Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 122 of 182
Found at i:39268713 original size:59 final size:60
Alignment explanation
Indices: 39268607--39268719 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
39268597 TTTAGCCTTT
*
39268607 AAACTTTTCAAAAATTATTTTTTGGCCCTCGAACTTTCTAAAAATTCAAATTTGATCATC
1 AAACTTTTCAAAAATTATTTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTGATCATC
* *
39268667 AAACTTTTTAAAAATTATGTTTTT-ACCCT-TAACTTTCTAAAAATTCAAATTTG
1 AAACTTTTCAAAAATTAT-TTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTG
39268720 GCCCTCGAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 23 0.47
60 21 0.43
61 5 0.10
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (60 bp):
AAACTTTTCAAAAATTATTTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTGATCATC
Found at i:39268724 original size:29 final size:30
Alignment explanation
Indices: 39268627--39268740 Score: 90
Period size: 30 Copynumber: 3.9 Consensus size: 30
39268617 AAAATTATTT
* *
39268627 TTTGGCCCTCGAACTTTCTAAAAATTCAAA
1 TTTGACCCTCAAACTTTCTAAAAATTCAAA
* * * **
39268657 TTTGATCATCAAACTTTTTAAAAATT-ATGT
1 TTTGACCCTCAAACTTTCTAAAAATTCA-AA
* *
39268687 TTTTACCCT-TAACTTTCTAAAAATTCAAA
1 TTTGACCCTCAAACTTTCTAAAAATTCAAA
* * *
39268716 TTTGGCCCTCGAACTTT-AAAAAATT
1 TTTGACCCTCAAACTTTCTAAAAATT
39268741 TCATTTTGAC
Statistics
Matches: 63, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
29 29 0.46
30 34 0.54
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTGACCCTCAAACTTTCTAAAAATTCAAA
Found at i:39268731 original size:59 final size:60
Alignment explanation
Indices: 39268607--39268740 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 60
39268597 TTTAGCCTTT
* * *
39268607 AAACTTTTCAAAAATTATTTTTTGGCCCTCGAACTTTCTAAAAATTCAAATTTGATCATC
1 AAACTTTTAAAAAATTATTTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTGACCATC
* * * *
39268667 AAACTTTTTAAAAATTATGTTTTT-ACCCT-TAACTTTCTAAAAATTCAAATTTGGCCCTC
1 AAACTTTTAAAAAATTAT-TTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTGACCATC
*
39268726 GAAC-TTTAAAAAATT
1 AAACTTTTAAAAAATT
39268741 TCATTTTGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
58 10 0.15
59 29 0.45
60 21 0.32
61 5 0.08
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (60 bp):
AAACTTTTAAAAAATTATTTTTTGACCCTCGAACTTTCTAAAAATTCAAATTTGACCATC
Found at i:39274140 original size:20 final size:19
Alignment explanation
Indices: 39274107--39274188 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 19
39274097 CATTTTACCC
*
39274107 AAAAAAAG-AGAGAAAAGA
1 AAAAAAAGAAAAGAAAAGA
39274125 AAATAAAAGAAAAGAAAAAGGA
1 AAA-AAAAGAAAAG-AAAA-GA
* *
39274147 AACAGAA-AAAAGAAAAGA
1 AAAAAAAGAAAAGAAAAGA
*
39274165 GAAAAAAGAAGAAGAAAAGA
1 AAAAAAAGAA-AAGAAAAGA
39274185 AAAA
1 AAAA
39274189 GGAGAGGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
18 9 0.18
19 11 0.22
20 20 0.39
21 7 0.14
22 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (19 bp):
AAAAAAAGAAAAGAAAAGA
Found at i:39274154 original size:6 final size:5
Alignment explanation
Indices: 39274117--39274187 Score: 65
Period size: 5 Copynumber: 14.2 Consensus size: 5
39274107 AAAAAAAGAG
* * * * *
39274117 AGAAA AGAAA ATAAA AGAAA AGAAAA AGGAA ACAGA A-AAA AGAAA AGAGA
1 AGAAA AGAAA AGAAA AGAAA AG-AAA AGAAA AGAAA AGAAA AGAAA AGAAA
39274167 A-AAA AGAAGA AGAAA AGAAA A
1 AGAAA AGAA-A AGAAA AGAAA A
39274188 AGGAGAGGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
4 6 0.11
5 37 0.70
6 10 0.19
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (5 bp):
AGAAA
Found at i:39274160 original size:7 final size:7
Alignment explanation
Indices: 39274108--39274174 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
39274098 ATTTTACCCA
39274108 AAAAAAG
1 AAAAAAG
39274115 AGAGAAAAG
1 A-A-AAAAG
39274124 AAAATAA-
1 AAAA-AAG
39274131 AAGAAAAG
1 AA-AAAAG
39274139 -AAAAAG
1 AAAAAAG
* *
39274145 GAAACAG
1 AAAAAAG
39274152 AAAAAAG
1 AAAAAAG
*
39274159 AAAAGAG
1 AAAAAAG
39274166 AAAAAAG
1 AAAAAAG
39274173 AA
1 AA
39274175 GAAGAAAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 5 0.10
7 32 0.65
8 6 0.12
9 6 0.12
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:39274179 original size:15 final size:15
Alignment explanation
Indices: 39274108--39274177 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 15
39274098 ATTTTACCCA
39274108 AAAAAAGAGAGAAAAG
1 AAAAAAGA-AGAAAAG
39274124 AAAATAA-AAGAAAAG
1 AAAA-AAGAAGAAAAG
39274139 -AAAAAG--GAAACAG
1 AAAAAAGAAGAAA-AG
*
39274152 AAAAAAGAA-AAGAG
1 AAAAAAGAAGAAAAG
39274166 AAAAAAGAAGAA
1 AAAAAAGAAGAA
39274178 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 15
0.74 0.02 0.24
Matches are distributed among these distances:
12 4 0.09
13 4 0.09
14 20 0.43
15 11 0.24
16 5 0.11
17 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAAAGAAGAAAAG
Found at i:39275190 original size:75 final size:75
Alignment explanation
Indices: 39275061--39275255 Score: 246
Period size: 75 Copynumber: 2.6 Consensus size: 75
39275051 ATGAAGTGAC
* * * * **
39275061 CATCATCTTGATAAGATACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAA
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCAAAGCTCAATACGAGTGAAA
*
39275126 CTTCAAACTA
66 CTTCAAACCA
* * * *
39275136 CATCTTCTTGATGAGATACAGAGAAGTGGACCGAAACAATGAAGTAAAGTTCAATACGAGTGAAA
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCAAAGCTCAATACGAGTGAAA
* *
39275201 CTTTAAACCC
66 CTTCAAACCA
* * *
39275211 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAATAATGAAGC
1 CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGC
39275256 GGTCATCTTC
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 101 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (75 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCAAAGCTCAATACGAGTGAAA
CTTCAAACCA
Found at i:39275267 original size:48 final size:48
Alignment explanation
Indices: 39275210--39275353 Score: 153
Period size: 48 Copynumber: 3.0 Consensus size: 48
39275200 ACTTTAAACC
* * * * *
39275210 CCATCTTCCTAATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGG
1 CCATCTTCCTGATGAGATACAGAGAAATGGACCAAAACAATGAAGCAG
* * * * *
39275258 TCATCTTCCTGATAAGATTCAAAAAAATGGACCAAAACAATGAAGCAG
1 CCATCTTCCTGATGAGATACAGAGAAATGGACCAAAACAATGAAGCAG
* * * * *
39275306 CCATCTTCTTGATGAGATACAGAGAAATAGACTAAAATAATGTAGCAG
1 CCATCTTCCTGATGAGATACAGAGAAATGGACCAAAACAATGAAGCAG
39275354 AGATCAAGAT
Statistics
Matches: 76, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (48 bp):
CCATCTTCCTGATGAGATACAGAGAAATGGACCAAAACAATGAAGCAG
Found at i:39275475 original size:48 final size:48
Alignment explanation
Indices: 39275403--39275495 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
39275393 TTCAAACCTC
* * * *
39275403 CATCTTCCTGATGAGATACCTAGAAGTGAATCAAAACGATGAAGCGAT
1 CATCTTCCTAATGAGATACATAGAAGTGAACCAAAACAATGAAGCGAT
*
39275451 CATCTTCCTAATGAGATACATAGAAGTGGACCAAAACAATGAAGC
1 CATCTTCCTAATGAGATACATAGAAGTGAACCAAAACAATGAAGC
39275496 AGAGCTCAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACATAGAAGTGAACCAAAACAATGAAGCGAT
Found at i:39275551 original size:144 final size:144
Alignment explanation
Indices: 39275290--39275593 Score: 342
Period size: 144 Copynumber: 2.1 Consensus size: 144
39275280 AAAAATGGAC
* * * * *
39275290 CAAAACAATGAAGCAGCCATCTTCTTGATGAGATACAGAGAAATAGACTAAAATAATGTAGCAGA
1 CAAAACAATGAAGCAGCCATCTTCCTAATGAGATACAGAGAAATAGACCAAAACAATGAAGCAGA
* * * * * *
39275355 GATCAAGATCCCTAAGTTATAGTGGAGTAGAATGAAACTTCAAACCTCCATCTTCCTGATGAGAT
66 GATCAACATCCCGAAGTTACAGTGGAATAGAACGAAACTTCAAAACTCCATCTTCCTGATGAGAT
**
39275420 ACCTAGAAGTGAAT
131 ACAGAGAAGTGAAT
* * * * *
39275434 CAAAACGATGAAGC-GATCATCTTCCTAATGAGATACATAGAAGTGGACCAAAACAATGAAGCAG
1 CAAAACAATGAAGCAG-CCATCTTCCTAATGAGATACAGAGAAATAGACCAAAACAATGAAGCAG
* * * * *
39275498 AGCTCAACATTCCCGAGGTTACAGTGGAATGGAGCGAAACTTCAAAACT-CATCTTCTTGATGAG
65 AGATCAACA-TCCCGAAGTTACAGTGGAATAGAACGAAACTTCAAAACTCCATCTTCCTGATGAG
* *
39275562 ATATAGAGAAGTGGAT
129 ATACAGAGAAGTGAAT
*
39275578 CAAAATAATGAAGCAG
1 CAAAACAATGAAGCAG
39275594 AGCTCAATGT
Statistics
Matches: 130, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
143 1 0.01
144 97 0.75
145 32 0.25
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (144 bp):
CAAAACAATGAAGCAGCCATCTTCCTAATGAGATACAGAGAAATAGACCAAAACAATGAAGCAGA
GATCAACATCCCGAAGTTACAGTGGAATAGAACGAAACTTCAAAACTCCATCTTCCTGATGAGAT
ACAGAGAAGTGAAT
Found at i:39275717 original size:93 final size:96
Alignment explanation
Indices: 39275450--39275720 Score: 334
Period size: 96 Copynumber: 2.9 Consensus size: 96
39275440 GATGAAGCGA
* * * * * *
39275450 TCATCTTCCTAATGAGATACATAGAAGTGGACCAAAACAATGAAGCAGAGCTCAACATTCC-CGA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGAGCTCAATA-TCCTCGA
*
39275514 GGTTACAGTGGAATGGAGCGAAACTTCAAAAC
65 GGTTACAGTGGAGTGGAGCGAAACTTCAAAAC
* * *
39275546 TCATCTTCTTGATGAGATATAGAGAAGTGGATCAAAATAATGAAGCAGAGCTCAATGTCCTTGAG
1 TCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGAGCTCAATATCCTCGAG
* * * *
39275611 GTCACAATGGAGTGGAGCGATACTTCAAACC
66 GTTACAGTGGAGTGGAGCGAAACTTCAAAAC
* * * *
39275642 T-ATCTTCTTGGTGAGATACAGA-AAGTGGGTCAAAATAA-GTAGCAGATCTCAATATCCTCGAG
1 TCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGAGCTCAATATCCTCGAG
*
39275704 GTTACAGTAGAGTGGAG
66 GTTACAGTGGAGTGGAG
39275721 TAAAACACCA
Statistics
Matches: 150, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
93 34 0.23
94 15 0.10
95 22 0.15
96 79 0.53
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (96 bp):
TCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGAGCTCAATATCCTCGAG
GTTACAGTGGAGTGGAGCGAAACTTCAAAAC
Found at i:39275949 original size:46 final size:46
Alignment explanation
Indices: 39275827--39275959 Score: 164
Period size: 45 Copynumber: 2.9 Consensus size: 46
39275817 GTTACATCAC
* *
39275827 CATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTAAAGCTAT
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCATATTAAAGCAAT
*
39275872 CATCCAATCTTTTACCCCT-AGTCAAGAGGGGCATATTTAAGCAA-
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCATATTAAAGCAAT
* * * * *
39275916 CTGTCTACTCTTTTATCCCTAAGTCAAGAGGGGCATATTGAAGC
1 C-ATCCAATCTTTTACCCCTAAGTCAAGAGGGGCATATTAAAGC
39275960 TGTAACAACT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
44 2 0.03
45 53 0.69
46 22 0.29
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (46 bp):
CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCATATTAAAGCAAT
Found at i:39278509 original size:45 final size:44
Alignment explanation
Indices: 39278414--39278680 Score: 253
Period size: 45 Copynumber: 6.0 Consensus size: 44
39278404 GAAGCTACCA
39278414 TCCAATCTTTTACCCCTAGTCAAGAGAGGGCAGATT-AAGGCCACCA-
1 TCCAATCTTTTA-CCCTAGTCAAGAG-GGGCAGATTGAA-GCCA-CAT
39278460 TCCAATCTTTTACTCCTAGTCAAGAGGGGCAGATTGAAGCCACAT
1 TCCAATCTTTTAC-CCTAGTCAAGAGGGGCAGATTGAAGCCACAT
*
39278505 TCCAATCTTTTACCCTTAGTCAAGAGAGGCAGATTGAAGCCACAT
1 TCCAATCTTTTACCC-TAGTCAAGAGGGGCAGATTGAAGCCACAT
* * *
39278550 TCTAATCTTTTACCCTTAATCAAGAGGGGCAGATTAAAG---C-T
1 TCCAATCTTTTACCC-TAGTCAAGAGGGGCAGATTGAAGCCACAT
* * * *
39278591 GTCCGATCTTTTACCTCTAATCAATAGGGGTAGATTGAAGCCACCA-
1 -TCCAATCTTTTACC-CTAGTCAAGAGGGGCAGATTGAAGCCA-CAT
* * * * *
39278637 TCTAGTCTTTTACCTCT-GATCCAGAGGGGCAGAATGAAGTCACA
1 TCCAATCTTTTACC-CTAG-TCAAGAGGGGCAGATTGAAGCCACA
39278681 CACACAAATC
Statistics
Matches: 190, Mismatches: 19, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 33 0.17
43 1 0.01
44 6 0.03
45 122 0.64
46 27 0.14
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (44 bp):
TCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGCCACAT
Found at i:39278646 original size:87 final size:87
Alignment explanation
Indices: 39278414--39278669 Score: 272
Period size: 87 Copynumber: 2.9 Consensus size: 87
39278404 GAAGCTACCA
*
39278414 TCCAATCTTTTACCCCTAGTCAAGAGAGGGCAGATT-AAGGCCACCATCCAATCTTTTACTCC-T
1 TCCAATCTTTTA-CCCTAGTCAAGAG-GGGCAGATTGAA-GCCACCATCTAATCTTTTAC-CCTT
* *
39278477 AGTCAAGAGGGGCAGATTGAAGCCACAT
62 AATCAAGAGGGGCAGATTAAAG-C-CAT
*
39278505 TCCAATCTTTTACCCTTAGTCAAGAGAGGCAGATTGAAGCCA-CATTCTAATCTTTTACCCTTAA
1 TCCAATCTTTTACCC-TAGTCAAGAGGGGCAGATTGAAGCCACCA-TCTAATCTTTTACCCTTAA
39278569 TCAAGAGGGGCAGATTAAAG-C-T
64 TCAAGAGGGGCAGATTAAAGCCAT
* * * * * *
39278591 GTCCGATCTTTTACCTCTAATCAATAGGGGTAGATTGAAGCCACCATCTAGTCTTTTA-CCTCTG
1 -TCCAATCTTTTACC-CTAGTCAAGAGGGGCAGATTGAAGCCACCATCTAATCTTTTACCCT-TA
*
39278655 ATCCAGAGGGGCAGA
63 ATCAAGAGGGGCAGA
39278670 ATGAAGTCAC
Statistics
Matches: 145, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
86 4 0.03
87 62 0.43
88 3 0.02
