACTATATACATATATAATATG
37031 -TATAAACTATATAACACTAATATAATATTG
1 TTATAAACTATAT-ACA-T-ATATAATA-TG
*
37061 TTATAAACTATCTACATATATA
1 TTATAAACTATATACATATATA
37083 GTTATATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
24 12 0.27
25 3 0.07
26 1 0.02
27 6 0.14
28 6 0.14
29 1 0.02
30 4 0.09
31 11 0.25
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (27 bp):
TTATAAACTATATACATATATAATATG
Found at i:37111 original size:21 final size:20
Alignment explanation
Indices: 37085--37127 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
37075 CATATATAGT
37085 TATATAAAATATATAGTTGTA
1 TATATAAAATATATAGTT-TA
**
37106 TATATACTATATATAGTTTA
1 TATATAAAATATATAGTTTA
37126 TA
1 TA
37128 CATACATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
TATATAAAATATATAGTTTA
Found at i:37158 original size:35 final size:36
Alignment explanation
Indices: 37114--37191 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
37104 TATATATACT
37114 ATATATAGTTTATACATACATG-TACTATAAGTTAC
1 ATATATAGTTTATACATACATGATACTATAAGTTAC
** * *
37149 ATATATAGTTTATATGTATATGTATACTATAGGTTAC
1 ATATATAGTTTATACATACATG-ATACTATAAGTTAC
37186 ATATAT
1 ATATAT
37192 TAACTATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 19 0.51
37 18 0.49
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (36 bp):
ATATATAGTTTATACATACATGATACTATAAGTTAC
Found at i:37225 original size:7 final size:7
Alignment explanation
Indices: 37213--37244 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
37203 TATGCATAGT
37213 GTTTAGG
1 GTTTAGG
37220 GTTTAGG
1 GTTTAGG
37227 GTTTAGG
1 GTTTAGG
37234 GTTTAGG
1 GTTTAGG
37241 GTTT
1 GTTT
37245 TTATAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:37417 original size:8 final size:8
Alignment explanation
Indices: 37403--37437 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
37393 TAGTTTATAC
37403 ATATATGT
1 ATATATGT
*
37411 GTATATGT
1 ATATATGT
37419 ATATATGT
1 ATATATGT
*
37427 ATATATAT
1 ATATATGT
37435 ATA
1 ATA
37438 CTATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (8 bp):
ATATATGT
Found at i:37421 original size:14 final size:14
Alignment explanation
Indices: 37398--37437 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
37388 TTATATAGTT
* *
37398 TATACATATATGTG
1 TATATATATATATG
*
37412 TATATGTATATATG
1 TATATATATATATG
37426 TATATATATATA
1 TATATATATATA
37438 CTATATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (14 bp):
TATATATATATATG
Found at i:37499 original size:15 final size:14
Alignment explanation
Indices: 37479--37602 Score: 58
Period size: 13 Copynumber: 8.1 Consensus size: 14
37469 ATATACTTTT
37479 TATAGTTTATACATA
1 TATAGTTTATA-ATA
*
37494 TATAGTTTAT-CTA
1 TATAGTTTATAATA
*
37507 TGTAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
37522 CATAATTTATATATATA
1 TAT-AGTT-TATA-ATA
37539 TATAGCTTATAATAATTA
1 TATAG-TT-T-ATAA-TA
37557 TATAGTTTATAATATAAA
1 TATAGTTTAT-A-AT--A
37575 TATAGTTTAT-ATA
1 TATAGTTTATAATA
37588 TATAGTTTAT-ATA
1 TATAGTTTATAATA
37601 TA
1 TA
37603 AACTTATATT
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
13 24 0.27
15 24 0.27
16 8 0.09
17 11 0.12
18 21 0.24
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:37512 original size:13 final size:15
Alignment explanation
Indices: 37479--37598 Score: 54
Period size: 15 Copynumber: 7.7 Consensus size: 15
37469 ATATACTTTT
37479 TATAGTTTATACATA
1 TATAGTTTATACATA
37494 TATAGTTTAT-C-TA
1 TATAGTTTATACATA
* * *
37507 TGTAGTTCATATAAACA
1 TATAGTT--TATACATA
* *
37524 TA-ATTTATATATATA
1 TATAGTT-TATACATA
37539 TATAGCTTATAATA-ATTA
1 TATAG-TT-T-ATACA-TA
*
37557 TATAGTTTATAATATAAA
1 TATAGTTTAT-ACAT--A
37575 TATAGTTTAT--ATA
1 TATAGTTTATACATA
37588 TATAGTTTATA
1 TATAGTTTATA
37599 TATAAACTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 27
0.71 0.07 0.23
Matches are distributed among these distances:
13 19 0.23
14 1 0.01
15 26 0.31
16 7 0.08
17 10 0.12
18 21 0.25
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:37538 original size:88 final size:88
Alignment explanation
Indices: 37351--37527 Score: 227
Period size: 88 Copynumber: 2.0 Consensus size: 88
37341 ATATATATAC
*
37351 TATATTAATATAATTTATAATTTATAAACTATATATTTTATATAGTTTATACATATATGTGTATA
1 TATATTAATATAAATTATAATTTATAAACTATATATTTTATATAGTTTATACATATATGTGTATA
* * * *
37416 TGTATATATGTATATATATATAC
66 TCTATATATGTATATAAACATAA
*
37439 TATATTAATATAAATTATATTTTATAAACTATATACTTTT-TATAGTTTATACATATATAGT-T-
1 TATATTAATATAAATTATAATTTATAAACTATATA-TTTTATATAGTTTATACATATAT-GTGTA
*
37501 TATCTATGTA-GTTCATATAAACATAA
64 TATCTATATATG-T-ATATAAACATAA
37527 T
1 T
37528 TTATATATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
86 1 0.01
87 9 0.12
88 62 0.79
89 6 0.08
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (88 bp):
TATATTAATATAAATTATAATTTATAAACTATATATTTTATATAGTTTATACATATATGTGTATA
TCTATATATGTATATAAACATAA
Found at i:37577 original size:18 final size:18
Alignment explanation
Indices: 37515--37591 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
37505 TATGTAGTTC
* *
37515 ATATAAACATAATTTAT-
1 ATATAAATATAGTTTATA
* *
37532 ATATATATATAGCTTATA
1 ATATAAATATAGTTTATA
*
37550 ATA-ATTATATAGTTTATA
1 ATATA-AATATAGTTTATA
37568 ATATAAATATAGTTTATA
1 ATATAAATATAGTTTATA
37586 TATATA
1 -ATATA
37592 GTTTATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
17 14 0.28
18 30 0.60
19 6 0.12
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (18 bp):
ATATAAATATAGTTTATA
Found at i:37599 original size:13 final size:13
Alignment explanation
Indices: 37569--37602 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
37559 TAGTTTATAA
*
37569 TATAAATATAGTT
1 TATATATATAGTT
37582 TATATATATAGTT
1 TATATATATAGTT
37595 TATATATA
1 TATATATA
37603 AACTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:37710 original size:27 final size:27
Alignment explanation
Indices: 37680--37736 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
37670 ATATACTTTA
*
37680 TATTTAAACTATATA-AATTATATAATT
1 TATTCAAACTATATATAATT-TATAATT
* * *
37707 TATTCATAGTATATATAATTTATATTT
1 TATTCAAACTATATATAATTTATAATT
37734 TAT
1 TAT
37737 ATATAGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTCAAACTATATATAATTTATAATT
Found at i:37737 original size:18 final size:18
Alignment explanation
Indices: 37716--37750 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37706 TTATTCATAG
37716 TATATATAATTTATATTT
1 TATATATAATTTATATTT
*
37734 TATATATAGTTTATATT
1 TATATATAATTTATATT
37751 AATAAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATATAATTTATATTT
Found at i:37742 original size:27 final size:28
Alignment explanation
Indices: 37689--37782 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 28
37679 ATATTTAAAC
37689 TATATA-AATTATATAATTTATTCATAG
1 TATATATAATTATATAATTTATTCATAG
*
37716 TATATATAATT-TATATTTTATAT-ATAG
1 TATATATAATTATATAATTTAT-TCATAG
** *
37743 TTTATATTAATAAACAATATAATTTATACATAG
1 --TATA-T-AT-AATTATATAATTTATTCATAG
37776 TATATAT
1 TATATAT
37783 TTAAATATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
27 19 0.36
28 5 0.09
29 6 0.11
30 2 0.04
31 6 0.11
32 2 0.04
33 13 0.25
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
