Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003257.1 Hibiscus syriacus cultivar Beakdansim tig00006843_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: 110696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:22385 original size:18 final size:19
Alignment explanation
Indices: 22350--22386 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
22340 CACGGAATGT
22350 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
22370 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
22387 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:23341 original size:2 final size:2
Alignment explanation
Indices: 23334--23384 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
23324 ATGATAAATT
23334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
23376 TA TT TA TA T
1 TA TA TA TA T
23385 TGAAAGAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:23909 original size:22 final size:22
Alignment explanation
Indices: 23883--23925 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23873 TAATAAATTA
23883 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
23905 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
23926 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23933 original size:54 final size:54
Alignment explanation
Indices: 23873--24439 Score: 306
Period size: 54 Copynumber: 10.6 Consensus size: 54
23863 ACAACTACAA
23873 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* * **
23927 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-AATCAATTCATAC
** *
23976 -AATCCA-TATTTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* * **
24029 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-AATCAATTCATAC
** ** * ** * * *
24078 -AATCCA-TATGTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-A-AA
1 TAATAAATTAT-TTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATAC
*
24130 TCAATCCAAA-T-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCAT
1 T-AAT--AAATTATTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATTCAT
24193 A-
53 AC
*
24194 TAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAA-TCTATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTC-ATAC
* * **
24243 TAATAAATTATTTAAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-AATCAATTCATAC
** * *
24292 -AATCCA-TATTTTAAAATAAATCAATCCATACAAAAAAATTATTTAAAATAAACCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCAT--------A-T-TTTAAAATAAATCAATTCATAC
*
24355 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
24409 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
24440 CAACTACAAT
Statistics
Matches: 393, Mismatches: 55, Indels: 130
0.68 0.10 0.22
Matches are distributed among these distances:
47 8 0.02
48 93 0.24
49 7 0.02
50 28 0.07
51 12 0.03
52 14 0.04
53 7 0.02
54 141 0.36
55 6 0.02
56 4 0.01
57 2 0.01
58 11 0.03
60 3 0.01
61 2 0.01
62 13 0.03
63 12 0.03
64 27 0.07
65 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
Found at i:23934 original size:22 final size:22
Alignment explanation
Indices: 23885--23933 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23875 ATAAATTATT
**
23885 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
23907 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
23930 TAAA
1 TAAA
23934 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:23943 original size:32 final size:32
Alignment explanation
Indices: 23905--24060 Score: 113
Period size: 32 Copynumber: 4.7 Consensus size: 32
23895 CAATCCATAT
23905 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
23937 TTTAAAATAAATCAATCCATAC-AACTACAA-TA
1 TTTAAAATAAATCAATTCATACTAA-TA-AATTA
* * * * * * *
23969 -AT-AAATCAATCCATATTTTAAAATAAATCAATCCAAA
1 TTTAAAATAAAT-CA-A-TTCATACT-AATAAAT---TA
24006 TTTTAAAATAAATCAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATTCATACTAATAAATTA
*
24039 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATTCATAC
24061 AACTACAATA
Statistics
Matches: 93, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
30 7 0.08
31 5 0.05
32 47 0.51
33 8 0.09
34 1 0.01
35 2 0.02
36 6 0.06
37 6 0.06
38 1 0.01
39 3 0.03
40 7 0.08
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:23980 original size:80 final size:81
Alignment explanation
Indices: 23887--24596 Score: 761
Period size: 80 Copynumber: 8.8 Consensus size: 81
23877 AAATTATTTA
*
23887 AAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
23952 TCCATACAACTACAAT
66 TCCATACAACTAAAAT
23968 -AATAAATCAATCCATATTTTAAAATAAATCAAT-C---C----AAA-T-TTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
24022 TTCATACTAA-TAAATTATTT
66 TCCATAC-AACTAAA--A--T
* * ** **
24042 AAAATAAATCAATCCATA----CAACTACAAT-AATAAAT-C-AATCCA-TATGTTAAAATAAAT
1 -AAATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTAT-TTAAAATAAAT
24099 CAATCCATACTAA-TAAATTATTT
63 CAATCCATAC-AACTAAA--A--T
* *
24122 AAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