89 4 0.03
90 48 0.33
91 24 0.17
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (87 bp):
TCCAATCTTTTACCCTAGTCAAGAGGGGCAGATTGAAGCCACCATCTAATCTTTTACCCTTAATC
AAGAGGGGCAGATTAAAGCCAT
Found at i:39278668 original size:132 final size:134
Alignment explanation
Indices: 39278417--39278680 Score: 304
Period size: 132 Copynumber: 2.0 Consensus size: 134
39278407 GCTACCATCC
* * *
39278417 AATCTTTTACCCCTAGTCAAGAGAGGGCAGATTAAGGCCACCATCCAATCTTTTACTCCTAGTCA
1 AATCTTTTACCCCTAATCAAGAGAGGGCAGATTAAAG-C-CCATCCAATCTTTTACTCCTAATCA
* *
39278482 AGAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCTTAGTCAAGAGAGGCAGATTGAAGCCA
64 AGAGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCTGAGTCAAGAGAGGCAGAATGAAGCCA
39278547 CATTCT
129 CATTCT
* ** *
39278553 AATCTTTTACCCTTAATCAAGAG-GGGCAGATTAAAG-CTGTCCGATCTTTTAC-CTCTAATCAA
1 AATCTTTTACCCCTAATCAAGAGAGGGCAGATTAAAGCCCATCCAATCTTTTACTC-CTAATCAA
* * * * * * *
39278615 TAGGGGTAGATTGAAGCCACCA-TCTAGTCTTTTACCTCTGA-TCCAGAGGGGCAGAATGAAGTC
65 GAGGGGCAGATTGAAGCCA-CATTCCAATCTTTTACC-CTGAGTCAAGAGAGGCAGAATGAAGCC
39278678 ACA
128 ACA
39278681 CACACAAATC
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
131 1 0.01
132 70 0.64
133 5 0.05
135 12 0.11
136 21 0.19
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (134 bp):
AATCTTTTACCCCTAATCAAGAGAGGGCAGATTAAAGCCCATCCAATCTTTTACTCCTAATCAAG
AGGGGCAGATTGAAGCCACATTCCAATCTTTTACCCTGAGTCAAGAGAGGCAGAATGAAGCCACA
TTCT
Found at i:39280407 original size:30 final size:27
Alignment explanation
Indices: 39280342--39280449 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 27
39280332 ACCTGTAAAG
*
39280342 TCCCTAAACTTTTC-AAAATTCCATTTTGA
1 TCCCTAAAC-TTTCAAAAATT--ATTTTTA
39280371 -CCCTAAACTTTCTAAAAATTATGTTTTA
1 TCCCTAAACTTTC-AAAAATTAT-TTTTA
*
39280399 TCCCCTAAACTTGTCAAAAAGTATTTTTA
1 T-CCCTAAACTT-TCAAAAATTATTTTTA
39280428 TCCCTCAAACTTTCCAAAAATT
1 TCCCT-AAACTTT-CAAAAATT
39280450 CAAATTTGAC
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
27 6 0.09
28 17 0.25
29 25 0.37
30 18 0.26
31 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (27 bp):
TCCCTAAACTTTCAAAAATTATTTTTA
Found at i:39282056 original size:183 final size:180
Alignment explanation
Indices: 39281774--39282255 Score: 557
Period size: 183 Copynumber: 2.7 Consensus size: 180
39281764 TTGAGCATCC
* * * *
39281774 TTAACGATTAGTACCTAAAGTGCTAAC-TAAATAAAACTTTAAGTACCTACTTTG-ATAAAAAAA
1 TTAACAATTGGTACCTAAAGTGGTAACAT-AATAAAACTTTAGGTACCTACTTTGTA-AAAAAAA
** *
39281837 AACCCTTTAGGTACCTAAATAGGAAAAGTTGCATAGTTTAAGTATCTAGAGTGGTAACAAATTAA
64 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTATCTA-AGTGGTAACAAATTAA
*
39281902 AAATGTCATTG-G-CATAATTTGGTTGGTTTGAA-T-TCTTTTTGTAACGAGAA
128 AAATGTCA-TGAGTCATAATTTGATTGGTTTGAATTGTCTTTTTGTAACGAGAA
* *
39281952 TTAACAGTTGGTACCTAAAGTGGTAACATAATAAAACTTTAGGTGCCTACTTTGGTCAAAACAAA
1 TTAACAATTGGTACCTAAAGTGGTAACATAATAAAACTTTAGGTACCTACTTT-GT---AA-AAA
* * *
39282017 AAAAAAACTTTAGGTATCTAAATGGGAAAAGTTGCATAGTATAAATATCTATAGTGGTAACAAAT
61 AAAAAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTATCTA-AGTGGTAACAAAT
* * * * * *
39282082 TAAAAATGTCATGAGTCATAATTTGATTTGTTTGAATTGTTTTTTTTTAATGTGAG
125 TAAAAATGTCATGAGTCATAATTTGATTGGTTTGAATTGTCTTTTTGTAACGAGAA
* * * * * * * *
39282138 TTAACAATTTGAATCTAAAATGGTAATAGAATAAAACTTTAGGTACTTACTTTGT--AAAAAATA
1 TTAACAATTGGTACCTAAAGTGGTAACATAATAAAACTTTAGGTACCTACTTTGTAAAAAAAAAA
*
39282201 AACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAACGTGGTAA
66 AACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTATCTAA-GTGGTAA
39282256 ATTTTGGGGA
Statistics
Matches: 258, Mismatches: 34, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
178 46 0.18
179 58 0.22
182 3 0.01
183 74 0.29
184 18 0.07
185 3 0.01
186 56 0.22
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (180 bp):
TTAACAATTGGTACCTAAAGTGGTAACATAATAAAACTTTAGGTACCTACTTTGTAAAAAAAAAA
AACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTATCTAAGTGGTAACAAATTAAAAA
TGTCATGAGTCATAATTTGATTGGTTTGAATTGTCTTTTTGTAACGAGAA
Found at i:39283534 original size:175 final size:176
Alignment explanation
Indices: 39282990--39283930 Score: 1114
Period size: 179 Copynumber: 5.3 Consensus size: 176
39282980 GCAATAGAAT
39282990 AAAACTTTAGGTACCTAAATGGGAAAA-TTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * * *
39283054 AAAT-TCATGTGTCATAATTTGATTGGTTTGAATTCTTTTTTTTTAATGTGAGTTAA-TAGCTGA
66 AAATGTCATGTGTCATAATTTGATTGGTTTGAATTC--TTTTTTTAACGTGAGTTAACGA-TTGG
** * *
39283117 TACCTAAAGTGGTAGGAAAATAAAACTTTAGGTACCTACTTTGATAAAA
128 TACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAA
* *
39283166 AAAACTTTAGGCACCTAAATGGGAAAAGTTTGCATAGTTTAAGTACCTAAAGTGGGAATAGATTA
1 AAAACTTTAGGTACCTAAATGGGAAAAG-TTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
** * *
39283231 AAAATGTCACATGTCATAATTTGATTGGTTTGAATTTTTTTTTTTTTTGTAACATGAGTTAACCG
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGAA-----TTCTTTTTT-TAACGTGAGTTAA-CG
* * *
39283296 -TTGCTACCTAAAGTGGCAATAGGATAAAACTTTAGGTACCTACTTTGGTAAAA
123 ATTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAA
* * *
39283349 AAAACTTTAGGTACTTAAAT-GGAAAAGTTGCATAGTTTTAAATACCTAAAGTGATAATAGATTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAG-TTTAAGTACCTAAAGTGGTAATAGATTA
* * * *
39283413 AAAATGTCATTTGTCATGATTTGATTGG-TTGAATACTTTTTTAAACGTGAGTTAACGATTGGTA
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGAATTCTTTTTTTAACGTGAGTTAACGATTGGTA
*
39283477 CCTAAAGTGGTAATAGAATAAAACTTT-GGATATCTAC-TTGGTAAAA
130 CCTAAAGTGGTAATAGAATAAAACTTTAGG-TACCTACTTTGGTAAAA
* * *
39283523 AAAACCTTTAGGTACCTAAATGGAAAAAGTTGCATAATTTAAGTACCTAAAGTGGTAATAAATTA
1 AAAA-CTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
* * * *
39283588 AAAATATCATGTGTCATAATTTGATTGGTTTGGATTTTTTTTTTTAACATGAGTTAACTG-TTGG
65 AAAATGTCATGTGTCATAATTTGATTGGTTT-GAATTCTTTTTTTAACGTGAGTTAAC-GATTGG
* *
39283652 TACCTAAAGTGGTAACAGAATAAAACTTTAGGTATCTACTTTGGTTAAAAA
128 TACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGG-T-AAAA
* * * * *
39283703 AAAACATTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAA-TAATCTAAAGTGGTAATAAAATA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGT-ACCTAAAGTGGTAATAGATTA
* * * *
39283767 AAAATGTCACGTGTCATAATTT-ATTTTGTTTGGATTCTTTTTTTTAAACGTGAGTTAACAATTG
65 AAAATGTCATGTGTCATAATTTGA-TTGGTTTGAATTC-TTTTTTT-AACGTGAGTTAACGATTG
* * * *
39283831 GTACCTAAAGTGGTAATAGAATAAAACTTTAAGCACTTACTTTGATAAAAAAA
127 GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGT---AAAA
** * *
39283884 AAAACTTTAGACACCTAAATGAGAAAGGTT-CATAGTTTAAGTACCTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTA
39283931 TTTTGATATT
Statistics
Matches: 660, Mismatches: 74, Indels: 58
0.83 0.09 0.07
Matches are distributed among these distances:
174 17 0.03
175 112 0.17
176 48 0.07
177 60 0.09
178 52 0.08
179 113 0.17
180 76 0.12
181 43 0.07
182 63 0.10
183 74 0.11
184 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (176 bp):
AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
AAATGTCATGTGTCATAATTTGATTGGTTTGAATTCTTTTTTTAACGTGAGTTAACGATTGGTAC
CTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAA
Found at i:39283761 original size:179 final size:178
Alignment explanation
Indices: 39282990--39283930 Score: 1145
Period size: 175 Copynumber: 5.3 Consensus size: 178
39282980 GCAATAGAAT
39282990 AAAACTTTAGGTACCTAAATGGGAAAA-TTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* * * *
39283054 AAAT-TCATGTGTCATAATTTGATTGGTTTGAATTCTTTTTTTTTAATGTGAGTTAA-TAGCTGA
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATT-TTTTTTTTTAACGTGAGTTAACT-GTTGG
** * *
39283117 TACCTAAAGTGGTAGGAAAATAAAACTTTAGGTACCTACTTTGAT-AAAA
129 TACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAAA
* *
39283166 AAAACTTTAGGCACCTAAATGGGAAAAGTTTGCATAGTTTAAGTACCTAAAGTGGGAATAGATTA
1 AAAACTTTAGGTACCTAAATGGGAAAAG-TTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTA
** * * *
39283231 AAAATGTCACATGTCATAATTTGATTGGTTTGAATTTTTTTTTTTTTTGTAACATGAGTTAACCG
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGGA----TTTTTTTTTT-TAACGTGAGTTAACTG
* * *
39283296 TTGCTACCTAAAGTGGCAATAGGATAAAACTTTAGGTACCTACTTTGGT-AAAA
125 TTGGTACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAAA
* * *
39283349 AAAACTTTAGGTACTTAAAT-GGAAAAGTTGCATAGTTTTAAATACCTAAAGTGATAATAGATTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAG-TTTAAGTACCTAAAGTGGTAATAGATTA
* * * ** *
39283413 AAAATGTCATTTGTCATGATTTGATTGG-TT-GAATACTTTTTTAAACGTGAGTTAAC-GATTGG
65 AAAATGTCATGTGTCATAATTTGATTGGTTTGGATTTTTTTTTTTAACGTGAGTTAACTG-TTGG
*
39283475 TACCTAAAGTGGTAATAGAATAAAACTTT-GGATATCTAC-TTGGTAAAAA
129 TACCTAAAGTGGTAATAGAATAAAACTTTAGG-TACCTACTTTGGTAAAAA
* * * *
39283524 AAACCTTTAGGTACCTAAATGGAAAAAGTTGCATAATTTAAGTACCTAAAGTGGTAATAAATTAA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
* *
39283589 AAATATCATGTGTCATAATTTGATTGGTTTGGATTTTTTTTTTTAACATGAGTTAACTGTTGGTA
66 AAATGTCATGTGTCATAATTTGATTGGTTTGGATTTTTTTTTTTAACGTGAGTTAACTGTTGGTA
* *
39283654 CCTAAAGTGGTAACAGAATAAAACTTTAGGTATCTACTTTGGTTAAAAA
131 CCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGG-TAAAAA
* * * * *
39283703 AAAACATTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAA-TAATCTAAAGTGGTAATAAAATA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGT-ACCTAAAGTGGTAATAGATTA
* * * **
39283767 AAAATGTCACGTGTCATAATTT-ATTTTGTTTGGATTCTTTTTTTTAAACGTGAGTTAACAATTG
65 AAAATGTCATGTGTCATAATTTGA-TTGGTTTGGATT-TTTTTTTTTAACGTGAGTTAACTGTTG
* * * *
39283831 GTACCTAAAGTGGTAATAGAATAAAACTTTAAGCACTTACTTTGATAAAAAAA
128 GTACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGT--AAAAA
** * *
39283884 AAAACTTTAGACACCTAAATGAGAAAGGTT-CATAGTTTAAGTACCTA
1 AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTA
39283931 TTTTGATATT
Statistics
Matches: 663, Mismatches: 76, Indels: 48
0.84 0.10 0.06
Matches are distributed among these distances:
174 8 0.01
175 120 0.18
176 48 0.07
177 60 0.09
178 49 0.07
179 119 0.18
180 77 0.12
181 40 0.06
182 65 0.10
183 77 0.12
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (178 bp):
AAAACTTTAGGTACCTAAATGGGAAAAGTTGCATAGTTTAAGTACCTAAAGTGGTAATAGATTAA
AAATGTCATGTGTCATAATTTGATTGGTTTGGATTTTTTTTTTTAACGTGAGTTAACTGTTGGTA
CCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGGTAAAAA
Found at i:39283812 original size:357 final size:358
Alignment explanation
Indices: 39282990--39283930 Score: 1221
Period size: 357 Copynumber: 2.6 Consensus size: 358
39282980 GCAATAGAAT
*
39282990 AAAACTTTAGGTACCTAAATGGGAAAA-TTGCATAGTTTAAGT-ACCTAAAGTGGTAATAGATTA
1 AAAACTTTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAA-TAACCTAAAGTGGTAATAGATTA
* * * * ** *
39283053 AAAAT-TCATGTGTCATAATTTGATTGGTTTGAATTCTTTTTTTTTAATGTGAGTTAATAGCTGA
65 AAAATGTCATGTGTCATAATTTGATTTGTTTGAATTCTTTTTTTTAAACGTGAGTTAACAATTGG
** *
39283117 TACCTAAAGTGGTAGGAAAATAAAACTTTAGGTACCTACTTTGATAAAAAAAACTTTAGGCACCT
130 TACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGATAAAAAAAACTTTAGGCACCT
* * * *
39283182 AAATGGGAAAAGTTTGCATAGTTTAAGTACCTAAAGTGGGAATAGATTAAAAATGTCACATGTCA
195 AAATGGAAAAAGTTTGCATAATTTAAGTACCTAAAGTGGGAATAAATTAAAAATATCACATGTCA
39283247 TAATTTGATTGGTTTGAATTTTTTTTTTTTTTGTAACATGAGTTAACCGTTGCTACCTAAAGTGG
260 TAATTTGATTGGTTTGAA---TTTTTTTTTTTGTAACATGAGTTAACCGTTGCTACCTAAAGTGG
* *
39283312 CAATAGGATAAAACTTTAGGTACCTACTTTGGTAAAA
322 CAACAGAATAAAACTTTAGGTACCTACTTTGGTAAAA
*
39283349 AAAACTTTAGGTACTTAAAT-GGAAAAGTTGCATAGTTTTAA-ATACCTAAAGTGATAATAGATT
1 AAAACTTTAGGTACTTAAATGGGAAAAGTTGCATAG-TTTAATA-ACCTAAAGTGGTAATAGATT
* * * * *
39283412 AAAAATGTCATTTGTCATGATTTGA-TTGGTTGAATAC--TTTTTTAAACGTGAGTTAACGATTG
64 AAAAATGTCATGTGTCATAATTTGATTTGTTTGAATTCTTTTTTTTAAACGTGAGTTAACAATTG
* * *
39283474 GTACCTAAAGTGGTAATAGAATAAAACTTT-GGATATCTAC-TTGGTAAAAAAAACCTTTAGGTA
129 GTACCTAAAGTGGTAATAGAATAAAACTTTAGG-TACCTACTTTGATAAAAAAAA-CTTTAGGCA
* **
39283537 CCTAAATGGAAAAAG-TTGCATAATTTAAGTACCTAAAGTGGTAATAAATTAAAAATATCATGTG
192 CCTAAATGGAAAAAGTTTGCATAATTTAAGTACCTAAAGTGGGAATAAATTAAAAATATCACATG
* * *
39283601 TCATAATTTGATTGGTTTGGA-TTTTTTTTTT-TAACATGAGTTAACTGTTGGTACCTAAAGTGG
257 TCATAATTTGATTGGTTTGAATTTTTTTTTTTGTAACATGAGTTAACCGTTGCTACCTAAAGTGG
* *
39283664 TAACAGAATAAAACTTTAGGTATCTACTTTGGTTAAAAA
322 CAACAGAATAAAACTTTAGGTACCTACTTTGG-T-AAAA
* * * *
39283703 AAAACATTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAATAATCTAAAGTGGTAATAAAATAA
1 AAAACTTTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAATAACCTAAAGTGGTAATAGATTAA
* *
39283768 AAATGTCACGTGTCATAATTT-ATTTTGTTTGGATTCTTTTTTTTAAACGTGAGTTAACAATTGG
66 AAATGTCATGTGTCATAATTTGA-TTTGTTTGAATTCTTTTTTTTAAACGTGAGTTAACAATTGG
