Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 32
Found at i:5026270 original size:29 final size:28
Alignment explanation
Indices: 5026237--5026315 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
5026227 TCTGTGCAGC
* *
5026237 TCGCCAGGAAGCCATGGCGACGTAGTAGG
1 TCGCC-GGAAGGCATGGCGACGTAGTAGA
5026266 TCGCCCGGAAGGCATGGCGACGTAGTAGA
1 TCG-CCGGAAGGCATGGCGACGTAGTAGA
*
5026295 TCGTCCGGAAGGCATGACGAC
1 TCG-CCGGAAGGCATGGCGAC
5026316 CTACGGCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 43 0.96
30 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.37, T:0.14
Consensus pattern (28 bp):
TCGCCGGAAGGCATGGCGACGTAGTAGA
Found at i:5030314 original size:54 final size:54
Alignment explanation
Indices: 5030250--5030662 Score: 281
Period size: 54 Copynumber: 7.6 Consensus size: 54
5030240 ACAACTACAA
*
5030250 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAC
* *** * *
5030304 TAATACATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCAATAC
* ** *
5030357 -CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCAATAC
* ** *
5030411 T-AT--A-T-TTTAAAATAAATCAATCCAAACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCAATAC
*
5030465 T-AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCAATAC
* * * *
5030524 TGATAAATTATTTAAAATAAATCGATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAC
*
5030578 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATTC-ATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TCAATAC
5030632 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
5030663 CAACTACAAT
Statistics
Matches: 311, Mismatches: 24, Indels: 48
0.81 0.06 0.13
Matches are distributed among these distances:
48 26 0.08
49 1 0.00
50 2 0.01
52 3 0.01
53 1 0.00
54 224 0.72
55 9 0.03
56 1 0.00
58 13 0.04
59 3 0.01
60 3 0.01
61 1 0.00
62 3 0.01
63 6 0.02
64 15 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAC
Found at i:5030391 original size:22 final size:23
Alignment explanation
Indices: 5030316--5030390 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
5030306 ATACATTATT
5030316 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
5030338 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
5030364 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
5030387 TAAA
1 TAAA
5030391 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:5030401 original size:32 final size:32
Alignment explanation
Indices: 5030362--5030608 Score: 257
Period size: 32 Copynumber: 8.7 Consensus size: 32
5030352 CAATCCATAT
5030362 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5030394 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5030416 TTTAAAATAAATCAATCCAAACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5030448 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5030470 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5030502 TTTAAAATAAATCAATCCATACTGATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
5030534 TTTAAAAT--A--AATCGAT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5030556 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
5030588 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
5030609 TTTTAAAATA
Statistics
Matches: 180, Mismatches: 5, Indels: 60
0.73 0.02 0.24
Matches are distributed among these distances:
22 34 0.19
23 5 0.03
24 4 0.02
26 15 0.08
27 12 0.07
28 15 0.08
30 4 0.02
31 5 0.03
32 86 0.48
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:5030499 original size:22 final size:22
Alignment explanation
Indices: 5030450--5030498 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5030440 ATAAATTATT
* **
5030450 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
5030472 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
5030495 TAAA
1 TAAA
5030499 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5030607 original size:86 final size:86
Alignment explanation
Indices: 5030416--5030608 Score: 359
Period size: 86 Copynumber: 2.2 Consensus size: 86
5030406 CAATCTATAT
*
5030416 TTTAAAATAAATCAATCCAAACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
5030481 TCAATCCATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
* *
5030502 TTTAAAATAAATCAATCCATACTGATAAATTATTTAAAATAAATCGATCTATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
5030567 TCAATCCATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
5030588 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
5030609 TTTTAAAATA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 104 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (86 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
TCAATCCATACTAATAAATTA
Found at i:5030614 original size:22 final size:22
Alignment explanation
Indices: 5030588--5030630 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5030578 TAATAAATTA
5030588 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
5030610 TTTAAAATAAATTAATTCATA
1 TTTAAAATAAATCAATCCATA
5030631 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5030646 original size:86 final size:85
Alignment explanation
Indices: 5030470--5030746 Score: 281
Period size: 86 Copynumber: 3.2 Consensus size: 85
5030460 CAATCTATAT
**
5030470 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTGATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A-
* *
5030535 TTAAAATAAATCGAT-CT-AT-A-T-
62 -TAAATTAATTC-ATACTAATAATTA
5030556 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
5030621 TTAATTCATACTAATAAATTA
66 TTAATTCATACTAAT-AATTA
* *
5030642 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAACCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
* *
5030700 ATCAATCAATCCATACAAATACATTA
65 AT---T-AATTCATACTAATA-ATTA
5030726 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
5030747 TTTTAAAATA
Statistics
Matches: 171, Mismatches: 8, Indels: 26
0.83 0.04 0.13
Matches are distributed among these distances:
80 30 0.18
81 11 0.06
82 3 0.02
83 3 0.02
84 38 0.22
85 8 0.05
86 78 0.46
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.34
Consensus pattern (85 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TTAATTCATACTAATAATTA
Found at i:5030738 original size:84 final size:80
Alignment explanation
Indices: 5030265--5030746 Score: 294
Period size: 80 Copynumber: 5.9 Consensus size: 80
5030255 AATTATTTAA
* * * * *
5030265 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATACATTATTTAAAATAAATCAAT
1 AATAAACCAATCCATATTTTAAAATAAATTAATCCATACAAATAAATTATTTAAAATAAATCAAT
5030330 CCATACAACTACAAT
66 CCATACAACTACAAT
* * *
5030345 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAACCAATCCATATTTTAAAATAAATTAATCCATACAAATAAATTATTTAAAATAAATCAAT
* * **
5030410 -C-TA-TATTTTAA-
66 CCATACAACTACAAT
* ** * * * * * **
5030421 AATAAATCAATCCA-AACTAATAAATTATTTAA--AATAAATCAATCTA-TATTTTAAAATAAAT
1 AATAAACCAATCCATATTTTA-AAATAAATTAATCCATACA--AATAAATTA-TTTAAAATAAAT
*
5030482 CAATCCATACTAA-TAAATTATTT
62 CAATCCATAC-AACTACA--A--T
* ** * * *
5030505 AAAATAAATCAATCCATACTGATAAATTATTTAAAATAAATCGAT-C---TATA-T-TTTAAAAT
1 --AATAAACCAATCCATA-TTTTAAA--A--T-AAATTAATCCATACAAATAAATTATTTAAAAT
*
5030564 AAATCAATCCATACTAA-TAAATTATTT
58 AAATCAATCCATAC-AACTACA--A--T
* * *
5030591 AAAATAAATCAATCCATATTTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAACCAATCCATATTTTAAAATAAATTAATCCATACAAATAAATTATTTAAAATAAATCA
5030656 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
*
5030673 AATAAACCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATACATTATTTAAAATAAAT
1 AATAAACCAATCCATATTTTAAAATAAAT---T-AATCCATACAAATAAATTATTTAAAATAAAT
5030738 CAATCCATA
62 CAATCCATA
5030747 TTTTAAAATA
Statistics
Matches: 326, Mismatches: 41, Indels: 66
0.75 0.09 0.15
Matches are distributed among these distances:
74 3 0.01
75 5 0.02
76 42 0.13
77 5 0.02
78 4 0.01
79 3 0.01
80 101 0.31
81 3 0.01
82 1 0.00
83 2 0.01
84 41 0.13
85 8 0.02
86 92 0.28
87 3 0.01
88 5 0.02
89 1 0.00
91 1 0.00
92 4 0.01
94 2 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAACCAATCCATATTTTAAAATAAATTAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:5030744 original size:32 final size:32
Alignment explanation
Indices: 5030698--5030808 Score: 107
Period size: 32 Copynumber: 3.8 Consensus size: 32
5030688 ATTTTAAAAT
*
5030698 AAATCAATCAATCCATACAAATACATTATTTA
1 AAATAAATCAATCCATACAAATACATTATTTA
5030730 AAATAAATCAAT-C---C--AT--A-T-TTTA
1 AAATAAATCAATCCATACAAATACATTATTTA
* * *
5030752 AAATAAATCAATTCATACTAATAAATTATTTA
1 AAATAAATCAATCCATACAAATACATTATTTA
*
5030784 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAAATACA
5030809 ATAATAAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
22 16 0.25
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.03
32 36 0.56
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (32 bp):
AAATAAATCAATCCATACAAATACATTATTTA
Found at i:5030752 original size:22 final size:22
Alignment explanation
Indices: 5030726--5030768 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5030716 AAATACATTA
5030726 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
5030748 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
5030769 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:5030757 original size:80 final size:79
Alignment explanation
Indices: 5030260--5030842 Score: 286
Period size: 80 Copynumber: 7.2 Consensus size: 79
5030250 TAATAAATTA
* *
5030260 TTTAAAATAAATCAATCCATATTTTAAAAT--A-AATCAATCTATACTAATACATTATTTAAAAT
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACAAATACATTATTTAAAAT
*
5030322 AAATCAATCCATACAAC
66 AAATCAATCCAT---AT
** * *
5030339 TACAATAATAAATCAATCCATATTTTAAAAT--A-AATCAATCCATACTAATAAATTATTTAAAA
1 TTTAA-AATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACAAATACATTATTTAAAA
*
5030401 TAAATCAATCTATAT
65 TAAATCAATCCATAT
* ** * ** **
5030416 TTTAAAATAAATCAATCCAAACTAATAAATTATTTAA--AATAAAT-C-AAT-C-TATATTTTAA
1 TTTAAAATAAATCAATCCATA-TTTTAAAATAAATAATCAATCCATACAAATACAT-TA-TTTAA
5030475 AATAAATCAATCCATACTAATAAATT
63 AATAAATCAAT-C---C--AT--A-T
** * * * *
5030501 ATTTAAAATAAATCAATCCATACTGATAAATTATTTAA-AATAAATCGAT-C---TATA-T-TTT
1 -TTTAAAATAAATCAATCCATA-TTTTAAA--A-TAAATAATCAATCCATACAAATACATTATTT
5030559 AAAATAAATCAATCCATACTAATAAATT
61 AAAATAAATCAAT-C---C--AT--A-T
* * *
5030587 ATTTAAAATAAATCAATCCATATTTTAAAATAAAT--T-AATTCATACTAATAAATTATTTAAAA
1 -TTTAAAATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACAAATACATTATTTAAAA
*
5030649 TAAATCAATCCATACAAC
65 TAAATCAATCCAT---AT
** *
5030667 TACAATAATAAACCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATACATTATTTAAA
1 TTTAA-AATAAATCAATCCATATTTTAAAATAAAT-AATCAATCCATACAAATACATTATTTAAA
5030732 ATAAATCAATCCATAT
64 ATAAATCAATCCATAT
* ** *
5030748 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACA--A-