TATATATAATTATATAATTTATTCATAG
Found at i:37842 original size:22 final size:20
Alignment explanation
Indices: 37689--37960 Score: 123
Period size: 20 Copynumber: 13.3 Consensus size: 20
37679 ATATTTAAAC
*
37689 TATATAAATTATATAATTTA
1 TATATAAACTATATAATTTA
*
37709 T-TCATAGTA-TATATAATTTA
1 TAT-ATA-AACTATATAATTTA
** *
37729 TAT-TTTA-TATATAGTTTA
1 TATATAAACTATATAATTTA
*
37747 TATTAATAAACAATATAATTTA
1 TA-T-ATAAACTATATAATTTA
* *
37769 TACAT--AGTATAT-ATTTA
1 TATATAAACTATATAATTTA
* **
37786 AATATGATTCATATATAATTTA
1 TATAT-AAAC-TATATAATTTA
*
37808 TATATTAACTATATAATTTA
1 TATATAAACTATATAATTTA
* *
37828 TATCAATAAATTATATAGTTTA
1 TAT--ATAAACTATATAATTTA
* **
37850 TATATAGTA-TATAATAATAAA
1 TATATA-AACTAT-ATAATTTA
* *
37871 AATATAAACTATATAGTTTA
1 TATATAAACTATATAATTTA
*
37891 TATTAATAAACTATATAGTTTA
1 TA-T-ATAAACTATATAATTTA
* *
37913 TACATAATA-TATATAGTTTA
1 TATATAA-ACTATATAATTTA
*
37933 TATATATA-TATATATATGTGTA
1 TATATAAACTATATA-AT-T-TA
37955 TATATA
1 TATATA
37961 TATTATAATT
Statistics
Matches: 194, Mismatches: 35, Indels: 44
0.71 0.13 0.16
Matches are distributed among these distances:
17 8 0.04
18 19 0.10
19 10 0.05
20 66 0.34
21 27 0.14
22 64 0.33
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (20 bp):
TATATAAACTATATAATTTA
Found at i:37843 original size:63 final size:62
Alignment explanation
Indices: 37689--37946 Score: 205
Period size: 63 Copynumber: 4.2 Consensus size: 62
37679 ATATTTAAAC
* * * * *
37689 TATATAAATTATATAATTTAT-TC-ATAGTA-TATATAATTTATAT-T-TTATATATAGTTTA
1 TATATAAACTATATAATTTATATCAATA-AACTATATAGTTTATATATAATATATATAATTTA
* * * *
37747 TATTAATAAACAATATAATTTATA-C-AT--AGTATATA-TTTAAATATGATTCATATATAATTT
1 TA-T-ATAAACTATATAATTTATATCAATAAACTATATAGTTTATATAT-AAT-ATATATAATTT
37807 A
62 A
* * * **
37808 TATATTAACTATATAATTTATATCAATAAATTATATAGTTTATATATAGTATATAATAATAAA
1 TATATAAACTATATAATTTATATCAATAAACTATATAGTTTATATATAATATAT-ATAATTTA
* * * * *
37871 AATATAAACTATATAGTTTATATTAATAAACTATATAGTTTATACATAATATATATAGTTTA
1 TATATAAACTATATAATTTATATCAATAAACTATATAGTTTATATATAATATATATAATTTA
*
37933 TATATATA-TATATA
1 TATATAAACTATATA
37947 TATGTGTATA
Statistics
Matches: 163, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
57 7 0.04
58 9 0.06
59 18 0.11
60 23 0.14
61 21 0.13
62 15 0.09
63 62 0.38
64 8 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (62 bp):
TATATAAACTATATAATTTATATCAATAAACTATATAGTTTATATATAATATATATAATTTA
Found at i:37844 original size:33 final size:32
Alignment explanation
Indices: 37796--37907 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 32
37786 AATATGATTC
* *
37796 ATAT-ATAATTTATATATTAACTATATAATTT
1 ATATAATAAATTATATATTAACTATATAGTTT
* *
37827 ATATCAATAAATTATATAGTTTA-TATATAGTAT
1 ATAT-AATAAATTATATA-TTAACTATATAGTTT
*
37860 ATAATAATAAA--A-ATATAAACTATATAGTTT
1 AT-ATAATAAATTATATATTAACTATATAGTTT
*
37890 ATATTAATAAACTATATA
1 ATA-TAATAAATTATATA
37908 GTTTATACAT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
29 3 0.05
30 21 0.32
31 5 0.08
32 1 0.02
33 30 0.46
34 5 0.08
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (32 bp):
ATATAATAAATTATATATTAACTATATAGTTT
Found at i:37924 original size:2 final size:2
Alignment explanation
Indices: 37919--37967 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
37909 TTTATACATA
* * *
37919 AT AT AT AT AGT TT AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37962 AT -T AT A
1 AT AT AT A
37968 ATTGTTTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39327 original size:21 final size:25
Alignment explanation
Indices: 39278--39373 Score: 78
Period size: 25 Copynumber: 3.8 Consensus size: 25
39268 TTAAAGTTAT
*
39278 AATATTTTA-TA-TAAATTAATGTAA
1 AATATTTTATTATTAATTTAAT-TAA
39302 GAA-ATATTTA-TATTAATTT-ATTAA
1 -AATAT-TTTATTATTAATTTAATTAA
39326 ATATATTTTATTATTAATTTAATTAAAA
1 A-ATATTTTATTATTAATTTAATT--AA
*
39354 AATATTTTCTT-TTAATTTAA
1 AATATTTTATTATTAATTTAA
39374 AAATATATGT
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
23 1 0.02
24 10 0.16
25 21 0.34
26 17 0.28
27 9 0.15
28 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATTTTATTATTAATTTAATTAA
Found at i:39359 original size:22 final size:21
Alignment explanation
Indices: 39334--39379 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
39324 AAATATATTT
39334 TATTATTAATTTAATTAAAAAA
1 TATT-TTAATTTAATTAAAAAA
** *
39356 TATTTTCTTTTAATTTAAAAA
1 TATTTTAATTTAATTAAAAAA
39377 TAT
1 TAT
39380 ATGTTATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTTTAATTTAATTAAAAAA
Found at i:39368 original size:26 final size:26
Alignment explanation
Indices: 39278--39373 Score: 96
Period size: 26 Copynumber: 3.8 Consensus size: 26
39268 TTAAAGTTAT
*
39278 AATATTTTA-TA-TAAATTAATGTAAGA
1 AATATTTTATTATTAATTTAAT-TAA-A
39304 AATA-TTTA-TATTAATTT-ATTAAA
1 AATATTTTATTATTAATTTAATTAAA
*
39327 TATATTTTATTATTAATTTAATTAAAA
1 AATATTTTATTATTAATTTAATT-AAA
*
39354 AATATTTTCTT-TTAATTTAA
1 AATATTTTATTATTAATTTAA
39374 AAATATATGT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
23 4 0.07
24 7 0.11
25 17 0.28
26 21 0.34
27 12 0.20
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATTTTATTATTAATTTAATTAAA
Found at i:39378 original size:50 final size:50
Alignment explanation
Indices: 39279--39386 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
39269 TAAAGTTATA
* *
39279 ATATTTTA-TATAAATTAATGTAAGAAATATTTATATTAATTTATTAAAT
1 ATATTTTATTATAAATTAATGTAAAAAATATTTATATTAATTTATAAAAT
* * *
39328 ATATTTTATTATTAATTTAAT-TAAAAAATATTTTCTTTTAATTTA-AAAAT
1 ATATTTTATTA-TAAATTAATGTAAAAAATA-TTTATATTAATTTATAAAAT
*
39378 ATATGTTAT
1 ATATTTTAT
39387 CTTTATCTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 8 0.16
50 22 0.44
51 20 0.40
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (50 bp):
ATATTTTATTATAAATTAATGTAAAAAATATTTATATTAATTTATAAAAT
Found at i:39436 original size:31 final size:31
Alignment explanation
Indices: 39369--39453 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
39359 TTTCTTTTAA
*
39369 TTTAAAAATATATGTTATCTTTATCTAACCT
1 TTTAAAAATATATGTTATCTTTATCTAACAT
* *
39400 ATTAAAAATATATGTTAT-TATTATTTTAA-AT
1 TTTAAAAATATATGTTATCT-TTA-TCTAACAT
*
39431 TTTAAAAGTATATATTTTATCTT
1 TTTAAAA--ATATATGTTATCTT
39454 AATTTACTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.02
31 27 0.61
32 4 0.09
33 11 0.25
34 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (31 bp):
TTTAAAAATATATGTTATCTTTATCTAACAT
Found at i:39579 original size:24 final size:23
Alignment explanation
Indices: 39531--39597 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
39521 ATTTTAACAT
39531 AAAATATATATTTTTAAATTTAA
1 AAAATATATATTTTTAAATTTAA
39554 AAAATATATATTTTTAAATTTAA
1 AAAATATATATTTTTAAATTTAA
*
39577 AAAATAAAATATTTTTAAATT
1 AAAAT-ATATATTTTTAAATT
39598 AAGTTAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 28 0.67
24 14 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATATATATTTTTAAATTTAA
Found at i:39593 original size:77 final size:77
Alignment explanation
Indices: 39512--39666 Score: 172
Period size: 77 Copynumber: 2.0 Consensus size: 77
39502 CTTATCTTAA
** * ** * *
39512 TTTTAAAATATTTTAA-CATAAAATATATATTTTTAAATTTAA-A-AAATATATATTTTTAAATT