* * * *
39283832 TACCTAAAGTGGTAATAGAATAAAACTTTAAGCACTTACTTTGATAAAAAAAAAAACTTTAGACA
130 TACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGAT---AAAAAAAACTTTAGGCA
* * *
39283897 CCTAAAT-GAGAAAGGTT-CATAGTTTAAGTACCTA
192 CCTAAATGGAAAAAGTTTGCATAATTTAAGTACCTA
39283931 TTTTGATATT
Statistics
Matches: 506, Mismatches: 55, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
352 58 0.11
353 12 0.02
354 64 0.13
355 25 0.05
357 135 0.27
358 84 0.17
359 49 0.10
360 55 0.11
361 24 0.05
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (358 bp):
AAAACTTTAGGTACTTAAATGGGAAAAGTTGCATAGTTTAATAACCTAAAGTGGTAATAGATTAA
AAATGTCATGTGTCATAATTTGATTTGTTTGAATTCTTTTTTTTAAACGTGAGTTAACAATTGGT
ACCTAAAGTGGTAATAGAATAAAACTTTAGGTACCTACTTTGATAAAAAAAACTTTAGGCACCTA
AATGGAAAAAGTTTGCATAATTTAAGTACCTAAAGTGGGAATAAATTAAAAATATCACATGTCAT
AATTTGATTGGTTTGAATTTTTTTTTTTGTAACATGAGTTAACCGTTGCTACCTAAAGTGGCAAC
AGAATAAAACTTTAGGTACCTACTTTGGTAAAA
Found at i:39291556 original size:9 final size:9
Alignment explanation
Indices: 39291544--39291610 Score: 66
Period size: 9 Copynumber: 7.2 Consensus size: 9
39291534 TTTTATTATT
39291544 TTTTAATAA
1 TTTTAATAA
39291553 TTTTAATAA
1 TTTTAATAA
*
39291562 TTTCATATAA
1 TTTTA-ATAA
39291572 TTCTTAATAA
1 TT-TTAATAA
39291582 TGTTTAA-ATA
1 T-TTTAATA-A
*
39291592 TTTTTAT-A
1 TTTTAATAA
39291600 TTTTAATAA
1 TTTTAATAA
39291609 TT
1 TT
39291611 ATTTGAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.15
9 21 0.44
10 17 0.35
11 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:39291556 original size:10 final size:10
Alignment explanation
Indices: 39291523--39291610 Score: 62
Period size: 10 Copynumber: 9.2 Consensus size: 10
39291513 ATGGACATTG
*
39291523 TTTTTAACAA
1 TTTTTAATAA
* *
39291533 TTTTTATTAT
1 TTTTTAATAA
39291543 TTTTTAATAA
1 TTTTTAATAA
39291553 -TTTTAATAA
1 TTTTTAATAA
*
39291562 -TTTCATATAA
1 TTTTTA-ATAA
*
39291572 TTCTTAATAA
1 TTTTTAATAA
*
39291582 TGTTTAA-ATA
1 TTTTTAATA-A
39291592 TTTTT-AT-A
1 TTTTTAATAA
39291600 -TTTTAATAA
1 TTTTTAATAA
39291609 TT
1 TT
39291611 ATTTGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
7 4 0.07
8 3 0.05
9 16 0.27
10 34 0.57
11 3 0.05
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:39291995 original size:26 final size:26
Alignment explanation
Indices: 39291960--39292011 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39291950 CTCATATTGC
* *
39291960 ATATTTTTATGATAGTAATTTAAATT
1 ATATTTTTATCATAATAATTTAAATT
39291986 ATATTTTTATCATAATAATTTAAATT
1 ATATTTTTATCATAATAATTTAAATT
39292012 TTATACAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (26 bp):
ATATTTTTATCATAATAATTTAAATT
Found at i:39293617 original size:2 final size:2
Alignment explanation
Indices: 39293610--39293641 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39293600 CTTTTCACAA
39293610 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
39293642 GTATGTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39293944 original size:10 final size:10
Alignment explanation
Indices: 39293929--39293959 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
39293919 AAACCTAAAA
39293929 TTAAAAATAT
1 TTAAAAATAT
39293939 TTAAAAATTAT
1 TTAAAAA-TAT
39293950 TTAAAAATAT
1 TTAAAAATAT
39293960 AATAATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:39293950 original size:11 final size:11
Alignment explanation
Indices: 39293929--39293957 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39293919 AAACCTAAAA
39293929 TTAAAAA-TAT
1 TTAAAAATTAT
39293939 TTAAAAATTAT
1 TTAAAAATTAT
39293950 TTAAAAAT
1 TTAAAAAT
39293958 ATAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAAATTAT
Found at i:39294110 original size:11 final size:10
Alignment explanation
Indices: 39294087--39294160 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
39294077 AGAGACATTG
39294087 TTTTTAATAT
1 TTTTTAATAT
*
39294097 TTTTTATTAGT
1 TTTTTAATA-T
* *
39294108 TTTTTAACAA
1 TTTTTAATAT
*
39294118 TTCTTAATTAT
1 TTTTTAA-TAT
*
39294129 TTTTAAATAT
1 TTTTTAATAT
*
39294139 TTTTT-TTAT
1 TTTTTAATAT
*
39294148 ATTTT-ATAT
1 TTTTTAATAT
39294157 TTTT
1 TTTT
39294161 AGTAATTATT
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
9 13 0.27
10 21 0.44
11 14 0.29
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:39294113 original size:21 final size:20
Alignment explanation
Indices: 39294087--39294160 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 20
39294077 AGAGACATTG
39294087 TTTTTAATATTTTTTATTAGT
1 TTTTTAATATTTTTTATTA-T
* * *
39294108 TTTTTAACAATTCTTAATTAT
1 TTTTTAA-TATTTTTTATTAT
*
39294129 TTTTAAATATTTTTT-TTAT
1 TTTTTAATATTTTTTATTAT
*
39294148 ATTTT-ATATTTTT
1 TTTTTAATATTTTT
39294161 AGTAATTATT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 8 0.19
19 7 0.16
20 5 0.12
21 14 0.33
22 9 0.21
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTTAATATTTTTTATTAT
Found at i:39294555 original size:26 final size:26
Alignment explanation
Indices: 39294526--39294580 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
39294516 ATATTTTTCA
* *
39294526 TATTTTTATGATAGTGATTTAAATTT
1 TATTTTTATCATAATGATTTAAATTT
39294552 TATTTTTATCATAATGATTTAAATTT
1 TATTTTTATCATAATGATTTAAATTT
39294578 TAT
1 TAT
39294581 ACAACTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (26 bp):
TATTTTTATCATAATGATTTAAATTT
Found at i:39298878 original size:18 final size:19
Alignment explanation
Indices: 39298845--39298880 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39298835 CGATATCATT
*
39298845 TTGTGCGTGATGTTGTTGC
1 TTGTGCGTGATATTGTTGC
39298864 TTGTG-GTGATATTGTTG
1 TTGTGCGTGATATTGTTG
39298881 TAAGCAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.08, C:0.06, G:0.36, T:0.50
Consensus pattern (19 bp):
TTGTGCGTGATATTGTTGC
Found at i:39300766 original size:17 final size:16
Alignment explanation
Indices: 39300744--39300788 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
39300734 TGGCAATATA
39300744 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
39300761 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
39300777 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
39300789 TGTGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:39300787 original size:10 final size:11
Alignment explanation
Indices: 39300744--39300789 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
39300734 TGGCAATATA
39300744 TTTCTTTTCTT
1 TTTCTTTTCTT
39300755 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
39300767 CTTC-TTTCTT
1 TTTCTTTTCTT
39300777 TTTC-TTTCTT
1 TTTCTTTTCTT
39300787 TTT
1 TTT
39300790 GTGAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:39307953 original size:13 final size:13
Alignment explanation
Indices: 39307935--39307966 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
39307925 ATAGAAGAAG
39307935 AATTACCTTGAAC
1 AATTACCTTGAAC
39307948 AATTACCTTGAAC
1 AATTACCTTGAAC
39307961 AATTAC
1 AATTAC
39307967 TTCAGTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (13 bp):
AATTACCTTGAAC
Found at i:39311448 original size:26 final size:27
Alignment explanation
Indices: 39311409--39311466 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
39311399 TTCTTCTCTC
39311409 TTCCAGTAGTTTTTCC-CAAAAGGGTT
1 TTCCAGTAGTTTTTCCTCAAAAGGGTT
*
39311435 TTCCATGTAG-TTTTCCTCGAAAGGGTT
1 TTCCA-GTAGTTTTTCCTCAAAAGGGTT
39311462 TTCCA
1 TTCCA
39311467 CGTAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (27 bp):
TTCCAGTAGTTTTTCCTCAAAAGGGTT
Found at i:39312798 original size:19 final size:19
Alignment explanation
Indices: 39312776--39312818 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
39312766 TTAATTTGTT
* *
39312776 TATTTTGCCATGACATTCA
1 TATTTTGCCATAACATCCA
39312795 TATTTTGCCATAACATCCA
1 TATTTTGCCATAACATCCA
39312814 TATTT
1 TATTT
39312819 GCATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (19 bp):
TATTTTGCCATAACATCCA
Found at i:39315941 original size:19 final size:18
Alignment explanation
Indices: 39315888--39315950 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 18
39315878 CAAAATAATC
39315888 AAAATAATTTTCAAAATTT
1 AAAATAATTTT-AAAATTT
39315907 GAAAATAATTTTAAAATTT
1 -AAAATAATTTTAAAATTT
39315926 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTT-T-AAAATT-T
39315946 AAAAT
1 AAAAT
39315951 TTGTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.10
18 6 0.15
19 13 0.32
20 17 0.43
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATAATTTTAAAATTT
Found at i:39320165 original size:15 final size:17
Alignment explanation
Indices: 39320145--39320180 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
39320135 AATAATTATT
39320145 TAATTTTTAAAA-A-AA
1 TAATTTTTAAAATATAA
39320160 TAA-TTTTAAAATATAA
1 TAATTTTTAAAATATAA
39320176 TAATT
1 TAATT
39320181 CACTATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 5 0.28
17 1 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTTAAAATATAA
Found at i:39320335 original size:10 final size:10
Alignment explanation
Indices: 39320320--39320409 Score: 89
Period size: 10 Copynumber: 9.2 Consensus size: 10
39320310 AGGTTCATTG
39320320 TTTTTAATAA
1 TTTTTAATAA
* *
39320330 TTTTTATTAGT
1 TTTTTAATA-A
39320341 TTTTTAATAA
1 TTTTTAATAA
39320351 --TTTAATAA
1 TTTTTAATAA
*
39320359 TTTTTTATAA
1 TTTTTAATAA
*
39320369 TTCTTAATAA
1 TTTTTAATAA
39320379 TTTTTAA-ATA
1 TTTTTAATA-A
*
39320389 TTTTTTAT-A
1 TTTTTAATAA
39320398 TTTTTAATAA
1 TTTTTAATAA
39320408 TT
1 TT
39320410 ATTTGAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
8 8 0.12
9 9 0.14
10 39 0.61
11 8 0.12
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:39320363 original size:39 final size:39
Alignment explanation
Indices: 39320320--39320409 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
39320310 AGGTTCATTG
* * * *
39320320 TTTTTAATAATTTTTATTAGTTTTTTAATAATTTAATA-A
1 TTTTTAATAATTCTTAATAATTTTTAAAT-ATTTAATATA
* **
39320359 TTTTTTATAATTCTTAATAATTTTTAAATATTTTTTATA
1 TTTTTAATAATTCTTAATAATTTTTAAATATTTAATATA
39320398 TTTTTAATAATT
1 TTTTTAATAATT
39320410 ATTTGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 6 0.14
39 36 0.86
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (39 bp):
TTTTTAATAATTCTTAATAATTTTTAAATATTTAATATA
Found at i:39326657 original size:31 final size:31
Alignment explanation
Indices: 39326619--39326681 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
39326609 TTATTGAAGT
39326619 GTCGGAGTCAACAGGACCTTCAACGAGTAGA
1 GTCGGAGTCAACAGGACCTTCAACGAGTAGA
39326650 GTCGGAGTCAACAGGACCTTCAACGAGTAGA
1 GTCGGAGTCAACAGGACCTTCAACGAGTAGA
39326681 G
1 G
39326682 ATAAAGGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.16
Consensus pattern (31 bp):
GTCGGAGTCAACAGGACCTTCAACGAGTAGA
Found at i:39327472 original size:41 final size:41
Alignment explanation
Indices: 39327317--39327474 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
39327307 GTTTTTCCAT
* * * ** *
39327317 AAACACCGCAAAAGGT-AAAGCAATAGCAACGTTTATAGGAA
1 AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTA-AGAAA
* * *
39327358 AAACACAGCTAAAGGTCAAAGCATTAGCGGCATTTAAGAAA
1 AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTAAGAAA
* * * * * *
39327399 AAATGCCACTAAAGGTCAGAGCATTAGTGGCGTTTATGAGA
1 AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTAAGAAA
*
39327440 AAACGCCGCTAAAGGTCATAGCATTAGCGGCGTTT
1 AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTT
39327475 TTCCCATAAA
Statistics
Matches: 96, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 81 0.84
42 15 0.16
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.20
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTAAGAAA
Found at i:39329010 original size:40 final size:40
Alignment explanation
Indices: 39328886--39329096 Score: 215
Period size: 41 Copynumber: 5.1 Consensus size: 40
39328876 TAAAAATTAG
* * *
39328886 AGGTTAAGCAATAGCAGCGTTTATGGAAAAAACGCTGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATGG-AAAAACGCCGCAAA
* *
39328927 AGGTAAAGCAAAAGCGACGTTTATGAGAAAAACGCCGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATG-GAAAAACGCCGCAAA
* * **
39328968 AGGTAAAGCAATAGCGGCATTTATGGGAAAACGCCATAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGAAAAACGCCGCAAA
* * *
39329008 AGGTAAAGCAATAGCGGCGTTTATGGGACAAACGCCGTAAT
1 AGGTAAAGCAATAGCGGCGTTTAT-GGAAAAACGCCGCAAA
** * *
39329049 AGGTATAGAGCAATAGCAGTGTTTTTTTGGGAAAACGCCGCAAA
1 AGGTA-A-AGCAATAGC-G-GCGTTTATGGAAAAACGCCGCAAA
39329093 AGGT
1 AGGT
39329097 TTAGAGTATT
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
40 35 0.25
41 73 0.52
42 2 0.01
43 9 0.06
44 17 0.12
45 5 0.04