1 TTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAAT-AATCAATCCATACAAATACATTAT
5030810 -T--AATAAATCAATCCATAT
59 TTAAAATAAATCAATCCATAT
5030828 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
5030843 AATTTTTATT
Statistics
Matches: 412, Mismatches: 49, Indels: 85
0.75 0.09 0.16
Matches are distributed among these distances:
74 1 0.00
75 2 0.00
76 34 0.08
77 12 0.03
78 5 0.01
79 6 0.01
80 149 0.36
81 13 0.03
82 7 0.02
83 3 0.01
84 41 0.10
85 9 0.02
86 119 0.29
88 4 0.01
89 1 0.00
90 6 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (79 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACAAATACATTATTTAAAAT
AAATCAATCCATAT
Found at i:5030777 original size:22 final size:22
Alignment explanation
Indices: 5030728--5030776 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5030718 ATACATTATT
**
5030728 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
5030750 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
5030773 TAAA
1 TAAA
5030777 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:5030785 original size:54 final size:54
Alignment explanation
Indices: 5030345--5030800 Score: 399
Period size: 54 Copynumber: 8.3 Consensus size: 54
5030335 CAACTACAAT
5030345 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
5030399 AATAAATCAATCTATATTTTAAAATAAATCAATCCAAACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
5030453 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** * *
5030507 AATAAATCAATCCATACTGATAAATTATTTAAAATAAATCGAT-CT-AT--A-T-TTTAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATTTAA
*
5030561 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAAT
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATA--CT--AATAAATT-AT
* *
5030626 TCAT
51 TTAA
* * *
5030630 ACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAC-AACTACA--A--T--
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
* * *
5030673 AATAAACCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATACATTATTTAA
1 AATAAATCAATCCATATTTTAAAAT--A--AATCAATCCATACTAATAAATTATTTAA
*
5030731 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
5030785 AATAAATCAATCCATA
1 AATAAATCAATCCATA
5030801 CAACTACAAT
Statistics
Matches: 331, Mismatches: 28, Indels: 86
0.74 0.06 0.19
Matches are distributed among these distances:
43 2 0.01
44 5 0.02
47 3 0.01
48 8 0.02
49 2 0.01
50 4 0.01
52 17 0.05
53 2 0.01
54 199 0.60
55 7 0.02
56 3 0.01
57 2 0.01
58 37 0.11
59 5 0.02
60 12 0.04
61 2 0.01
62 2 0.01
63 4 0.01
64 2 0.01
66 1 0.00
67 1 0.00
68 6 0.02
69 5 0.02
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:5031021 original size:22 final size:22
Alignment explanation
Indices: 5030995--5031134 Score: 98
Period size: 22 Copynumber: 6.5 Consensus size: 22
5030985 TAATAAATTA
5030995 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
5031017 TTTAAAATAAATCAATCTATACT
1 TTTAAAATAAATCAATCTATA-T
** * * * *
5031040 AATAAATTAATTAAAATATATTAT
1 TTTAAAATAAAT-CAATCTA-TAT
* *
5031064 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATCAATCTATAT
*
5031086 TTT---AT-AAT-AA-AT-TAT
1 TTTAAAATAAATCAATCTATAT
5031101 TTTAAAATAAATCAAT-TCATAT
1 TTTAAAATAAATCAATCT-ATAT
*
5031123 TTTATAATAAAT
1 TTTAAAATAAAT
5031135 TATTTTAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
15 6 0.07
17 2 0.02
18 5 0.05
19 5 0.05
20 3 0.03
22 41 0.45
23 14 0.15
24 14 0.15
25 2 0.02
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:5031101 original size:15 final size:15
Alignment explanation
Indices: 5031083--5031167 Score: 57
Period size: 15 Copynumber: 5.3 Consensus size: 15
5031073 AATAAATCCA
5031083 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
5031098 TATTTTAAAATAAATCAATT
1 TATTTT---AT-AAT-AAAT
5031118 CATATTTTATAATAAAT
1 --TATTTTATAATAAAT
*
5031135 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
* *
5031150 AACTTTAT--TAAAT
1 TATTTTATAATAAAT
5031163 TATTT
1 TATTT
5031168 AAAATTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.15
15 25 0.45
17 3 0.05
18 5 0.09
19 5 0.09
20 3 0.05
22 6 0.11
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:5031102 original size:37 final size:37
Alignment explanation
Indices: 5030985--5031151 Score: 175
Period size: 37 Copynumber: 4.7 Consensus size: 37
5030975 CGTGTGACAC
* *
5030985 TAATAAATTA-TTTAAAATAAATCAATCTATATTTTA
1 TAATAAATTATTTTAAAATAAATAAATCCATATTTTA
* * * * * * *
5031021 AAATAAATCAATCTATACT-AATAAAT---TA-ATTA
1 TAATAAATTATTTTAAAATAAATAAATCCATATTTTA
* *
5031053 AAATATATTATTTTAAAATAAATAAATCCATATTTTA
1 TAATAAATTATTTTAAAATAAATAAATCCATATTTTA
* *
5031090 TAATAAATTATTTTAAAATAAATCAATTCATATTTTA
1 TAATAAATTATTTTAAAATAAATAAATCCATATTTTA
5031127 TAATAAATTATTTTAAAATAAATAA
1 TAATAAATTATTTTAAAATAAATAA
5031152 CTTTATTAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
32 16 0.15
33 9 0.08
36 16 0.15
37 65 0.61
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (37 bp):
TAATAAATTATTTTAAAATAAATAAATCCATATTTTA
Found at i:5036016 original size:24 final size:24
Alignment explanation
Indices: 5035966--5036039 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 24
5035956 TTTAATCAAA
* *
5035966 ATATTAATTATTAAAATATTTAAAAT
1 ATATTTATTATT--AATATTTATAAT
*
5035992 ATATTTATTATTAATATTTCTAAT
1 ATATTTATTATTAATATTTATAAT
* * *
5036016 A-ATATAATATT-ATATTTTTAAT
1 ATATTTATTATTAATATTTATAAT
5036038 AT
1 AT
5036040 TATAATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 11 0.27
23 8 0.20
24 11 0.27
26 11 0.27
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTATTATTAATATTTATAAT
Found at i:5036026 original size:26 final size:26
Alignment explanation
Indices: 5035963--5036028 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
5035953 CATTTTAATC
5035963 AAAATAT-TA-ATTATTAAAATATTT
1 AAAATATATATATTATTAAAATATTT
* *
5035987 AAAATATATTTATTATTAATAT-TTCT
1 AAAATATATATATTATTAAAATATT-T
5036013 AATAATATA-ATATTAT
1 AA-AATATATATATTAT
5036029 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 7 0.20
25 3 0.09
26 19 0.54
27 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATATATATTATTAAAATATTT
Found at i:5036037 original size:22 final size:23
Alignment explanation
Indices: 5036000--5036046 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5035990 ATATATTTAT
5036000 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
5036023 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
5036045 TA
1 TA
5036047 AAACAATCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:5036202 original size:27 final size:28
Alignment explanation
Indices: 5036114--5036218 Score: 78
Period size: 27 Copynumber: 3.9 Consensus size: 28
5036104 ATATATATAA
* *
5036114 TAAATTA-TTAATAA-AATTTATATTAT
1 TAAATTATTTAATAATAAATAATATTAT
* * *
5036140 T-TATTAATTTCAT-AGAAATAATATTAT
1 TAAATT-ATTTAATAATAAATAATATTAT
5036167 TAAATTA-TTAATAATAAATAATATTATT
1 TAAATTATTTAATAATAAATAATATTA-T
* *
5036195 TACA-TATTTAATATTAATATAATA
1 TAAATTATTTAATAATAA-ATAATA
5036219 ATCTAATAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.05
26 7 0.11
27 30 0.48
28 16 0.26
29 6 0.10
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (28 bp):
TAAATTATTTAATAATAAATAATATTAT
Found at i:5036259 original size:23 final size:23
Alignment explanation
Indices: 5036233--5036277 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5036223 AATAATATTT
5036233 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
5036256 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
5036278 ATATAACTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:5039655 original size:11 final size:11
Alignment explanation
Indices: 5039639--5039666 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5039629 TGAGCCTTTT
5039639 CGAGCTGTTCA
1 CGAGCTGTTCA
5039650 CGAGCTGTTCA
1 CGAGCTGTTCA
5039661 CGAGCT
1 CGAGCT
5039667 TCAGTTCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.25
Consensus pattern (11 bp):
CGAGCTGTTCA
Found at i:5060373 original size:57 final size:57
Alignment explanation
Indices: 5060285--5060399 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
5060275 GATGAATATA
5060285 AGTTACTTATCAAAAAAATATGTGATTATACAAAAATATTTGATTTTTGTGGTGAGT
1 AGTTACTTATCAAAAAAATATGTGATTATACAAAAATATTTGATTTTTGTGGTGAGT
5060342 AGTTACTTATCAAAAAAATATGTGATTATACAAAAATATTTGATTTTTGTGGTGAGT
1 AGTTACTTATCAAAAAAATATGTGATTATACAAAAATATTTGATTTTTGTGGTGAGT
5060399 A
1 A
5060400 TATTTTAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (57 bp):
AGTTACTTATCAAAAAAATATGTGATTATACAAAAATATTTGATTTTTGTGGTGAGT
Found at i:5065850 original size:20 final size:21
Alignment explanation
Indices: 5065827--5065883 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
5065817 AACCTAAAAG
5065827 TAAAAAATAAAAAAAAT-AAA
1 TAAAAAATAAAAAAAATCAAA
* *
5065847 T-AAACATTAAAAAAATCAAA
1 TAAAAAATAAAAAAAATCAAA
* * *
5065867 GAGAAAATAAAATAAAT
1 TAAAAAATAAAAAAAAT
5065884 TAAAAATTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (21 bp):
TAAAAAATAAAAAAAATCAAA
Found at i:5067655 original size:106 final size:106
Alignment explanation
Indices: 5067478--5068467 Score: 1604
Period size: 106 Copynumber: 9.3 Consensus size: 106
5067468 TGTTTCGAGG
* * **
5067478 CCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
*
5067543 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
5067584 CCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCA
1 CCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
*
5067648 GCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
5067690 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAAAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* ** * *
5067755 CCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTAGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
5067796 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * * * * *
5067861 CCGTCTCTTCGTTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
66 CGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
5067903 CTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTATTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* *
5067968 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTAGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
5068009 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
*
5068074 CGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
5068115 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
5068180 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
5068221 CCAATATCCTTCACTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
*
5068286 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
5068327 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
5068392 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