1 TTTTAAAATAAGTTAATAATAAAATATAT-TTAATAAA-TTAATATAAAAATAT-TTTTTAAAGT
39574 TAAAAAATAAAATAT
63 TAAAAAATAAAATAT
*
39589 TTTTAAATTAAGTTAATAATAAAATATATTTAATAAATTAATATAAAAATATTTTTTAAAGTTAA
1 TTTTAAAATAAGTTAATAATAAAATATATTTAATAAATTAATATAAAAATATTTTTTAAAGTTAA
* *
39654 TATATAAAATAT
66 AAAATAAAATAT
39666 T
1 T
39667 ATGAATTCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
76 4 0.06
77 43 0.66
78 18 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (77 bp):
TTTTAAAATAAGTTAATAATAAAATATATTTAATAAATTAATATAAAAATATTTTTTAAAGTTAA
AAAATAAAATAT
Found at i:39606 original size:24 final size:24
Alignment explanation
Indices: 39538--39666 Score: 104
Period size: 23 Copynumber: 5.2 Consensus size: 24
39528 CATAAAATAT
*
39538 ATATTTTTAAATTTAAAAAAT-AT
1 ATATTTTTAAATTTAAAAAATAAA
39561 ATATTTTTAAATTTAAAAAATAAA
1 ATATTTTTAAATTTAAAAAATAAA
39585 ATATTTTTAAA-TTAAGTTAATAATAAA
1 ATATTTTTAAATTTAA---AA-AATAAA
* *
39612 ATATATTTAATAAA-TTAATATA-AAA
1 ATAT-TTT--TAAATTTAAAAAATAAA
* * *
39637 ATATTTTTTAAAGTTAATATATAAA
1 ATA-TTTTTAAATTTAAAAAATAAA
39662 ATATT
1 ATATT
39667 ATGAATTCAA
Statistics
Matches: 92, Mismatches: 3, Indels: 21
0.79 0.03 0.18
Matches are distributed among these distances:
23 29 0.32
24 22 0.24
25 15 0.16
26 4 0.04
27 11 0.12
28 3 0.03
30 8 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATATTTTTAAATTTAAAAAATAAA
Found at i:39616 original size:53 final size:50
Alignment explanation
Indices: 39559--39665 Score: 119
Period size: 53 Copynumber: 2.1 Consensus size: 50
39549 TTTAAAAAAT
* *
39559 ATATATTT-TTAAATTTAAAAAATAAAATATTTTTAAATTAAGTTAATA-ATAAA
1 ATATATTTAATAAA-TTAAAAAA-AAAATATTTTT---TAAAGTTAATATATAAA
* *
39612 ATATATTTAATAAATTAATATAAAAATATTTTTTAAAGTTAATATATAAA
1 ATATATTTAATAAATTAAAAAAAAAATATTTTTTAAAGTTAATATATAAA
39662 ATAT
1 ATAT
39666 TATGAATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
49 10 0.21
50 9 0.19
52 11 0.23
53 14 0.29
54 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (50 bp):
ATATATTTAATAAATTAAAAAAAAAATATTTTTTAAAGTTAATATATAAA
Found at i:39620 original size:27 final size:26
Alignment explanation
Indices: 39579--39665 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 26
39569 AAATTTAAAA
*
39579 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AATTAAGTTAAT
*
39606 AATAAAATATATTTAA-TAAATTAAT
1 AATAAAATATATTTAATTAAGTTAAT
*
39631 -ATAAAA-ATATTT-TTTAAAGTTAAT
1 AATAAAATATATTTAATT-AAGTTAAT
39655 ATATAAAATAT
1 A-ATAAAATAT
39666 TATGAATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
23 7 0.14
24 13 0.25
25 8 0.16
26 8 0.16
27 15 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATAAAATATATTTAATTAAGTTAAT
Found at i:39637 original size:25 final size:25
Alignment explanation
Indices: 39580--39666 Score: 90
Period size: 25 Copynumber: 3.4 Consensus size: 25
39570 AATTTAAAAA
*
39580 ATAAAATATTTTTAAATTAAGTTAATA-
1 ATAAAATA-TTTT-AA-TAAATTAATAT
39607 ATAAAATATATTTAATAAATTAATAT
1 ATAAAATAT-TTTAATAAATTAATAT
*
39633 A-AAAATATTTT-TTAAAGTTAATAT
1 ATAAAATATTTTAATAAA-TTAATAT
39657 ATAAAATATT
1 ATAAAATATT
39667 ATGAATTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.07
24 11 0.20
25 24 0.44
26 4 0.07
27 11 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAAAATATTTTAATAAATTAATAT
Found at i:39679 original size:77 final size:78
Alignment explanation
Indices: 39529--39681 Score: 179
Period size: 77 Copynumber: 2.0 Consensus size: 78
39519 ATATTTTAAC
** * * *
39529 ATAAAATATATATTTTTAAATTTAAAAAATATATATTTTTAAATTTAAAAAATAAAATATTTTTA
1 ATAAAATATATATTAATAAATTTAAAAAAAATATATTTTTAAAGTTAAAAAATAAAATATTTATA
39594 AATTAAGTTAATA
66 AATTAAGTTAATA
* *
39607 ATAAAATATAT-TTAATAAA-TTAATATAAAAATAT-TTTTTAAAGTTAATATATAAAATA-TTA
1 ATAAAATATATATTAATAAATTTAA-A-AAAAATATATTTTTAAAGTTAAAAAATAAAATATTTA
*
39668 TGAATTCAAGTTAA
64 TAAATT-AAGTTAA
39682 ATTTATACAG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
76 11 0.17
77 35 0.55
78 18 0.28
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (78 bp):
ATAAAATATATATTAATAAATTTAAAAAAAATATATTTTTAAAGTTAAAAAATAAAATATTTATA
AATTAAGTTAATA
Found at i:46916 original size:2 final size:2
Alignment explanation
Indices: 46909--46937 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46899 ACATACATAC
46909 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
46938 CACACACACA
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:52578 original size:18 final size:18
Alignment explanation
Indices: 52555--52609 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
52545 GGGTTCGATT
52555 GGGTCGGACATGCAGGTC
1 GGGTCGGACATGCAGGTC
52573 GGGTCGGACATGCAGGTC
1 GGGTCGGACATGCAGGTC
*
52591 GGGTCAGG-CATGCAAGTC
1 GGGTC-GGACATGCAGGTC
52609 G
1 G
52610 AATCTGGTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 33 0.94
19 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (18 bp):
GGGTCGGACATGCAGGTC
Found at i:53146 original size:30 final size:30
Alignment explanation
Indices: 53112--53174 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
53102 ATTTAGATTT
* * *
53112 AAATTTAATCAAAATTTTATTTTGGTCCTC
1 AAATTTAATCAAAATTTCAATTTAGTCCTC
* *
53142 AAATTTAGTTAAAATTTCAATTTAGTCCTC
1 AAATTTAATCAAAATTTCAATTTAGTCCTC
53172 AAA
1 AAA
53175 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (30 bp):
AAATTTAATCAAAATTTCAATTTAGTCCTC
Found at i:56758 original size:2 final size:2
Alignment explanation
Indices: 56751--56787 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56741 CCGTCCCGAT
56751 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 T
56788 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56815 original size:33 final size:33
Alignment explanation
Indices: 56773--56877 Score: 185
Period size: 33 Copynumber: 3.2 Consensus size: 33
56763 TATATATATA
56773 TATATATATATATATTTTAT-TTTTTATATTAAT
1 TATATATATA-ATATTTTATATTTTTATATTAAT
*
56806 TATATATATACTATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
56839 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
56872 TATATA
1 TATATA
56878 ATACAAATCT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.12
33 61 0.88
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:56829 original size:7 final size:7
Alignment explanation
Indices: 56783--56868 Score: 59
Period size: 7 Copynumber: 11.9 Consensus size: 7
56773 TATATATATA
56783 TATATTT
1 TATATTT
*
56790 TATTTTT
1 TATATTT
56797 TATATTAAT
1 TATATT--T
*
56806 TATATATA
1 TATAT-TT
56814 TACTATTT
1 TA-TATTT
56822 TATATTT
1 TATATTT
*
56829 T-TATAT
1 TATATTT
*
56835 TA-ATTA
1 TATATTT
*
56841 TATATAT
1 TATATTT
*
56848 AATATTT
1 TATATTT
56855 TATATTTT
1 TATA-TTT
56863 TATATT
1 TATATT
56869 AATTATATAA
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
6 9 0.15
7 29 0.48
8 12 0.20
9 9 0.15
10 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (7 bp):
TATATTT
Found at i:61419 original size:8 final size:8
Alignment explanation
Indices: 61406--61430 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61396 TTGATCCCTC
61406 TTAAAATT
1 TTAAAATT
61414 TTAAAATT
1 TTAAAATT
61422 TTAAAATT
1 TTAAAATT
61430 T
1 T
61431 ATGCCCGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAAAATT
Found at i:69472 original size:35 final size:35
Alignment explanation
Indices: 69426--69496 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
69416 TCACATGTTA
69426 ACTTTGACTCAAATCATTGAATTTGAGTAAAGTTG
1 ACTTTGACTCAAATCATTGAATTTGAGTAAAGTTG
*
69461 ACTTTGACTCAAATCATTGAATTTTAGTAAAGTTG
1 ACTTTGACTCAAATCATTGAATTTGAGTAAAGTTG
69496 A
1 A
69497 ATTTCACGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (35 bp):
ACTTTGACTCAAATCATTGAATTTGAGTAAAGTTG
Found at i:76579 original size:16 final size:16
Alignment explanation
Indices: 76553--76594 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
76543 AGAAAGAAGT
76553 AAAGAAAAGTATGGGTG
1 AAAG-AAAGTATGGGTG
76570 AAAGAAAGTATGGGTG
1 AAAGAAAGTATGGGTG
76586 AAAGAAAGT
1 AAAGAAAGT
76595 CAGAAGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (16 bp):
AAAGAAAGTATGGGTG
Found at i:79871 original size:14 final size:14
Alignment explanation
Indices: 79852--79912 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
79842 TTGTTATATT
79852 TTATATTAATATAA
1 TTATATTAATATAA
* *
79866 TTATATAAATATTA
1 TTATATTAATATAA
* * *
79880 TTATTTTTATTAAAA
1 TTA-TATTAATATAA
* *
79895 TAATATTTATATAA
1 TTATATTAATATAA
79909 TTAT
1 TTAT
79913 TATTTATTTA
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
14 25 0.76
15 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:79889 original size:20 final size:20
Alignment explanation
Indices: 79866--79921 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 20
79856 ATTAATATAA
79866 TTATATAAATATTATTATTT
1 TTATATAAATATTATTATTT
*
79886 TTAT-TAAA-A-TA--ATAT
1 TTATATAAATATTATTATTT
*
79901 TTATATAATTATTATTTATTT
1 TTATATAAATATTA-TTATTT
79922 AAATTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 11
0.66 0.07 0.27
Matches are distributed among these distances:
15 7 0.26
16 3 0.11
17 3 0.11
18 3 0.11
19 4 0.15
20 4 0.15
21 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATAAATATTATTATTT
Found at i:79892 original size:32 final size:33
Alignment explanation
Indices: 79848--79924 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
79838 ATAGTTGTTA
*
79848 TATTTTATATTAATATAATTATATAAAT-ATTAT
1 TATTTTATATTAAAATAA-TATATAAATAATTAT
* *
79881 TATTTT-TATTAAAATAATATTTATATAATTAT
1 TATTTTATATTAAAATAATATATAAATAATTAT
79913 TA-TTTAT-TTAAA
1 TATTTTATATTAAA
79925 TTTATTACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 15 0.38
32 18 0.46
33 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATTTTATATTAAAATAATATATAAATAATTAT
Found at i:79912 original size:23 final size:24
Alignment explanation
Indices: 79854--79915 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 24
79844 GTTATATTTT
*
79854 ATATTAATATAATTA-TATAAATA
1 ATATTTATATAATTATTATAAATA
* *
79877 TTA-TTAT-T-TTTATTA-AAATA
1 ATATTTATATAATTATTATAAATA
79897 ATATTTATATAATTATTAT
1 ATATTTATATAATTATTAT
79916 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 9
0.67 0.12 0.21
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 4 0.14
23 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTATATAATTATTATAAATA
Found at i:81751 original size:42 final size:42
Alignment explanation
Indices: 81651--81742 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
81641 GATGCAATAG
* * * *
81651 GGGTACATGCCCAGCCCTCTAATTCATATGACATCTCCTCAA
1 GGGTACATGTCAAGCCCACCAATTCATATGACATCTCCTCAA
* * *
81693 GGGTATATGTCAAGCCCACCAATTCATATGCCATCTCCTCAT
1 GGGTACATGTCAAGCCCACCAATTCATATGACATCTCCTCAA
*
81735 GGTTACAT
1 GGGTACAT
81743 TCCTAGCCCT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.28
Consensus pattern (42 bp):
GGGTACATGTCAAGCCCACCAATTCATATGACATCTCCTCAA
Found at i:82392 original size:19 final size:19
Alignment explanation
Indices: 82356--82393 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
82346 TATTCCAATT
*
82356 GAAATTTAAAATTGTATTC
1 GAAATTTAAAATTATATTC
82375 GAAA-TTAAAAGTTATATTC
1 GAAATTTAAAA-TTATATTC
82394 CAAGTATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (19 bp):
GAAATTTAAAATTATATTC
Found at i:83335 original size:277 final size:274
Alignment explanation
Indices: 82759--83490 Score: 821
Period size: 277 Copynumber: 2.6 Consensus size: 274
82749 TGTTGCGTCT
* * * ** *
82759 CCGGGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTAACATACCAATCGAAGGC-
1 CCGGGGGACATGAGTCACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT-GAAAGCT
* * * *
82823 GCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTTCCCTCAAACATAATAGGTACTGACATAA
65 GCCCCCAG-AAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTACATGA
* *** * * * *
82888 ATAGTGTTCCTC-GGGGGTTTAGGGTTATATAATAGGGTAATGATAACATATTCTCTAACAAAAT
129 ATAGTG-CCCTCAGGGGACAT-GAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAAT
* * * * * * *
82952 AATGGAATGCGCCCCCCGAGAACGCGCTTTCACCACTTTGCCAAGTTCCCTCAAACATAATAGGT
192 AATGGAAGGCCCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAAAATAATAGGC
83017 ACTGATATGAATAGTGCCC
257 ACT-ATATGAATAGTGCCC
** * ** * * *
83036 ATGAGGG-TTTAGGGTTACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGAAAGCT
1 CCGGGGGACAT-GAGTCACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGCT
83100 GCATCCCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTACATG
65 GC--CCCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTACATG
* * *
83165 AATAGTGCCCCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATA
128 AATAGTGCCCTCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATA
*
83230 ATGGAAGGCACCCCCCCGAAAACGCGCTTTCACCATTTTGCCAAGTCCCCTAAAAAATAATAGGG
193 ATGGAAGGC-CCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAAAATAATA-GG
83295 CA-T-TCATGAATAGTGCCC
256 CACTAT-ATGAATAGTGCCC
* * * *
83313 CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCTCTGACAAAATAATGGAAGAAT
1 CCGGGGGACATGAGTCACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAG-CT
* * * * **** *
83378 CCCCCCCGGAAACGTGTTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGG-GCATT-CATG
65 -GCCCCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTAC-TTACATG
*
83441 AATAGTGCCCTCAGGGGACATAAGTGACATAATAGGGGCAATGATAACAT
128 AATAGTGCCCTCAGGGGACATGAGTGACATAATA-GGGCAATGATAACAT
83491 GAATAATGGA
Statistics
Matches: 383, Mismatches: 59, Indels: 26
0.82 0.13 0.06
Matches are distributed among these distances:
276 44 0.11
277 217 0.57
278 113 0.30
279 9 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (274 bp):
CCGGGGGACATGAGTCACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGCTG
CCCCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTACATGAAT
AGTGCCCTCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAATG
GAAGGCCCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAAAATAATAGGCACTA
TATGAATAGTGCCC
Found at i:83366 original size:138 final size:138
Alignment explanation
Indices: 82759--83490 Score: 791
Period size: 139 Copynumber: 5.3 Consensus size: 138
82749 TGTTGCGTCT
* * * * ** *
82759 CCGGGGGACATGACTCACATAATAGGGCAATGATAACATATTCTCTAACATACCAATCGAAGGC-
1 CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCA
* * * *
82823 GCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTTCCCTCAAACATAATAGGTACTGACATAA
