Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 93 of 310
Found at i:29797941 original size:42 final size:41
Alignment explanation
Indices: 29797817--29798040 Score: 178
Period size: 43 Copynumber: 5.3 Consensus size: 41
29797807 ATGTGACCTT
* * * * *
29797817 TAGCGGCGTTTTTCACTAAAGCGTCGCTAAAAGTCTTATTCTT
1 TAGCGGCGTTTTTC-TTAAAGCGCCGCT-AAAGTCATGTTCTA
* * * * *
29797860 TAGCAGCATTTTTCTTAAAGTGCCGCTAAAAGTCTTGTTCTT
1 TAGCGGCGTTTTTCTTAAAGCGCCGCT-AAAGTCATGTTCTA
29797902 TAGCGGCGTTTTTCTTAAAGCGCCGCTAAAGTTCATGTTCTA
1 TAGCGGCGTTTTTCTTAAAGCGCCGCTAAAG-TCATGTTCTA
* ** * * * *
29797944 TAGCGGTGTTTGTGGTAAAAGTGCCACTAAAGGTCATGTTCCA
1 TAGCGGCGTTT-TTCTTAAAGCGCCGCTAAA-GTCATGTTCTA
* * * *
29797987 TAGCGGCATTTTTGTGAGAAACGCCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTTTCTTA-AAGCGCCGCTAAA-GTCATGTTCTA
*
29798030 TAGTGGCGTTT
1 TAGCGGCGTTT
29798041 GCGAAATTTT
Statistics
Matches: 149, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.03
42 70 0.47
43 74 0.50
44 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
TAGCGGCGTTTTTCTTAAAGCGCCGCTAAAGTCATGTTCTA
Found at i:29803558 original size:14 final size:15
Alignment explanation
Indices: 29803539--29803595 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
29803529 AATCTTTAAG
29803539 GATATG-CAATCTTA
1 GATATGACAATCTTA
29803553 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
29803570 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
29803589 GATATGA
1 GATATGA
29803596 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:29803580 original size:36 final size:38
Alignment explanation
Indices: 29803539--29803617 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
29803529 AATCTTTAAG
29803539 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
29803575 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
29803615 GAT
1 GAT
29803618 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:29803586 original size:19 final size:19
Alignment explanation
Indices: 29803539--29803617 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
29803529 AATCTTTAAG
29803539 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29803558 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29803575 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29803594 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
29803615 GAT
1 GAT
29803618 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29809235 original size:7 final size:7
Alignment explanation
Indices: 29809225--29809289 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
29809215 AAAAAAAAGG
29809225 GAAAAAA
1 GAAAAAA
29809232 G--AAAA
1 GAAAAAA
29809237 GAAAAAGA
1 GAAAAA-A
29809245 GAAAAAA
1 GAAAAAA
29809252 -ATAAAAA
1 GA-AAAAA
29809259 GAAAAAA
1 GAAAAAA
*
29809266 G--AGAA
1 GAAAAAA
29809271 -AAAAAA
1 GAAAAAA
29809277 GAAAAAA
1 GAAAAAA
29809284 GAAAAA
1 GAAAAA
29809290 TGGAGAGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
5 8 0.17
6 4 0.08
7 28 0.58
8 8 0.17
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:29809252 original size:16 final size:15
Alignment explanation
Indices: 29809215--29809289 Score: 71
Period size: 16 Copynumber: 4.9 Consensus size: 15
29809205 CTTCTATTTC
**
29809215 AAAAAAAAGGGAAA-
1 AAAAAAAAGAAAAAG
*
29809229 AAAGAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
29809244 AGAAAAAAATAAAAAG
1 A-AAAAAAAGAAAAAG
* *
29809260 AAAAAAGAGAAAAAA
1 AAAAAAAAGAAAAAG
29809275 AAGAAAAAAGAAAAA
1 AA-AAAAAAGAAAAA
29809290 TGGAGAGGCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.22
15 14 0.29
16 24 0.49
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:29809252 original size:23 final size:22
Alignment explanation
Indices: 29809226--29809289 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 22
29809216 AAAAAAAGGG
*
29809226 AAAAAAGAAAAGAAAAAGAGAA
1 AAAAAAAAAAAGAAAAAGAGAA
*
29809248 AAAAATAAAAAGAAAAAAGAGAAA
1 AAAAAAAAAAAG-AAAAAGAG-AA
29809272 AAAAAGAAAAAAGAAAAA
1 AAAAA-AAAAAAGAAAAA
29809290 TGGAGAGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 10 0.28
23 8 0.22
24 12 0.33
25 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAAAGAGAA
Found at i:29810381 original size:84 final size:84
Alignment explanation
Indices: 29810237--29810932 Score: 1048
Period size: 84 Copynumber: 8.3 Consensus size: 84
29810227 CAACATTCAG
29810237 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
29810302 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * *
29810321 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTATATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
29810386 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * *
29810405 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTATATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
29810470 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * *
29810489 CGTCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTATATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
29810554 GTGGAGCAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* *