5068433 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
5068468 CGAGCAAAAT
Statistics
Matches: 822, Mismatches: 59, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 724 0.88
107 97 0.12
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:5068181 original size:531 final size:530
Alignment explanation
Indices: 5067478--5068467 Score: 1667
Period size: 531 Copynumber: 1.9 Consensus size: 530
5067468 TGTTTCGAGG
* *
5067478 CCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGAGAAATTGTTTGTTGACAACCAG
5067543 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAGTTG
66 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAGTTG
* *
5067608 AAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAA
131 AAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAA
* *
5067673 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAAT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCACTATGAAGTTGAAATTGGCTCCGAAATTGGGAAAT
* * * *
5067738 TGTTTGTTGAAAACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTAGAGTCCAATAT
261 TGTTTATTGAAAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTAGAGTCCAATAT
* * *
5067803 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCTC
326 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCC
* * *
5067868 TTCGTTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTG
391 TTCG-TCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
5067933 ACTCTGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCG
455 ACTCTGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCG
5067998 TTGTCTAGAGT
520 TTGTCTAGAGT
* * *
5068009 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGAGAAATTGTTTGTTGACAACCAG
* *
5068074 CGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-CTGTGAAGTT
66 CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTC-GTGAAGTT
* *
5068138 GAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
130 GAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGA
*
5068203 ACTTGCGTTGTCTGGAGTCCAATATCCTTCACTATGAAGTTGAAATTGGCTCTGAAATTGGGAAA
195 ACTTGCGTTGTCTGGAGTCCAATATCCTTCACTATGAAGTTGAAATTGGCTCCGAAATTGGGAAA
* * *
5068268 TTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
260 TTGTTTATTGAAAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTAGAGTCCAATA
*
5068333 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
325 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCC
* * *
5068398 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
390 CTTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
5068463 GCTCT
455 ACTCT
5068468 CGAGCAAAAT
Statistics
Matches: 426, Mismatches: 32, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
530 59 0.14
531 367 0.86
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (530 bp):
CCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGAGAAATTGTTTGTTGACAACCAG
CAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTCGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCACTATGAAGTTGAAATTGGCTCCGAAATTGGGAAAT
TGTTTATTGAAAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTAGAGTCCAATAT
CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCC
TTCGTCGTGAAGTTGAACTTGCGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGA
CTCTGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGT
TGTCTAGAGT
Found at i:5075654 original size:52 final size:52
Alignment explanation
Indices: 5075598--5075699 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
5075588 TTTTTATTTG
* * *
5075598 TATTTTTTAT-ACTTTTTTTATAATTTAAATTGATATAATTCATATATAATAA
1 TATTTTTTATGA-ATTTATTATAATTTAAATTAATATAATTCATATATAATAA
* * *
5075650 TATTTTTTTTGAATTTATTATAGTTTAAATTAATATGATTCATATATAAT
1 TATTTTTTATGAATTTATTATAATTTAAATTAATATAATTCATATATAAT
5075700 TGTAAGTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 42 0.98
53 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (52 bp):
TATTTTTTATGAATTTATTATAATTTAAATTAATATAATTCATATATAATAA
Found at i:5076236 original size:29 final size:32
Alignment explanation
Indices: 5076182--5076249 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 32
5076172 GAGGACTAAT
*
5076182 TTAAAAT-TTAAAATATAATTTAGATATGAAA
1 TTAAAATATTAAAATATAATTTAGATATCAAA
*
5076213 TTAAAATATTAAAA-A-AA-TTAGATATCAAT
1 TTAAAATATTAAAATATAATTTAGATATCAAA
5076242 TTAAAATA
1 TTAAAATA
5076250 AAACCATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 18 0.53
30 2 0.06
31 8 0.24
32 6 0.18
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (32 bp):
TTAAAATATTAAAATATAATTTAGATATCAAA
Found at i:5077717 original size:137 final size:134
Alignment explanation
Indices: 5077448--5077716 Score: 434
Period size: 137 Copynumber: 2.0 Consensus size: 134
5077438 CTAACTTATC
* *
5077448 CCTTTGTAATGCTTGGGTATAGTATAACCAATCATTGTTGTGTAATTAGGCTATTCTGTTTTGTT
1 CCTTTGTAATGCTTGGGTATAATATAACCAATCATTGTTGTGTAATTAGGCTATTCTATTTTGTT
* *
5077513 GATTGGTTATTGGTTGTATCAAAACCTTACTGTTGTGGTAATAAAATGCTGAATTATCCAAAAAA
66 GATTAGTTATTGGTTGTATCAAAACC-T-CTGTTGTGGTAATAAAATGCTGAATTATCAAAAAAA
5077578 AAAAAG
129 AAAAAG
* *
5077584 CCTTTGTAATGCTTGGGGTATAATATAACCAATTATTGTTGTGTAATTAGGCTGTTCTATTTTGT
1 CCTTTGTAATGCTT-GGGTATAATATAACCAATCATTGTTGTGTAATTAGGCTATTCTATTTTGT
5077649 TGATTAGTTATTGGTTGTATCAAAA-C-CTGTTGTGGTAATAAAATGCTGAATTATCAAAAAAGA
65 TGATTAGTTATTGGTTGTATCAAAACCTCTGTTGTGGTAATAAAATGCTGAATTATCAAAAAA-A
5077712 AAAAA
129 AAAAA
5077717 AGAAAAAAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
133 34 0.27
134 6 0.05
136 15 0.12
137 70 0.56
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (134 bp):
CCTTTGTAATGCTTGGGTATAATATAACCAATCATTGTTGTGTAATTAGGCTATTCTATTTTGTT
GATTAGTTATTGGTTGTATCAAAACCTCTGTTGTGGTAATAAAATGCTGAATTATCAAAAAAAAA
AAAG
Found at i:5077950 original size:26 final size:24
Alignment explanation
Indices: 5077912--5077964 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
5077902 TCAAATTCAT
*
5077912 TTATAATTATTTATTAAT-AAATTA
1 TTATAATTATTTAAT-ATGAAATTA
5077936 TTATAATATATTTTAATATGAAATTA
1 TTATAAT-TA-TTTAATATGAAATTA
5077962 TTA
1 TTA
5077965 ATTTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 4 0.16
26 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATAATTATTTAATATGAAATTA
Found at i:5078140 original size:6 final size:6
Alignment explanation
Indices: 5078129--5078156 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5078119 TTTCATTATT
5078129 CTCACC CTCACC CTCACC CTCACC CTCA
1 CTCACC CTCACC CTCACC CTCACC CTCA
5078157 AAGCTCTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.64, G:0.00, T:0.18
Consensus pattern (6 bp):
CTCACC
Found at i:5080597 original size:81 final size:85
Alignment explanation
Indices: 5080498--5080725 Score: 266
Period size: 90 Copynumber: 2.7 Consensus size: 85
5080488 ACCTTCCCCA
* * * * *
5080498 CCTCCTCCGGCTAATGTTCCAACTCCGCCTTCCCCAAAATCTCCACCTTCACTTCCAC-CT-C-A
1 CCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCACCTTCACATCCACACTACGA
*
5080560 -GATAGTTTTTAGTTCACCG
66 GGATAATTTTTAGTTCACCG
** * * *
5080579 CCTCCTCCAGCTTCTGTTCCAACGCCACCTTCCTCAAAGTCTCCACGTTCACCACCAGCAACACT
1 CCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCACCTTCA-CATC--C-ACACT
*
5080644 ACCGAGGATAATTTTTAGTTCCCCG
62 A-CGAGGATAATTTTTAGTTCACCG
*
5080669 CCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCACCTTCACCTCCA
1 CCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCACCTTCACATCCA
5080726 GCAACACCAC
Statistics
Matches: 120, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
81 43 0.36
82 2 0.02
84 1 0.01
85 2 0.02
86 3 0.03
87 1 0.01
88 1 0.01
89 3 0.03
90 64 0.53
ACGTcount: A:0.21, C:0.42, G:0.10, T:0.27
Consensus pattern (85 bp):
CCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCACCTTCACATCCACACTACGA
GGATAATTTTTAGTTCACCG
Found at i:5080693 original size:90 final size:90
Alignment explanation
Indices: 5080560--5080732 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 90
5080550 TTCCACCTCA
* ** *
5080560 GATAGTTTTTAGTTCACCGCCTCCTCCAGCTTCTGTTCCAACGCCACCTTCCTCAAAGTCTCCAC
1 GATAATTTTTAGTTCACCGCCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCAC
*
5080625 GTTCACCACCAGCAACACTACCGAG
66 CTTCACCACCAGCAACACTACCGAG
*
5080650 GATAATTTTTAGTTCCCCGCCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCAC
1 GATAATTTTTAGTTCACCGCCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCAC
*
5080715 CTTCACCTCCAGCAACAC
66 CTTCACCACCAGCAACAC
5080733 CACCAACTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.23, C:0.40, G:0.11, T:0.26
Consensus pattern (90 bp):
GATAATTTTTAGTTCACCGCCTCCTCCAGCTAATGTTCCAACGCCACCTTCCTCAAAATCTCCAC
CTTCACCACCAGCAACACTACCGAG
Found at i:5087946 original size:24 final size:23
Alignment explanation
Indices: 5087895--5087946 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
5087885 TTCAATGGTC
5087895 CTTTTTACGAGGAATATTTTGTT
1 CTTTTTACGAGGAATATTTTGTT
5087918 CTTTTTACGAGGAATATTTTGTT
1 CTTTTTACGAGGAATATTTTGTT
5087941 CTTTTT
1 CTTTTT
5087947 GAATTGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (23 bp):
CTTTTTACGAGGAATATTTTGTT
Found at i:5095678 original size:182 final size:182
Alignment explanation
Indices: 5095387--5096111 Score: 1008
Period size: 182 Copynumber: 4.0 Consensus size: 182
5095377 ATACAAATAG
* * * ** * ** *
5095387 AAAATGTATCGCTCCATAGCAATATTACAGGTAAAAATATGAAAAAACCGGTCTCAAAATGAAAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACAAGTCTCAAAATGACAA
* * * *
5095452 AACCGGTAAA-ACGATATTGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
66 AACCGATAAAGA-AATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
5095516 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
130 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
*
5095569 AAAATGTATTGATCCATAACAATATAACAACTAAAAATATGACAAAACAAGTCTCAAAAATGACA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACAAGTCTC-AAAATGACA
***
5095634 AAACCGATAAA-AAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGATTTTTT
65 AAACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA-CACTT
*
5095698 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTTGATACTTTAAAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTT-AAA
** ** *
5095753 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCCCAAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACAAGTCTCAAAATGACAA
* * *** * *
5095818 ATCCGGTAAAGCGCTATCGGATATGTTGAAAGTGTCAATAATTTAATATAAATATCGACACTTTC
66 AACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT-
* **
5095883 T-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATG
130 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
*
5095935 AAAATGTATTGATCCATAACAATATAACAACTAAAAATATGACAAAATCAA-TCTCAAAATGACA
1 AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAA-CAAGTCTCAAAATGACA
* * *