1 -AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
24187 ATCCATATAACTACAAT
65 ATCCATACAACTAAAAT
*
24204 -AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
*
24268 TCCATACAACTACAAT
66 TCCATACAACTAAAAT
* * *
24284 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAAAAATTATTTAAAATAAACCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
24348 TCCATACTAA-TAAATTATTT
66 TCCATAC-AACTAAA--A--T
24368 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 -AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
24433 ATCCATACAACTACAAT
65 ATCCATACAACTAAAAT
*
24450 -AATAAATCAATCCATATTTAAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
* ***
24514 TTCATA-TTTTAAAAT
66 TCCATACAACTAAAAT
* * *
24529 AAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 AAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
24594 AAT
60 AAT
24597 TATTTTAAAA
Statistics
Matches: 549, Mismatches: 40, Indels: 75
0.83 0.06 0.11
Matches are distributed among these distances:
70 24 0.04
71 3 0.01
72 11 0.02
73 3 0.01
74 1 0.00
75 1 0.00
76 17 0.03
78 2 0.00
79 7 0.01
80 306 0.56
81 3 0.01
82 5 0.01
83 3 0.01
84 13 0.02
85 6 0.01
86 141 0.26
87 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (81 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
TCCATACAACTAAAAT
Found at i:23993 original size:22 final size:22
Alignment explanation
Indices: 23968--24027 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
23958 CAACTACAAT
23968 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
23990 AATAAATCAATCCAAATTTTAA
1 AATAAATCAATCCATATTTTAA
*
24012 AATAAATCAATTCATA
1 AATAAATCAATCCATA
24028 CTAATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:24052 original size:134 final size:133
Alignment explanation
Indices: 23942--24271 Score: 456
Period size: 134 Copynumber: 2.5 Consensus size: 133
23932 AATTATTTAA
* *
23942 AATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT-A-T-TTTAAAATAAATCAAT
1 AATAAATCAATCCATA-AACTAAAATAAATAAATCAATACTAATAATTATTTAAAATAAATCAAT
24001 CCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
65 CCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
*
24066 CAAT
130 AAAT
*** * *
24070 AATAAATCAATCCATATGTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATAAACTAAAATAAATAAATCAATACTAAT-AATTATTTAAAATAAATCAAT
*
24135 CCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATAACTA
65 CCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTA
*
24200 CAAT
130 AAAT
*** * *
24204 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATAAACTAAAATAAATAAATCAATACTAAT-AATTATTTAAAATAAATCAAT
24269 CCA
65 CCA
24272 TACAACTACA
Statistics
Matches: 185, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
127 5 0.03
128 25 0.14
129 1 0.01
130 2 0.01
132 1 0.01
133 1 0.01
134 150 0.81
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (133 bp):
AATAAATCAATCCATAAACTAAAATAAATAAATCAATACTAATAATTATTTAAAATAAATCAATC
CAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAA
AAT
Found at i:24059 original size:102 final size:102
Alignment explanation
Indices: 23883--24385 Score: 568
Period size: 102 Copynumber: 4.7 Consensus size: 102
23873 TAATAAATTA
*
23883 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
23948 TCAATCCATACAACTACAATAATAAATCAATCCATAT
66 TCAATCCATACAACTACAATAATAAATCAATCCATAT
23985 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
24050 TCAATCCATACAACTACAATAATAAATCAATCCATAT
66 TCAATCCATACAACTACAATAATAAATCAATCCATAT
* * ** * ** * * *
24087 GTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-A-AATCAATCCAAA-T-TTTAAAA
1 TTTAAAATAAATCAATCCA-AATTTTAAAATAAATCAATTCATACT-AAT--AAATTATTTAAAA
* *
24148 TAAATCAATTCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
62 TAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATAT
** *
24195 AACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAA
1 ---TTTAA-AATAAATCAATCCAAATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAA
24259 ATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
61 ATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
* *
24301 TTTAAAATAAATCAATCCATACAAAAAAATTATTTAAAATAAACCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAAT-C---C----AAA-T-TTTAAAATAAATCAATTCATACTAATAAATTAT
24366 TTAAAATAAATCAATCCATA
56 TTAAAATAAATCAATCCATA
24386 TTTTAAAATA
Statistics
Matches: 337, Mismatches: 32, Indels: 54
0.80 0.08 0.13
Matches are distributed among these distances:
101 2 0.01
102 158 0.47
103 19 0.06
104 4 0.01
106 19 0.06
108 18 0.05
110 7 0.02
111 16 0.05
112 91 0.27
113 3 0.01
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (102 bp):
TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
TCAATCCATACAACTACAATAATAAATCAATCCATAT
Found at i:24116 original size:22 final size:23
Alignment explanation
Indices: 24041--24115 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
24031 ATAAATTATT
24041 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