29810573 CGCCTTAATCCCCTAAGCGGTAGGGTAACAGGTTAAATTTGCATATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
29810638 GTGGAGTAGATCGAAGACT
66 GTGGAGCAGATCGAAGACT
* * *
29810657 CGCCTTAATCCCCTAAGCAGTACGGTAATAGG-----TTCGCAGATCTTATCTCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
*
29810717 GCGGAGCAGATCGACGATGACT
66 GTGGAGCAGATCGA--A-GACT
* *
29810739 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGTAGATCTTATCTCCCTAAGTAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
29810804 GTGGAGCATATCGAAGACC
66 GTGGAGCAGATCGAAGACT
* *
29810823 CGCCTTAATCCCCTAAGAAGTAGGGTAACAGGTTAAATTTACAGATCTTA--TCCCTAAGCAGTA
1 CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
* *
29810886 G-CGAGCAGATTGAAGACAAT
66 GTGGAGCAGATCGAAGAC--T
* *
29810906 GCACCTTAACCCCCTAAGCAGTAGGGT
1 -CGCCTTAATCCCCTAAGCAGTAGGGT
29810933 CCAAGATGAT
Statistics
Matches: 568, Mismatches: 33, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
79 38 0.07
81 14 0.02
82 47 0.08
84 431 0.76
85 1 0.00
87 37 0.07
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (84 bp):
CGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTA
GTGGAGCAGATCGAAGACT
Found at i:29811696 original size:19 final size:19
Alignment explanation
Indices: 29811672--29811750 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
29811662 AATCTTTAAG
29811672 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29811691 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29811710 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29811727 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
29811748 GAT
1 GAT
29811751 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29811702 original size:36 final size:36
Alignment explanation
Indices: 29811662--29811749 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 36
29811652 ATGGAAATAT
29811662 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGACAATCTTAGATATGATATGC
29811698 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG--ACAATCTTAGATATGATATGC
*
29811734 AATCTTGAAGATATGA
1 AATCTTTAAGATATGA
29811750 TCTTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
AATCTTTAAGATATGACAATCTTAGATATGATATGC
Found at i:29812236 original size:24 final size:24
Alignment explanation
Indices: 29812209--29812262 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
29812199 AAATGTTCTA
*
29812209 TTTATTCATT-TTTTATATGCTAT
1 TTTATTAATTCTTTTATATGCTAT
29812232 GTTTAATTAATTCTTTTATATGCTAT
1 -TTT-ATTAATTCTTTTATATGCTAT
29812258 TTTAT
1 TTTAT
29812263 AATATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 9 0.33
26 13 0.48
ACGTcount: A:0.24, C:0.07, G:0.06, T:0.63
Consensus pattern (24 bp):
TTTATTAATTCTTTTATATGCTAT
Found at i:29812551 original size:106 final size:106
Alignment explanation
Indices: 29812417--29812627 Score: 413
Period size: 106 Copynumber: 2.0 Consensus size: 106
29812407 TATTATTTAT
*
29812417 GTTTGTATGGAAATGTTAGAATATTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCT
1 GTTTGTATGGAAATGTTAGAATACTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCT
29812482 AAAACGTCATTTAAAATAATATTCCAAGGTTTTTTTAAAAC
66 AAAACGTCATTTAAAATAATATTCCAAGGTTTTTTTAAAAC
29812523 GTTTGTATGGAAATGTTAGAATACTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCT
1 GTTTGTATGGAAATGTTAGAATACTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCT
29812588 AAAACGTCATTTAAAATAATATTCCAAGGTTTTTTTAAAA
66 AAAACGTCATTTAAAATAATATTCCAAGGTTTTTTTAAAA
29812628 AAATAAAAGG
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (106 bp):
GTTTGTATGGAAATGTTAGAATACTTTGTACATCTATGCTTCATGATGCATTAATATGTCATCCT
AAAACGTCATTTAAAATAATATTCCAAGGTTTTTTTAAAAC
Found at i:29816052 original size:44 final size:44
Alignment explanation
Indices: 29816003--29816816 Score: 1450
Period size: 44 Copynumber: 18.5 Consensus size: 44
29815993 CAAATGTCAG
* * * *
29816003 ATCTGCTATCTTCGATCTGTTCTCTGTCAATACAGAGATGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * * * * *
29816047 ATCTGCTATCTTCGATCTTCTCTCTGACAATACAAAAACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * *
29816091 ATCTATCATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816135 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816179 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816223 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816267 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816311 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816355 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816399 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816443 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816487 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816531 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816575 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816619 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
29816663 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
*
29816707 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGATGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * *
29816751 ATCTGTCATCTTCGATCTACTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
*
29816795 ATCTGTCATCTTT-GATCTGCTC
1 ATCTGTTAT-TTTCGATCTGCTC
29816817 ACGCCAAATC
Statistics
Matches: 746, Mismatches: 23, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
44 744 1.00
45 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (44 bp):
ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
Found at i:29816162 original size:132 final size:132
Alignment explanation
Indices: 29816003--29816960 Score: 1536
Period size: 132 Copynumber: 7.4 Consensus size: 132
29815993 CAAATGTCAG
* * * * * * *
29816003 ATCTGCTATCTTCGATCTGTTCTCTGTCAATACAGAGATGCCAAATCTGCTATCTTCGATCTTCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
* * * * * *
29816068 CTCTGACAATACAAAAACGCCAAATCTATCATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816133 AA
131 AA
29816135 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
29816200 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816265 AA
131 AA
29816267 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
29816332 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816397 AA
131 AA
29816399 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
29816464 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816529 AA
131 AA
29816531 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
29816596 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816661 AA
131 AA
29816663 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
1 ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
* * * *
29816728 CTCTGTCAATACAGAGATGCCAAATCTGTCATCTTCGATCTACTCTCTGTCAATACAGAGACGCC
66 CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
29816793 AA
131 AA
* * *
29816795 ATCTGTCATCTTT-GA-------TCTG-C--T-C----ACGCCAAATCTGTCATCTTCGATCTGC
1 ATCTGTTAT-TTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGC
* * * *
29816844 TCTCTATCAATAGAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGC
65 TCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGC
29816909 CAA
130 CAA
** *
29816912 ATCTGCCATCTTT-GATCTGCTCTCTGTCAATACAGAGATGCCAAATCTG
1 ATCTGTTAT-TTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTG
29816961 CTATCGGTGA
Statistics
Matches: 782, Mismatches: 28, Indels: 32
0.93 0.03 0.04
Matches are distributed among these distances:
117 101 0.13
121 1 0.00
122 1 0.00
124 5 0.01
125 5 0.01
127 1 0.00
128 1 0.00
132 664 0.85
133 3 0.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (132 bp):
ATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCT
CTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCC
AA
Found at i:29816830 original size:29 final size:29
Alignment explanation
Indices: 29816788--29816845 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
29816778 CAATACAGAG
*
29816788 ACGCCAAATCTGTCATCTTTGATCTGCTC
1 ACGCCAAATCTGTCATCTTCGATCTGCTC
29816817 ACGCCAAATCTGTCATCTTCGATCTGCTC
1 ACGCCAAATCTGTCATCTTCGATCTGCTC
29816846 TCTATCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (29 bp):
ACGCCAAATCTGTCATCTTCGATCTGCTC
Found at i:29816840 original size:161 final size:161
Alignment explanation
Indices: 29816656--29816960 Score: 511
Period size: 161 Copynumber: 1.9 Consensus size: 161
29816646 CAATACAGAG
* * * * *
29816656 ACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATTTTCG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTTATCTTCG
* *
29816721 ATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGTCATCTTCGATCTACTCTCTGTCAATACAG
66 ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTCGATCTACTCTCTGTCAATACAG
29816786 AGACGCCAAATCTGTCATCTTTGATCTGCTC
131 AGACGCCAAATCTGTCATCTTTGATCTGCTC
*
29816817 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATAGAGAGACACCAAATCTGTTATCTTCG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTTATCTTCG
* *
29816882 ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTTGATCTGCTCTCTGTCAATACAG
66 ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTCGATCTACTCTCTGTCAATACAG
*
29816947 AGATGCCAAATCTG
131 AGACGCCAAATCTG
29816961 CTATCGGTGA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
161 133 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (161 bp):
ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTTATCTTCG
ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTCGATCTACTCTCTGTCAATACAG
AGACGCCAAATCTGTCATCTTTGATCTGCTC
Found at i:29816843 original size:117 final size:117
Alignment explanation
Indices: 29816700--29816933 Score: 387
Period size: 117 Copynumber: 2.0 Consensus size: 117
29816690 CAATACAGAG
* * * **
29816700 ACGCCAAATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGTCATCTTCG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCG
*
29816765 ATCTACTCTCTGTCAATACAGAGACGCCAAATCTGTCATCTTTGATCTGCTC
66 ATCTACTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTTGATCTGCTC
* *
29816817 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATAGAGAGACACCAAATCTGTTATCTTCG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCG
*
29816882 ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTTGATCTGCTC
66 ATCTACTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTTGATCTGCTC
29816934 TCTGTCAATA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (117 bp):
ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCG
ATCTACTCTCTGTCAATACAGAGACGCCAAATCTGCCATCTTTGATCTGCTC
Found at i:29816868 original size:73 final size:73
Alignment explanation
Indices: 29816746--29816889 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
29816736 ATACAGAGAT
* * *
29816746 GCCAAATCTGTCATCTTCGATCTACTCTCTGTCAATACAGAGACGCCAAATCTGTCATCTTTGAT
1 GCCAAATCTGTCATCTTCGATCTACTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCGAT
29816811 CTGCTCAC
66 CTGCTCAC
* * *
29816819 GCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATAGAGAGACACCAAATCTGTTATCTTCGAT
1 GCCAAATCTGTCATCTTCGATCTACTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCGAT
29816884 CTGCTC
66 CTGCTC
29816890 TCTGTCAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (73 bp):
GCCAAATCTGTCATCTTCGATCTACTCTCTATCAATACAGAGACACCAAATCTGTCATCTTCGAT
CTGCTCAC
Found at i:29816870 original size:44 final size:44
Alignment explanation
Indices: 29816817--29816960 Score: 225
Period size: 44 Copynumber: 3.3 Consensus size: 44
29816807 TGATCTGCTC
* *
29816817 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTATCAATAGAGAG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTGTCAATACAGAG
* *
29816861 ACACCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTGTCAATACAGAG
* *
29816905 ACGCCAAATCTGCCATCTTTGATCTGCTCTCTGTCAATACAGAG
1 ACGCCAAATCTGTCATCTTCGATCTGCTCTCTGTCAATACAGAG
*
29816949 ATGCCAAATCTG
1 ACGCCAAATCTG
29816961 CTATCGGTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (44 bp):
ACGCCAAATCTGTCATCTTCGATCTGCTCTCTGTCAATACAGAG
Found at i:29828963 original size:5 final size:5
Alignment explanation
Indices: 29828942--29829027 Score: 56
Period size: 5 Copynumber: 17.4 Consensus size: 5
29828932 TTGTACAAAG
* * *
29828942 TAATA -AATA AAATTA TAATA TAATA TAATA T-ATAA TGAAAA TGATA
1 TAATA TAATA TAA-TA TAATA TAATA TAATA TAAT-A T-AATA TAATA
* *
29828988 TAAT- GAATA AAATA T-ATA TTAATA TAATA TAATA T-ATA TA
1 TAATA TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TA
29829028 TGAGAAAGCG
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 16 0.25
5 38 0.59
6 9 0.14
7 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:29829015 original size:24 final size:22
Alignment explanation
Indices: 29828944--29829028 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 22
29828934 GTACAAAGTA
29828944 ATAA-ATAAAAT-TATAATATAAT
1 ATAATATAAAATATAT-AT-TAAT
* * *
29828966 ATAATATATAATGA-A-AATGAT
1 ATAATATAAAAT-ATATATTAAT
29828987 ATAATGAATAAAATATATATTAAT
1 ATAAT--ATAAAATATATATTAAT
*
29829011 ATAATATAATATATATAT
1 ATAATATAAAATATATAT
29829029 GAGAAAGCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
21 8 0.16
22 18 0.37
23 13 0.27
24 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATATAAAATATATATTAAT
Found at i:29846104 original size:21 final size:22
Alignment explanation
Indices: 29846062--29846104 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29846052 TAAAAAAATG
*
29846062 AATTCAAAAATTTTATTGATTA
1 AATTCAAAAATTTTATTAATTA
* *
29846084 AATTGAAAATTTTTA-TAATTA
1 AATTCAAAAATTTTATTAATTA
29846105 GTTGACCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTCAAAAATTTTATTAATTA
Found at i:29850649 original size:78 final size:79
Alignment explanation
Indices: 29850541--29850698 Score: 246
Period size: 78 Copynumber: 2.0 Consensus size: 79
29850531 AAAATTTATA
* * * * *
29850541 TAATAAAAACATGAATATATTATATGTTAAACTTGATTATGATAT-GATATGTAATTTAAATACG
1 TAATAAAAACATGAATATATTATATATTAAACTTGATTATGATATAGAGATATAATATAAATACA
29850605 ATATCAATTTTAAC
66 ATATCAATTTTAAC
* *
29850619 TAATAAAAACATGAATATATTTTATATTAAACTTGATTATGATATAGAGATATGATATAAATACA
1 TAATAAAAACATGAATATATTATATATTAAACTTGATTATGATATAGAGATATAATATAAATACA
29850684 ATATCAATTTTAAC
66 ATATCAATTTTAAC
29850698 T
1 T
29850699 CTAGAATCTA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 43 0.60
79 29 0.40
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (79 bp):
TAATAAAAACATGAATATATTATATATTAAACTTGATTATGATATAGAGATATAATATAAATACA
ATATCAATTTTAAC
Found at i:29851264 original size:36 final size:36
Alignment explanation
Indices: 29851216--29851287 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
29851206 TTGCTATTAT
*
29851216 AACATTCAATAAATCCGCAGTTTGAATTTGAACATC
1 AACATTCAATAAATCCGCAGTGTGAATTTGAACATC
* * * *
29851252 AACATTCCATAAATCTGGAGTGTGCATTTGAACATC
1 AACATTCAATAAATCCGCAGTGTGAATTTGAACATC
29851288 TACAATCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (36 bp):
AACATTCAATAAATCCGCAGTGTGAATTTGAACATC
Found at i:29854134 original size:3 final size:3
Alignment explanation
Indices: 29854126--29854175 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
29854116 GAACGATGAC
* * *