5095999 AAACCGATAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
65 AAACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
5096064 TGGAATTTAAAAGAGAAGAAGTTATAGTGCCTATGAAGTATCGATACT
130 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACT
5096112 CTTTAAATTT
Statistics
Matches: 480, Mismatches: 56, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
181 1 0.00
182 245 0.51
183 139 0.29
184 95 0.20
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACAAGTCTCAAAATGACAA
AACCGATAAAGAAATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT
GGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAA
Found at i:5107903 original size:87 final size:87
Alignment explanation
Indices: 5107801--5107963 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
5107791 AAATAGGTCA
* *
5107801 ATATAAGCACTACCTATTACATTATATAAGCTCTACCTAATATGTTATTATACTTGGTAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
5107866 CCGGTTAAATGCTTATTTTATT
66 CCGGTTAAATGCTTATTTTATT
* * *
5107888 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
*
5107953 CTGGTTAAATG
66 CCGGTTAAATG
5107964 ATATAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
CCGGTTAAATGCTTATTTTATT
Found at i:5107935 original size:23 final size:23
Alignment explanation
Indices: 5107885--5107929 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5107875 TGCTTATTTT
*
5107885 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
5107908 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
5107930 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:5112457 original size:24 final size:24
Alignment explanation
Indices: 5112425--5112476 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5112415 CTTGAGAGAC
5112425 TGCAGAAAATTGAGGAATTTGAGG
1 TGCAGAAAATTGAGGAATTTGAGG
*
5112449 TGCAGAAAATTGAGGAATTTGATG
1 TGCAGAAAATTGAGGAATTTGAGG
5112473 TGCA
1 TGCA
5112477 TAACGTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27
Consensus pattern (24 bp):
TGCAGAAAATTGAGGAATTTGAGG
Found at i:5122300 original size:32 final size:31
Alignment explanation
Indices: 5122224--5122332 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 31
5122214 CAAATGTTAC
* *
5122224 AAAACAATCATTAAATTC-ATCTCAA-TATTTT
1 AAAATAATCATTAAATTCTAT-T-AATTATTAT
5122255 AAAATAAAT-ATTAAATTCTATTAAGTTATTAT
1 AAAAT-AATCATTAAATTCTATTAA-TTATTAT
*
5122287 AAAATAATCATTAAAAAT-TATTAAATTA-TAT
1 AAAATAATCATT-AAATTCTATT-AATTATTAT
* *
5122318 AAAATGATTATTAAA
1 AAAATAATCATTAAA
5122333 AAAACTAGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
30 5 0.08
31 30 0.45
32 25 0.38
33 6 0.09
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAATAATCATTAAATTCTATTAATTATTAT
Found at i:5122335 original size:32 final size:32
Alignment explanation
Indices: 5122273--5122334 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
5122263 TATTAAATTC
*
5122273 TATTAAGTTATTATAAAATAATCATTAAAAAT
1 TATTAAATTATTATAAAATAATCATTAAAAAT
* *
5122305 TATTAAATTA-TATAAAATGATTATTAAAAA
1 TATTAAATTATTATAAAATAATCATTAAAAA
5122335 AACTAGTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (32 bp):
TATTAAATTATTATAAAATAATCATTAAAAAT
Found at i:5129584 original size:60 final size:61
Alignment explanation
Indices: 5129449--5129625 Score: 186
Period size: 60 Copynumber: 2.9 Consensus size: 61
5129439 TGTATAATTT
* *
5129449 AGGATAAAATTGAAATGTTCAAAAACTTTGGAGAACAATTTAGAATGAAGATCGTAGTTTA
1 AGGATAAAATTGAAATGTTCAAAAACTTTGAAGAACAATTTAGAATGAAGATCATAGTTTA
* * * *
5129510 GGGACAAAGA-TGAAATGTTC-AAAAGTTTGAAGAATAATTTAGAATGATAG-TCATAGTTTA
1 AGGATAAA-ATTGAAATGTTCAAAAACTTTGAAGAACAATTTAGAATGA-AGATCATAGTTTA
* * * *
5129570 AGGATAAAATTGAAATATTTAAAAA-TTT-AAGGACCAATTTAAAATGAGAGAT-ATAG
1 AGGATAAAATTGAAATGTTCAAAAACTTTGAA-GAACAATTTAGAATGA-AGATCATAG
5129626 ATTGGGGATG
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
59 3 0.03
60 69 0.72
61 23 0.24
62 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.29
Consensus pattern (61 bp):
AGGATAAAATTGAAATGTTCAAAAACTTTGAAGAACAATTTAGAATGAAGATCATAGTTTA
Found at i:5131598 original size:31 final size:31
Alignment explanation
Indices: 5131563--5131647 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
5131553 TTAAGCTCGC
*
5131563 GAGTTTTCGAGTCGAGTCGAGTTTCATTTTA
1 GAGTTTTCGAGTCGAGTCGAGCTTCATTTTA
*
5131594 GAGTTTTCGAGTCGAGTTGAGCTTCATTTTA
1 GAGTTTTCGAGTCGAGTCGAGCTTCATTTTA
*
5131625 GAGTTTTTGAGTCGAGTCGAGCT
1 GAGTTTTCGAGTCGAGTCGAGCT
5131648 CAGCACTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (31 bp):
GAGTTTTCGAGTCGAGTCGAGCTTCATTTTA
Found at i:5132838 original size:22 final size:23
Alignment explanation
Indices: 5132812--5132867 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5132802 CACTCTATAT
* *
5132812 ATTATTTTTTTTCAAT-TAAATA
1 ATTATTTTTATTCAATAAAAATA
*
5132834 ATTATTTTTATTGAATAAAAATA
1 ATTATTTTTATTCAATAAAAATA
5132857 A-TATTTTTATT
1 ATTATTTTTATT
5132868 ATTTCGGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTATTTTTATTCAATAAAAATA
Found at i:5144952 original size:18 final size:18
Alignment explanation
Indices: 5144931--5144974 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5144921 GTCGTCGTCG
*
5144931 TCATCGTCATAATAATAA
1 TCATCATCATAATAATAA
5144949 TCATCATCATAATAATAA
1 TCATCATCATAATAATAA
*
5144967 TAATCATC
1 TCATCATC
5144975 TTCATCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (18 bp):
TCATCATCATAATAATAA
Found at i:5144963 original size:21 final size:21
Alignment explanation
Indices: 5144939--5144979 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5144929 CGTCATCGTC
5144939 ATAATAATAATCATCATCATA
1 ATAATAATAATCATCATCATA
*
5144960 ATAATAATAATCATCTTCAT
1 ATAATAATAATCATCATCAT
5144980 CACCCTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATAATAATCATCATCATA
Found at i:5155432 original size:55 final size:56
Alignment explanation
Indices: 5155366--5155561 Score: 173
Period size: 56 Copynumber: 3.5 Consensus size: 56
5155356 TATTTTTTAG
*
5155366 ATATATTCGATTTC-AGACCCCTATTTTTATGCTTCTTAAT-AGCAACAAATGATAC
1 ATATACTCGATTTCGAGACCCCTATTTTTATGCTTCTTAATGA-CAACAAATGATAC
* * * * *
5155421 ATATACTCGATTTCGGGGCCTCTATTTTTATGCTTCTTAATGACAACAACTGATAG
1 ATATACTCGATTTCGAGACCCCTATTTTTATGCTTCTTAATGACAACAAATGATAC
* * ** * * * * *
5155477 ATATACTAGATTTTGAGGTCTCTATTTTTATACTTATTAATGGA-AACAACTGATAG
1 ATATACTCGATTTCGAGACCCCTATTTTTATGCTTCTTAAT-GACAACAAATGATAC
* * * * *
5155533 ATATATTCAATTTTGAGATCCTTATTTTT
1 ATATACTCGATTTCGAGACCCCTATTTTT
5155562 TGGGTTCCTA
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
55 13 0.11
56 104 0.87
57 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (56 bp):
ATATACTCGATTTCGAGACCCCTATTTTTATGCTTCTTAATGACAACAAATGATAC
Found at i:5155454 original size:56 final size:55
Alignment explanation
Indices: 5155363--5155537 Score: 199
Period size: 56 Copynumber: 3.1 Consensus size: 55
5155353 TCCTATTTTT
* * * * *
5155363 TAGATATATTCGATTTC-AGACCCCTATTTTTATGCTTCTTAATAGCAACAAATGA
1 TAGATATACTAGATTTCGAGGCCTCTATTTTTATGCTTCTTAAT-GCAACAACTGA
* * *
5155418 TACATATACTCGATTTCGGGGCCTCTATTTTTATGCTTCTTAATGACAACAACTGA
1 TAGATATACTAGATTTCGAGGCCTCTATTTTTATGCTTCTTAATG-CAACAACTGA
* * * * *
5155474 TAGATATACTAGATTTTGAGGTCTCTATTTTTATACTTATTAATGGAAACAACTGA
1 TAGATATACTAGATTTCGAGGCCTCTATTTTTATGCTTCTTAAT-GCAACAACTGA
5155530 TAGATATA
1 TAGATATA
5155538 TTCAATTTTG
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
55 16 0.16
56 86 0.83
57 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (55 bp):
TAGATATACTAGATTTCGAGGCCTCTATTTTTATGCTTCTTAATGCAACAACTGA
Found at i:5155559 original size:56 final size:56
Alignment explanation
Indices: 5155386--5155561 Score: 189
Period size: 56 Copynumber: 3.1 Consensus size: 56
5155376 TTTCAGACCC
* * * * * **
5155386 CTATTTTTATGCTTCTTAATAGCAACAAATGATACATATACTCGATTTCG-GGGCCT
1 CTATTTTTATGCTTCTTAAT-GAAACAACTGATAGATATACTCAATTTTGAGATCCT
*
5155442 CTATTTTTATGCTTCTTAATGACAACAACTGATAGATATACT-AGATTTTGAGGT-CT
1 CTATTTTTATGCTTCTTAATGA-AACAACTGATAGATATACTCA-ATTTTGAGATCCT
* * *
5155498 CTATTTTTATACTTATTAATGGAAACAACTGATAGATATATTCAATTTTGAGATCCT
1 CTATTTTTATGCTTCTTAAT-GAAACAACTGATAGATATACTCAATTTTGAGATCCT
5155555 -TATTTTT
1 CTATTTTT
5155562 TGGGTTCCTA
Statistics
Matches: 104, Mismatches: 10, Indels: 12
0.83 0.08 0.10
Matches are distributed among these distances:
55 1 0.01
56 96 0.92
57 7 0.07
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (56 bp):
CTATTTTTATGCTTCTTAATGAAACAACTGATAGATATACTCAATTTTGAGATCCT
Found at i:5155948 original size:28 final size:28
Alignment explanation
Indices: 5155916--5155971 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
5155906 TCTTTTATAT
5155916 TTTTCAATTATATATCTTCTTCATAACA
1 TTTTCAATTATATATCTTCTTCATAACA
**
5155944 TTTTCGGTTATATATCTTCTTCATAACA
1 TTTTCAATTATATATCTTCTTCATAACA
5155972 AATCTTATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTTCAATTATATATCTTCTTCATAACA
Found at i:5155979 original size:25 final size:27
Alignment explanation
Indices: 5155923--5155979 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
5155913 TATTTTTCAA
**
5155923 TTATATATCTTCTTCATAACATTTTCGG
1 TTATATATCTTCTTCATAACATAATC-G
5155951 TTATATATCTTCTTCATAACA-AATC-
1 TTATATATCTTCTTCATAACATAATCG
5155976 TTAT
1 TTAT
5155980 CCATTCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 4 0.15
27 2 0.07
28 21 0.78
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.49
Consensus pattern (27 bp):
TTATATATCTTCTTCATAACATAATCG
Found at i:5159587 original size:2 final size:2
Alignment explanation
Indices: 5159580--5159671 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
5159570 AATGAAGTCC
5159580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5159622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5159664 AT AT AT AT
1 AT AT AT AT
5159672 GTTTACAGAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5163197 original size:135 final size:135
Alignment explanation
Indices: 5162945--5163206 Score: 382
Period size: 135 Copynumber: 1.9 Consensus size: 135
5162935 GAGAAGTGAA
*
5162945 GCTCCGGTTGCTGCTTGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
1 GCTCCGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
* * *
5163010 GGAGATGGTTGTGGCTGAGAAGACCATCTCTTGCCTTCTTGACCGTCATCTGTATCAAACATGAA
66 GGAGATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTCACCATCATCTGTATCAAACATGAA
5163075 GAGAG
131 GAGAG
* * * * *
5163080 GCTCTGGTTGCTGCTGGGGATATGACGAAGTTCTATACAGAGGCTTTGATTCTGAAAAATGAGCA
1 GCTCCGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
* * * * *
5163145 -GATGATGATTGTGGTTGTGAGGACCATCTCTTGCCTTCTTCAGCATCTTCTGTATCAAACAT
66 GGA-GATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTCACCATCATCTGTATCAAACAT
5163207 ATGCTGATCC
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
134 2 0.02
135 110 0.98