66 CCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACT-TCATGA
*
82888 ATAGTGTTCC
130 ATAGTG-CCC
* ** * * * * * *
82898 TCGGGGG-TTTAGGGTTATATAATAGGGTAATGATAACATATTCTCTAACAAAATAATGGAATGC
1 CCGGGGGACAT-GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
* * *
82962 -GCCCCCCGAGAACGCGCTTTCACCACTTTGCCAAGTTCCCTCAAACATAATAGGTACTGAT-AT
65 ACCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACT--TCAT
83025 GAATAGTGCCC
128 GAATAGTGCCC
** * ** * * * *
83036 ATGAGGG-TTTAGGGTTACATAATAAGGCAATGATAACATATTCTCTGACAAAATAATGAAAGCT
1 CCGGGGGACAT-GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAG--
* *
83100 GCA-TCCCCAG-AAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTACA
63 GCACCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTT-CA
83163 TGAATAGTGCCC
127 TGAATAGTGCCC
* *
83175 CCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAATGGAAGGCA
1 CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCA
* * * *
83240 CCCCCCCGAAAACGCGCTTTCACCATTTTGCCAAGTCCCCTAAAAAATAATAGG-GCATTCATGA
66 CCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTAC-TTCATGA
83304 ATAGTGCCC
130 ATAGTGCCC
* *
83313 CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCTCTGACAAAATAATGGAA-GAA
1 CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCA
* * * **** *
83377 TCCCCCCCGGAAACGTGTTTTCACCACTTTGTTGTGTCCCCTCAAACATAATAGG-GCATTCATG
66 -CCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTAC-TTCATG
83441 AATAGTGCCC
129 AATAGTGCCC
* * *
83451 TCAGGGGACATAAGTGACATAATAGGGGCAATGATAACAT
1 CCGGGGGACATGAGTGACATAATA-GGGCAATGATAACAT
83491 GAATAATGGA
Statistics
Matches: 515, Mismatches: 65, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
137 6 0.01
138 218 0.42
139 283 0.55
140 8 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (138 bp):
CCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCA
CCCCCCCGAAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTTCATGAA
TAGTGCCC
Found at i:86747 original size:22 final size:22
Alignment explanation
Indices: 86714--86757 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
86704 TTAAAATGAT
86714 TAATTATAATTATTTAATATAA
1 TAATTATAATTATTTAATATAA
*
86736 TAATTCAT-ATTATTTATTATAA
1 TAATT-ATAATTATTTAATATAA
86758 AAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTATAATTATTTAATATAA
Found at i:96026 original size:32 final size:32
Alignment explanation
Indices: 95977--96052 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
95967 TCATTGGGCA
* *
95977 TAAGAGCCAACCTAAGAGAGTACCTTGAGGCC
1 TAAGAGCCTACCCAAGAGAGTACCTTGAGGCC
* *
96009 TTAGAGCCTACCCAAGAGAGTACCTTGGGGCC
1 TAAGAGCCTACCCAAGAGAGTACCTTGAGGCC
96041 TAAGAGCCTACC
1 TAAGAGCCTACC
96053 TAAGGGTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (32 bp):
TAAGAGCCTACCCAAGAGAGTACCTTGAGGCC
Found at i:110051 original size:85 final size:85
Alignment explanation
Indices: 109908--110085 Score: 302
Period size: 85 Copynumber: 2.1 Consensus size: 85
109898 ATACAATCAC
* * *
109908 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
*
109973 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
109993 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCCTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
110058 AATGCGCGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
110078 GACGCACA
1 GACACACA
110086 GTTGCGCGTC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:110097 original size:85 final size:85
Alignment explanation
Indices: 109908--110127 Score: 278
Period size: 85 Copynumber: 2.6 Consensus size: 85
109898 ATACAATCAC
* * * * *
109908 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGCGCGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
*
109973 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* * *
109993 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCCTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGCGCGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
110058 AATGCGCGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
* ** * * * * *
110078 GACGCACAGTTGCGCGTCATCTTAAATTTATGTCGGTGGCTTCAACGACA
1 GACACACAAATGCGCGTCATCTT-CATTTATGACGGGGGCCTCAATGACA
110128 GGAAAATGTG
Statistics
Matches: 118, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 98 0.83
86 20 0.17
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (85 bp):
GACACACAAATGCGCGTCATCTTCATTTATGACGGGGGCCTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:116683 original size:15 final size:15
Alignment explanation
Indices: 116663--116692 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
116653 GTTGATGACT
116663 TTTACCATTAATAAA
1 TTTACCATTAATAAA
116678 TTTACCATTAATAAA
1 TTTACCATTAATAAA
116693 GAAATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTACCATTAATAAA
Found at i:125549 original size:11 final size:11
Alignment explanation
Indices: 125533--125558 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
125523 CAAAAATTAT
125533 ATATATATATA
1 ATATATATATA
125544 ATATATATATA
1 ATATATATATA
125555 ATAT
1 ATAT
125559 TTTAAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATATA
Found at i:127463 original size:18 final size:18
Alignment explanation
Indices: 127440--127479 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
127430 GTCATCTTCT
127440 GCTGCTAGAGGATCCCCA
1 GCTGCTAGAGGATCCCCA
127458 GCTGCTAGAGGATCCCCA
1 GCTGCTAGAGGATCCCCA
127476 GCTG
1 GCTG
127480 ACTGTCCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.30, T:0.17
Consensus pattern (18 bp):
GCTGCTAGAGGATCCCCA
Found at i:128256 original size:6 final size:6
Alignment explanation
Indices: 128244--128306 Score: 92
Period size: 6 Copynumber: 10.7 Consensus size: 6
128234 TGAATATTAT
*
128244 TTAT-A TTATTA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
* *
128291 TAATAA TAATAA TTAT
1 TTATAA TTATAA TTAT
128307 TTTATTATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 4 0.07
6 50 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATAA
Found at i:128320 original size:18 final size:17
Alignment explanation
Indices: 128238--128316 Score: 52
Period size: 18 Copynumber: 4.5 Consensus size: 17
128228 TTCATTTGAA
128238 TATTATT-TATATTATTAT
1 TATTATTATA-ATTATT-T
* *
128256 TATAATTATAATTATAAT
1 TATTATTATAATTAT-TT
* *
128274 TATAATTATAATTATAAT
1 TATTATTATAATTAT-TT
* * *
128292 AATAATAATAATTATTT
1 TATTATTATAATTATTT
128309 TATTATTA
1 TATTATTA
128317 ATAAATATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.12
18 43 0.84
19 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTATAATTATTT
Found at i:133915 original size:15 final size:15
Alignment explanation
Indices: 133892--133928 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
133882 TTTGGGATCA
*
133892 ATACCTTTTGCATAC
1 ATACATTTTGCATAC
133907 ATACATTTTGCATAC
1 ATACATTTTGCATAC
*
133922 ATTCATT
1 ATACATT
133929 ATTCATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (15 bp):
ATACATTTTGCATAC
Found at i:143156 original size:113 final size:113
Alignment explanation
Indices: 142807--143370 Score: 839
Period size: 113 Copynumber: 5.0 Consensus size: 113
142797 TAGCAAAGAT