29854126 TAT TAT TAT TAA TAT TAT TAT CAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29854174 TA
1 TA
29854176 CTCCATATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29862485 original size:48 final size:47
Alignment explanation
Indices: 29862421--29862532 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 47
29862411 AGTGATAATT
29862421 TTAAATTTTCAATACTATTCGATATTTT-TTAAATTTATGCAAATT-TAA
1 TTAAA-TTTCAATACTATTCGATATTTTATT-AATTTATGC-AATTATAA
* * *
29862469 TTAAATTTGCAATACTATTTGATATTTTATTCATTTATGCAATTATAG
1 TTAAATTT-CAATACTATTCGATATTTTATTAATTTATGCAATTATAA
29862517 TTAATATTTCAATACT
1 TTAA-ATTTCAATACT
29862533 GCTTGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
47 7 0.12
48 44 0.77
49 6 0.11
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (47 bp):
TTAAATTTCAATACTATTCGATATTTTATTAATTTATGCAATTATAA
Found at i:29862539 original size:48 final size:45
Alignment explanation
Indices: 29862421--29862555 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 45
29862411 AGTGATAATT
*
29862421 TTAAATTTTCAATACTATTCGATATTTTTTAAATTTATGCAAATTTAA
1 TTAAA-TTTCAATACTATT-GATATTTTTT-CATTTATGCAAATTTAA
*
29862469 TTAAATTTGCAATACTATTTGATATTTTATTCATTTATGC-AATTATAG
1 TTAAATTT-CAATACTA-TTGATATTTT-TTCATTTATGCAAATT-TAA
* *
29862517 TTAATATTTCAATACTGCTTGATTTTTTTTTCATTTATG
1 TTAA-ATTTCAATACT-ATTGA-TATTTTTTCATTTATG
29862556 ATGTTTGCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
47 7 0.09
48 56 0.74
49 13 0.17
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.53
Consensus pattern (45 bp):
TTAAATTTCAATACTATTGATATTTTTTCATTTATGCAAATTTAA
Found at i:29863557 original size:7 final size:7
Alignment explanation
Indices: 29863545--29863569 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29863535 AGTCGTTTCA
29863545 TATTTAG
1 TATTTAG
29863552 TATTTAG
1 TATTTAG
29863559 TATTTAG
1 TATTTAG
29863566 TATT
1 TATT
29863570 ATGTATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:29867934 original size:127 final size:126
Alignment explanation
Indices: 29867698--29868079 Score: 593
Period size: 126 Copynumber: 3.0 Consensus size: 126
29867688 TTATAGCCTC
** * *
29867698 ATTTTTCTATGAACTACTGTAATAAAAGAGTGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTT
1 ATTTTTCTATGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTA
* * *
29867763 ACAATGCATTCTGCTTGAAGCGTTTTCGACACTATTTATTCAGAAATGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAATGTCTACTCAGAATT
* *
29867824 ATTTTTCTATGAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCAAAAAATTTTGCT
1 ATTTTTCTATGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTC-AGAAATTTTGCT
* * * *
29867889 AACAGTGCATCCTGCTTGAAGCGTTTTCGATACTATTTGTCCAGAAACGTCTATTCAGAATT
65 AACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAATGTCTACTCAGAATT
* * * *
29867951 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCAACGTGGGAGCTTTTTTTAGAAATTTTGCTG
1 ATTTTTCTATGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTA
*
29868016 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAATGTCTACTCAAAATT
66 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAATGTCTACTCAGAATT
29868077 ATT
1 ATT
29868080 CTTGTAGAAA
Statistics
Matches: 231, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
126 118 0.51
127 113 0.49
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (126 bp):
ATTTTTCTATGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTA
ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAATGTCTACTCAGAATT
Found at i:29868647 original size:20 final size:20
Alignment explanation
Indices: 29868606--29868690 Score: 101
Period size: 19 Copynumber: 4.5 Consensus size: 20
29868596 GCGATAATGT
*
29868606 ATCAATTAACCCCAAA-TTA
1 ATCAATTAACCCTAAATTTA
*
29868625 ATCAACTAACCCTAAATTTA
1 ATCAATTAACCCTAAATTTA
29868645 ATCAATTAACCCT-AATTTA
1 ATCAATTAACCCTAAATTTA
*
29868664 ATCAA-T---CCTTAATTTA
1 ATCAATTAACCCTAAATTTA
29868680 ATCAATTAACC
1 ATCAATTAACC
29868691 TTAATACCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
15 3 0.05
16 11 0.19
17 1 0.02
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCAATTAACCCTAAATTTA
Found at i:29868685 original size:35 final size:37
Alignment explanation
Indices: 29868606--29868695 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 37
29868596 GCGATAATGT
* *
29868606 ATCAATTAACCCCAAATTAATCAACTAACCCTAAATTTA
1 ATCAATTAACCCTAATTTAATCAACT-A-CCTAAATTTA
*
29868645 ATCAATTAACCCTAATTTAATCAA-T-CCTTAATTTA
1 ATCAATTAACCCTAATTTAATCAACTACCTAAATTTA
*
29868680 ATCAATTAACCTTAAT
1 ATCAATTAACCCTAAT
29868696 ACCCTAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 24 0.51
38 1 0.02
39 22 0.47
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.34
Consensus pattern (37 bp):
ATCAATTAACCCTAATTTAATCAACTACCTAAATTTA
Found at i:29868836 original size:16 final size:16
Alignment explanation
Indices: 29868817--29868874 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
29868807 CCCTAAATCT
*
29868817 TAAAAAACACTAACCT
1 TAAAAAACACTAACCC
** *
29868833 TAAATCA-ATTAAACCC
1 TAAAAAACACT-AACCC
*
29868849 TAAAAAACCCTAACCC
1 TAAAAAACACTAACCC