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (135 bp):
GCTCCGGTTGCTGCTGGGGATATGACAAAGTTCTATACAAAAGCTTTGATTCTGAAAAACGAGCA
GGAGATGATTGTGGCTGAGAAGACCATCTCTTGCCTTCTTCACCATCATCTGTATCAAACATGAA
GAGAG
Found at i:5177188 original size:19 final size:18
Alignment explanation
Indices: 5177164--5177211 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
5177154 TTAATAATTT
5177164 AATATTAATATCTTTAAAA
1 AATATTAATA-CTTTAAAA
*
5177183 AATATT-ATAGTTTAAAA
1 AATATTAATACTTTAAAA
5177200 ATATTATTAATA
1 A-A-TATTAATA
5177212 AATTATCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 10 0.40
20 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAATACTTTAAAA
Found at i:5180470 original size:24 final size:24
Alignment explanation
Indices: 5180426--5180472 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5180416 TCTTAAGTTG
*
5180426 TAATAATTTAAAAAATTTAATCTT
1 TAATAATTTAAAAAATATAATCTT
5180450 TAAT-ATTTAAAAAATAATAATCT
1 TAATAATTTAAAAAAT-ATAATCT
5180473 AATATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATTTAAAAAATATAATCTT
Found at i:5180479 original size:24 final size:23
Alignment explanation
Indices: 5180426--5180482 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
5180416 TCTTAAGTTG
*
5180426 TAATA-ATTTAAAAAATTTAATC
1 TAATATATTTAAAAAATATAATC
*
5180448 T-TTAATATTTAAAAAATAATAATC
1 TAAT-ATATTTAAAAAAT-ATAATC
5180472 TAATATATTTA
1 TAATATATTTA
5180483 TTATGATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.04
22 2 0.07
23 11 0.39
24 13 0.46
25 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATATATTTAAAAAATATAATC
Found at i:5181679 original size:17 final size:17
Alignment explanation
Indices: 5181657--5181723 Score: 107
Period size: 17 Copynumber: 3.8 Consensus size: 17
5181647 TAATTTAAAT
5181657 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
5181674 AATAATTTGTTGTAAGACA
1 AATAATTTGTT-TAA-ACA
*
5181693 AATAATTTATTTAAACA
1 AATAATTTGTTTAAACA
5181710 AATAATTTGTTTAA
1 AATAATTTGTTTAA
5181724 TATTTTATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 27 0.59
18 6 0.13
19 13 0.28
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (17 bp):
AATAATTTGTTTAAACA
Found at i:5195406 original size:17 final size:19
Alignment explanation
Indices: 5195384--5195419 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5195374 GATTTACATG
5195384 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
5195401 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
5195420 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:5195640 original size:31 final size:31
Alignment explanation
Indices: 5195545--5195653 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
5195535 AGAGTTGAGG
* *
5195545 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTCTTT-GGGACATATGGACA
* * ** *
5195576 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTTTGGGACATATGGACA
*
5195607 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTAGGTTCTTTGGGACATATGGACA
* *
5195638 G-TTGCCGAGGTTCTTT
1 GTTTACCTAGGTTCTTT
5195654 ATGACCTCTG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.20
31 48 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTTGGGACATATGGACA
Found at i:5195660 original size:30 final size:30
Alignment explanation
Indices: 5195568--5195674 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
5195558 TTTCGAGACA
* * * *
5195568 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
5195599 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
5195630 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
5195660 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
5195675 GGTCTGTGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:5199081 original size:64 final size:63
Alignment explanation
Indices: 5198995--5199156 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 63
5198985 ATTGTTTAAG
* * * *
5198995 ATGCATCGATGCACATA-CAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATATGATT
1 ATGCATCGATGCATA-AGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATT
5199058 T
63 T
* *
5199059 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTT
1 ATGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTT
*
5199123 ATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 ATGCATCGATGCATAAG-G-AGTGCATCGATGCAT
5199157 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 2 0.02
64 61 0.71
65 22 0.26
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTT
Found at i:5199156 original size:65 final size:65
Alignment explanation
Indices: 5199032--5199156 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
5199022 ATGCATGAAT
*
5199032 TTAAATAGAAAACATCGAATATGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
* *
5199097 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT
5199157 ACCTTCATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 1 0.02
64 32 0.58
65 22 0.40
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
Found at i:5199906 original size:31 final size:31
Alignment explanation
Indices: 5199817--5199925 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
5199807 AGAGTCGAGG
* * *
5199817 GTTTACCTATG-TCTTTCGAGACATATGGATA
1 GTTTACCTAGGTTCTTT-GGGACATATGGACA
* * ** *
5199848 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTTTGGGACATATGGACA
*
5199879 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTAGGTTCTTTGGGACATATGGACA
* *
5199910 G-TTGCCGAGGTTCTTT
1 GTTTACCTAGGTTCTTT
5199926 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTTGGGACATATGGACA
Found at i:5199932 original size:30 final size:30
Alignment explanation
Indices: 5199871--5199946 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
5199861 CTAAGGAACA
* *
5199871 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
5199902 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
5199932 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
5199947 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:5200081 original size:16 final size:16
Alignment explanation
Indices: 5200062--5200092 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5200052 TATACATGGG
*
5200062 CAATGAAATTGAAAGA
1 CAATGAAAGTGAAAGA
5200078 CAATGAAAGTGAAAG
1 CAATGAAAGTGAAAG
5200093 TGATAAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (16 bp):
CAATGAAAGTGAAAGA
Found at i:5202546 original size:3 final size:3
Alignment explanation
Indices: 5202538--5202844 Score: 524
Period size: 3 Copynumber: 105.0 Consensus size: 3
5202528 CTAACGGTTT
5202538 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5202586 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA A-A AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA
5202631 AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5202677 AGA A-A AG- AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
5202722 AGA AGA AAA AAA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5202769 AG- AGA AGA AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5202815 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5202845 GGAGAAGGAG
Statistics
Matches: 292, Mismatches: 2, Indels: 20
0.93 0.01 0.06
Matches are distributed among these distances:
2 18 0.06
3 271 0.93
4 3 0.01
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5202853 original size:6 final size:6
Alignment explanation
Indices: 5202538--5203074 Score: 178
Period size: 6 Copynumber: 89.7 Consensus size: 6
5202528 CTAACGGTTT
* * * * * * * *
5202538 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * * * *
5202586 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAAG AAAAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
5202634 AGAAGA AGAAGAAG AGAAGA AGAA-G AAAAGA AGAAGA AGAAGA AGAAAAG
1 AGAAGG AGAAG--G AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AG-AAGG
* * * * * * * **
5202684 AGAAGA AGAAGA AGAAGAAG AGAAGA AGAAGA AGAAGA AGAAGA AAAAAA
1 AGAAGG AGAAGG AGAAG--G AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * *
5202734 AGAAGA AGAA-G AGAAGA AGAAGA AGAAGA AGAAGAAG AGAAGA AGAA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG--G AGAAGG AGAAGG
* * * * * * * * *
5202782 AAAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * *
5202830 AGAAGA AGAAGA AG-AGG AGAAGG AGGAGG AG-AGG AGGAGG AG-AGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * * *
5202875 AGGAGG AGGAGG AGGAGG AGGAGAG AGGAGG AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAG-G AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * *
5202924 AGGAGG AG-AGG AGGAGG AGGAGG AGGAGG AGGAGG AGGA-G AGAAGAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG-G
* * * ** * * *
5202971 AGGAGG AGGAGG AGAAGA AGAAAA AGAA-G AGGAGG AGGAGG AGGAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * *
5203018 -GGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG ATG-AGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG A-GAAGG
*
5203065 AGGAGG AGAA
1 AGAAGG AGAA
5203075 TCAAACATAG
Statistics
Matches: 470, Mismatches: 40, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
5 42 0.09
6 397 0.84
7 16 0.03
8 15 0.03
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:5202856 original size:3 final size:3
Alignment explanation
Indices: 5202843--5203072 Score: 319
Period size: 3 Copynumber: 78.0 Consensus size: 3
5202833 AGAAGAAGAA
*
5202843 GAG GAG AAG GAG GAG GA- GAG GAG GAG GA- GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
5202889 GAG GAG GAG AGAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA- GAG
1 GAG GAG GAG -GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
*
5202934 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA- GAG AAG AGAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG -GAG GAG GAG
* * * * * *
5202979 GAG GA- GAA GAA GAA AAA GAA GAG GAG GAG GAG GAG GAG G-G GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
*
5203025 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAT GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
5203073 AATCAAACAT
Statistics
Matches: 210, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
2 12 0.06
3 193 0.92
4 5 0.02
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:5205068 original size:2 final size:2
Alignment explanation
Indices: 5205061--5205088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5205051 GGGTCAGCTA
5205061 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
5205089 TACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5213498 original size:26 final size:26
Alignment explanation
Indices: 5213463--5213527 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
5213453 TGATAAGTTA
*
5213463 ATATTAAATTTAATAAATTAAATCAT
1 ATATTTAATTTAATAAATTAAATCAT
* * ** *
5213489 ATGTTTAATTTGATAAATTATGTTAT
1 ATATTTAATTTAATAAATTAAATCAT