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (40 bp):
AGGTAAAGCAATAGCGGCGTTTATGGAAAAACGCCGCAAA
Found at i:39329014 original size:81 final size:82
Alignment explanation
Indices: 39328886--39329067 Score: 222
Period size: 81 Copynumber: 2.2 Consensus size: 82
39328876 TAAAAATTAG
* * **
39328886 AGGTTAAGCAATAGCAGCGTTTATGGAAAAAACGCTGCAAAAGGTAAAGCAAAAGCGACGTTTAT
1 AGGTAAAGCAATAGCAGCATTTATGGAAAAAACGCCACAAAAGGTAAAGCAAAAGCGACGTTTAT
39328951 GAGAAAAACGCCGCAAA
66 GAGAAAAACGCCGCAAA
* * * * *
39328968 AGGTAAAGCAATAGCGGCATTTATGG-GAAAACGCCATAAAAGGTAAAGCAATAGCGGCGTTTAT
1 AGGTAAAGCAATAGCAGCATTTATGGAAAAAACGCCACAAAAGGTAAAGCAAAAGCGACGTTTAT
* * * *
39329032 GGGACAAACGCCGTAAT
66 GAGAAAAACGCCGCAAA
39329049 AGGTATAGAGCAATAGCAG
1 AGGTA-A-AGCAATAGCAG
39329068 TGTTTTTTTG
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 50 0.60
82 24 0.29
83 10 0.12
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.17
Consensus pattern (82 bp):
AGGTAAAGCAATAGCAGCATTTATGGAAAAAACGCCACAAAAGGTAAAGCAAAAGCGACGTTTAT
GAGAAAAACGCCGCAAA
Found at i:39329117 original size:44 final size:45
Alignment explanation
Indices: 39328956--39329102 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 45
39328946 TTTATGAGAA
** *
39328956 AAACGCCGCAAAAGGTA-A-AGCAATAGC-G-GCATTTATGGGA-
1 AAACGCCGCAAAAGGTATAGAGCAATAGCAGTGTTTTTTTGGGAC
** ** *
39328996 AAACGCCATAAAAGGTA-A-AGCAATAGC-G-GCGTTTATGGGAC
1 AAACGCCGCAAAAGGTATAGAGCAATAGCAGTGTTTTTTTGGGAC
* *
39329037 AAACGCCGTAATAGGTATAGAGCAATAGCAGTGTTTTTTTGGGA-
1 AAACGCCGCAAAAGGTATAGAGCAATAGCAGTGTTTTTTTGGGAC
*
39329081 AAACGCCGCAAAAGGTTTAGAG
1 AAACGCCGCAAAAGGTATAGAG
39329103 TATTAGTGGT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 37 0.41
41 15 0.16
42 1 0.01
43 9 0.10
44 20 0.22
45 9 0.10
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (45 bp):
AAACGCCGCAAAAGGTATAGAGCAATAGCAGTGTTTTTTTGGGAC
Found at i:39329935 original size:14 final size:14
Alignment explanation
Indices: 39329916--39329961 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
39329906 AGGGTTTGGA
39329916 TTTGTTCATCCTTG
1 TTTGTTCATCCTTG
*
39329930 TTTG-T--TCCTGG
1 TTTGTTCATCCTTG
39329941 TTTGTTCATCCTTG
1 TTTGTTCATCCTTG
39329955 TTTGTTC
1 TTTGTTC
39329962 CTTGTTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.33
12 1 0.04
13 1 0.04
14 16 0.59
ACGTcount: A:0.04, C:0.20, G:0.17, T:0.59
Consensus pattern (14 bp):
TTTGTTCATCCTTG
Found at i:39329950 original size:25 final size:25
Alignment explanation
Indices: 39329916--39329963 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
39329906 AGGGTTTGGA
39329916 TTTGTTCATCCTTGTTTGTTCCTGG
1 TTTGTTCATCCTTGTTTGTTCCTGG
39329941 TTTGTTCATCCTTGTTTGTTCCT
1 TTTGTTCATCCTTGTTTGTTCCT
39329964 TGTTCGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.21, G:0.17, T:0.58
Consensus pattern (25 bp):
TTTGTTCATCCTTGTTTGTTCCTGG
Found at i:39329963 original size:11 final size:11
Alignment explanation
Indices: 39329924--39329967 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
39329914 GATTTGTTCA
39329924 TCCTTGTTTGT
1 TCCTTGTTTGT
*
39329935 TCCTGGTTTGTT
1 TCCTTGTTTG-T
39329947 CATCCTTGTTTGT
1 --TCCTTGTTTGT
39329960 TCCTTGTT
1 TCCTTGTT
39329968 CGTTTCAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 17 0.61
12 1 0.04
13 1 0.04
14 9 0.32
ACGTcount: A:0.02, C:0.20, G:0.18, T:0.59
Consensus pattern (11 bp):
TCCTTGTTTGT
Found at i:39333317 original size:20 final size:20
Alignment explanation
Indices: 39333266--39333309 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
39333256 GTTGTAATTA
39333266 TTTACTAATATTTCAACTAT
1 TTTACTAATATTTCAACTAT
39333286 TTTACTAATATTTCAACTAT
1 TTTACTAATATTTCAACTAT
39333306 TTTA
1 TTTA
39333310 TGTGTATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTACTAATATTTCAACTAT
Found at i:39334915 original size:12 final size:12
Alignment explanation
Indices: 39334894--39334924 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39334884 AAATATGATG
39334894 AACTTCAGCTAC
1 AACTTCAGCTAC
*
39334906 AACTTTAGCTAC
1 AACTTCAGCTAC
39334918 AACTTCA
1 AACTTCA
39334925 AGCCAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (12 bp):
AACTTCAGCTAC
Found at i:39335373 original size:43 final size:43
Alignment explanation
Indices: 39335303--39335407 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
39335293 GAGAAAAGCG
* * * *
39335303 AAGACCATCTTCTTTAGCAGCATTTGTGGGGAAAGTGCCGCTA
1 AAGACCATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTA
* ** *
39335346 AAGGCCATGTTCTTTAGCGGTGTTTGTGTGAAAAGCGCCGCTA
1 AAGACCATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTA
39335389 AAGACCATGTTCTTTAGCG
1 AAGACCATGTTCTTTAGCG
39335408 ACGTTATCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (43 bp):
AAGACCATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCCGCTA
Found at i:39336986 original size:31 final size:30
Alignment explanation
Indices: 39336961--39337026 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
39336951 ATTTTCGAGG
*
39336961 AATTTAGGGATCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATCAAAATTGAAATTTTCGGAA
* *
39336992 AATTTGGGATTAAAATTGAACTTTT-GGAA
1 AATTTGGGATCAAAATTGAAATTTTCGGAA
39337021 AATTTG
1 AATTTG
39337027 AGGTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 10 0.30
30 18 0.55
31 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGATCAAAATTGAAATTTTCGGAA
Found at i:39337037 original size:30 final size:30
Alignment explanation
Indices: 39336961--39337026 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
39336951 ATTTTCGAGG
* *
39336961 AATTTAGGGATCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATTAAAATTGAAACTTTTGGAA
39336992 AATTTGGGATTAAAATTG-AACTTTTGGAA
1 AATTTGGGATTAAAATTGAAACTTTTGGAA
39337021 AATTTG
1 AATTTG
39337027 AGGTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 16 0.48
30 12 0.36
31 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGATTAAAATTGAAACTTTTGGAA
Found at i:39337045 original size:29 final size:28
Alignment explanation
Indices: 39336984--39337078 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
39336974 AAATTGAAAT
39336984 TTTTGGAAAATTTG-GGATTAAAAT-TGAA
1 TTTTGGAAAATTTGAGG-TTAAAATGTG-A
39337012 CTTTTGGAAAATTTGAGGTTGAAAATGTGA
1 -TTTTGGAAAATTTGAGGTT-AAAATGTGA
** * * *
39337042 TTTTCAAAAATTTAAGGGTAAAAATGGTAA
1 TTTTGGAAAATTTGA-GGTTAAAAT-GTGA
39337072 TTTTGGA
1 TTTTGGA
39337079 TGTTCAAGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
29 33 0.61
30 19 0.35
31 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (28 bp):
TTTTGGAAAATTTGAGGTTAAAATGTGA
Found at i:39337087 original size:29 final size:29
Alignment explanation
Indices: 39337055--39337162 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 29
39337045 TCAAAAATTT
*
39337055 AAGGGTAAAAATGGTAATTTTGGATGTTC
1 AAGGGTAAAAATGGTAATTTTGGAAGTTC
*
39337084 AAGGG-AAAAATGGTAATTTTTAAGAAGTTC
1 AAGGGTAAAAATGGTAA-TTTT-GGAAGTTC
* * *
39337114 GAGGGTAAAAAT-GTGATTTTTGGAAGTTT
1 AAGGGTAAAAATGGT-AATTTTGGAAGTTC
* *
39337143 GAGGAT-AAAATGGTAATTTT
1 AAGGGTAAAAATGGTAATTTT
39337163 TTGTCAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
28 21 0.32
29 22 0.33
30 16 0.24
31 7 0.11
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
AAGGGTAAAAATGGTAATTTTGGAAGTTC
Found at i:39337162 original size:28 final size:28
Alignment explanation
Indices: 39337062--39337162 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
39337052 TTTAAGGGTA
* *
39337062 AAAATGGTAATTTTGGATGTTCAAGGGA-
1 AAAATGGTAATTTTGGAAGTTCGA-GGAT
* *
39337090 AAAATGGTAATTTTTAAGAAGTTCGAGGGT
1 AAAATGGTAA-TTTT-GGAAGTTCGAGGAT
* *
39337120 AAAAAT-GTGATTTTTGGAAGTTTGAGGAT
1 -AAAATGGT-AATTTTGGAAGTTCGAGGAT
39337149 AAAATGGTAATTTT
1 AAAATGGTAATTTT
39337163 TTGTCAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 20 0.34
29 19 0.33
30 13 0.22
31 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAGTTCGAGGAT
Found at i:39337993 original size:16 final size:17
Alignment explanation
Indices: 39337953--39337995 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
39337943 AATTAAATTT
39337953 TAAATTTAAACTCAAAA
1 TAAATTTAAACTCAAAA
39337970 TAAATTTAAACTCAAAA
1 TAAATTTAAACTCAAAA
39337987 T-AATTTAAA
1 TAAATTTAAA
39337996 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATTTAAACTCAAAA
Found at i:39338517 original size:49 final size:49
Alignment explanation
Indices: 39338464--39338693 Score: 164
Period size: 50 Copynumber: 4.7 Consensus size: 49
39338454 CACCGTTGTA
*
39338464 ACCTCAA-CCTTTCCCTTCATATCTCCATGGTATCGGATTCGATGTTACG
1 ACCTCAATCC-TTCCCTTCATATCTCCATGGTATCGGATTCGCTGTTACG
* ** * *
39338513 ACCTCAATCCTTCCCATCGCATCTTCTAAGGTATCGGATTCGCTG-T-CG
1 ACCTCAATCCTTCCCTTCATATC-TCCATGGTATCGGATTCGCTGTTACG
* * * * *
39338561 CAGCCTCAATCCTTCCTTTCATCTCTTCATGGTATCGGGTTCGCCGTTACG
1 -A-CCTCAATCCTTCCCTTCATATCTCCATGGTATCGGATTCGCTGTTACG
* * * * * **
39338612 ACCTCAA-CCTTTCCTATCATATTTTCTAAGGTACCGGATTCG-TCGTCGCG
1 ACCTCAATCCTTCCCT-TCATA-TCTCCATGGTATCGGATTCGCT-GTTACG
** * *
39338662 GTCTCAATCCTTCCCTTCATCTCTTCATGGTA
1 ACCTCAATCCTTCCCTTCATATCTCCATGGTA
39338694 CCGAGTTTAC
Statistics
Matches: 135, Mismatches: 36, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
48 8 0.06
49 52 0.39
50 66 0.49
51 9 0.07
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.35
Consensus pattern (49 bp):
ACCTCAATCCTTCCCTTCATATCTCCATGGTATCGGATTCGCTGTTACG
Found at i:39338766 original size:149 final size:149
Alignment explanation
Indices: 39338607--39339338 Score: 448
Period size: 149 Copynumber: 4.9 Consensus size: 149
39338597 GGGTTCGCCG
* * * * * *
39338607 TTACGACCTCAACCTTTC-CTATCATATTTTCTAAGGTACCG-GATTCGTCGTCGCGGTCTCAAT
1 TTACGACCTCAACCTTTCTC-ATCACATCTTCTAAGGCACCGAG-CTCGCCGTCGCGGCCTCAA-
* * * *
39338670 CC-TTCCCTTCATCTCTTCATGGTACCGAGTTTACCGTTATGGCCTCAACCTTTCCCATTGCATC
63 CCTTTCCCTTCATATCTTCATGGTACCGAGTTCACCGTTACGGCCTCAACCTTTCCCATTACATC
39338734 TTCTTAGGTACCAGGTTTACCA
128 TTCTTAGGTACCAGGTTTACCA
* * * *
39338756 TTACGGCCTCAACCTTTCTCATCACATCTTCTAAGGCATCGAGCTCGCCGTTGTGGCCTCAACCT
1 TTACGACCTCAACCTTTCTCATCACATCTTCTAAGGCACCGAGCTCGCCGTCGCGGCCTCAACCT
** * * * *
39338821 TTCCCTTTGTATGTTCATGGTACCGAGTTCACCGTTGCGGCCTCAACCTTTCCCATTACATTTTT
66 TTCCCTTCATATCTTCATGGTACCGAGTTCACCGTTACGGCCTCAACCTTTCCCATTACATCTTC
*** *
39338886 TTAGGTACC-GAACT-CGTCG
131 TTAGGTACCAGGTTTAC--CA
* * * * *** * * * **
39338905 TTGCGACCTTAACCTTTCCCTTTGTATCTTCGT--GGTACCGGGTTTACCG-CTGCGGCCTCAAC
1 TTACGACCTCAACCTTTCTCATCACATCTTC-TAAGGCACCGAGCTCGCCGTC-GCGGCCTCAAC
* ** * * * *
39338967 CTTTCCCATCACCTCTTCTTAGGTACCGGGTTCACCGTTGCGGCCTAAATCC-TTCCC-TT-CAT
64 CTTTCCCTTCATATCTTCAT-GGTACCGAGTTCACCGTTACGGCCTCAA-CCTTTCCCATTACAT
**
39339029 CTAT-TTATGGTACCAGGTTTACTG
127 CT-TCTTA-GGTACCAGGTTTACCA
* * * ** * * * * *
39339053 TTGCGGCCTCAACCTTTCCCATTGCATCTTCTTAGGTACC-AGGTTCGCCGTTGTGGCCTCAACC
1 TTACGACCTCAACCTTTCTCATCACATCTTCTAAGGCACCGA-GCTCGCCGTCGCGGCCTCAACC
* * * * * * * * **
39339117 TTTCCCATCATATCTTCTAAGGTATCGGGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCT
65 TTTCCCTTCATATCTTC-ATGGTACCGAGTTCACCGTTACGGCCTCAACCTTTCCCATTACATCT
** ** *
39339182 TC-GGGGTACCAGGTTCGCCG
129 TCTTAGGTACCAGGTTTACCA
* * * * * * * * * * *
39339202 TTGCGGCCTTAACCTTTCTCATTACATCTTCTTAGGTACCGGGCTCGCCGTTGCGGCTTTAATCT
1 TTACGACCTCAACCTTTCTCATCACATCTTCTAAGGCACCGAGCTCGCCGTCGCGGCCTCAACCT
** * * * * * *
39339267 TTCCCTTTGTATCTTCGTGGTACCGGGTTCACCATTACGACCTCAACCTTTCCCATCACATCTTT
66 TTCCCTTCATATCTTCATGGTACCGAGTTCACCGTTACGGCCTCAACCTTTCCCATTACATCTTC
39339332 TTAGGTA
131 TTAGGTA
39339339 TCGGATTCAT
Statistics
Matches: 455, Mismatches: 104, Indels: 48
0.75 0.17 0.08
Matches are distributed among these distances:
147 9 0.02
148 112 0.25
149 321 0.71
150 9 0.02
151 4 0.01
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (149 bp):
TTACGACCTCAACCTTTCTCATCACATCTTCTAAGGCACCGAGCTCGCCGTCGCGGCCTCAACCT
TTCCCTTCATATCTTCATGGTACCGAGTTCACCGTTACGGCCTCAACCTTTCCCATTACATCTTC
TTAGGTACCAGGTTTACCA
Found at i:39338767 original size:99 final size:99
Alignment explanation
Indices: 39338465--39339516 Score: 623
Period size: 99 Copynumber: 10.6 Consensus size: 99
39338455 ACCGTTGTAA
* * * ** * *
39338465 CCTCAACCTTTCCCTTCATATCTCCATGGTATCG-GATTCGATGTTACGACCTCAATCC-TTCCC
1 CCTCAACCTTTCCCTTCATCTCTTCATGGTACCGAG-TTCGCCGTTGCGGCCTCAA-CCTTTCCC
** * * * * * * *
39338528 ATCGCATCTTCTAAGGTATCGGATTCGCTGTCGCAG
64 ATTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * * * *
39338564 CCTCAATCC-TTCCTTTCATCTCTTCATGGTATCGGGTTCGCCGTTACGACCTCAACCTTTCCTA
1 CCTCAA-CCTTTCCCTTCATCTCTTCATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCCA
* * * * * ** *