29868865 TAAAAAACAC
1 TAAAAAACAC
29868875 GGGCAAAATG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 2 0.06
16 28 0.90
17 1 0.03
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (16 bp):
TAAAAAACACTAACCC
Found at i:29868837 original size:23 final size:23
Alignment explanation
Indices: 29868786--29868838 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
29868776 CCCTTAAATT
* * *
29868786 CTAAACCTTAAAAACCCCTAACC
1 CTAAATCTTAAAAAACACTAACC
29868809 CTAAATCTTAAAAAACACTAACC
1 CTAAATCTTAAAAAACACTAACC
*
29868832 TTAAATC
1 CTAAATC
29868839 AATTAAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (23 bp):
CTAAATCTTAAAAAACACTAACC
Found at i:29869750 original size:19 final size:21
Alignment explanation
Indices: 29869714--29869757 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
29869704 AATAATTAAT
*
29869714 TATTTTGTAGAATTTTAAAAA
1 TATTTTGTAGAATATTAAAAA
*
29869735 TATTTT-TAGAA-ATTAAAAC
1 TATTTTGTAGAATATTAAAAA
29869754 TATT
1 TATT
29869758 AAAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 5 0.24
21 6 0.29
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
TATTTTGTAGAATATTAAAAA
Found at i:29878178 original size:16 final size:17
Alignment explanation
Indices: 29878157--29878194 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
29878147 TTCTATATGG
*
29878157 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
29878173 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
29878191 ATTT
1 ATTT
29878195 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:29878373 original size:16 final size:17
Alignment explanation
Indices: 29878338--29878375 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29878328 ACTTTTTATT
*
29878338 TTTTTATTATTTGAATA
1 TTTTTATAATTTGAATA
*
29878355 TTTTTATAATTTTAA-A
1 TTTTTATAATTTGAATA
29878371 TTTTT
1 TTTTT
29878376 TGTTGAGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTATAATTTGAATA
Found at i:29887758 original size:47 final size:49
Alignment explanation
Indices: 29887687--29887861 Score: 150
Period size: 47 Copynumber: 3.7 Consensus size: 49
29887677 AAGGTGTAAT
* * *
29887687 GCCGATGCCACGTCCCAGACATGGTCTTACACTGGCTCATC-CATC-AA
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCGAA
* * *
29887734 GTCGATGTCATGTCCCAGACATGGTCTTACACTGACT-ATCGAAATCGAG
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCATC-AAATCGAA
* * * * **
29887783 GCCGACGTAATATCCCAGATATGGTCTTACACTGGCTC-TCATAAT-GTG
1 GCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCATCA-AATCGAA
*
29887831 GCTGATG-CATGTCCCAG-CTAT-GTCTTACACT
1 GCCGATGTCATGTCCCAGAC-ATGGTCTTACACT
29887862 AGCGAACAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
46 13 0.12
47 43 0.41
48 11 0.11
49 37 0.36
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
GCCGATGTCATGTCCCAGACATGGTCTTACACTGGCTCATCAAATCGAA
Found at i:29889523 original size:10 final size:10
Alignment explanation
Indices: 29889508--29889533 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29889498 CTCTAGCGAG
29889508 TTAGTTCTGC
1 TTAGTTCTGC
29889518 TTAGTTCTGC
1 TTAGTTCTGC
29889528 TTAGTT
1 TTAGTT
29889534 GTTGTACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.54
Consensus pattern (10 bp):
TTAGTTCTGC
Found at i:29892506 original size:16 final size:16
Alignment explanation
Indices: 29892481--29892511 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29892471 GGTAAGAAAT
*
29892481 TTGTATTCTGTATCTG
1 TTGTAATCTGTATCTG
29892497 TTGTAATCTGTATCT
1 TTGTAATCTGTATCT
29892512 ATAACTGATA
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:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (16 bp):
TTGTAATCTGTATCTG
Found at i:29896411 original size:3 final size:3
Alignment explanation
Indices: 29896403--29896436 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29896393 ATATATATTT
29896403 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29896437 TCATCACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29896679 original size:22 final size:21
Alignment explanation
Indices: 29896637--29896679 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
29896627 CTGAGATAAT
* *
29896637 TTAAATGAAAGAATTATAATA
1 TTAAATGAAAGAATAAAAATA
*
29896658 TTAAATTGAAATAATAAAAATA
1 TTAAA-TGAAAGAATAAAAATA
29896680 GGTATTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAATGAAAGAATAAAAATA
Found at i:29899492 original size:11 final size:11
Alignment explanation
Indices: 29899476--29899500 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29899466 TTGTGTGTTC
29899476 TTTATTTTATT
1 TTTATTTTATT
29899487 TTTATTTTATT
1 TTTATTTTATT
29899498 TTT
1 TTT
29899501 TTCACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:29906103 original size:18 final size:18
Alignment explanation
Indices: 29906077--29906111 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29906067 TATAACAATG
29906077 GAAAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAAAGAAA
*
29906095 GAAAGAAAAAAAAAGAA
1 GAAAAAAAAAAAAAGAA
29906112 CAACGAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAAAGAAA
Found at i:29912805 original size:33 final size:33
Alignment explanation
Indices: 29912764--29912830 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29912754 CCGTTTATGG
29912764 ATTTATTCACTTGTAACGTTCATAGTGTGACAT
1 ATTTATTCACTTGTAACGTTCATAGTGTGACAT
29912797 ATTTATTCACTTGTAACGTTCATAGTGTGACAT
1 ATTTATTCACTTGTAACGTTCATAGTGTGACAT
29912830 A
1 A
29912831 CCTAAATCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
ATTTATTCACTTGTAACGTTCATAGTGTGACAT
Found at i:29914936 original size:93 final size:93
Alignment explanation
Indices: 29914777--29914949 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
29914767 AGGATATTTG
* * * * * *
29914777 GGCATCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTTTGGATGTGAATGTCCAAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCGAACGCCCAAACTCGTTGAG
29914842 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
29914870 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCGAACGCCCAAACTCGTTGAG
29914935 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
29914950 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCGAACGCCCAAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29914947 original size:46 final size:44
Alignment explanation
Indices: 29914784--29914955 Score: 150
Period size: 46 Copynumber: 3.8 Consensus size: 44
29914774 TTGGGCATCT
* * * *
29914784 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTTTGGATGTGAATGTCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATG-GAACGCCC
* * * * *
29914830 AAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAGGCATCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAAC---GC--CC
*
29914877 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGAATGCGAACGCCC
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG-ATG-GAACGCCC
*
29914923 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATG
1 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG
29914956 GGCGGGTTAC
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 56 0.56
47 25 0.25
48 4 0.04
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (44 bp):
GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAACGCCC
Found at i:29915370 original size:19 final size:19
Alignment explanation
Indices: 29915346--29915443 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
29915336 AATCTTTAAG
29915346 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29915365 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29915384 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29915401 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
29915420 AATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
29915441 GAT
1 GAT
29915444 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.66
21 8 0.11
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29915376 original size:36 final size:35
Alignment explanation
Indices: 29915336--29915419 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 35
29915326 ATGGAAGTAT
29915336 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTT-A-GATATGACAATCTTAGATATGATATGC
29915372 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGATATG--ACAATCTTAGATATGATATGC
29915408 AATC-TTAGATAT
1 AATCTTTAGATAT
29915420 AATATGCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 36 0.80
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
AATCTTTAGATATGACAATCTTAGATATGATATGC
Found at i:29918321 original size:147 final size:147
Alignment explanation
Indices: 29918054--29918348 Score: 572
Period size: 147 Copynumber: 2.0 Consensus size: 147
29918044 GAAAATGAAA
29918054 AATAAAAATGGCCTGAAAATTGAATATATGTTTTTCTAATAAATGAAGTTCAAAAATGGAAATAA
1 AATAAAAATGGCCTGAAAATTGAATATATGTTTTTCTAATAAATGAAGTTCAAAAATGGAAATAA
*
29918119 ATCATTTGTTCATAGTGAATCATTGAATGTGGAAATATTAAATATATTTTCTCATAGATTCTTTT
66 ATCATTTGGTCATAGTGAATCATTGAATGTGGAAATATTAAATATATTTTCTCATAGATTCTTTT
*
29918184 ATGGTAAAGTTCTCATG
131 ATGGTAAAATTCTCATG
29918201 AATAAAAATGGCCTGAAAATTGAATATATGTTTTTCTAATAAATGAAGTTCAAAAATGGAAATAA
1 AATAAAAATGGCCTGAAAATTGAATATATGTTTTTCTAATAAATGAAGTTCAAAAATGGAAATAA
29918266 ATCATTTGGTCATAGTGAATCATTGAATGTGGAAATATTAAATATATTTTCTCATAGATTCTTTT
66 ATCATTTGGTCATAGTGAATCATTGAATGTGGAAATATTAAATATATTTTCTCATAGATTCTTTT
29918331 ATGGTAAAATTCTCATG
131 ATGGTAAAATTCTCATG
29918348 A
1 A
29918349 TTTTAACAGA
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (147 bp):
AATAAAAATGGCCTGAAAATTGAATATATGTTTTTCTAATAAATGAAGTTCAAAAATGGAAATAA
ATCATTTGGTCATAGTGAATCATTGAATGTGGAAATATTAAATATATTTTCTCATAGATTCTTTT
ATGGTAAAATTCTCATG
Found at i:29922066 original size:6 final size:6
Alignment explanation
Indices: 29922028--29922071 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
29922018 ACAGTACCTA
* * *
29922028 AACAGT AATCAGT AACGGT AGCAGT AACCGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
29922072 TTCGACACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:29922378 original size:40 final size:40
Alignment explanation
Indices: 29922329--29922414 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