24063 CTACAATAATAAATCAATCCATA-TGT
1 -T--AA-AATAAATCAATCCATACTAA
24089 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
24112 TAAA
1 TAAA
24116 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:24250 original size:22 final size:22
Alignment explanation
Indices: 24177--24250 Score: 53
Period size: 22 Copynumber: 3.2 Consensus size: 22
24167 AAATTATTTA
24177 AAATAAATCAATCCATATAACTACA-
1 AAATAAATCAAT-C-TAT-ACTA-AT
* **
24202 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCTATACTAAT
24224 AAAATAAATCAATCTATACTAAT
1 -AAATAAATCAATCTATACTAAT
24247 AAAT
1 AAAT
24251 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
22 20 0.51
23 4 0.10
24 2 0.05
25 2 0.05
26 11 0.28
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAAATCAATCTATACTAAT
Found at i:24287 original size:40 final size:39
Alignment explanation
Indices: 24163--24385 Score: 128
Period size: 32 Copynumber: 5.8 Consensus size: 39
24153 CAATTCATAC
24163 TAATAAATTATTTAAAATAAATCAATCCATATAACTACAA
1 TAATAAATTATTTAAAATAAATCAATCCATA-AACTACAA
24203 TAATAAATCAATCCATATTTTAAAATAAATCAAT-C-T--A-TAC--
1 TAAT--A--AAT---TA-TTTAAAATAAATCAATCCATAAACTACAA
24243 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TAATAAATTATTTAAAATAAATCAATCCATA-AACTACAA
24283 TAATAAATCAATCCATATTTTAAAATAAATCAATCC----A-TACAA
1 TAAT--A--AAT---TA-TTTAAAATAAATCAATCCATAAACTACAA
*
24325 -AA-AAATTATTTAAAATAAACCAATCC----A-TAC--
1 TAATAAATTATTTAAAATAAATCAATCCATAAACTACAA
24355 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
24386 TTTTAAAATA
Statistics
Matches: 152, Mismatches: 2, Indels: 63
0.70 0.01 0.29
Matches are distributed among these distances:
31 2 0.01
32 60 0.39
33 5 0.03
34 1 0.01
36 6 0.04
37 1 0.01
38 5 0.03
40 12 0.08
41 2 0.01
42 10 0.07
43 2 0.01
44 6 0.04
46 1 0.01
47 5 0.03
48 34 0.22
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (39 bp):
TAATAAATTATTTAAAATAAATCAATCCATAAACTACAA
Found at i:24329 original size:22 final size:22
Alignment explanation
Indices: 24256--24330 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
24246 TAAATTATTT
24256 AAAATAAATCAATCCATACAACTA
1 AAAATAAATCAATCCATACAA--A
****
24280 CAATAATAAATCAATCCATATTTT
1 -AA-AATAAATCAATCCATACAAA
24304 AAAATAAATCAATCCATACAAA
1 AAAATAAATCAATCCATACAAA
24326 AAAAT
1 AAAAT
24331 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 21 0.51
23 2 0.05
25 2 0.05
26 16 0.39
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAAATCAATCCATACAAA
Found at i:24343 original size:134 final size:130
Alignment explanation
Indices: 23985--24330 Score: 427
Period size: 134 Copynumber: 2.6 Consensus size: 130
23975 CAATCCATAT
23985 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTC--AC-AAT-AATTATTTAAAATAAA
* * * *
24050 TCAATCCATACAACTACAATAATAAATCAATCCATATGTTAAAATAAATCAATCCATACTAATAA
62 TCAATCCATACAAATAAAATAATAAATCAATCCATATATTAAAATAAATCAATCAATACTAATAA
24115 ATTA
127 ATTA
24119 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTC--AC-AAT-AATTATTTAAAATAAA
* * * * *
24184 TCAATCCATATAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAA
62 TCAATCCATACAAATAAAATAATAAATCAATCCATATATTAAAATAAATCAATCAATACTAATAA
24249 ATTA
127 ATTA
* **
24253 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAA-TC-C-AT-A-T-TTTAAAATAAA
1 TTTAAAATAAATCAATCC--A-AATTTTAA-AATAAATCAATTCACAATAATTATTTAAAATAAA
24312 TCAATCCATACAAA-AAAAT
62 TCAATCCATACAAATAAAAT
24331 TATTTAAAAT
Statistics
Matches: 199, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
127 4 0.02
128 23 0.12
129 1 0.01
130 1 0.01
132 2 0.01
134 150 0.75
136 1 0.01
137 7 0.04
138 10 0.05
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (130 bp):
TTTAAAATAAATCAATCCAAATTTTAAAATAAATCAATTCACAATAATTATTTAAAATAAATCAA
TCCATACAAATAAAATAATAAATCAATCCATATATTAAAATAAATCAATCAATACTAATAAATTA
Found at i:24391 original size:22 final size:22
Alignment explanation
Indices: 24365--24407 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
24355 TAATAAATTA
24365 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
24387 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
24408 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24391 original size:134 final size:131
Alignment explanation
Indices: 24253--24573 Score: 366
Period size: 134 Copynumber: 2.4 Consensus size: 131
24243 TAATAAATTA
*
24253 TTTAAAATAAATCAATCCATAC-AACTACA-A-T-AATAAATCAATCCATATTTTAAAATA-AAT
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATA----AAAATACAAT
**
24313 CAATCCATACAAAAAAATTATTT-AAAATAAACCAATCCATACTAATAAATTATTTAAAATAAAT
61 -AATAAAT-C-AAAAAA-TATTTAAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAAT
24377 CAATCCATAT
122 CAATCCATAT
* *
24387 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATAAAAATACAATAA
*** * *
24452 TAAATCAATCCATATTTAAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTC
63 TAAATCAAAAAATATTTAAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
24517 ATAT