5213515 ATATTTAATTTAA
1 ATATTTAATTTAA
5213528 ACTTATGACA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (26 bp):
ATATTTAATTTAATAAATTAAATCAT
Found at i:5217385 original size:64 final size:65
Alignment explanation
Indices: 5217246--5217388 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 65
5217236 AATTGTTCAG
* * *
5217246 TGTGTATCGATGCA-CAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAAGGCAATT
* * * * * **
5217310 AGTGCATCGATGCATAAGG-AGTGCATCGATACACCCCCTT-AAGATTGAAACATCGAAGGTGAT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATACA-CCCATTAAAAATGGAAACATCGAAGGCAAT
5217373 T
65 T
*
5217374 TGTGTACCGATGCAT
1 TGTGTATCGATGCAT
5217389 GGGTAGTGCA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
64 56 0.88
65 8 0.12
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (65 bp):
TGTGTATCGATGCATAAGGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAAGGCAATT
Found at i:5218881 original size:23 final size:23
Alignment explanation
Indices: 5218851--5218917 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
5218841 ACCTTATATA
*
5218851 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTATACGCG
* * **
5218874 GCACTTCGGTGCAATTGTACATG
1 GCACTTCGGTGCATTTATACGCG
5218897 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTATACG
5218918 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTATACGCG
Found at i:5222823 original size:64 final size:64
Alignment explanation
Indices: 5222735--5223005 Score: 229
Period size: 64 Copynumber: 4.2 Consensus size: 64
5222725 CAATGAAGGT
* * *
5222735 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTCCTTATTAATGAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTTCATTATTAATGAG
* * * *
5222799 ATGCATCAATGCA-TACCTTATGCATCGATGCACTAATTGCATTTGATG-TTCTATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTTC-ATTATTAATGA
5222862 G
64 G
* * * * * *
5222863 ATGCATTGATGCACT-CCTTATGCATCGATGCATTGATTGTATTCGATGTTATTATT-TTAA-AA
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTT-TCATTATTAATGA
5222925 GG
64 -G
* * * *
5222927 ATGCATCGATGCAGTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TT-TTAAAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATG-T-TTCATTATTAATG
5222989 -G
63 AG
5222990 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
5223006 TATGAATGTG
Statistics
Matches: 168, Mismatches: 26, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
63 7 0.04
64 150 0.89
65 9 0.05
66 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTTCATTATTAATGAG
Found at i:5227138 original size:64 final size:62
Alignment explanation
Indices: 5227001--5227276 Score: 222
Period size: 64 Copynumber: 4.2 Consensus size: 62
5226991 CAATGAAGGT
* * *
5227001 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAATGCATTCGATGTTTCCTTTTAAGAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTTCATTTTAAGAG
* * * *
5227062 ATGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGCATTTGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTTCATT-TTAA-GAG
* *
5227126 ATGCATTGATGCACT-CCTTATGCATCGATGCATCGATGCATTGATTGCATTCGATGTTATTATT
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT--A---A---A-TGCATTCGATGTT-TCATT
*
5227190 TTAAAAGG
56 TTAAGA-G
* * *
5227198 ATGCATCGATGCAGTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TTTTAA-AG
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATG-T-TTCATTTTAAGA-
5227260 G
62 G
5227261 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
5227277 TATGAATGTG
Statistics
Matches: 176, Mismatches: 19, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
60 2 0.01
61 27 0.15
62 18 0.10
63 8 0.05
64 61 0.35
65 5 0.03
66 1 0.01
68 2 0.01
71 1 0.01
72 45 0.26
73 6 0.03
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTTCATTTTAAGAG
Found at i:5227160 original size:72 final size:72
Alignment explanation
Indices: 5227081--5227231 Score: 198
Period size: 72 Copynumber: 2.1 Consensus size: 72
5227071 TGCATACCTT
* ** *
5227081 ATGCATCGATGCACTAATTGCATTTGATGTT-TTATTATTAATGGGATGCATTGATGCACT-CCT
1 ATGCATCGATGCACTAATTGCATTCGATGTTATTATT-TTAAAAGGATGCATCGATGCACTACC-
5227144 TATGCATCG
64 TATGCATCG
* * * *
5227153 ATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAAAAGGATGCATCGATGCAGTAGCTA
1 ATGCATCGATGCACTAATTGCATTCGATGTTATTATTTTAAAAGGATGCATCGATGCACTACCTA
5227218 TGCATCG
66 TGCATCG
5227225 ATGCATC
1 ATGCATC
5227232 AAAGGCATTC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 63 0.91
73 6 0.09
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (72 bp):
ATGCATCGATGCACTAATTGCATTCGATGTTATTATTTTAAAAGGATGCATCGATGCACTACCTA
TGCATCG
Found at i:5227166 original size:16 final size:18
Alignment explanation
Indices: 5227145--5227181 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
5227135 TGCACTCCTT
5227145 ATGCATCGA-TGCA-TCG
1 ATGCATCGATTGCATTCG
*
5227161 ATGCATTGATTGCATTCG
1 ATGCATCGATTGCATTCG
5227179 ATG
1 ATG
5227182 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (18 bp):
ATGCATCGATTGCATTCG
Found at i:5230404 original size:24 final size:24
Alignment explanation
Indices: 5230377--5230461 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 24
5230367 GACTATGATG
5230377 AAAATGATGATCAAGATGACAACA
1 AAAATGATGATCAAGATGACAACA
* * *
5230401 AAAATGATGGTCGTGATGATGATGAA-A
1 AAAATGATGATC---AAGATGA-CAACA
*
5230428 ATAATTGATGATCAAGATGACAACA
1 A-AAATGATGATCAAGATGACAACA
5230453 AAAATGATG
1 AAAATGATG
5230462 GTTGTGATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
24 20 0.43
25 8 0.17
27 8 0.17
28 11 0.23
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.22
Consensus pattern (24 bp):
AAAATGATGATCAAGATGACAACA
Found at i:5230443 original size:52 final size:52
Alignment explanation
Indices: 5230381--5230481 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
5230371 ATGATGAAAA
5230381 TGATGATCAAGATGACAACAAAAATGATGGTCGTGATGATGATGAAAATAAT
1 TGATGATCAAGATGACAACAAAAATGATGGTCGTGATGATGATGAAAATAAT
*
5230433 TGATGATCAAGATGACAACAAAAATGATGGTTGTGATGATGATGAAAAT
1 TGATGATCAAGATGACAACAAAAATGATGGTCGTGATGATGATGAAAAT
5230482 GAAGATGGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.26
Consensus pattern (52 bp):
TGATGATCAAGATGACAACAAAAATGATGGTCGTGATGATGATGAAAATAAT
Found at i:5235042 original size:201 final size:201
Alignment explanation
Indices: 5234697--5235099 Score: 806
Period size: 201 Copynumber: 2.0 Consensus size: 201
5234687 TGGGCTAAGA
5234697 AGGAAGTGATTTGGAGCATTATGGGAGGGCAAACAACCGAACAAGGGGATTGTTCTAAATTCAAT
1 AGGAAGTGATTTGGAGCATTATGGGAGGGCAAACAACCGAACAAGGGGATTGTTCTAAATTCAAT
5234762 GGTAACATTCAACATTGCTGTAAGAAGGATCCAACCGTAGTGGATCTATTGCCGGGAACACTTTA
66 GGTAACATTCAACATTGCTGTAAGAAGGATCCAACCGTAGTGGATCTATTGCCGGGAACACTTTA
5234827 TAATCAGCAGATTGTGAATTGCTGTAAAGGGGAGTGCTAAACTCGTGGGTGCAAGATCCAGCCAC
131 TAATCAGCAGATTGTGAATTGCTGTAAAGGGGAGTGCTAAACTCGTGGGTGCAAGATCCAGCCAC
5234892 TGCAGC
196 TGCAGC
5234898 AGGAAGTGATTTGGAGCATTATGGGAGGGCAAACAACCGAACAAGGGGATTGTTCTAAATTCAAT
1 AGGAAGTGATTTGGAGCATTATGGGAGGGCAAACAACCGAACAAGGGGATTGTTCTAAATTCAAT
5234963 GGTAACATTCAACATTGCTGTAAGAAGGATCCAACCGTAGTGGATCTATTGCCGGGAACACTTTA
66 GGTAACATTCAACATTGCTGTAAGAAGGATCCAACCGTAGTGGATCTATTGCCGGGAACACTTTA
5235028 TAATCAGCAGATTGTGAATTGCTGTAAAGGGGAGTGCTAAACTCGTGGGTGCAAGATCCAGCCAC
131 TAATCAGCAGATTGTGAATTGCTGTAAAGGGGAGTGCTAAACTCGTGGGTGCAAGATCCAGCCAC
5235093 TGCAGC
196 TGCAGC
5235099 A
1 A
5235100 AGCTCATTCC
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 202 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (201 bp):
AGGAAGTGATTTGGAGCATTATGGGAGGGCAAACAACCGAACAAGGGGATTGTTCTAAATTCAAT
GGTAACATTCAACATTGCTGTAAGAAGGATCCAACCGTAGTGGATCTATTGCCGGGAACACTTTA
TAATCAGCAGATTGTGAATTGCTGTAAAGGGGAGTGCTAAACTCGTGGGTGCAAGATCCAGCCAC
TGCAGC
Found at i:5236615 original size:16 final size:17
Alignment explanation
Indices: 5236579--5236619 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5236569 GATTGTGACA
*
5236579 ATATCTTTAAATTTTTAT
1 ATAT-TTTAAAATTTTAT
5236597 ATATTTTAAAATTTT-T
1 ATATTTTAAAATTTTAT
5236613 ATATTTT
1 ATATTTT
5236620 TTTATTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 10 0.45
18 4 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTTAAAATTTTAT
Found at i:5236621 original size:18 final size:18
Alignment explanation
Indices: 5236587--5236620 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5236577 CAATATCTTT
5236587 AAATTTTTATATATTTTA
1 AAATTTTTATATATTTTA
5236605 AAATTTTTATAT-TTTT
1 AAATTTTTATATATTTT
5236621 TTATTAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AAATTTTTATATATTTTA
Found at i:5239811 original size:2 final size:2
Alignment explanation
Indices: 5239804--5239851 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5239794 GGTGAATCTG
5239804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5239846 AT AT AT
1 AT AT AT
5239852 CCAATATAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5242530 original size:209 final size:210
Alignment explanation
Indices: 5241927--5242736 Score: 1130
Period size: 209 Copynumber: 3.8 Consensus size: 210
5241917 ATTTAAGAAT
* *
5241927 TAAATTGAAC-AATATGAAATTACAAATAAAACTTTAAATAAATTAAA-AACACATCGATGAGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-C-ATAAGGG
* *
5241990 ATCAAATCGAAATAATTTCAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACCCA
64 ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCA
* * * *
5242055 TTTAAAAAGTTATGGGCCAATTAAAAAAATGAATTAAGTAATAAGTATGGATCAATTTCATATGC
129 TTTAAAAAGTTATGGGCCAATTAAAAATA-GAAATAAGTAATAAGTATGGGTCAATTTCAGATGC
5242120 AAATAAAATTTGGAGGAC
193 AAATAAAATTTGGAGGAC
* * * *
5242138 TAAATTGAACAAATTTTAAATTAAAAAATAAAAAATTAAATAAATTAAACAACACACATTGATGA
1 TAAATTGAACAAATATGAAATT-ACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A--A
*
5242203 GGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTATAA-TAT
61 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAGTACTA-AATTAT
* * *
5242267 ACCCATTTAAAAAGTTATGGGCTAATTTAAAAACAGAAATAAATAATAAGTATGGGTCAATTTCA
124 ACCCATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCA
5242332 GATGCAAATAAAATTTGGAGGAC
188 GATGCAAATAAAATTTGGAGGAC
*
5242355 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* * * * *
5242418 CAAATTGAAATAATTTTAAATTTTGAGGTTAAAATTAATTCAAAAAGTACTAAATTATACTCATT
66 CAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCATT
* * * *
5242483 TAAAAAGTTATGAGTCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCGGGTGCAA
131 TAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
5242548 ATAAAATTTGGAGGAC
195 ATAAAATTTGGAGGAC
* * *
5242564 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATATATTAAACAAGACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* * *
5242627 CAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAGGTACTAAATTATACTCAT
66 CAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAA-GTACTAAATTATACCCAT
* * *
5242692 TTAAAAGGTTATGGGCCAATTAATAAATATAAATAAGTATTAAGT
130 TTAAAAAGTTATGGGCCAATTAA-AAATAGAAATAAGTAATAAGT
5242737 TGAGAAAAAA
Statistics
Matches: 542, Mismatches: 44, Indels: 27
0.88 0.07 0.04
Matches are distributed among these distances:
208 2 0.00
209 201 0.37
210 95 0.18
211 10 0.02
212 11 0.02
213 25 0.05
214 6 0.01
215 1 0.00
216 75 0.14
217 106 0.20
218 10 0.02
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (210 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
CAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCATT
TAAAAAGTTATGGGCCAATTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAAA
TAAAATTTGGAGGAC
Found at i:5242801 original size:20 final size:20
Alignment explanation
Indices: 5242776--5242840 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
5242766 GATATATATA
5242776 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
*
5242796 ATATAAAATATAT-GTATTAT
1 ATATAAACTATATAGT-TTAT
*
5242816 ATATAAACCATATAGTTTAT
1 ATATAAACTATATAGTTTAT
5242836 ATATA
1 ATATA
5242841 TATTATGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
ATATAAACTATATAGTTTAT
Found at i:5242868 original size:31 final size:31
Alignment explanation
Indices: 5242803--5242869 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
5242793 TATATATAAA
* * *
5242803 ATATATGTATTATATATAAACCATATAGTTT
1 ATATATATATTATATATAAACCATAAAGTAT
* **
5242834 ATATATATATTATGTATAAAGTATAAAGTAT
1 ATATATATATTATATATAAACCATAAAGTAT
5242865 ATATA
1 ATATA
5242870 CCATGTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (31 bp):
ATATATATATTATATATAAACCATAAAGTAT
Found at i:5242875 original size:27 final size:28
Alignment explanation
Indices: 5242835--5242895 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
5242825 ATATAGTTTA
** * * *
5242835 TATATATATTATGTATAAAGTATAA-AG
1 TATATATACCATGTAAAAACTATAATAC
5242862 TATATATACCATGTAAAAACTATAATAC
1 TATATATACCATGTAAAAACTATAATAC
5242890 TATATA
1 TATATA
5242896 GTTTATATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (28 bp):
TATATATACCATGTAAAAACTATAATAC
Found at i:5242949 original size:11 final size:11
Alignment explanation
Indices: 5242935--5242969 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5242925 CTACATAGTT
5242935 TATATAAATTA
1 TATATAAATTA
*
5242946 TATATGAATTA
1 TATATAAATTA
*
5242957 TATATAAACTA
1 TATATAAATTA
5242968 TA
1 TA
5242970 CAATTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (11 bp):
TATATAAATTA
Found at i:5243150 original size:12 final size:13
Alignment explanation
Indices: 5243125--5243171 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
5243115 TACTATAGTT
5243125 TATATTTATATAC
1 TATATTTATATAC
*
5243138 TATATTTTATACTATT
1 TATA-TTTATA-TA-C
5243154 TATATTTATATAC
1 TATATTTATATAC
5243167 TATAT
1 TATAT
5243172 ATATGAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 9 0.31
14 8 0.28
15 8 0.28
16 4 0.14
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:5243167 original size:17 final size:17
Alignment explanation
Indices: 5243123--5243175 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
5243113 CATACTATAG
5243123 TTTATATTTATATAC--
1 TTTATATTTATATACTA
5243138 --TATATTT-TATACTA
1 TTTATATTTATATACTA
5243152 TTTATATTTATATACTA
1 TTTATATTTATATACTA
*
5243169 TATATAT
1 TTTATAT
5243176 GAACTATAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.16
13 7 0.22
16 7 0.22
17 13 0.41
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATATTTATATACTA
Found at i:5243172 original size:15 final size:15
Alignment explanation
Indices: 5243125--5243173 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
5243115 TACTATAGTT
5243125 TATATTTATATACTA
1 TATATTTATATACTA
*
5243140 TAT-TTTATACTA-TT
1 TATATTTATA-TACTA
5243154 TATATTTATATACTA
1 TATATTTATATACTA
5243169 TATAT
1 TATAT
5243174 ATGAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTTATATACTA
Found at i:5243251 original size:18 final size:18
Alignment explanation
Indices: 5243230--5243306 Score: 82
Period size: 18 Copynumber: 3.9 Consensus size: 18
5243220 AAGGTTGATA
*
5243230 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
*
5243248 TTTACATATAAACTATAG
1 TTTACATATGAACTATAG
5243266 TTAATATTTACATATGAACTATAG
1 ------TTTACATATGAACTATAG
5243290 TTTACATATGAACTATA
1 TTTACATATGAACTATA
5243307 TATAAACTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 33 0.66
24 17 0.34
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:5243274 original size:42 final size:42
Alignment explanation
Indices: 5243185--5243306 Score: 149
Period size: 42 Copynumber: 2.8 Consensus size: 42
5243175 TGAACTATAG
* *
5243185 TTTACATATGAACTATA-TATATAAATATATATACTA-AGGTTGATA
1 TTTACATATGAACTATAGT-T-TACATATA-A-ACTATA-GTTAATA
*
5243230 TTTATATATGAACTATAGTTTACATATAAACTATAGTTAATA
1 TTTACATATGAACTATAGTTTACATATAAACTATAGTTAATA
*
5243272 TTTACATATGAACTATAGTTTACATATGAACTATA
1 TTTACATATGAACTATAGTTTACATATAAACTATA
5243307 TATAAACTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
42 43 0.61
43 2 0.03
44 7 0.10
45 17 0.24
46 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (42 bp):
TTTACATATGAACTATAGTTTACATATAAACTATAGTTAATA
Found at i:5243338 original size:2 final size:2
Alignment explanation
Indices: 5243333--5243449 Score: 62
Period size: 2 Copynumber: 56.5 Consensus size: 2
5243323 TACATATGAC
*
5243333 AT AT AT AT AT AT AT ACT AT AGT -T GAT AT TT AT AT ACT AT AT A-
1 AT AT AT AT AT AT AT A-T AT A-T AT -AT AT AT AT AT A-T AT AT AT
* * * * * *
5243375 AT TT AC AT AT GAC CT AT AT AT AT ACT AT AGT TT AT AT TT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT
*
5243418 AT -T AT AT -T AT AT AT AT AT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
5243450 CTACATAGTA
Statistics
Matches: 87, Mismatches: 16, Indels: 24
0.69 0.13 0.19
Matches are distributed among these distances:
1 4 0.05
2 72 0.83
3 11 0.13
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5243371 original size:55 final size:51
Alignment explanation
Indices: 5243307--5243424 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 51
5243297 ATGAACTATA
* *
5243307 TATAAACTATATAGTTTACATATGACATATATATATATATACTATAGTTGATATT
1 TATATACTATATAATTTACATATGAC----ATATATATATACTATAGTTGATATT
* *
5243362 TATATACTATATAATTTACATATGACCTATATATATACTATAGTTTATATT
1 TATATACTATATAATTTACATATGACATATATATATACTATAGTTGATATT
*
5243413 TATATATTATAT
1 TATATACTATAT
5243425 TATATATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
51 34 0.59
55 24 0.41
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (51 bp):
TATATACTATATAATTTACATATGACATATATATATACTATAGTTGATATT
Found at i:5243446 original size:51 final size:50
Alignment explanation
Indices: 5243339--5243452 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 50
5243329 TGACATATAT
* * *
5243339 ATATATATACTATAGTTGATATTTATATACTATATAATTTACATATGACC
1 ATATATATACTATAGTTGATATTTATATACTATATAATATACATATAAAC
* * *
5243389 TATATATATACTATAGTTTATATTTATATATTATATTATATATATATATAAAC
1 -ATATATATACTATAGTTGATATTTATATACTATA-TA-ATATACATATAAAC
5243442 -TATATATACTA
1 ATATATATACTA
5243453 CATAGTATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 43 0.78
52 2 0.04
53 10 0.18
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (50 bp):
ATATATATACTATAGTTGATATTTATATACTATATAATATACATATAAAC
Found at i:5243562 original size:7 final size:7
Alignment explanation
Indices: 5243523--5243590 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
5243513 GTTTATTAGT
5243523 ATATATA
1 ATATATA
5243530 A-ACTATA
1 ATA-TATA
5243537 ATA-AT-
1 ATATATA
*
5243542 ATAGATA
1 ATATATA
5243549 GATATATA
1 -ATATATA
5243557 ATATAT-
1 ATATATA
5243563 ATATATA
1 ATATATA
*
5243570 CTATATA
1 ATATATA
*
5243577 TTATATA
1 ATATATA
*
5243584 GTATATA
1 ATATATA
5243591 TAAACTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 11 0.22
7 30 0.59
8 7 0.14
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:5243581 original size:18 final size:18
Alignment explanation
Indices: 5243550--5243713 Score: 84
Period size: 18 Copynumber: 8.9 Consensus size: 18
5243540 ATATAGATAG
*
5243550 ATATATAATATATATATAT
1 ATATATACTATATAT-TAT
* *
5243569 ACTATATATTATATAGTAT
1 A-TATATACTATATATTAT
* *
5243588 ATATAAACTATATAGTAT
1 ATATATACTATATATTAT
* *
5243606 ATATAAACTCTATATTAT
1 ATATATACTATATATTAT
* *
5243624 ATAGTTCATTACTATATATAAC
1 ATA--T-A-TACTATATATTAT
* * **
5243646 CTATATAGTATATGGTAT
1 ATATATACTATATATTAT
* *
5243664 ATACAAACTATATATTAT
1 ATATATACTATATATTAT
*
5243682 ATAGT-T-C-AT-TAGTAT
1 ATA-TATACTATATATTAT
*
5243697 ATATAAACTATATATTA
1 ATATATACTATATATTA
5243714 ATTTATTAAT
Statistics
Matches: 108, Mismatches: 27, Indels: 21
0.69 0.17 0.13
Matches are distributed among these distances:
14 1 0.01
15 8 0.07
16 3 0.03
17 3 0.03
18 61 0.56
19 6 0.06
20 14 0.13
21 1 0.01
22 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATATACTATATATTAT
Found at i:5243606 original size:7 final size:7
Alignment explanation
Indices: 5243546--5243608 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
5243536 AATAATATAG
5243546 ATAGATAT
1 ATAG-TAT
*
5243554 ATAATAT
1 ATAGTAT
5243561 ATA-TAT
1 ATAGTAT
*
5243567 ATACTAT
1 ATAGTAT
*
5243574 ATATTAT
1 ATAGTAT
5243581 ATAGTAT
1 ATAGTAT
5243588 ATA-TA-
1 ATAGTAT
*
5243593 A-ACTAT
1 ATAGTAT
5243599 ATAGTAT
1 ATAGTAT
5243606 ATA
1 ATA
5243609 TAAACTCTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 9 0.19
7 31 0.66
8 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (7 bp):
ATAGTAT
Found at i:5243626 original size:2 final size:2
Alignment explanation
Indices: 5243522--5243610 Score: 69
Period size: 2 Copynumber: 44.0 Consensus size: 2
5243512 AGTTTATTAG
* * *
5243522 TA TA TA TA AA CTA TA -A TA -A TA TA GA TA GA TA TA TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5243562 TA TA TA TA CTA TA TA T- TA TA TA GTA TA TA TA AA CTA TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA
5243605 TA TA TA
1 TA TA TA
5243611 AACTCTATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
1 4 0.06
2 58 0.83
3 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:5243658 original size:33 final size:32
Alignment explanation
Indices: 5243603--5243713 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 32
5243593 AACTATATAG
*
5243603 TATATATAAACTCTATATTATATAGTTCATTA
1 TATATATAAACTATATATTATATAGTTCATTA
* * *
5243635 CTATATATAACCTATATAGTATAT-G------G
1 -TATATATAAACTATATATTATATAGTTCATTA
*
5243661 TATATACAAACTATATATTATATAGTTCATTA
1 TATATATAAACTATATATTATATAGTTCATTA
5243693 GTATATATAAACTATATATTA
1 -TATATATAAACTATATATTA
5243714 ATTTATTAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
25 20 0.33
26 1 0.02
32 1 0.02
33 39 0.64