142807 TCAAATCCATCACTTGATGGATCAG-TATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
142871 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
142920 TCAAATCCATCACTTGATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
142984 AGAAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
143032 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
143097 AGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * * * * * ** * *
143145 TTAAATTCATCACTCGGTGGATCAG-TAATGCCAGTTAGAGTTCATAATGAGAATAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCT-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * **
143209 AAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGATT-AACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTG-TTCAACCTTTTGC
* * * * *
143258 TTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATTTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
143323 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
143371 ATGACTCTAT
Statistics
Matches: 407, Mismatches: 38, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
112 112 0.28
113 292 0.72
114 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:143350 original size:24 final size:23
Alignment explanation
Indices: 143307--143351 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
143297 GTTCATAATG
*
143307 AGAAGAATTCATTTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
143330 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
143352 AGCTTGTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:143782 original size:27 final size:24
Alignment explanation
Indices: 143707--143786 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
143697 TTTTCATTTG
*
143707 ATTATTATT-TATTATTATTAT-T
1 ATTATTATTATTTTATTATTATAT
* *
143729 ATTATTATAATAATTATTATTAT-T
1 ATTATTATTAT-TTTATTATTATAT
143753 ATTATTATTATTTTATTATTA-AT
1 ATTATTATTATTTTATTATTATAT
*
143776 AAATATTATTA
1 -ATTATTATTA
143787 CAGGCCCAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.16
23 11 0.22
24 31 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTATTATTATTTTATTATTATAT
Found at i:143786 original size:3 final size:3
Alignment explanation
Indices: 143707--143773 Score: 100
Period size: 3 Copynumber: 22.3 Consensus size: 3
143697 TTTTCATTTG
* *
143707 ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATA ATA ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
143753 ATT ATT ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
143774 ATAAATATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:145174 original size:3 final size:3
Alignment explanation
Indices: 145166--145195 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
145156 TTTACTTTTA
*
145166 ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
145196 TAGCCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:145404 original size:20 final size:19
Alignment explanation
Indices: 145379--145420 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
145369 CTATTTTATA
145379 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
145399 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
145418 AAT
1 AAT
145421 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:145422 original size:119 final size:117
Alignment explanation
Indices: 145275--145511 Score: 300
Period size: 120 Copynumber: 2.0 Consensus size: 117
145265 ATTTTAATCC
* * * *
145275 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAG-GGTAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGAT-GTCTTAAAACAACTAGAAGT-
* *
145337 CATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
64 CATTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* ** *
145393 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGATGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGATGTCTTAAAACAACTAGAAGTC
**
145458 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
145511 T
1 T
145512 AATATATATT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
118 19 0.18
119 28 0.27
120 35 0.34
121 19 0.18
122 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGATGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:147629 original size:31 final size:31
Alignment explanation
Indices: 147572--147630 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
147562 GTAAAATTTT
*
147572 TGTTTATAATATTATAATATTATTTTTATTA
1 TGTTTATAATATTATAATAATATTTTTATTA
*
147603 TGTTTATAATATTAATTATAAT-TTTTTA
1 TGTTTATAATATT-ATAATAATATTTTTA
147631 ACATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TGTTTATAATATTATAATAATATTTTTATTA
Found at i:147700 original size:9 final size:9
Alignment explanation
Indices: 147663--147720 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
147653 TCACATCTTT
147663 AATATCTATA
1 AATAT-TATA
*
147673 AATATTAAAA
1 AATATT-ATA
*
147683 AATTATTATC
1 AA-TATTATA
147693 AATATTATA
1 AATATTATA
*
147702 AATATAATA
1 AATATTATA
*
147711 AAAATTATA
1 AATATTATA
147720 A
1 A
147721 CATAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 23 0.59
10 12 0.31
11 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATTATA
Found at i:152001 original size:28 final size:28
Alignment explanation
Indices: 151955--152029 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
151945 TGCTTGCAAG
* * *
151955 CACTAACTCGATGAAATAATGTTTCAAA
1 CACTAACTCAACGAAATAATATTTCAAA
* * * *
151983 TACTAACTTAACGACATAATATTTCAAG
1 CACTAACTCAACGAAATAATATTTCAAA
152011 CACTAACTCAACGAAATAA
1 CACTAACTCAACGAAATAA
152030 CGTAAACGTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (28 bp):
CACTAACTCAACGAAATAATATTTCAAA
Found at i:154445 original size:24 final size:24
Alignment explanation
Indices: 154432--154525 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
154422 AAACATAATT
154432 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
154456 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
154480 CATGTC-AGTATCATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * *
154503 CAGGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
154526 TCAAATCAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.32
24 42 0.68
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:156120 original size:18 final size:18
Alignment explanation
Indices: 156085--156127 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
156075 AAAGATATTA
156085 AAAT-AATAAAAGCGATT
1 AAATAAATAAAAGCGATT
156102 AAATAAATAAAAG-GAATT
1 AAATAAATAAAAGCG-ATT
156120 AAAGTAAA
1 AAA-TAAA
156128 AATAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAAGCGATT
Found at i:163840 original size:17 final size:17
Alignment explanation
Indices: 163818--163853 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
163808 GTCAACAGAA
*
163818 GTCAACGCCGGTCAACG
1 GTCAACGCCAGTCAACG
*
163835 GTCAACGCTAGTCAACG
1 GTCAACGCCAGTCAACG
163852 GT
1 GT
163854 TCAGGTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.17
Consensus pattern (17 bp):
GTCAACGCCAGTCAACG
Found at i:165432 original size:17 final size:18
Alignment explanation
Indices: 165410--165444 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
165400 AAATTCATGT
*
165410 GAAACAT-CTATATATTA