39338628 TCATATTTTCTAAGGTACCGGATTCGTCGTCGCGG
65 TTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* ** **
39338663 TCTCAATCC-TTCCCTTCATCTCTTCATGGTACCGAGTTTACCGTTATGGCCTCAACCTTTCCCA
1 CCTCAA-CCTTTCCCTTCATCTCTTCATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCCA
* * * * *
39338727 TTGCATCTTCTTAGGTACCAGGTTTACCATTACGG
65 TTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * * * * *
39338762 CCTCAACCTTTCTCATCA-CATCTTCTAAGGCATCGAGCTCGCCGTTGTGGCCTCAACCTTTCCC
1 CCTCAACCTTTCCCTTCATC-TCTTC-ATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCC
* ** * * *
39338826 TTTGTATGTTCAT-GGTACCGAGTTCACCGTTGCGG
64 ATTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * ** * * *
39338861 CCTCAACCTTTCCCATTACATTTTTTTA-GGTACCGAACTCGTCGTTGCGACCTTAACCTTTCCC
1 CCTCAACCTTTCCC-TT-CATCTCTTCATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCC
* ** * * *
39338925 TTTGTATCTTCGT-GGTACCGGGTTTACCGCTGCGG
64 ATTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * * * *
39338960 CCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGGGTTCACCGTTGCGGCCTAAATCC-TTCCC
1 CCTCAACCTTTCCCTTCATCTCTTCAT-GGTACCGAGTTCGCCGTTGCGGCCTCAA-CCTTTCCC
* * *
39339024 -TT-CATCTAT-TTATGGTACCAGGTTTACTGTTGCGG
64 ATTACATCT-TCTTA-GGTACCGGGTTCACCGTTGCGG
*
39339059 CCTCAACCTTTCCCATTGCATCTTCTT-A-GGTACC-AGGTTCGCCGTTGTGGCCTCAACCTTTC
1 CCTCAACCTTTCCC-TT-CATC-TCTTCATGGTACCGA-GTTCGCCGTTGCGGCCTCAACCTTTC
* * * * * *
39339121 CCATCATATCTTCTAAGGTATCGGGCTCGCCGTTGCGG
62 CCATTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
** * ** * *
39339159 CCTCAACCTTTCCCTTTGTATCTTCGGGGTACC-AGGTTCGCCGTTGCGGCCTTAACCTTTCTCA
1 CCTCAACCTTTCCCTTCATCTCTTCATGGTACCGA-GTTCGCCGTTGCGGCCTCAACCTTTCCCA
* *
39339223 TTACATCTTCTTAGGTACCGGGCTCGCCGTTGCGG
65 TTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * ** * * * * * * *
39339258 CTTTAATCTTTCCCTTTGTATCTTCGTGGTACCGGGTTCACCATTACGACCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTCATCTCTTCATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCCAT
* * * * * * *
39339323 CACATCTTTTTAGGTATCGGATTCATCGTCGCGA
66 TACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * * *
39339357 CCTCCATCC-TTCCCTTTATCTTTTCATGGTA-CTAGATTCGTCGTTGCGGCCTCAACCTTTCCC
1 CCT-CAACCTTTCCCTTCATCTCTTCATGGTACCGAG-TTCGCCGTTGCGGCCTCAACCTTTCCC
* * * * *
39339420 ATCACCTCTTCTTAGGTACCGGGTTCGCCATTGCAG
64 ATTACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
* * * * *
39339456 CCTCAACCTTTCCTTTCACATATTTTAAT-GTACC-AGATTCGTCGTTGCGGCCTCAATCCTT
1 CCTCAACCTTTCCCTT--CATCTCTTCATGGTACCGAG-TTCGCCGTTGCGGCCTCAA-CCTT
39339517 CCCTATCAAA
Statistics
Matches: 754, Mismatches: 166, Indels: 64
0.77 0.17 0.07
Matches are distributed among these distances:
97 14 0.02
98 18 0.02
99 584 0.77
100 107 0.14
101 27 0.04
102 4 0.01
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.35
Consensus pattern (99 bp):
CCTCAACCTTTCCCTTCATCTCTTCATGGTACCGAGTTCGCCGTTGCGGCCTCAACCTTTCCCAT
TACATCTTCTTAGGTACCGGGTTCACCGTTGCGG
Found at i:39339072 original size:347 final size:346
Alignment explanation
Indices: 39338584--39339468 Score: 1130
Period size: 347 Copynumber: 2.5 Consensus size: 346
39338574 TCCTTTCATC
* * * ** * * * *
39338584 TCTTCATGGTATCGGGTTCGCCGTTACGACCTCAACCTTTCCTATCATATTTTCTAAGGTACCGG
1 TCTTCGTGGTACCGGGTTCACCACTACGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGG
* * * * **
39338649 ATTCGTCGTCGCGGTCTCAATCCTTCCCTTCATCTCTTCATGGTACC-GAGTTTACCGTTATGGC
66 ATTCATCGTCGCGGCCTCAATCCTTCCCTTCATCT-TTTATGGTACCAG-GTTTACTGTTGCGGC
** * *
39338713 CTCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTTACCATTACGGCCTCAACCTTTCTCAT
129 CTCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCAT
* * *
39338778 CACATCTTCTAAGGCATCGAGCTCGCCGTTGTGGCCTCAACCTTTCCCTTTGTATGTTCATGGTA
194 CACATCTTCTAAGGCATCGAGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCTTCAGGGTA
* * *
39338843 CC-GAGTTCACCGTTGCGGCCTCAACCTTTCCCATTACATTTTTTTAGGTACCGAACTCGTCGTT
259 CCAG-GTTCACCGTTGCGGCCTCAACCTTTCCCATTACATCTTCTTAGGTACCGAACTCGCCGTT
39338907 GCGACCTTAACCTTTCCCTTTGTA
323 GCGACCTTAACCTTTCCCTTTGTA
* * * * *
39338931 TCTTCGTGGTACCGGGTTTACCGCTGCGGCCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGG
1 TCTTCGTGGTACCGGGTTCACCACTACGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGG
* * * *
39338996 GTTCACCGTTGCGGCCTAAATCCTTCCCTTCATCTATTTATGGTACCAGGTTTACTGTTGCGGCC
66 ATTCATCGTCGCGGCCTCAATCCTTCCCTTCATCT-TTTATGGTACCAGGTTTACTGTTGCGGCC
* *
39339061 TCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCGTTGTGGCCTCAACCTTTCCCATC
130 TCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCATC
* * * *
39339126 ATATCTTCTAAGGTATCGGGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCTTCGGGGTAC
195 ACATCTTCTAAGGCATCGAGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCTTCAGGGTAC
* * * **
39339191 CAGGTTCGCCGTTGCGGCCTTAACCTTTCTCATTACATCTTCTTAGGTACCGGGCTCGCCGTTGC
260 CAGGTTCACCGTTGCGGCCTCAACCTTTCCCATTACATCTTCTTAGGTACCGAACTCGCCGTTGC
* * *
39339256 GGCTTTAATCTTTCCCTTTGTA
325 GACCTTAACCTTTCCCTTTGTA
* * *
39339278 TCTTCGTGGTACCGGGTTCACCATTACGACCTCAACCTTTCCCATCACATCTTTTTAGGTATCGG
1 TCTTCGTGGTACCGGGTTCACCACTACGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGG
* * * * *
39339343 ATTCATCGTCGCGACCTCCATCCTTCCCTTTATCTTTTCATGGTACTA-GATT-CGTCGTTGCGG
66 ATTCATCGTCGCGGCCTCAATCCTTCCCTTCATCTTTT-ATGGTACCAGGTTTAC-T-GTTGCGG
** * * *
39339406 CCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGGGTTCGCCATTGCAGCCTCAACCTTTCC
128 CCTCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCC
39339469 TTTCACATAT
Statistics
Matches: 462, Mismatches: 71, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
345 1 0.00
346 7 0.02
347 452 0.98
348 2 0.00
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.35
Consensus pattern (346 bp):
TCTTCGTGGTACCGGGTTCACCACTACGACCTCAACCTTTCCCATCACATCTTCTTAGGTACCGG
ATTCATCGTCGCGGCCTCAATCCTTCCCTTCATCTTTTATGGTACCAGGTTTACTGTTGCGGCCT
CAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCATTGCGGCCTCAACCTTTCCCATCA
CATCTTCTAAGGCATCGAGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCTTCAGGGTACC
AGGTTCACCGTTGCGGCCTCAACCTTTCCCATTACATCTTCTTAGGTACCGAACTCGCCGTTGCG
ACCTTAACCTTTCCCTTTGTA
Found at i:39339313 original size:248 final size:247
Alignment explanation
Indices: 39338812--39339338 Score: 619
Period size: 248 Copynumber: 2.1 Consensus size: 247
39338802 GCCGTTGTGG
* * * *
39338812 CCTCAACCTTTCCCTTTGTATGTTCAT-GGTACCGAGTTCACCGTTGCGGCCTCAACCTTTCCCA
1 CCTCAACCTTTCCCATTGCATCTTCTTAGGTACCGAGTTCACCGTTGCGGCCTCAACCTTTCCCA
* * * * * * *
39338876 TTACATTTTTTTAGGTACCGAACTCGTCGTTGCGACCTTAACCTTTCCCTTTGTATCTTCGTGGT
66 TCACATCTTCTAAGGTACCGAACTCGCCGTTGCGACCTCAACCTTTCCCTTTGTATCTTCGGGGT
* * * *
39338941 ACCGGGTTTACCGCTGCGGCCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGGGTTCACCGTT
131 ACCAGGTTCACCGCTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGCTCACCGTT
* ** * *
39339006 GCGGCCTAAATCCTTCCCTTCATCTATTTATGGTACCAGGTTTACTGTTGCGG
196 GCGGCCTAAATCCTTCCCTT-ATCTATTTATGGTACCAGGTTCACCATTACGA
* *
39339059 CCTCAACCTTTCCCATTGCATCTTCTTAGGTACC-AGGTTCGCCGTTGTGGCCTCAACCTTTCCC
1 CCTCAACCTTTCCCATTGCATCTTCTTAGGTACCGA-GTTCACCGTTGCGGCCTCAACCTTTCCC
* * ** *
39339123 ATCATATCTTCTAAGGTATCGGGCTCGCCGTTGCGGCCTCAACCTTTCCCTTTGTATCTTCGGGG
65 ATCACATCTTCTAAGGTACCGAACTCGCCGTTGCGACCTCAACCTTTCCCTTTGTATCTTCGGGG
* * * * * *
39339188 TACCAGGTTCGCCGTTGCGGCCTTAACCTTTCTCATTACATCTTCTTAGGTACCGGGCTCGCCGT
130 TACCAGGTTCACCGCTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGCTCACCGT
* * * * * *
39339253 TGCGGCTTTAATCTTTCCCTT-TGTATCTTCGTGGTACCGGGTTCACCATTACGA
195 TGCGGCCTAAATCCTTCCCTTATCTAT-TT-ATGGTACCAGGTTCACCATTACGA
** *
39339307 CCTCAACCTTTCCCATCACATCTTTTTAGGTA
1 CCTCAACCTTTCCCATTGCATCTTCTTAGGTA
39339339 TCGGATTCAT
Statistics
Matches: 234, Mismatches: 42, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
246 4 0.02
247 26 0.11
248 204 0.87
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.35
Consensus pattern (247 bp):
CCTCAACCTTTCCCATTGCATCTTCTTAGGTACCGAGTTCACCGTTGCGGCCTCAACCTTTCCCA
TCACATCTTCTAAGGTACCGAACTCGCCGTTGCGACCTCAACCTTTCCCTTTGTATCTTCGGGGT
ACCAGGTTCACCGCTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGCTCACCGTT
GCGGCCTAAATCCTTCCCTTATCTATTTATGGTACCAGGTTCACCATTACGA
Found at i:39339489 original size:50 final size:50
Alignment explanation
Indices: 39338710--39339524 Score: 267
Period size: 50 Copynumber: 16.4 Consensus size: 50
39338700 TTACCGTTAT
** * * ** *
39338710 GGCCTCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTTACCATTAC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * * * *
39338760 GGCCTCAACCTTTCTCATCACATCTTCTAAGGCATC-GAGCTCGCCGTTGT
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGA-TTCGCCATTGC
* *** * * * *
39338810 GGCCTCAACCTTTCCCTTTGTATGTTCAT-GGTACC-GAGTTCACCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGA-TTCGCCATTGC
* * * * * *
39338859 GGCCTCAACCTTTCCCATTACATTTTTTTAGGTACC-GAACTCGTCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAG-ATTCGCCATTGC
* * * *** * * * * ** **
39338909 GACCTTAACCTTTCCCTTTGTATCTTCGT-GGTACCGGGTTTACCGCTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * *
39338958 GGCCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGGGTTCACCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * ** **
39339008 GGCCTAAATCC-TTCCCTTCATC-TA-T-TTATGGTACCAGGTTTACTGTTGC
1 GGCCTCAA-CCTTTCCCATCA-CATATTCTTA-GGTACCAGATTCGCCATTGC
** * * * *
39339057 GGCCTCAACCTTTCCCATTGCATCTTCTTAGGTACCAGGTTCGCCGTTGT
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * ** *
39339107 GGCCTCAACCTTTCCCATCATATCTTCTAAGGTATCGGGCTCGCCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* *** * ** * *
39339157 GGCCTCAACCTTTCCCTTTGTATCTTC-GGGGTACCAGGTTCGCCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * ** *
39339206 GGCCTTAACCTTTCTCATTACATCTTCTTAGGTACCGGGCTCGCCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * *** * * * * * *
39339256 GGCTTTAATCTTTCCCTTTGTATCTTCGT-GGTACCGGGTTCACCATTAC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * ** * *
39339305 GACCTCAACCTTTCCCATCACATCTTTTTAGGTATCGGATTCATCGTCGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* * * * * * * * *
39339355 GACCTCCATCC-TTCCCTTTATC-TTTTCAT-GGTACTAGATTCGTCGTTGC
1 GGCCT-CAACCTTTCCCATCA-CATATTCTTAGGTACCAGATTCGCCATTGC
* * * *
39339404 GGCCTCAACCTTTCCCATCACCTCTTCTTAGGTACCGGGTTCGCCATTGC
1 GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
* ** * * *
39339454 AGCCTCAACCTTTCCTTTCACATATT-TTAATGTACCAGATTCGTCGTTGC
1 GGCCTCAACCTTTCCCATCACATATTCTT-AGGTACCAGATTCGCCATTGC
39339504 GGCCTCAATCC-TTCCCTATCA
1 GGCCTCAA-CCTTTCCC-ATCA
39339525 AACCTATAGA
Statistics
Matches: 582, Mismatches: 161, Indels: 43
0.74 0.20 0.05
Matches are distributed among these distances:
48 11 0.02
49 211 0.36
50 343 0.59
51 17 0.03
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (50 bp):
GGCCTCAACCTTTCCCATCACATATTCTTAGGTACCAGATTCGCCATTGC
Found at i:39342469 original size:57 final size:59
Alignment explanation
Indices: 39342377--39342500 Score: 189
Period size: 57 Copynumber: 2.1 Consensus size: 59
39342367 AAAAAAATGG
**
39342377 TGAAAATGGAGAAACGAGAAATCATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAACGAGAAATCATTTGGAAATGATTATGACTTTCTCCAAAATGAAAA
* *
39342436 TGAAAATGGAGAAACG-G-AATCATTTGTAAATGATTCTGACTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAACGAGAAATCATTTGGAAATGATTATGACTTTCTCCAAAATGAAAA
*
39342493 CGAAAATG
1 TGAAAATG
39342501 AATTTTTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 43 0.72
58 1 0.02
59 16 0.27
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (59 bp):
TGAAAATGGAGAAACGAGAAATCATTTGGAAATGATTATGACTTTCTCCAAAATGAAAA
Found at i:39348351 original size:15 final size:15
Alignment explanation
Indices: 39348331--39348384 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
39348321 ATATTACAAA
39348331 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
39348346 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
39348363 GAATATTTATTATTAAA
1 --ATATTTATTATTAAT
39348380 ATATT
1 ATATT
39348385 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:39348448 original size:16 final size:16
Alignment explanation
Indices: 39348417--39348453 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
39348407 ATGTGAAGAA
39348417 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
39348433 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
39348449 TATTA
1 TATTA
39348454 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:39348574 original size:13 final size:13
Alignment explanation