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (32 bp):
TATATATAAACTATATATTATATAGTTCATTA
Found at i:5243664 original size:58 final size:58
Alignment explanation
Indices: 5243497--5243710 Score: 199
Period size: 58 Copynumber: 3.7 Consensus size: 58
5243487 CCTAAACCCT
* * * * *
5243497 AACTATACATTATATAGTTTATTAGTATATATAAACTATAATAATATAGATAG-ATATA-T
1 AACTATATATTATATAGTTCATTACTATATATAAACTAT-ATAGTAT--ATAGTATATACA
* * * * * *
5243556 AA-TATATA-TATATA-CT-ATATATTATATAGTATA-TATAAACTATATAGTATATATA
1 AACTATATATTATATAGTTCAT-TACTATATA-TAAACTATATAGTATATAGTATATACA
* * *
5243611 AACTCTATATTATATAGTTCATTACTATATATAACCTATATAGTATATGGTATATACA
1 AACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATATAGTATATACA
*
5243669 AACTATATATTATATAGTTCATTAGTATATATAAACTATATA
1 AACTATATATTATATAGTTCATTACTATATATAAACTATATA
5243711 TTAATTTATT
Statistics
Matches: 127, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
53 4 0.03
54 5 0.04
55 9 0.07
56 17 0.13
57 17 0.13
58 71 0.56
59 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (58 bp):
AACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATATAGTATATACA
Found at i:5243708 original size:26 final size:26
Alignment explanation
Indices: 5243690--5243742 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
5243680 ATATAGTTCA
5243690 TTAGTATATATAAAC-TATATATTAAT
1 TTAGTA-ATATAAACATATATATTAAT
*
5243716 TTATTAATATAAACATATATATTAAT
1 TTAGTAATATAAACATATATATTAAT
5243742 T
1 T
5243743 GAAAGAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAGTAATATAAACATATATATTAAT
Found at i:5245992 original size:59 final size:59
Alignment explanation
Indices: 5245908--5246024 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 59
5245898 AATATGACTC
*
5245908 TTATTTTAAATTGGACTCTAAAC-TTTATATATTTCAATTTCAT-ATCTAAACTATGACAA
1 TTATTTTAAATTGGACTCTAAACTTTTA-ATATTTCAATTTCATCCTC-AAACTATGACAA
* *
5245967 TTATTTTAAATTAG-TTCTCAAACTTTTGAATATTTCAATTTCATCCTCAAACTATGAC
1 TTATTTTAAATTGGACTCT-AAACTTTT-AATATTTCAATTTCATCCTCAAACTATGAC
5246025 CTTTGTTCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
58 3 0.06
59 17 0.33
60 28 0.55
61 3 0.06
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.44
Consensus pattern (59 bp):
TTATTTTAAATTGGACTCTAAACTTTTAATATTTCAATTTCATCCTCAAACTATGACAA
Found at i:5246463 original size:16 final size:16
Alignment explanation
Indices: 5246444--5246474 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5246434 TCAATTACAG
5246444 GTCAGGTTGAAAACAT
1 GTCAGGTTGAAAACAT
5246460 GTCAGGTTGAAAACA
1 GTCAGGTTGAAAACA
5246475 GACCGGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (16 bp):
GTCAGGTTGAAAACAT
Found at i:5248992 original size:2 final size:2
Alignment explanation
Indices: 5248987--5249019 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5248977 AAGATTTTTA
5248987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5249020 GGGGAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5249342 original size:2 final size:2
Alignment explanation
Indices: 5249337--5249363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5249327 TAAAGATTTT
5249337 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5249364 GGGGAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5254916 original size:2 final size:2
Alignment explanation
Indices: 5254909--5254934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5254899 AAGGAAGCTT
5254909 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5254935 ACTTTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5257536 original size:16 final size:16
Alignment explanation
Indices: 5257487--5257528 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
5257477 TTTATTCACG
5257487 TTATTTTAAAATTAAA
1 TTATTTTAAAATTAAA
5257503 TTATTTTAAAATTAAA
1 TTATTTTAAAATTAAA
5257519 TTAATTTTAA
1 TT-ATTTTAA
5257529 TTTAAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTTTAAAATTAAA
Found at i:5259681 original size:3 final size:3
Alignment explanation
Indices: 5259673--5259715 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
5259663 CGACGTTAAG
* * * *
5259673 TGA TGA TGA TGA TGG TGA TGA TGA TGA TGG TGG TGG TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
5259716 CATGGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:5259692 original size:15 final size:15
Alignment explanation
Indices: 5259672--5259715 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
5259662 TCGACGTTAA
5259672 GTGATGATGATGATG
1 GTGATGATGATGATG
5259687 GTGATGATGATGATG
1 GTGATGATGATGATG
* *
5259702 GTGGTGGTGATGAT
1 GTGATGATGATGAT
5259716 CATGGTGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.34
Consensus pattern (15 bp):
GTGATGATGATGATG
Found at i:5259720 original size:18 final size:18
Alignment explanation
Indices: 5259672--5259722 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
5259662 TCGACGTTAA
*
5259672 GTGATGATGATGATGGTG
1 GTGATGATGATGGTGGTG
*
5259690 ATGATGATGATGGTGGTG
1 GTGATGATGATGGTGGTG
*
5259708 GTGATGATCATGGTG
1 GTGATGATGATGGTG
5259723 ACGATAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.02, G:0.43, T:0.33
Consensus pattern (18 bp):
GTGATGATGATGGTGGTG
Found at i:5260742 original size:58 final size:58
Alignment explanation
Indices: 5260652--5260768 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
5260642 TCCGCAATAA
5260652 AATCCGCAACCGTAATTCGATACTATGCGCCGAGCTGGCCAAGTTGACCTTTACTTCC
1 AATCCGCAACCGTAATTCGATACTATGCGCCGAGCTGGCCAAGTTGACCTTTACTTCC
5260710 AATCCGCAACCGTAATTCGATACTATGCGCCGAGCTGGCCAAGTTGACCTTTACTTCC
1 AATCCGCAACCGTAATTCGATACTATGCGCCGAGCTGGCCAAGTTGACCTTTACTTCC
5260768 A
1 A
5260769 CAAGCTGGCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (58 bp):
AATCCGCAACCGTAATTCGATACTATGCGCCGAGCTGGCCAAGTTGACCTTTACTTCC
Found at i:5267347 original size:43 final size:39
Alignment explanation
Indices: 5267295--5267391 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 39
5267285 TTCACGAATG
5267295 TAAATGAACGAACAAGTCCTTTGTTCATATTCGTTCATTTAA
1 TAAATGAACGAACAA-T-C-TTGTTCATATTCGTTCATTTAA
* *
5267337 TTAAACGAACGTAA-AATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACG-AACAATCTTGTTCATATTCGTTCATTTAA
*
5267377 TAAATAAACGAACAA
1 TAAATGAACGAACAA
5267392 AAACGAACTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
38 2 0.04
39 10 0.21
40 21 0.44
41 1 0.02
42 1 0.02
43 11 0.23
44 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (39 bp):
TAAATGAACGAACAATCTTGTTCATATTCGTTCATTTAA
Found at i:5268579 original size:4 final size:4
Alignment explanation
Indices: 5268570--5268703 Score: 268
Period size: 4 Copynumber: 33.5 Consensus size: 4
5268560 GAAGAGTATG
5268570 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5268618 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
5268666 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
5268704 GTTATGATGT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 130 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:5269352 original size:114 final size:121
Alignment explanation
Indices: 5269125--5269366 Score: 417
Period size: 123 Copynumber: 2.0 Consensus size: 121
5269115 TGGTAATTGC
5269125 TGCAACAAGACTGCCATGCAAAACCAACCAAATACAGCTTATTATAACTATTTTGGAGAGGATGG
1 TGCAACAAGACTGCCATGCAAAACCAACCAAATACAGCTTATTATAAC-ATTTTGGAGAGGA-GG
5269190 AGGGTACTACATTTTCTAATCATTTAATTTTACGAAATGTGATATGTGTAACATTGTT
64 AGGGTACTACATTTTCTAATCATTTAATTTTACGAAATGTGATATGTGTAACATTGTT
5269248 TGCAACAAGACTGCCATGCAAAACCAACCAAATACAGCTTA-TAT-AC-TTTTGGAGA-G-GGAG
1 TGCAACAAGACTGCCATGCAAAACCAACCAAATACAGCTTATTATAACATTTTGGAGAGGAGGAG
5269308 GGTACTACA-TTTCTAATCA-TTAATTTTACGAAATGTGATATGTGTAACATTGTT
66 GGTACTACATTTTCTAATCATTTAATTTTACGAAATGTGATATGTGTAACATTGTT
5269362 TGCAA
1 TGCAA
5269367 AGTTTAAATC
Statistics
Matches: 119, Mismatches: 0, Indels: 9
0.93 0.00 0.07
Matches are distributed among these distances:
114 40 0.34
115 10 0.08
116 13 0.11
118 1 0.01
119 9 0.08
121 2 0.02
122 3 0.03
123 41 0.34
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (121 bp):
TGCAACAAGACTGCCATGCAAAACCAACCAAATACAGCTTATTATAACATTTTGGAGAGGAGGAG
GGTACTACATTTTCTAATCATTTAATTTTACGAAATGTGATATGTGTAACATTGTT
Found at i:5286319 original size:33 final size:32
Alignment explanation
Indices: 5286264--5286364 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
5286254 TCCGAACCAG
* *
5286264 CTTCTGCCGCCGCC-CGTTCTTCCTCCGAACCC-
1 CTTCTGCCACCGCCAC-TGCTTCCTCC-AACCCA
*
5286296 CTTTCTGCCTCCGCCACTGCTTCCTCCAAGCCCA
1 C-TTCTGCCACCGCCACTGCTTCCTCCAA-CCCA
* *
5286330 CTTCAGCCACCGCCATTGCTTCCTCCAAACCCA
1 CTTCTGCCACCGCCACTGCTTCCTCC-AACCCA
5286363 CT
1 CT
5286365 CCAGCCGCCG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.05
33 52 0.88
34 4 0.07
ACGTcount: A:0.13, C:0.50, G:0.12, T:0.25
Consensus pattern (32 bp):
CTTCTGCCACCGCCACTGCTTCCTCCAACCCA
Found at i:5286370 original size:33 final size:33
Alignment explanation
Indices: 5286306--5286378 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
5286296 CTTTCTGCCT
* * *
5286306 CCGCCACTGCTTCCTCCAAGCCCACTTCAGCCA
1 CCGCCATTGCTTCCTCCAAACCCACTCCAGCCA
*
5286339 CCGCCATTGCTTCCTCCAAACCCACTCCAGCCG
1 CCGCCATTGCTTCCTCCAAACCCACTCCAGCCA
5286372 CCGCCAT
1 CCGCCAT
5286379 CTCCGCTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.18, C:0.52, G:0.12, T:0.18
Consensus pattern (33 bp):
CCGCCATTGCTTCCTCCAAACCCACTCCAGCCA
Found at i:5290527 original size:14 final size:14
Alignment explanation
Indices: 5290510--5290545 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5290500 TAAGTCATTG
*
5290510 ATATTCATTCATAT
1 ATATTCATTAATAT
*
5290524 ATATACATTAATAT
1 ATATTCATTAATAT
5290538 ATATTCAT
1 ATATTCAT
5290546 GTACATCACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTCATTAATAT
Found at i:5294714 original size:32 final size:32
Alignment explanation
Indices: 5294673--5294742 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
5294663 CAAGGTGTTG
*
5294673 GCAAATCTAATGCAGTTATGCAACAGAAGGAT
1 GCAAATCTAATGCAGTTATGAAACAGAAGGAT
5294705 GCAAATCTAATGCAGTTATGAAACAGAAGGAT
1 GCAAATCTAATGCAGTTATGAAACAGAAGGAT
*
5294737 GAAAAT
1 GCAAAT
5294743 AATTTAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (32 bp):
GCAAATCTAATGCAGTTATGAAACAGAAGGAT
Found at i:5300120 original size:23 final size:23
Alignment explanation
Indices: 5300058--5300120 Score: 56
Period size: 27 Copynumber: 2.6 Consensus size: 23
5300048 AGTTGAGCAC
* *
5300058 TAAATTTTTATAAATAAATCGAT
1 TAAATTTTTATAAATAAATCAAA
5300081 TGAATATTATTTAATAAATTAAAT-AAA
1 T-AA-ATT-TTT-ATAAA-TAAATCAAA
5300108 TAAATTTTTATAA
1 TAAATTTTTATAA
5300121 CTCATATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
23 5 0.15
24 5 0.15
25 6 0.18
26 5 0.15
27 7 0.21
28 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (23 bp):
TAAATTTTTATAAATAAATCAAA
Done.