1 GAAACATACCATATATTA
165427 GAAACATACCATATATTA
1 GAAACATACCATATATTA
165445 AAATCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
GAAACATACCATATATTA
Found at i:166555 original size:18 final size:19
Alignment explanation
Indices: 166534--166576 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
166524 ACATTTATAA
* *
166534 TATAAGTTATATTTATT-T
1 TATAAGATATATTAATTAT
166552 TATAAAGATATATTAATTAT
1 TAT-AAGATATATTAATTAT
166572 TATAA
1 TATAA
166577 TATTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TATAAGATATATTAATTAT
Found at i:166555 original size:23 final size:22
Alignment explanation
Indices: 166526--166610 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 22
166516 AATTAAATAC
*
166526 ATTTATAATATAAGTTATATTT
1 ATTTATAATATAAGTTATATTA
*
166548 ATTT-T-ATA-AAGATATATTA
1 ATTTATAATATAAGTTATATTA
* *
166567 ATTATTATAATATTAATTTA-AATA
1 A-T-TTATAATA-TAAGTTATATTA
166591 CATTTATAATATAAGTTATA
1 -ATTTATAATATAAGTTATA
166611 AAACTAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
19 10 0.20
20 4 0.08
21 3 0.06
22 11 0.22
23 12 0.24
24 4 0.08
25 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTATAATATAAGTTATATTA
Found at i:166619 original size:35 final size:35
Alignment explanation
Indices: 166504--166625 Score: 105
Period size: 33 Copynumber: 3.6 Consensus size: 35
166494 AGTTTTAATC
166504 AGTTATAAAACTAA-TTAAATACATTTATAATATA
1 AGTTATAAAACTAATTTAAATACATTTATAATATA
** * * *
166538 AGTTAT--ATTTATTTTATAA-AGATATATTAAT-T-
1 AGTTATAAAACTAATTTA-AATACATTTA-TAATATA
* *
166570 A-TTATAATATTAATTTAAATACATTTATAATATA
1 AGTTATAAAACTAATTTAAATACATTTATAATATA
*
166604 AGTTATAAAACTAATTAAAATA
1 AGTTATAAAACTAATTTAAATA
166626 TAATAATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
31 4 0.06
32 10 0.15
33 22 0.33
34 13 0.20
35 17 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (35 bp):
AGTTATAAAACTAATTTAAATACATTTATAATATA
Found at i:166920 original size:17 final size:16
Alignment explanation
Indices: 166873--166920 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
166863 AATGTTACAA
166873 ATATATTTTAATTAATT
1 ATATATTTTAA-TAATT
* *
166890 CTATAATTTAATAATT
1 ATATATTTTAATAATT
*
166906 GATATATTTTTATAA
1 -ATATATTTTAATAA
166921 AATAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATATTTTAATAATT
Found at i:168144 original size:9 final size:9
Alignment explanation
Indices: 168130--168360 Score: 56
Period size: 9 Copynumber: 23.7 Consensus size: 9
168120 TATATATATA
168130 TATATAAAC
1 TATATAAAC
*
168139 TATATAGAAA
1 TATATA-AAC
168149 T-TATATAA-
1 TATATA-AAC
168157 TATATAAAC
1 TATATAAAC
* **
168166 TATGTAATT
1 TATATAAAC
* * *
168175 TATTTATAT
1 TATATAAAC
*
168184 TATATATAAT
1 TATATA-AAC
*
168194 TATATATGAAT
1 TATATA--AAC
168205 TATATATAAC
1 TATATA-AAC
168215 TATATAAAC
1 TATATAAAC
168224 TATATATAGAC
1 TATATA-A-AC
***
168235 TATATAGTT
1 TATATAAAC
168244 TATATATATA-
1 TATATA-A-AC
*
168254 TATATATAC
1 TATATAAAC
*
168263 TATATATAAAT
1 --TATATAAAC
**
168274 TATATAATT
1 TATATAAAC
168283 TATATATTAAC
1 TATATA--AAC
*
168294 TATATAAAAT
1 TATAT-AAAC
*
168304 TATATATATTATT
1 TATATA-A--A-C
168317 TATATAAAC
1 TATATAAAC
* *
168326 TACATATAC
1 TATATAAAC
168335 TATATAATTTAC
1 TATATAA---AC
168347 -ATATAAAC
1 TATATAAAC
168355 TATATA
1 TATATA
168361 TAAAACTATA
Statistics
Matches: 169, Mismatches: 30, Indels: 46
0.69 0.12 0.19
Matches are distributed among these distances:
8 6 0.04
9 80 0.47
10 35 0.21
11 36 0.21
12 5 0.03
13 7 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (9 bp):
TATATAAAC
Found at i:168368 original size:12 final size:12
Alignment explanation
Indices: 168347--168404 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
168337 TATAATTTAC
168347 ATAT-AAACTAT
1 ATATAAAACTAT
168358 ATATAAAACTAT
1 ATATAAAACTAT
*
168370 ATAT--AACCAT
1 ATATAAAACTAT
**
168380 ATATACTAC-AT
1 ATATAAAACTAT
168391 ATATAAAA-TAT
1 ATATAAAACTAT
168402 ATA
1 ATA
168405 GTTTATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.23
11 17 0.44
12 13 0.33
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAAAACTAT
Found at i:168374 original size:2 final size:2
Alignment explanation
Indices: 168052--168362 Score: 156
Period size: 2 Copynumber: 158.5 Consensus size: 2
168042 TAAAAAATTG
* * * * *
168052 AT AT AT AT AT AT AT AT AT A- AG CT AT GT AGT TT GT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
168093 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
* * * * * *
168135 AA ACT AT AT AG AA AT -T AT AT A- AT AT AT AA ACT AT GT A- AT TT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
168176 AT TT AT AT -T AT AT AT A- AT -T AT AT AT GA- AT -T AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
168213 ACT AT AT AA ACT AT AT AT AG ACT AT AT AGT TT AT AT AT AT AT AT
1 A-T AT AT AT A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* *
168257 AT AT ACT AT AT AT AA AT -T AT AT A- AT TT AT AT AT -T A- ACT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
168297 AT A- AA AT -T AT AT AT AT -T AT TT AT AT AA ACT AC AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT
* * *
168338 AT A- AT TT AC AT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A
168363 AAACTATATA
Statistics
Matches: 233, Mismatches: 44, Indels: 64
0.68 0.13 0.19
Matches are distributed among these distances:
1 19 0.08
2 199 0.85
3 15 0.06
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:168443 original size:20 final size:20
Alignment explanation
Indices: 168204--168444 Score: 100
Period size: 20 Copynumber: 11.9 Consensus size: 20
168194 TATATATGAA
**
168204 TTATATAT-AACTATATAAA
1 TTATATATAAACTATATAGT
* *
168223 CTATATATAGACTATATAGT
1 TTATATATAAACTATATAGT
*
168243 TTATATATATA-TATATA-T
1 TTATATATAAACTATATAGT
* * *
168261 ACTATATATAAATTATATAAT
1 -TTATATATAAACTATATAGT
* **
168282 TTATATATTAACTATATAAAA
1 TTATATATAAACTATAT-AGT
* *
168303 TTATATATATTA-TTTATA-T
1 TTATATATA-AACTATATAGT
** * * *
168322 AAACTACATATACTATATAAT
1 TTA-TATATAAACTATATAGT
*
168343 TTACATATAAACTATATA-T
1 TTATATATAAACTATATAGT
* * *
168362 AAAACTATATATAACCATATATACT
1 ----TTATATATAAAC-TATATAGT
** *
168387 ACATATATAAAATATATAGT
1 TTATATATAAACTATATAGT
*
168407 TTAT-TAATAAACCATATAGT
1 TTATAT-ATAAACTATATAGT
*
168427 TTATATATGAACTATATA
1 TTATATATAAACTATATA
168445 TAAACTAAGG
Statistics
Matches: 166, Mismatches: 39, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.01
19 27 0.16
20 95 0.57
21 26 0.16
22 1 0.01
23 9 0.05
24 6 0.04
25 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (20 bp):
TTATATATAAACTATATAGT
Found at i:170279 original size:9 final size:10
Alignment explanation
Indices: 170264--170418 Score: 75
Period size: 11 Copynumber: 14.7 Consensus size: 10
170254 TATACATATT
170264 ATATATATAA
1 ATATATATAA
170274 AT-TATAT-A
1 ATATATATAA
*
170282 ATTTATTAATGAA
1 ATATA-T-AT-AA
170295 ATATATATAA
1 ATATATATAA
*
170305 TATATATATAT
1 -ATATATATAA
*
170316 ATATATATAT
1 ATATATATAA
170326 ATATATTATAA
1 ATATA-TATAA
*
170337 ACCATATA-AA
1 A-TATATATAA
* *
170347 CTATATATACTT
1 ATATATATA--A
*
170359 TTATATATGAA
1 ATATATAT-AA
*
170370 CTATATATAA
1 ATATATATAA
170380 ATTATATATAA