Indices: 39348558--39348592 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39348548 ATGTATGTTT
*
39348558 AATAATATTGAAA
1 AATAATATTAAAA
*
39348571 AATACTATTAAAA
1 AATAATATTAAAA
39348584 AATAATATT
1 AATAATATT
39348593 TTATATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (13 bp):
AATAATATTAAAA
Found at i:39349089 original size:3 final size:3
Alignment explanation
Indices: 39349081--39349109 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39349071 ATTATTTCAA
39349081 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39349110 ACTTTGATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39351515 original size:43 final size:43
Alignment explanation
Indices: 39351454--39351535 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
39351444 AAAAAGCGTG
* * *
39351454 GCTAAAGAGCATGGTCTTTAGCAACGCTTTTTCCACAAATGCT
1 GCTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAATGCT
**
39351497 GCTAAAGAACATGGTCTTTAACGGCGCTTTTCCCACAAA
1 GCTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAA
39351536 CGCCACTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAATGCT
Found at i:39351545 original size:43 final size:43
Alignment explanation
Indices: 39351455--39351545 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
39351445 AAAAGCGTGG
* * * * **
39351455 CTAAAGAGCATGGTCTTTAGCAACGCTTTTTCCACAAATGCTG
1 CTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAACGCCA
**
39351498 CTAAAGAACATGGTCTTTAACGGCGCTTTTCCCACAAACGCCA
1 CTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAACGCCA
39351541 CTAAA
1 CTAAA
39351546 ATTAACAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
CTAAAGAACATGGTCTTTAACAACGCTTTTCCCACAAACGCCA
Found at i:39355826 original size:41 final size:39
Alignment explanation
Indices: 39355759--39356180 Score: 371
Period size: 41 Copynumber: 10.3 Consensus size: 39
39355749 CTCAATTAAA
* * *
39355759 TGACTTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACAT
1 TGACCTTTAGCGGCGCTTT-TCATAAGCGCCGCTATTGC-T
*
39355800 TGACCTTTATCGGCGCCTTTTCATAAGCGCCGCTATTGCTT
1 TGACCTTTAGCGGCG-CTTTTCATAAGCGCCGCTATTGC-T
** * *
39355841 TGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTACAT
1 TGACCTTTAGCGGCGCTT-TTCATAAGCGCCGCTATTGC-T
* *
39355882 TGACCTTTAGCGACGCTTTTTCATAAGCGTCGCTATTGCT
1 TGACCTTTAGCGGCGC-TTTTCATAAGCGCCGCTATTGCT
**
39355922 CTGACCTTTAGCGGCGCTTGACTATAAGCGCCGCTATTGCT
1 -TGACCTTTAGCGGCGCTTTTC-ATAAGCGCCGCTATTGCT
* ** *
39355963 CTGACCTTTAGCGGTGCTTGACCATAAGTGCCGCTATTGCTT
1 -TGACCTTTAGCGGCGCTT-TTCATAAGCGCCGCTATTGC-T
* * * * *
39356005 TGACCTGTAGCAGTGCTTTCCCATAAGCGCCGCTATTACAT
1 TGACCTTTAGCGGCGCTTT-TCATAAGCGCCGCTATTGC-T
* * *
39356046 TGACCTTTAGTGGCGCTTGCTCATAAGCGTCGCTATTGCT
1 TGACCTTTAGCGGCGCTT-TTCATAAGCGCCGCTATTGCT
* *
39356086 CTAACTTTTAGCGGCG-TTTTCCCATAAGCGCCGCTATTGCT
1 -TGACCTTTAGCGGCGCTTTT--CATAAGCGCCGCTATTGCT
* * *
39356127 CTGATCTTTAGCAGCGCTTTTCCATAAGTGCCGCTATTGCT
1 -TGACCTTTAGCGGCGCTTTT-CATAAGCGCCGCTATTGCT
*
39356168 CT-ACCTTTTGCGG
1 -TGACCTTTAGCGG
39356181 GGTTTATGTA
Statistics
Matches: 316, Mismatches: 52, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.00
40 18 0.06
41 285 0.90
42 12 0.04
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (39 bp):
TGACCTTTAGCGGCGCTTTTCATAAGCGCCGCTATTGCT
Found at i:39355903 original size:82 final size:82
Alignment explanation
Indices: 39355759--39356180 Score: 499
Period size: 82 Copynumber: 5.2 Consensus size: 82
39355749 CTCAATTAAA
* * *
39355759 TGACTTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTATCGGCGCCTTTTCAT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTTTTCAT
*
39355824 AAGCGCCGCTATTGCTT
66 AAGCGCCGCTATTGCTC
* * *
39355841 TGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTACATTGACCTTTAGCGACGCTTTTTCAT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTTTTCAT
*
39355906 AAGCGTCGCTATTGCTC
66 AAGCGCCGCTATTGCTC
** * * * ***
39355923 TGACCTTTAGCGGCGCTTGACTATAAGCGCCGCTATTGC-TCTGACCTTTAGCGGTGCTTGACCA
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACAT-TGACCTTTAGCGGCGCTTTTTCA
* *
39355987 TAAGTGCCGCTATTGCTT
65 TAAGCGCCGCTATTGCTC
* * * * **
39356005 TGACCTGTAGCAGTGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGTGGCGCTTGCTCAT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTTTTCAT
*
39356070 AAGCGTCGCTATTGCTC
66 AAGCGCCGCTATTGCTC
* * * * * * *
39356087 TAACTTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGC-TCTGATCTTTAGCAGCGCTTTTCCA
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACAT-TGACCTTTAGCGGCGCTTTTTCA
*
39356151 TAAGTGCCGCTATTGCTC
65 TAAGCGCCGCTATTGCTC
*
39356169 T-ACCTTTTGCGG
1 TGACCTTTAGCGG
39356181 GGTTTATGTA
Statistics
Matches: 286, Mismatches: 51, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
81 11 0.04
82 274 0.96
83 1 0.00
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (82 bp):
TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTTTTCAT
AAGCGCCGCTATTGCTC
Found at i:39355988 original size:123 final size:121
Alignment explanation
Indices: 39355759--39356164 Score: 485
Period size: 123 Copynumber: 3.3 Consensus size: 121
39355749 CTCAATTAAA
* * * *
39355759 TGACTTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTATCGGCGCCTT-TTCA
1 TGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCG-CTTGCT-A
* * *
39355823 TAAGCGCCGCTATTGCTTTGACCTTTAGCGGCGCTTGCCCATAAGCACCGCTATTACAT
64 TAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGC-T
** * *
39355882 TGACCTTTAGC-GACGCTTTTTCATAAGCGTCGCTATTGC-TCTGACCTTTAGCGGCGCTTGACT
1 TGACCTTTAGCAG-CGCTTTCCCATAAGCGCCGCTATTACAT-TGACCTTTAGCGGCGCTTG-CT
* * *
39355945 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGCTTGACCATAAGTGCCGCTATTGCTT
63 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGC-T
* * *
39356005 TGACCTGTAGCAGTGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGTGGCGCTTGCTCAT
1 TGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTGCT-AT
* * * * *
39356070 AAGCGTCGCTATTGCTCTAACTTTTAGCGGCGTTTTCCCATAAGCGCCGCTATTGCT
65 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCT
* * *
39356127 CTGATCTTTAGCAGCGCTTTTCCATAAGTGCCGCTATT
1 -TGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTATT
39356165 GCTCTACCTT
Statistics
Matches: 241, Mismatches: 34, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
122 8 0.03
123 230 0.95
124 3 0.01
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (121 bp):
TGACCTTTAGCAGCGCTTTCCCATAAGCGCCGCTATTACATTGACCTTTAGCGGCGCTTGCTATA
AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCT
Found at i:39356967 original size:28 final size:27
Alignment explanation
Indices: 39356917--39356969 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
39356907 CTTTTTGAAA
*
39356917 TTTTAGAATTTAATCCCTTTATTTTAT
1 TTTTAGAATTTAATCCCTCTATTTTAT
* *
39356944 TTTTAGAAATTTATTCTCTCTATTTT
1 TTTTAG-AATTTAATCCCTCTATTTT
39356970 TTAGATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTAGAATTTAATCCCTCTATTTTAT
Found at i:39358697 original size:11 final size:10
Alignment explanation
Indices: 39358679--39358721 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
39358669 TTAATATGTA
39358679 TTTA-TTATT
1 TTTATTTATT
39358688 TTTATGTTATT
1 TTTAT-TTATT
39358699 TTTATTTATT
1 TTTATTTATT
*
39358709 TGTTATTCATT
1 T-TTATTTATT
39358720 TT
1 TT
39358722 ATGACATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 4 0.13
10 7 0.23
11 19 0.63
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTATTTATT
Found at i:39358703 original size:17 final size:19
Alignment explanation
Indices: 39358661--39358715 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
39358651 TATTATTCAT
* *
39358661 TTTAATATTTAATATG-TA
1 TTTATTATTTATTATGTTA
39358679 TTTATTATTT-TTATGTTA
1 TTTATTATTTATTATGTTA
39358697 TTT-TTATTTATT-TGTTA
1 TTTATTATTTATTATGTTA
39358714 TT
1 TT
39358716 CATTTTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 17 0.52
18 16 0.48
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTATTATTTATTATGTTA
Found at i:39358901 original size:23 final size:22
Alignment explanation
Indices: 39358856--39358902 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
39358846 TTCACTATAC
*
39358856 TTTTATTCTAATAATATTGCTA
1 TTTTATTCTAATAATATTACTA
* *
39358878 TTTTATTACTATTACTATTACTA
1 TTTTATT-CTAATAATATTACTA
39358901 TT
1 TT
39358903 ATTTTATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATTCTAATAATATTACTA
Found at i:39364547 original size:48 final size:48
Alignment explanation
Indices: 39364488--39364881 Score: 457
Period size: 48 Copynumber: 8.2 Consensus size: 48
39364478 TTTAGGAAGA
* * * * *
39364488 CAGATTGAAGCTACCAAATCCAATCTTATACCTCTAAATCCAAAGGGA
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * * * *
39364536 CAGATTAAAGCTACCACATCAAATCTTATACACTTAAATCTAG-GGTGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGG-GG
* * *
39364584 CATATTAAAGTCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * *
39364632 CAGATTAAAGCCACCATATCCAATCTTATACCCCTAAATCTAGAGGGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * * *
39364680 CAAATTGAAGCCACCACATCCAATATTATACGCCTAAATCTAGAGGGA
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * *
39364728 CAGATTGAAGCCACTATATCAAATCTTATACCCCTAAATCCAGAGGGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * *
39364776 TAGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCTAGAGGGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
* * * * *
39364824 CAAATTGAAGCCACCAAATCAAATCTTATACCACTAAATCCAGAGAGG
1 CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
*
39364872 TAGATTGAAG
1 CAGATTGAAG
39364882 TTGCAAAACC
Statistics
Matches: 292, Mismatches: 52, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
47 2 0.01
48 288 0.99
49 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (48 bp):
CAGATTGAAGCCACCACATCCAATCTTATACCCCTAAATCCAGAGGGG
Found at i:39367021 original size:10 final size:10
Alignment explanation
Indices: 39366994--39367026 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
39366984 TTAATGTGTA
39366994 TTTA-TTATT
1 TTTAGTTATT
39367003 TTTATGTTATT
1 TTTA-GTTATT
39367014 TTTAGTTATT
1 TTTAGTTATT
39367024 TTT
1 TTT
39367027 TATTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 9 0.41
11 9 0.41
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (10 bp):
TTTAGTTATT
Found at i:39367028 original size:11 final size:11
Alignment explanation
Indices: 39366998--39367026 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
39366988 TGTGTATTTA
39366998 TTATTTTTATG
1 TTATTTTTATG
39367009 TTATTTTTA-G
1 TTATTTTTATG
39367019 TTATTTTT
1 TTATTTTT
39367027 TATTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TTATTTTTATG
Found at i:39367035 original size:21 final size:20
Alignment explanation
Indices: 39366994--39367036 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39366984 TTAATGTGTA
*
39366994 TTTATTATTTTTATGTTATT
1 TTTATTATTTTTATGTCATT
39367014 TTTAGTTATTTTTTAT-TCATT
1 TTTA-TTA-TTTTTATGTCATT
39367035 TT
1 TT
39367037 ATGACATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTATTATTTTTATGTCATT
Found at i:39370158 original size:177 final size:177
Alignment explanation
Indices: 39369940--39370263 Score: 594
Period size: 177 Copynumber: 1.8 Consensus size: 177
39369930 TCTTCTCCTC
* * *
39369940 CACTGCCAACACCTACTGCACCTTCATGGCCACCGGCTCCGTCTTTGCCTATAACACCAGCACCA
1 CACTACCAACACCTACAGCACCTTCATGGCCACCGGCTCCGTCTTTGCCTACAACACCAGCACCA
*
39370005 ACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTACTGGCCCTTGGGC
66 ACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTACTGACCCTTGGGC
39370070 ACCAGCTCCTGCACCTTGGGCACCATCTCCAATATCTTCTCCACCTT
131 ACCAGCTCCTGCACCTTGGGCACCATCTCCAATATCTTCTCCACCTT
* *
39370117 CACTACCAACACCTACAGCACCTTCATTGCCACCTGCTCCGTCTTTGCCTACAACACCAGCACCA
1 CACTACCAACACCTACAGCACCTTCATGGCCACCGGCTCCGTCTTTGCCTACAACACCAGCACCA
39370182 ACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTACTGACCCTTGGGC
66 ACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTACTGACCCTTGGGC
39370247 ACCAGCTCCTGCACCTT
131 ACCAGCTCCTGCACCTT
39370264 CATGGCCACC
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
177 141 1.00
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.22
Consensus pattern (177 bp):
CACTACCAACACCTACAGCACCTTCATGGCCACCGGCTCCGTCTTTGCCTACAACACCAGCACCA
ACTCCTGAGCCTTGGGCACCAACTACAGTTTCAGTGCCAGAAACAACAGTTACTGACCCTTGGGC
ACCAGCTCCTGCACCTTGGGCACCATCTCCAATATCTTCTCCACCTT
Found at i:39371317 original size:25 final size:23
Alignment explanation
Indices: 39371272--39371318 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