128 ATAT
*
24521 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATA
24574 CTAATAAATT
Statistics
Matches: 167, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
133 5 0.03
134 129 0.77
135 3 0.02
136 10 0.06
137 3 0.02
138 1 0.01
140 16 0.10
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (131 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATAAAAATACAATAATAA
ATCAAAAAATATTTAAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
T
Found at i:24416 original size:22 final size:22
Alignment explanation
Indices: 24367--24415 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
24357 ATAAATTATT
**
24367 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
24389 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
24412 TAAA
1 TAAA
24416 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24457 original size:26 final size:24
Alignment explanation
Indices: 24422--24488 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
24412 TAAATTATTT
24422 AAAATAAATCAATCCATACAACTA
1 AAAATAAATCAATCCATACAACTA
**
24446 CAATAATAAATCAATCCAT--ATTTA
1 -AA-AATAAATCAATCCATACAACTA
24470 AAAATAAATCAATCCATAC
1 AAAATAAATCAATCCATAC
24489 TAATAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 15 0.41
23 2 0.05
24 3 0.08
25 2 0.05
26 15 0.41
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATAAATCAATCCATACAACTA
Found at i:24496 original size:22 final size:22
Alignment explanation
Indices: 24423--24496 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 22
24413 AAATTATTTA
24423 AAATAAATCAATCCATAC-AACT
1 AAATAAATCAATCCATACTAA-T
*
24445 ACAATAATAAATCAATCCATATTTAA-
1 ---A-AATAAATCAATCCATA-CTAAT
24471 AAATAAATCAATCCATACTAAT
1 AAATAAATCAATCCATACTAAT
24493 AAAT
1 AAAT
24497 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
21 3 0.07
22 20 0.47
23 1 0.02
25 1 0.02
26 16 0.37
28 2 0.05
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:24532 original size:54 final size:52
Alignment explanation
Indices: 24450--24663 Score: 244
Period size: 54 Copynumber: 4.1 Consensus size: 52
24440 CAACTACAAT
* *
24450 AATAAATCAATCCATATTTAAAAATAAATCAATCCATACTAATAAATTA-TTTAA
1 AATAAATCAATCCATATTTTAAAATAAAT-AAT-TATA-TAATAAATTATTTTAA
*
24504 AATAAATCAATTCATATTTTAAAATAAATCAATCTATACTAATAAATTA-TTTAA
1 AATAAATCAATCCATATTTTAAAATAAAT-AAT-TATA-TAATAAATTATTTTAA
* * *
24558 AATAAATCAATCCATA--CT--AATAAATTATT-TAAAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATAATTATATAATAAATTATTTTAA
* * *
24605 AATAAATCAATCCATATTTTATAATAAATTATTTTATAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATAATTATATAATAAATTATTTTAA
24657 AATAAAT
1 AATAAAT
24664 AACCTTATTA
Statistics
Matches: 145, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
46 9 0.06
47 23 0.16
48 1 0.01
49 3 0.02
50 7 0.05
51 11 0.08
52 25 0.17
54 66 0.46
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (52 bp):
AATAAATCAATCCATATTTTAAAATAAATAATTATATAATAAATTATTTTAA
Found at i:24559 original size:166 final size:162
Alignment explanation
Indices: 24124--24596 Score: 629
Period size: 166 Copynumber: 2.9 Consensus size: 162
24114 AATTATTTAA
* *
24124 AATAAATCAATCCAAATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * *
24189 CCATATAACTACAAT-AATAAATCAAT-C-CAT-A-T-TTTAAAATAAATCAATCTATACTAATA
66 CCATAT--CTA-AATAAAT-AATCTATACTAATAATTATTTAAAATAAATCAATCCATACTAATA
24248 AATTATTTAAAATAAATCAATCCATACAACTACAAT
127 AATTATTTAAAATAAATCAATCCATACAACTACAAT
* * *
24284 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAAAAAATTATTTAAAATAAACCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * * *
24349 CCATA-CT-AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA
66 CCATATCTAAATAAATAATCTATACT-AAT-AAT---TA-TTTAAAATAAATCAATCCATACTAA
24412 TAAATTATTTAAAATAAATCAATCCATACAACTACAAT
125 TAAATTATTTAAAATAAATCAATCCATACAACTACAAT
*
24450 AATAAATCAATCCATATTTAAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
24515 TCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATA
66 CCATA-TCT-AAATAAAT-AATCTATACTAAT-AATTATTTAAAATAAATCAATCCATACTAATA
24580 AATTATTTAAAATAAAT
127 AATTATTTAAAATAAAT
24597 TATTTTAAAA
Statistics
Matches: 273, Mismatches: 23, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
155 6 0.02
156 3 0.01
157 2 0.01
158 2 0.01
160 66 0.24
164 1 0.00
166 171 0.63
167 2 0.01
168 1 0.00
170 13 0.05
171 6 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (162 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATCTAAATAAATAATCTATACTAATAATTATTTAAAATAAATCAATCCATACTAATAAATT
ATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:24563 original size:14 final size:14
Alignment explanation
Indices: 24544--24611 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
24534 AATCTATACT
24544 AATAAATTATTTAA
1 AATAAATTATTTAA
* * *
24558 AATAAATCAATCCATACT
1 AATAAAT-TAT--TTA-A
24576 AATAAATTATTTAA
1 AATAAATTATTTAA
24590 AATAAATTATTTTAA
1 AATAAATTA-TTTAA
24605 AATAAAT
1 AATAAAT