1 A-TATATATAA
* *
170391 ACCATGTAT-A
1 A-TATATATAA
*
170401 CTATATATAA
1 ATATATATAA
170411 ACTATATA
1 A-TATATA
170419 GTTTATTAAT
Statistics
Matches: 112, Mismatches: 18, Indels: 29
0.70 0.11 0.18
Matches are distributed among these distances:
8 3 0.03
9 17 0.15
10 27 0.24
11 48 0.43
12 11 0.10
13 6 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATATATAA
Found at i:170355 original size:2 final size:2
Alignment explanation
Indices: 170254--170335 Score: 70
Period size: 2 Copynumber: 44.0 Consensus size: 2
170244 AAAAATAAAC
* * *
170254 TA TA CA TA T- TA TA TA TA TA AA T- TA TA TA -A TT 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
*
170291 TGA AA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
170332 TA TA
1 TA TA
170336 AACCATATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
1 7 0.11
2 56 0.88
3 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:170414 original size:11 final size:11
Alignment explanation
Indices: 170296--170418 Score: 80
Period size: 11 Copynumber: 11.5 Consensus size: 11
170286 ATTAATGAAA
170296 TATATATAATA-
1 TATATATAA-AC
*
170307 TATATATATA-
1 TATATATAAAC
*
170317 TATATATATA-
1 TATATATAAAC
170327 TATATTATAAAC
1 TATA-TATAAAC
*
170339 --CATATAAAC
1 TATATATAAAC
***
170348 TATATATACTTT
1 TATATATA-AAC
*
170360 TATATATGAAC
1 TATATATAAAC
*
170371 TATATATAAAT
1 TATATATAAAC
170382 TATATATAAAC
1 TATATATAAAC
* *
170393 CATGTAT--AC
1 TATATATAAAC
170402 TATATATAAAC
1 TATATATAAAC
170413 TATATA
1 TATATA
170419 GTTTATTAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
9 14 0.16
10 16 0.18
11 50 0.57
12 7 0.08
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (11 bp):
TATATATAAAC
Found at i:171172 original size:31 final size:31
Alignment explanation
Indices: 171136--171195 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
171126 GATAGTTATG
*
171136 CTATATTGGTTAC-TCATGAACTATATATATA
1 CTATATAGGTTACAT-ATGAACTATATATATA
*
171167 CTATATAGTTTACATATGAACTATATATA
1 CTATATAGGTTACATATGAACTATATATA
171196 AAAACTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (31 bp):
CTATATAGGTTACATATGAACTATATATATA
Found at i:171189 original size:20 final size:20
Alignment explanation
Indices: 171166--171235 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
171156 CTATATATAT
171166 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
** *
171186 ACTATATA-TAAAAACTATATAA
1 ACTATATAGT--TTAC-ATATGA
171208 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
171228 ACTATATA
1 ACTATATA
171236 TATAAACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 1 0.03
20 21 0.52
21 4 0.10
22 13 0.32
23 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (20 bp):
ACTATATAGTTTACATATGA
Found at i:171216 original size:42 final size:42
Alignment explanation
Indices: 171154--171250 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
171144 GTTACTCATG
171154 AACTATATATATACTATATAGTTTACATATGAACTATATATAAA
1 AACTATATA-A-ACTATATAGTTTACATATGAACTATATATAAA
*
171198 AACTATATAAACTATATAGTTTACATATGAACTATATATATA
1 AACTATATAAACTATATAGTTTACATATGAACTATATATAAA
*
171240 AACTATTTAAA
1 AACTATATAAA
171251 ATTCAAAGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 41 0.80
43 1 0.02
44 9 0.18
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38
Consensus pattern (42 bp):
AACTATATAAACTATATAGTTTACATATGAACTATATATAAA
Found at i:171235 original size:22 final size:22
Alignment explanation
Indices: 171168--171237 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
171158 ATATATATAC
171168 TATATAGTTTACATATGAACTA
1 TATATAGTTTACATATGAACTA
*** *
171190 TATATA-AAAACTATATAAAC--
1 TATATAGTTTAC-ATATGAACTA
171210 TATATAGTTTACATATGAACTA
1 TATATAGTTTACATATGAACTA
171232 TATATA
1 TATATA
171238 TAAACTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 13 0.36
21 4 0.11
22 19 0.53
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (22 bp):
TATATAGTTTACATATGAACTA
Found at i:171276 original size:42 final size:42
Alignment explanation
Indices: 171230--171310 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
171220 ACATATGAAC
*
171230 TATATATATAAACTATTTAAAATTCAAAGTA-ATACTATAGTT
1 TATATATATAAACTATAT-AAATTCAAAGTATATACTATAGTT
* *
171272 TATATTTATATACTATATAAATTCAAAGTATATACTATA
1 TATATATATAAACTATATAAATTCAAAGTATATACTATA
171311 TACTTTGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (42 bp):
TATATATATAAACTATATAAATTCAAAGTATATACTATAGTT
Found at i:171926 original size:8 final size:8
Alignment explanation
Indices: 171913--171937 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
171903 ACTTGTTTTT
171913 CGCTCAAA
1 CGCTCAAA
171921 CGCTCAAA
1 CGCTCAAA
171929 CGCTCAAA
1 CGCTCAAA
171937 C
1 C
171938 CCTAAACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (8 bp):
CGCTCAAA
Found at i:172303 original size:45 final size:46
Alignment explanation
Indices: 172232--172328 Score: 117
Period size: 45 Copynumber: 2.1 Consensus size: 46
172222 CTCTTCTTTT
* *
172232 TCTTCTGTTAATCTTCTCTAACCCT-AATCTAA-CTAAGACTATTCA
1 TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATC-AAGACTATTCA
* * * *
172277 TCTTTTGTTCATCTTCCCTAAACCTAAATCTAATCGAGACTCTTCA
1 TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATCAAGACTATTCA
172323 TCTTCT
1 TCTTCT
172329 TCTGTCTCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 21 0.49
46 21 0.49
47 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (46 bp):
TCTTCTGTTAATCTTCCCTAAACCTAAATCTAATCAAGACTATTCA
Found at i:174257 original size:22 final size:22
Alignment explanation
Indices: 174206--174248 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
174196 TTCAATTTTT
*
174206 TAATTTATTTTATTATGTTTTCA
1 TAATTT-TATTATTATGTTTTCA
174229 TAATTTTATTATTAT-TTTTC
1 TAATTTTATTATTATGTTTTC
174249 TTTATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TAATTTTATTATTATGTTTTCA
Found at i:175580 original size:56 final size:56
Alignment explanation
Indices: 175509--175656 Score: 219
Period size: 56 Copynumber: 2.7 Consensus size: 56
175499 ATATTTAAAT
* *
175509 TAATT-ATTTAATTAATCATGTTCAATAAATAAATTATTTTAACTTTTAATGATTA
1 TAATTAATTTAATTAATCATGTTCAATAAATAAATTATTTTAACTTGTAATAATTA
**
175564 TAATTAATTTAATTAATCATGTTCAATTCCA-AAATTATTTTAACTTGTAATAATTA
1 TAATTAATTTAATTAATCATGTTCAA-TAAATAAATTATTTTAACTTGTAATAATTA
* *
175620 TAATTAATTTAATAAATAATGTTCAATAAATAAATTA
1 TAATTAATTTAATTAATCATGTTCAATAAATAAATTA
175657 ATAAAATTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
55 7 0.09
56 73 0.89
57 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (56 bp):
TAATTAATTTAATTAATCATGTTCAATAAATAAATTATTTTAACTTGTAATAATTA
Found at i:175671 original size:14 final size:12
Alignment explanation
Indices: 175619--175672 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 12
175609 TGTAATAATT
*
175619 ATAATTAATTTA
1 ATAAATAATTTA
175631 ATAAATAATGTTCA
1 ATAAATAAT-TT-A
*
175645 ATAAATAAATTA
1 ATAAATAATTTA
175657 ATAAAATTAATTTA
1 AT-AAA-TAATTTA
175671 AT
1 AT
175673 GATTATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 11 0.31
13 7 0.20
14 17 0.49
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (12 bp):
ATAAATAATTTA
Done.