39371262 AACTTTGTAG
*
39371272 AACATTAAACTCTGATAAAATAA
1 AACATTAAAATCTGATAAAATAA
*
39371295 AACATTATAAATCTTATACAAATA
1 AACATTA-AAATCTGATA-AAATA
39371319 TTATCGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
AACATTAAAATCTGATAAAATAA
Found at i:39372962 original size:22 final size:23
Alignment explanation
Indices: 39372926--39372970 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
39372916 TTTGGTAGAA
*
39372926 TTAATTCACATAATTTTTATATT
1 TTAATTCACATAATTTTAATATT
*
39372949 TTAATTTA-ATAATTTTAATATT
1 TTAATTCACATAATTTTAATATT
39372971 ATTATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATTCACATAATTTTAATATT
Found at i:39373105 original size:18 final size:17
Alignment explanation
Indices: 39373083--39373141 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
39373073 AAAATGAAAC
39373083 ATTAAAAATATTTAAGA
1 ATTAAAAATATTTAAGA
** *
39373100 ATTTAAAAGA-ATAAAACA
1 A-TTAAAA-ATATTTAAGA
39373118 A-TAAAAATATTTAAGAA
1 ATTAAAAATATTTAAG-A
39373135 ATTAAAA
1 ATTAAAA
39373142 GAATAAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
15 1 0.03
16 9 0.29
17 3 0.10
18 17 0.55
19 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (17 bp):
ATTAAAAATATTTAAGA
Found at i:39373123 original size:34 final size:34
Alignment explanation
Indices: 39373070--39373152 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
39373060 GTGTGGATGA
* * * *
39373070 AAAAAAATGAAACATTAAAAATATTTAAGAATTT
1 AAAAGAATAAAACAATAAAAATATTTAAGAAATT
39373104 AAAAGAATAAAACAATAAAAATATTTAAGAAATT
1 AAAAGAATAAAACAATAAAAATATTTAAGAAATT
39373138 AAAAGAATAAAACAA
1 AAAAGAATAAAACAA
39373153 GCATGCTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (34 bp):
AAAAGAATAAAACAATAAAAATATTTAAGAAATT
Found at i:39373129 original size:26 final size:26
Alignment explanation
Indices: 39373100--39373149 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39373090 ATATTTAAGA
39373100 ATTTAA-AAGAATAAAACAATAAAAAT
1 ATTTAAGAA-AATAAAACAATAAAAAT
* *
39373126 ATTTAAGAAATTAAAAGAATAAAA
1 ATTTAAGAAAATAAAACAATAAAA
39373150 CAAGCATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (26 bp):
ATTTAAGAAAATAAAACAATAAAAAT
Found at i:39392569 original size:86 final size:86
Alignment explanation
Indices: 39392424--39392592 Score: 241
Period size: 86 Copynumber: 2.0 Consensus size: 86
39392414 CTTGGCGTAT
* * * * *
39392424 AAATGGAATACTCATGTCTCGAAATGAACATGAGATTATGTATAAATGGAAGACTCATGTCTCGA
1 AAATGAAATACTCATGACTCAAAATGAACATGAGATTACGTATAAAAGGAAGACTCATGTCTCGA
* *
39392489 GATGAGCATGATGTTATGTAA
66 GATAAGCATGAGGTTATGTAA
* *
39392510 AAATGAAATACTCGTGACTCAAAATGAGCATGAGATTACGTA-AGAAAGGAAGACTCATGTCTCG
1 AAATGAAATACTCATGACTCAAAATGAACATGAGATTACGTATA-AAAGGAAGACTCATGTCTCG
39392574 AGATAAGCATGAGGTTATG
65 AGATAAGCATGAGGTTATG
39392593 ATTATAAGGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 1 0.01
86 72 0.99
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (86 bp):
AAATGAAATACTCATGACTCAAAATGAACATGAGATTACGTATAAAAGGAAGACTCATGTCTCGA
GATAAGCATGAGGTTATGTAA
Found at i:39392606 original size:43 final size:43
Alignment explanation
Indices: 39392424--39392592 Score: 173
Period size: 43 Copynumber: 3.9 Consensus size: 43
39392414 CTTGGCGTAT
* *
39392424 AAATGGAATACTCATGTCTCGAAATGAA-CATGAGATTATGTAT
1 AAATGGAAGACTCATGTCTCGAAAT-AAGCATGAGATTATGTAA
* *
39392467 AAATGGAAGACTCATGTCTCGAGATGAGCATGATG-TTATGTAA
1 AAATGGAAGACTCATGTCTCGAAATAAGCATGA-GATTATGTAA
* * * * * * *
39392510 AAATGAAATACTCGTGACTCAAAATGAGCATGAGATTACGTAA
1 AAATGGAAGACTCATGTCTCGAAATAAGCATGAGATTATGTAA
* *
39392553 GAAA-GGAAGACTCATGTCTCGAGATAAGCATGAGGTTATG
1 -AAATGGAAGACTCATGTCTCGAAATAAGCATGAGATTATG
39392593 ATTATAAGGA
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
42 2 0.02
43 96 0.94
44 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (43 bp):
AAATGGAAGACTCATGTCTCGAAATAAGCATGAGATTATGTAA
Found at i:39396918 original size:16 final size:17
Alignment explanation
Indices: 39396899--39396939 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
39396889 TAATCTTTTA
39396899 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
39396915 AAAA-TATTAAAATAAT
1 AAAATTATAAAAATAAT
39396931 AAAATTATA
1 AAAATTATA
39396940 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 10 0.48
17 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:39398551 original size:20 final size:20
Alignment explanation
Indices: 39398526--39398581 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
39398516 AAAATTATAA
39398526 TTTTATAATTTTTATAA-AAT
1 TTTTATAATTTTTA-AAGAAT
*
39398546 TTTTAT-TTTTTTAAAGTAAT
1 TTTTATAATTTTTAAAG-AAT
*
39398566 TTTTA-AATTTTAAAAG
1 TTTTATAATTTTTAAAG
39398582 GTTTAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.07
19 6 0.20
20 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTATAATTTTTAAAGAAT
Found at i:39399027 original size:51 final size:51
Alignment explanation
Indices: 39398958--39399235 Score: 119
Period size: 51 Copynumber: 5.4 Consensus size: 51
39398948 CAGTTGACAC
39398958 TTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCAATCCATAA
1 TTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCAATCCATAA
* * * * * * *
39399009 TTTC-AGTCTCAACTCAGTAGCAACGGT---CG-CA-ACTTCCT-CATTATACTTGGCAC
1 TTTCAAGTC-CAACCCAGTA--AA-GGTGGGCGTTATTCTCCCTGCA--ATCCAT---AA
* *
39399062 TTTCAAGTCCAACCCAATAAAGGTGGGCGTTATTCTCCCTGTAATCCATAA
1 TTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCAATCCATAA
* ** ** ** * **** *
39399113 TTTC-AGTCTCAACTCAGTAGCAACTTTCGCG--ACTTCCTCATTGCACTTGGCAC
1 TTTCAAGTC-CAACCCAGTA--AAGGTGGGCGTTA-TT-CTCCCTGCAATCCATAA
* *
39399166 TTTCAAGTCCAACCCAGTAAAGGTGGACGTTATTCTCCTTGCAATCCATAA
1 TTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCAATCCATAA
*
39399217 TTTC-AGTCTCAACTCAGTA
1 TTTCAAGTC-CAACCCAGTA
39399236 GCAACGGTCA
Statistics
Matches: 157, Mismatches: 45, Indels: 50
0.62 0.18 0.20
Matches are distributed among these distances:
48 2 0.01
49 5 0.03
50 20 0.13
51 59 0.38
52 4 0.03
53 45 0.29
54 16 0.10
55 5 0.03
56 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (51 bp):
TTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCAATCCATAA
Found at i:39399116 original size:104 final size:104
Alignment explanation
Indices: 39398936--39399360 Score: 661
Period size: 104 Copynumber: 4.1 Consensus size: 104
39398926 TTGTGTCGTG
* *
39398936 ACTTCCTCATTGCAGTTGACACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
1 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
*
39399001 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCGCA
66 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACA
** * *
39399040 ACTTCCTCATTATACTTGGCACTTTCAAGTCCAACCCAATAAAGGTGGGCGTTATTCTCCCTGTA
1 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
** * *
39399105 ATCCATAATTTCAGTCTCAACTCAGTAGCAACTTTCGCG
66 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACA
* *
39399144 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGACGTTATTCTCCTTGCA
1 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
*
39399209 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACG
66 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACA
* *
39399248 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAATGTGGGTGTTATTCTCCCTGCA
1 ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
* * * *
39399313 ATCCATAATATCAGTCTCAACTTAGTAACAATGGTCACA
66 ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACA
*
39399352 ACTTACTCA
1 ACTTCCTCA
39399361 ACCTTAGGTC
Statistics
Matches: 293, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 293 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (104 bp):
ACTTCCTCATTGCACTTGGCACTTTCAAGTCCAACCCAGTAAAGGTGGGCGTTATTCTCCCTGCA
ATCCATAATTTCAGTCTCAACTCAGTAGCAACGGTCACA
Found at i:39399966 original size:15 final size:16
Alignment explanation
Indices: 39399937--39399970 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39399927 AGTTAAACTT
*
39399937 GGTCTCTGTATTGCGA
1 GGTCTCTGTACTGCGA
39399953 GGTCT-TGTACTGCGA
1 GGTCTCTGTACTGCGA
39399968 GGT
1 GGT
39399971 TACATGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (16 bp):
GGTCTCTGTACTGCGA
Found at i:39404916 original size:29 final size:31
Alignment explanation
Indices: 39404858--39404918 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
39404848 TTATATGAAA
39404858 TTGAAGAAAAAGGAAAGAAAGAGAAGGAGCAAT
1 TTGAAGAAAAAGGAAAG--AGAGAAGGAGCAAT
*
39404891 TTGAAGAGAAAGGAAAG-GAGAA-GAGCAA
1 TTGAAGAAAAAGGAAAGAGAGAAGGAGCAA
39404919 GGAGTAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 6 0.22
30 5 0.19
33 16 0.59
ACGTcount: A:0.56, C:0.03, G:0.33, T:0.08
Consensus pattern (31 bp):
TTGAAGAAAAAGGAAAGAGAGAAGGAGCAAT
Found at i:39404930 original size:33 final size:31
Alignment explanation
Indices: 39404859--39404932 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
39404849 TATATGAAAT
*
39404859 TGAAGAAAAAGGAAAGAAAGAGAAGGAGCAA
1 TGAAGAGAAAGGAAAGAAAGAGAAGGAGCAA
*
39404890 TTTGAAGAGAAAGGAAAGGAGAAGAGCAAGGAGTAA
1 --TGAAGAGAAAGGAAA-GA-AAGAG-AAGGAGCAA
39404926 -GAAGAGA
1 TGAAGAGA
39404933 CAAAATCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 21 0.58
34 2 0.06
35 5 0.14
36 8 0.22
ACGTcount: A:0.55, C:0.03, G:0.35, T:0.07
Consensus pattern (31 bp):
TGAAGAGAAAGGAAAGAAAGAGAAGGAGCAA
Found at i:39405026 original size:16 final size:17
Alignment explanation
Indices: 39404991--39405031 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
39404981 AGATTAAAAA
*
39404991 TATTAATTTTATGTGTT
1 TATTAATTTTATGTATT
39405008 TA-TAATTTTA-GTATAT
1 TATTAATTTTATGTAT-T
39405024 TATTAATT
1 TATTAATT
39405032 ATGATGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (17 bp):
TATTAATTTTATGTATT
Found at i:39405116 original size:20 final size:21
Alignment explanation
Indices: 39405074--39405116 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
39405064 GATAAATATT
*
39405074 AATTGTGTGATTAATTGGTGA
1 AATTGTGTGATTAATTGGAGA
* *
39405095 AATTGTG-GATTTATTTGAGA
1 AATTGTGTGATTAATTGGAGA
39405115 AA
1 AA
39405117 ATAAAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
AATTGTGTGATTAATTGGAGA
Found at i:39405376 original size:25 final size:24
Alignment explanation
Indices: 39405272--39405379 Score: 110
Period size: 25 Copynumber: 4.2 Consensus size: 24
39405262 ACACTAGCGC
39405272 GCTCTCCGTTATTTTAGCACGTAT-TGT
1 GCTCTCCGTTA--TTAGCAC-T-TGTGT
39405299 GCTCTCCGTTATTAGCACTGTGTGT
1 GCTCTCCGTTATTAGCACT-TGTGT
*
39405324 GCTCTCCGTTATTAGCACTTCGTAT
1 GCTCTCCGTTATTAGCACTT-GTGT
** *
39405349 GCTCTCCGTTACCCAGCACTTTTGT
1 GCTCTCCGTTA-TTAGCACTTGTGT
39405374 GCTCTC
1 GCTCTC
39405380 TGTTTAGTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
24 3 0.04
25 51 0.71
26 7 0.10
27 11 0.15
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.40
Consensus pattern (24 bp):
GCTCTCCGTTATTAGCACTTGTGT
Found at i:39407744 original size:6 final size:6
Alignment explanation
Indices: 39407724--39407768 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
39407714 TTTAATGGAT
* *
39407724 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
39407769 TCAAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 8 0.24
6 25 0.76
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:39407746 original size:17 final size:17
Alignment explanation
Indices: 39407724--39407767 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
39407714 TTTAATGGAT
*
39407724 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
39407741 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
39407758 TTTAAATTTA
1 TTTAAATTTA
39407768 ATCAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:39408350 original size:28 final size:28
Alignment explanation
Indices: 39408319--39408375 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39408309 ATTCGAATAT
39408319 ACACACTCAGTAGTAGATCAGAACACTC
1 ACACACTCAGTAGTAGATCAGAACACTC
39408347 ACACACTCAGTAGTAGATCAGAACACTC
1 ACACACTCAGTAGTAGATCAGAACACTC
39408375 A
1 A
39408376 AGCACCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (28 bp):
ACACACTCAGTAGTAGATCAGAACACTC
Found at i:39408571 original size:9 final size:9
Alignment explanation
Indices: 39408557--39408590 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
39408547 TAGCCATTAA
39408557 TAATAATAT
1 TAATAATAT
39408566 TAATAATAT
1 TAATAATAT
39408575 TAATAA-AT
1 TAATAATAT
*
39408583 CAATAATA
1 TAATAATA
39408591 AAAAAAGCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATAATAT
Found at i:39409317 original size:34 final size:32
Alignment explanation
Indices: 39409249--39409310 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