24612 CAATCCATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 16 0.37
15 16 0.37
17 4 0.09
18 7 0.16
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:24604 original size:134 final size:132
Alignment explanation
Indices: 24323--24620 Score: 453
Period size: 134 Copynumber: 2.2 Consensus size: 132
24313 CAATCCATAC
*
24323 AAAA-AAATTA-TTTAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
1 AAAATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
24386 TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
66 TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
24451 AT
131 AT
* * *
24453 -AAATCAATCCATATTTAAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTC
1 AAAATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
*
24517 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAA-TA-
63 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTAC
*
24580 AATTATTT
127 AA-TA-AT
24588 AAAATAAATTATTTTAAAATAAATCAATCCATA
1 AAAATAAATTATTTTAAAATAAATCAATCCATA
24621 TTTTATAATA
Statistics
Matches: 151, Mismatches: 8, Indels: 15
0.87 0.05 0.09
Matches are distributed among these distances:
129 3 0.02
130 3 0.02
133 27 0.18
134 108 0.72
135 3 0.02
136 7 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (132 bp):
AAAATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
AT
Found at i:24605 original size:15 final size:15
Alignment explanation
Indices: 24576--24663 Score: 88
Period size: 15 Copynumber: 5.5 Consensus size: 15
24566 AATCCATACT
24576 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
24590 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
24605 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
24627 AATAAATTATTTTAT
1 AATAAATTATTTTAA
24642 AATAAATTATTTTAA
1 AATAAATTATTTTAA
24657 AATAAAT
1 AATAAAT
24664 AACCTTATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
14 9 0.14
15 37 0.58
17 1 0.02
18 3 0.05
19 3 0.05
20 1 0.02
22 10 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:24611 original size:47 final size:46
Alignment explanation
Indices: 24544--24686 Score: 170
Period size: 52 Copynumber: 3.1 Consensus size: 46
24534 AATCTATACT
24544 AATAAATTA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA-TAATAAATTATTTAA
*
24590 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAT
1 AATAAATTATTTTAAAATAAATCAATCC--A---TATAATAAATTA-TTTAA
*
24642 AATAAATTATTTTAAAATAAAT-AA-CC-T-TATTAAATTATTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATATAATAAATTATTTAA
24684 AAT
1 AAT
24687 TATTCTAATA
Statistics
Matches: 87, Mismatches: 3, Indels: 18
0.81 0.03 0.17
Matches are distributed among these distances:
42 7 0.08
43 9 0.10
44 1 0.01
46 9 0.10
47 18 0.21
49 1 0.01
50 2 0.02
51 12 0.14
52 28 0.32
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (46 bp):
AATAAATTATTTTAAAATAAATCAATCCATATAATAAATTATTTAA
Found at i:24997 original size:12 final size:12
Alignment explanation
Indices: 24980--25049 Score: 63
Period size: 13 Copynumber: 5.7 Consensus size: 12
24970 ATATTTGATT
24980 TTAATTTTAATA
1 TTAATTTTAATA
24992 TTAATTTTTAA-A
1 TTAA-TTTTAATA
* *
25004 -TAAATTAAATA
1 TTAATTTTAATA
25015 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
25028 TTATATTATATATA
1 TTA-ATTTTA-ATA
25042 TTAATTTT
1 TTAATTTT
25050 TTAAATTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
10 4 0.09
11 4 0.09
12 8 0.17
13 23 0.50
14 7 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:25014 original size:23 final size:24
Alignment explanation
Indices: 24982--25055 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 24
24972 ATTTGATTTT
*
24982 AATTTTAATATTAATTTTTAAATA
1 AATTATAATATTAATTTTTAAATA
25006 AATTA-AATATTAATTTTTAATATTA
1 AATTATAATATTAATTTTTAA-A-TA
*
25031 TATTATATATATTAATTTTTTAAAT
1 AATTATA-ATATTAA-TTTTTAAAT
25056 TTATTTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 15 0.35
24 5 0.12
25 6 0.14
26 2 0.05
27 8 0.19
28 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATAATATTAATTTTTAAATA
Found at i:25059 original size:23 final size:23
Alignment explanation
Indices: 24951--25059 Score: 62
Period size: 27 Copynumber: 4.5 Consensus size: 23
24941 AGGTTTTATA
*
24951 TTTAATTTTATATTATATTATATTT
1 TTTAAATTTATA-TATATTA-ATTT
*
24976 GATTTTAATTT-TA-ATATTAA-TT
1 --TTTAAATTTATATATATTAATTT
** *
24998 TTTAAATAAATTAAATATTAATTT
1 TTTAAATTTA-TATATATTAATTT
*
25022 TTAATATTATATTATATATATTAATTT
1 TT--TA-AAT-TTATATATATTAATTT
25049 TTTAAATTTAT
1 TTTAAATTTAT
25060 TTTATATCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
20 6 0.09
22 4 0.06
23 12 0.19
24 12 0.19
25 2 0.03
26 4 0.06
27 23 0.36
28 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (23 bp):
TTTAAATTTATATATATTAATTT
Found at i:25091 original size:31 final size:28
Alignment explanation
Indices: 25019--25091 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
25009 TAAATATTAA
* *
25019 TTTTTAATATTATATTATATATATTAAT
1 TTTTTAATATTATTTTATATATATAAAT
25047 TTTTTAA-ATTTATTTTATATCATATAAAT
1 TTTTTAATA-TTATTTTATAT-ATATAAAT
25076 TGTTTTATATATTATT
1 T-TTTTA-ATATTATT
25092 AAAATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 17 0.45
29 8 0.21
30 5 0.13
31 6 0.16
32 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
TTTTTAATATTATTTTATATATATAAAT
Found at i:29888 original size:3 final size:3
Alignment explanation
Indices: 29872--29953 Score: 83
Period size: 3 Copynumber: 25.3 Consensus size: 3
29862 AGTTTAAAAA
* *
29872 TAT TATT TATT TAT TAT TAC TAT TAC TAT TAT TAT CTAT TAT TAT TAT
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
29920 TATT TAT TAT TAT TATT TAT TATT TAT TTT TAT T
1 TA-T TAT TAT TAT TA-T TAT TA-T TAT TAT TAT T
29954 TTTGTAGGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
3 49 0.72
4 19 0.28
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29895 original size:13 final size:13
Alignment explanation
Indices: 29879--29943 Score: 78
Period size: 13 Copynumber: 4.8 Consensus size: 13
29869 AAATATTATT
29879 TATTTATTATTAC
1 TATTTATTATTAC
29892 TATTACTATTATTATC
1 TATT--TATTATTA-C
*
29908 TA-TTATTATTAT
1 TATTTATTATTAC
*
29920 TATTTATTATTAT
1 TATTTATTATTAC
29933 TATTTATTATT
1 TATTTATTATT
29944 TATTTTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
12 2 0.04
13 33 0.70
15 9 0.19
16 3 0.06
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTATTATTAC
Found at i:29943 original size:16 final size:16
Alignment explanation
Indices: 29882--29936 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
29872 TATTATTTAT
29882 TTATTATTA-CTATTA
1 TTATTATTATCTATTA
*
29897 CTATTATTATCTATTA
1 TTATTATTATCTATTA
*
29913 TTATTATTATTTATTA
1 TTATTATTATCTATTA
29929 TTATTATT
1 TTATTATT
29937 TATTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATTATCTATTA
Found at i:29951 original size:13 final size:13
Alignment explanation
Indices: 29872--29956 Score: 66
Period size: 13 Copynumber: 6.1 Consensus size: 13
29862 AGTTTAAAAA
29872 TATTATTTATTTAT
1 TATTATTTATTT-T
29886 TATTACTATTACTATTAT
1 TATTA-T-TTA-T-TT-T
*
29904 TATCTA-TTATTAT
1 TAT-TATTTATTTT
*
29917 TATTATTTATTAT
1 TATTATTTATTTT
29930 TATTATTTATTATT
1 TATTATTTATT-TT
29944 TATT-TTTATTTT
1 TATTATTTATTTT
29956 T
1 T
29957 GTAGGTGCCA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.08
13 28 0.45
14 11 0.18
15 2 0.03
16 6 0.10
17 1 0.02
18 7 0.11
19 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:29952 original size:10 final size:10
Alignment explanation
Indices: 29872--29954 Score: 82
Period size: 10 Copynumber: 8.1 Consensus size: 10
29862 AGTTTAAAAA
29872 TATTATTTATT
1 TATTA-TTATT
29883 TATTATTACTAT
1 TATTATTA-T-T
*
29895 TACTATTA-T
1 TATTATTATT
29904 TATCTATTA-T
1 TAT-TATTATT
29914 TATTATTATT
1 TATTATTATT
29924 TATTATTA-T
1 TATTATTATT
29933 TATTTATTATT
1 TA-TTATTATT
*
29944 TATTTTTATT
1 TATTATTATT
29954 T
1 T
29955 TTGTAGGTGC
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
9 11 0.17
10 35 0.56
11 9 0.14
12 8 0.13
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATTATT
Found at i:29956 original size:7 final size:7
Alignment explanation
Indices: 29878--29953 Score: 75
Period size: 7 Copynumber: 10.3 Consensus size: 7
29868 AAAATATTAT
29878 TTATTTA
1 TTATTTA
29885 TTATTACTA
1 TTATT--TA
29894 TTACTATTA
1 TTA-T-TTA
*
29903 TTATCTA
1 TTATTTA
29910 TTATTATTA
1 TTA-T-TTA
29919 TTATTTA
1 TTATTTA
29926 TTA-TTA
1 TTATTTA
29932 TTATTTA
1 TTATTTA
29939 TTATTTA
1 TTATTTA
29946 TT-TTTA
1 TTATTTA
29952 TT
1 TT
29954 TTTGTAGGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
6 12 0.20
7 28 0.47
8 3 0.05
9 15 0.25
10 1 0.02
11 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:31724 original size:11 final size:11
Alignment explanation
Indices: 31708--31733 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31698 TTTTTATTTG
31708 ATTTATTTATT
1 ATTTATTTATT
31719 ATTTATTTATT
1 ATTTATTTATT
31730 ATTT
1 ATTT
31734 CTCATCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:43807 original size:35 final size:35
Alignment explanation
Indices: 43768--43837 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
43758 TTACATTGAG
43768 ATAAACTTGATGAAATAACATACGTAAGTGAGAAT
1 ATAAACTTGATGAAATAACATACGTAAGTGAGAAT
*
43803 ATAAACTTGATGAAATAACCTACGTAAGTGAGAAT
1 ATAAACTTGATGAAATAACATACGTAAGTGAGAAT
43838 TATTAGTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (35 bp):
ATAAACTTGATGAAATAACATACGTAAGTGAGAAT
Found at i:47781 original size:9 final size:10
Alignment explanation
Indices: 47752--47784 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
47742 AAAACAAAAA
47752 TCCCAGTTTT
1 TCCCAGTTTT
47762 TCCCAGTTTTT
1 TCCCAG-TTTT
47773 TCCC-GTTTT
1 TCCCAGTTTT
47782 TCC
1 TCC
47785 GGTTTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 7 0.32
11 8 0.36
ACGTcount: A:0.06, C:0.33, G:0.09, T:0.52
Consensus pattern (10 bp):
TCCCAGTTTT
Found at i:48943 original size:31 final size:31
Alignment explanation