39409239 TATTTACGCG
* * *
39409249 TTTAGTCCTTTTGCTTTTTTTATTTGTTTCAA
1 TTTAGTCCTTTTGCATTTTTTAATTATTTCAA
39409281 TTTAGTCCTTTTTGCATTTTTTAATTATTT
1 TTTAGTCC-TTTTGCATTTTTTAATTATTT
39409311 ATAATTTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.66
Consensus pattern (32 bp):
TTTAGTCCTTTTGCATTTTTTAATTATTTCAA
Found at i:39409638 original size:29 final size:28
Alignment explanation
Indices: 39409605--39409759 Score: 74
Period size: 29 Copynumber: 5.4 Consensus size: 28
39409595 GAAATTATCA
*
39409605 TTTTACCCCCAAACTTTCCAAAATCTCAT
1 TTTTAACCCC-AACTTTCCAAAATCTCAT
* *
39409634 TTTTAACCCCGATTTTACCAAAAT-TACCA-
1 TTTTAACCCCAACTTT-CCAAAATCT--CAT
* *
39409663 TTTT-ACGCCCGAACTTTCTAAAATCCCAT
1 TTTTAAC-CCC-AACTTTCCAAAATCTCAT
*
39409692 TTTTAACCCCGA-TTTCACCAAAAT-TACCA-
1 TTTTAACCCCAACTTT--CCAAAATCT--CAT
*
39409721 TTTT-ACCTCTGAACTTTCCAAAAT-TCCAT
1 TTTTAACC-C-CAACTTTCCAAAATCT-CAT
39409750 TTTTAACCCC
1 TTTTAACCCC
39409760 GATTTCATCA
Statistics
Matches: 96, Mismatches: 13, Indels: 35
0.67 0.09 0.24
Matches are distributed among these distances:
27 3 0.03
28 16 0.17
29 60 0.62
30 14 0.15
31 3 0.03
ACGTcount: A:0.30, C:0.31, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTTAACCCCAACTTTCCAAAATCTCAT
Found at i:39409801 original size:59 final size:58
Alignment explanation
Indices: 39409596--39410138 Score: 711
Period size: 58 Copynumber: 9.3 Consensus size: 58
39409586 AACTGTCCAG
* ** *
39409596 AAATTATCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTTACCA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCA
* *
39409654 AAATTACCATTTTACGCCC-GAACTTTCTAAAATCCCATTTTTAACCCCGATTTCACCA
1 AAATTACCATTTTAC-CCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCA
* *
39409712 AAATTACCATTTTACCTCTGAACTTTCCAAAAT-TCCATTTTTAACCCCGATTTCATCAA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCT-CATTTTTAACCCCGATTTCA-CCA
*
39409771 AAATTACCATTTTACCCCTGAACTTTCCAAAATC-CTATTTTTTACCCCGATTTCACCA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTC-ATTTTTAACCCCGATTTCACCA
* * * *
39409829 AAATTACCATTTTGCCTCC-GAACTTTCCAAAATCTCGTTCTTAAGCCCGATTTCACCA
1 AAATTACCATTTTACC-CCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCA
* * * *
39409887 AAATTACAATTTTACCCTTGAAC-TTCCTAAAATTTCATTTTTAACCCTGATTTCACCA
1 AAATTACCATTTTACCCCTGAACTTTCC-AAAATCTCATTTTTAACCCCGATTTCACCA
* * * * *
39409945 AAATTACCATTTTGCCCGTGAACTTTCCAAAATCTCATTTTTAACCTCAATTTCACAAA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCAC-CA
* *
39410004 AAATTACCATTTTA-CCCTCAAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACCAA
1 AAATTACCATTTTACCCCT-GAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACC-A
* * *
39410063 AAATTACCACTTTACCCCTGAACTTTCCAAAATCTCATTTTGAACCTCGATTTCACCAA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACC-A
39410122 AAATTACCATTTTACCC
1 AAATTACCATTTTACCC
39410139 TCGAAAGTCA
Statistics
Matches: 424, Mismatches: 46, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
57 7 0.02
58 238 0.56
59 175 0.41
60 4 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCA
Found at i:39409901 original size:175 final size:172
Alignment explanation
Indices: 39409596--39410138 Score: 732
Period size: 175 Copynumber: 3.1 Consensus size: 172
39409586 AACTGTCCAG
* ** *
39409596 AAATTATCATTTTACCCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTTACCAAAATTAC
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAATTAC
*
39409661 CATTTTACGCCCGAACTTTCTAAAATCCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTA
66 CATTTTAC-CCCGAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACCAAAATTACCATTTTA
39409726 CCTCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAA
130 CC-CTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CAA
*
39409771 AAATTACCATTTTACCCCTGAACTTTCCAAAATC-CTATTTTTTACCCCGATTTCACCAAAATTA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTC-ATTTTTAACCCCGATTTCACCAAAATTA
* * * * * *
39409835 CCATTTTGCCTCCGAACTTTCCAAAATCTCGTTCTTAAGCCCGATTTCACCAAAATTACAATTTT
65 CCATTTTACC-CCGAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACCAAAATTACCATTTT
* * *
39409900 ACCCTTGAAC-TTCCTAAAATTTCATTTTTAACCCTGATTTCACCA
129 ACCC-TGAACTTTCC-AAAATTCCATTTTTAACCCCGATTTCACAA
* * * * *
39409945 AAATTACCATTTTGCCCGTGAACTTTCCAAAATCTCATTTTTAACCTCAATTTCACAAAAAATTA
1 AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCAC-CAAAATTA
* *
39410010 CCATTTTACCCTCAAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCACTT
65 CCATTTTACCC-CGAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACC-AAAATTACCATTT
* *
39410075 TACCCCTGAACTTTCCAAAA-TCTCATTTTGAACCTCGATTTCACCAA
128 TA-CCCTGAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCA-CAA
39410122 AAATTACCATTTTACCC
1 AAATTACCATTTTACCC
39410139 TCGAAAGTCA
Statistics
Matches: 321, Mismatches: 35, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
174 59 0.18
175 198 0.62
176 39 0.12
177 25 0.08
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (172 bp):
AAATTACCATTTTACCCCTGAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAATTAC
CATTTTACCCCGAACTTTCTAAAATCTCATTTTTAACCCCGATTTCACCAAAATTACCATTTTAC
CCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACAA
Found at i:39410017 original size:30 final size:29
Alignment explanation
Indices: 39409983--39410161 Score: 81
Period size: 28 Copynumber: 6.1 Consensus size: 29
39409973 AAAATCTCAT
39409983 TTTTAACCTCAATTTCACAAAAAATTACCA
1 TTTTAACCTCAATTTCAC-AAAAATTACCA
* *
39410013 TTTTACCCTCAAACTTT--CTAAAA-T-CTCA
1 TTTTAACCTC-AA-TTTCACAAAAATTAC-CA
* *
39410041 TTTTTAACCCCGATTTCACCAAAAATTACCA
1 -TTTTAACCTCAATTTCA-CAAAAATTACCA
* * *
39410072 CTTTACCCCTGAACTTTC-C-AAAA-T-CTCA
1 TTTTA-ACCTCAA-TTTCACAAAAATTAC-CA
*
39410100 TTTTGAACCTCGATTTCACCAAAAATTACCA
1 TTTT-AACCTCAATTTCA-CAAAAATTACCA
* **
39410131 TTTTACCCTCGAAAGT--CAAAAATTACCA
1 TTTTAACCTC-AATTTCACAAAAATTACCA
39410159 TTT
1 TTT
39410162 CACCCCCAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 40
0.65 0.11 0.24
Matches are distributed among these distances:
27 9 0.08
28 29 0.26
29 18 0.16
30 29 0.26
31 17 0.15
32 9 0.08
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTAACCTCAATTTCACAAAAATTACCA
Found at i:39412961 original size:20 final size:21
Alignment explanation
Indices: 39412919--39412961 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
39412909 GATAAATATT
*
39412919 AATTGTGTGATTAATTGGTGA
1 AATTGTGTGATTAATTGGAGA
* *
39412940 AATTGTG-GATTTATTTGAGA
1 AATTGTGTGATTAATTGGAGA
39412960 AA
1 AA
39412962 ATAAAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (21 bp):
AATTGTGTGATTAATTGGAGA
Found at i:39413165 original size:25 final size:24
Alignment explanation
Indices: 39413116--39413219 Score: 86
Period size: 25 Copynumber: 4.2 Consensus size: 24
39413106 ACATTAGCGC
* *
39413116 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTCCACTATTAGCACT-TGTGT
39413141 GCTCTCCACTATTAGCACTTCGTGT
1 GCTCTCCACTATTAGCACTT-GTGT
* *
39413166 GGTCT-C-CGATTAGCACTTAGTGT
1 GCTCTCCACTATTAGCACTT-GTGT
* ** *
39413189 GCTCTCCAATACCCAGCACTTTTGT
1 GCTCTCCACTA-TTAGCACTTGTGT
39413214 GCTCTC
1 GCTCTC
39413220 TGTTTAGTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
23 19 0.30
24 3 0.05
25 35 0.55
26 7 0.11
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (24 bp):
GCTCTCCACTATTAGCACTTGTGT
Found at i:39413181 original size:23 final size:23
Alignment explanation
Indices: 39413126--39413195 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
39413116 GCTCTCTATT
*
39413126 ATTAGCACTGT-GTGTGCTCTCCACT
1 ATTAGCACT-TAGTGTGCTCT-C-CG
* *
39413151 ATTAGCACTTCGTGTGGTCTCCG
1 ATTAGCACTTAGTGTGCTCTCCG
39413174 ATTAGCACTTAGTGTGCTCTCC
1 ATTAGCACTTAGTGTGCTCTCC
39413196 AATACCCAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 21 0.52
24 2 0.05
25 17 0.43
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (23 bp):
ATTAGCACTTAGTGTGCTCTCCG
Found at i:39413863 original size:20 final size:20
Alignment explanation
Indices: 39413833--39413879 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39413823 TGCCCCTTTT
39413833 GTATC-ATTTTTAAAGAAAA
1 GTATCGATTTTTAAAGAAAA
* *
39413852 GTATCGATTTTTGATGAAAA
1 GTATCGATTTTTAAAGAAAA
*
39413872 ATATCGAT
1 GTATCGAT
39413880 ACCTTTGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
GTATCGATTTTTAAAGAAAA
Found at i:39414535 original size:163 final size:163
Alignment explanation
Indices: 39414265--39414582 Score: 519
Period size: 163 Copynumber: 2.0 Consensus size: 163
39414255 GAACCGCCAG
* *
39414265 ACCAATTTCCTCCTCAGTGAAAGGCAAACATAGAAAGGTATTCATGCCATTAATAACATGAACGT
1 ACCAATTTCCTCCTCACTGAAAGGCAAACATAAAAAGGTATTCATGCCATTAATAACATGAACGT
* * *
39414330 CAATTCCCGACAAAGTCTTTGTGGCATCTCTCCGACCTCTAGACGTAAAAAAGTCAGCAAAGTAA
66 CAATTCCCGACAAAGTCTTTATGGCATCCCTCCGACCTCTAGACATAAAAAAGTCAGCAAAGTAA
39414395 TCACATGCCACTTGTGCCATCTCATACCATAAC
131 TCACATGCCACTTGTGCCATCTCATACCATAAC
** *
39414428 ACCAATTTCCTCCTCACTGAAAGGTGAACATAAAAAGGTATTCATGCCATTAGTAACATGAACGT
1 ACCAATTTCCTCCTCACTGAAAGGCAAACATAAAAAGGTATTCATGCCATTAATAACATGAACGT
** * * *
39414493 CAATTCCTTATAGAGTCTTTATGGCATCCCTCCGACCTCTAGACATAAACAAGTCAGCAAAGTAA
66 CAATTCCCGACAAAGTCTTTATGGCATCCCTCCGACCTCTAGACATAAAAAAGTCAGCAAAGTAA
39414558 TCACATGCCACTTGTGCCATCTCAT
131 TCACATGCCACTTGTGCCATCTCAT
39414583 CCTCACCCAA
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
163 142 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (163 bp):
ACCAATTTCCTCCTCACTGAAAGGCAAACATAAAAAGGTATTCATGCCATTAATAACATGAACGT
CAATTCCCGACAAAGTCTTTATGGCATCCCTCCGACCTCTAGACATAAAAAAGTCAGCAAAGTAA
TCACATGCCACTTGTGCCATCTCATACCATAAC
Found at i:39417848 original size:6 final size:6
Alignment explanation
Indices: 39417837--39417869 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
39417827 GAGATCCGGT
39417837 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
39417870 TGGAGTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:39417926 original size:25 final size:24
Alignment explanation
Indices: 39417893--39417946 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
39417883 GGGGGATTTT
* *
39417893 TTATTTTATTTAATATTAATATAA
1 TTATTTTATATAATATAAATATAA
39417917 TTATATTTATATAATATAAATATAA
1 TTAT-TTTATATAATATAAATATAA
*
39417942 GTATT
1 TTATT
39417947 AATATGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTTATATAATATAAATATAA
Found at i:39417931 original size:19 final size:21
Alignment explanation
Indices: 39417899--39417940 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
39417889 TTTTTTATTT
*
39417899 TATTTAATATTAATATAATTA
1 TATTTAATATTAATATAAATA
39417920 TATTT-ATA-TAATATAAATA
1 TATTTAATATTAATATAAATA
39417939 TA
1 TA
39417941 AGTATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 3 0.15
21 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTAATATTAATATAAATA
Found at i:39417956 original size:19 final size:18
Alignment explanation
Indices: 39417906--39417956 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
39417896 TTTTATTTAA
* **
39417906 TATTAATATAATTATATT
1 TATTAATATAAATATAAG
39417924 TATATAATATAAATATAAG
1 TAT-TAATATAAATATAAG
39417943 TATTAATATGAAAT
1 TATTAATAT-AAAT
39417957 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
TATTAATATAAATATAAG
Found at i:39417985 original size:29 final size:28
Alignment explanation
Indices: 39417953--39418027 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
39417943 TATTAATATG
*
39417953 AAATTTAAATTTATTATTATAT-TTTTT
1 AAATTTATATTTATTATTATATATTTTT
*
39417980 GAAAATATT-TATTTATTTTTATATATTTTT
1 --AAAT-TTATATTTATTATTATATATTTTT
39418010 AAATTTATATATTATTAT
1 AAATTTATAT-TTATTAT
39418028 CTAAAATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 2 0.05
28 7 0.18
29 23 0.59
30 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
AAATTTATATTTATTATTATATATTTTT
Found at i:39418720 original size:2 final size:2
Alignment explanation
Indices: 39418702--39418738 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
39418692 GAGATATGAG
* *
39418702 AT AT AG AT AT AT GT 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 AT AT AT AT A
39418739 GACTCATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:39424037 original size:18 final size:18
Alignment explanation
Indices: 39424014--39424057 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
39424004 AGTAGCCGAG
39424014 AGCCATTTAATGACCAAA
1 AGCCATTTAATGACCAAA
39424032 AGCCATTTAATGACCAAA
1 AGCCATTTAATGACCAAA
39424050 AGCCATTT
1 AGCCATTT
39424058 TGGTACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (18 bp):
AGCCATTTAATGACCAAA
Done.