Indices: 48907--48981 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
48897 TTTTTACTTG
48907 TCAACAATTGTCAGTGACATTGTTGAATTTA
1 TCAACAATTGTCAGTGACATTGTTGAATTTA
48938 TCAACAATTGTCAGTGACATTGTTGAATTTA
1 TCAACAATTGTCAGTGACATTGTTGAATTTA
48969 TCAACAATTGTCA
1 TCAACAATTGTCA
48982 ACAATTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (31 bp):
TCAACAATTGTCAGTGACATTGTTGAATTTA
Found at i:49140 original size:2 final size:2
Alignment explanation
Indices: 49133--49164 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49123 CCGCCCCGAT
49133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49165 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49187 original size:32 final size:33
Alignment explanation
Indices: 49151--49233 Score: 141
Period size: 34 Copynumber: 2.5 Consensus size: 33
49141 TATATATATA
49151 TATATATATAATATTTTTA-TTTTTATATTAAT
1 TATATATATAATATTTTTATTTTTTATATTAAT
49183 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATA-TTTTTATTTTTTATATTAAT
*
49217 TATATATAAAATATTTT
1 TATATATATAATATTTT
49234 CGGGTTCGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 13 0.27
33 10 0.21
34 25 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATATATAATATTTTTATTTTTTATATTAAT
Found at i:49187 original size:34 final size:34
Alignment explanation
Indices: 49139--49233 Score: 133
Period size: 34 Copynumber: 2.8 Consensus size: 34
49129 CGATTATATA
49139 TATATATATATATATATATATAATATTTTTA-TTTT
1 TATAT-TA-ATATATATATATAATATTTTTATTTTT
49174 TATATTAAT-TATATATATAATATTTTTTATTTTT
1 TATATTAATATATATATATAATA-TTTTTATTTTT
*
49208 TATATTAAT-TATATATAAAATATTTT
1 TATATTAATATATATATATAATATTTT
49234 CGGGTTCGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
32 13 0.23
33 12 0.21
34 27 0.47
35 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATTAATATATATATATAATATTTTTATTTTT
Found at i:54801 original size:2 final size:2
Alignment explanation
Indices: 54794--54841 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
54784 TATGAAAATA
54794 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
54836 AT AT AT
1 AT AT AT
54842 GGTAATATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54923 original size:33 final size:33
Alignment explanation
Indices: 54881--54946 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
54871 TTAACTTTCA
* * * *
54881 GCTATATGGTTATGGTGTGATTTTGTCGATTTG
1 GCTATATGGTCATGGTATGAGTTTGTCAATTTG
54914 GCTATATGGTCATGGTATGAGTTTGTCAATTTG
1 GCTATATGGTCATGGTATGAGTTTGTCAATTTG
54947 AATATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (33 bp):
GCTATATGGTCATGGTATGAGTTTGTCAATTTG
Found at i:55671 original size:17 final size:16
Alignment explanation
Indices: 55640--55705 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
55630 TATTTTCTCA
*
55640 AAATTTTACTAATAAT
1 AAATTTTAATAATAAT
55656 AAATTTT-A-AATAAT
1 AAATTTTAATAATAAT
*
55670 AAGATGTT-ATAAATAA-
1 AA-ATTTTAAT-AATAAT
*
55686 AAATTTTAATCATAA-
1 AAATTTTAATAATAAT
55701 AAATT
1 AAATT
55706 AATAAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
14 8 0.19
15 18 0.43
16 11 0.26
17 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATTTTAATAATAAT
Found at i:55719 original size:14 final size:14
Alignment explanation
Indices: 55640--55694 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 14
55630 TATTTTCTCA
55640 AAATTTTACTAATAAT
1 AAATTTTA--AATAAT
55656 AAATTTTAAATAAT
1 AAATTTTAAATAAT
55670 AAGATGTTATAAATAA-
1 AA-AT-TT-TAAATAAT
55686 AAATTTTAA
1 AAATTTTAA
55695 TCATAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.08
14 10 0.28
15 4 0.11
16 12 0.33
17 7 0.19
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (14 bp):
AAATTTTAAATAAT
Found at i:59802 original size:20 final size:20
Alignment explanation
Indices: 59757--59795 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59747 TCATTTAGTC
* *
59757 TTTATTTTTCTCTTAAATTA
1 TTTATTCTTCTCTAAAATTA
59777 TTTATTCTTCTCTAAAATT
1 TTTATTCTTCTCTAAAATT
59796 TTATATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTCTTCTCTAAAATTA
Found at i:70391 original size:22 final size:22
Alignment explanation
Indices: 70346--70391 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
70336 TAACCGGTTT
* * **
70346 GGTGGGTCTGATCAACTGCGTC
1 GGTGGGTCAGATCAACCGAATC
70368 GGTGGGTCAGATCAACCGAATC
1 GGTGGGTCAGATCAACCGAATC
70390 GG
1 GG
70392 GTAAGTGGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.22, G:0.37, T:0.22
Consensus pattern (22 bp):
GGTGGGTCAGATCAACCGAATC
Found at i:71197 original size:13 final size:13
Alignment explanation
Indices: 71179--71204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71169 GTTCATTCTA
71179 TTTCAATTCCGAT
1 TTTCAATTCCGAT
71192 TTTCAATTCCGAT
1 TTTCAATTCCGAT
71205 AAATTTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTCAATTCCGAT
Found at i:71584 original size:25 final size:23
Alignment explanation
Indices: 71531--71584 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
71521 TAATATGTAT
* **
71531 TTTTTATTTTAAAAATTATTTGT
1 TTTTTATTTTAAAAATTAATTAA
71554 TGTTTTATTTTTAAAAATATAATTAA
1 T-TTTTA-TTTTAAAAAT-TAATTAA
71580 TTTTT
1 TTTTT
71585 TTATAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 5 0.20
25 14 0.56
26 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTATTTTAAAAATTAATTAA
Found at i:79046 original size:2 final size:2
Alignment explanation
Indices: 79039--79073 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79029 TTTCTTTTTC
79039 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 T
79074 TAGGTGGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82973 original size:159 final size:158
Alignment explanation
Indices: 82685--83002 Score: 627
Period size: 159 Copynumber: 2.0 Consensus size: 158
82675 CCGATGAGGA
82685 GATTTCCAGGCTCTTCACTTTGATTAACCTGACGGGACCAGAAGTCCAGCAAACCTTCTCCACAT
1 GATTTCCAGGCTCTTCACTTTGATTAACCTGACGGGACCAGAAGTCCAGCAAACCTTCTCCACAT
82750 GTTCCAAGCATTGTGCCAATCTCCCTCTGCAGCATATATCAAGACCAAGCTTACAGAGGTATACA
66 GTTCCAAGCATTGTGCCAATCTCCCTCTGCAGCATATATCAAGACCAAGCTTACAGAGGTATACA
82815 TTTTATTGGAGAATGATGTAATTCTTTT
131 TTTTATTGGAGAATGATGTAATTCTTTT
82843 GATTTCCAGGCTCTTCACTTTGATTAACCTGACGGGACCAGAAGTCCAGCAAAACCTTCTCCACA
1 GATTTCCAGGCTCTTCACTTTGATTAACCTGACGGGACCAGAAGTCCAGC-AAACCTTCTCCACA
82908 TGTTCCAAGCATTGTGCCAATCTCCCTCTGCAGCATATATCAAGACCAAGCTTACAGAGGTATAC
65 TGTTCCAAGCATTGTGCCAATCTCCCTCTGCAGCATATATCAAGACCAAGCTTACAGAGGTATAC
82973 ATTTTATTGGAGAATGATGTAATTCTTTT
130 ATTTTATTGGAGAATGATGTAATTCTTTT
83002 G
1 G
83003 CTGGATATTA
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 50 0.31
159 109 0.69
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (158 bp):
GATTTCCAGGCTCTTCACTTTGATTAACCTGACGGGACCAGAAGTCCAGCAAACCTTCTCCACAT
GTTCCAAGCATTGTGCCAATCTCCCTCTGCAGCATATATCAAGACCAAGCTTACAGAGGTATACA
TTTTATTGGAGAATGATGTAATTCTTTT
Found at i:89064 original size:19 final size:20
Alignment explanation
Indices: 89028--89069 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
89018 ATATGACCCA
*
89028 AAAAAAAAAAACTTTACCTC
1 AAAAAAAAAAACTATACCTC
*
89048 AAAAACAAAAAC-ATACCTC
1 AAAAAAAAAAACTATACCTC
89067 AAA
1 AAA
89070 TGACTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAAAAAAAAACTATACCTC
Found at i:97315 original size:2 final size:2
Alignment explanation
Indices: 97304--97399 Score: 63
Period size: 2 Copynumber: 54.0 Consensus size: 2
97294 GAACCCGAAA
* * *
97304 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
97341 -T AT AT AT AT A- AT -T A- AT AT AA AT A- AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97376 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
97400 CGGGGCAGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
1 12 0.16
2 64 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:97325 original size:9 final size:8
Alignment explanation
Indices: 97303--97394 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 8
97293 CGAACCCGAA
*
97303 AATATTAT
1 AATATAAT
97311 ATATATAATT
1 A-ATATAA-T
*
97321 AATATAAA
1 AATATAAT
97329 AATATAA-
1 AATATAAT
*
97336 AATATTAT
1 AATATAAT
97344 ATATATAATT
1 A-ATATAA-T
97354 AATATAAAT
1 AATAT-AAT
97363 AATATAA-
1 AATATAAT
*
97370 AATATTAT
1 AATATAAT
97378 ATATATATAT
1 A-ATATA-AT
97388 ATATATA
1 A-ATATA
97395 TATATCGGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
7 12 0.17
8 12 0.17
9 30 0.43
10 15 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATAAT
Found at i:97338 original size:33 final size:34
Alignment explanation
Indices: 97301--97384 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
97291 TTCGAACCCG
97301 AAAATATTATATATATAATTAATATAAA-AATAT
1 AAAATATTATATATATAATTAATATAAATAATAT
97334 AAAATATTATATATATAATTAATATAAATAATAT
1 AAAATATTATATATATAATTAATATAAATAATAT
97368 AAAATATTATATATATA
1 AAAATATTATATATATA
97385 TATATATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 28 0.56
34 22 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAATAATAT
Found at i:97390 original size:42 final size:42
Alignment explanation
Indices: 97313--97392 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
97303 AATATTATAT
*
97313 ATATAATTAATATAAAAATATAAAATATTATATATATAATTA
1 ATATAAATAATATAAAAATATAAAATATTATATATATAATTA
* *
97355 ATATAAATAATAT-AAAATATTATATATATATATATATA
1 ATATAAATAATATAAAAATATAAAATAT-TATATATATA
97393 TATATATCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 12 0.35
42 22 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (42 bp):
ATATAAATAATATAAAAATATAAAATATTATATATATAATTA
Found at i:107390 original size:28 final size:28
Alignment explanation
Indices: 107323--107382 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
107313 AAAATATATT
* *
107323 TTCATTCTCTAAAATTGTATAAATTTAAA
1 TTCA-TCTTTAAAATTGTAAAAATTTAAA
* *
107352 TTTATCTTTAAAATTTTAAAAATTTAAA
1 TTCATCTTTAAAATTGTAAAAATTTAAA
107380 TTC
1 TTC
107383 GTTTTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (28 bp):
TTCATCTTTAAAATTGTAAAAATTTAAA
Done.