29922319 ATTCGTTTCA
* * **
29922329 TCAGAAATTTTACAGTTCAATGCAGTATACGTAACAATAT
1 TCAGTAATTTCACAGTTCAATGCAGTATACAAAACAATAT
* * *
29922369 TCAGTAATTTCACAGTTCAATTCGGTATTCAAAACAATAT
1 TCAGTAATTTCACAGTTCAATGCAGTATACAAAACAATAT
29922409 TCAGTA
1 TCAGTA
29922415 TCCCATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (40 bp):
TCAGTAATTTCACAGTTCAATGCAGTATACAAAACAATAT
Found at i:29924408 original size:26 final size:26
Alignment explanation
Indices: 29924363--29924434 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
29924353 CCTCTTTAAT
*
29924363 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCAATA
29924388 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
29924414 AACTAGGGCATAAGCTCTTTT
1 AACTGGGGCATAAGCCCTTTT
29924435 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 10 0.23
26 33 0.77
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:29924509 original size:20 final size:20
Alignment explanation
Indices: 29924484--29924558 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
29924474 TTATGATTAC
*
29924484 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
29924504 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29924524 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
29924544 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
29924559 TCCCACATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29924515 original size:11 final size:11
Alignment explanation
Indices: 29924484--29924539 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29924474 TTATGATTAC
29924484 ATCATGTGCAT
1 ATCATGTGCAT
* *
29924495 TTCA--TACAT
1 ATCATGTGCAT
29924504 ATCATGTGCAT
1 ATCATGTGCAT
*
29924515 ATCA--TACAT
1 ATCATGTGCAT
29924524 ATCATGTGCAT
1 ATCATGTGCAT
29924535 ATCAT
1 ATCAT
29924540 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29924556 original size:9 final size:10
Alignment explanation
Indices: 29924501--29924557 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
29924491 GCATTTCATA
29924501 CATATCATGT
1 CATATCATGT
*
29924511 GCATATCAT-A
1 -CATATCATGT
29924521 CATATCATGT
1 CATATCATGT
*
29924531 GCATATCATAT
1 -CATATCATGT
29924542 CA-ATCATGT
1 CATATCATGT
29924551 -ATATCAT
1 CATATCAT
29924558 ATCCCACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:29926195 original size:27 final size:27
Alignment explanation
Indices: 29926165--29926342 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29926155 ATATTGAGTC
* * * *
29926165 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29926192 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29926219 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29926247 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29926274 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29926301 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29926328 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29926343 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29926304 original size:82 final size:81
Alignment explanation
Indices: 29926186--29926341 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29926176 TGCTATATAA
* *
29926186 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29926251 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29926268 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29926332 CACTTAGTGC
65 CACTTAGTGC
29926342 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29934258 original size:27 final size:27
Alignment explanation
Indices: 29934228--29934405 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29934218 ATATTGAGTC
* * * *
29934228 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29934255 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29934282 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29934310 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29934337 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29934364 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29934391 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29934406 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29934367 original size:82 final size:81
Alignment explanation
Indices: 29934249--29934404 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29934239 TGCTATATAA
* *
29934249 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29934314 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29934331 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29934395 CACTTAGTGC
65 CACTTAGTGC
29934405 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29936868 original size:17 final size:17
Alignment explanation
Indices: 29936828--29936868 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
29936818 TTTACCCAAA
*
29936828 TGGGCCAGAAAGCCCAT
1 TGGGCCCGAAAGCCCAT
29936845 TGGGCCCGAAAGCCCAT
1 TGGGCCCGAAAGCCCAT
29936862 TGGGCCC
1 TGGGCCC
29936869 AACTTCAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.22, C:0.34, G:0.32, T:0.12
Consensus pattern (17 bp):
TGGGCCCGAAAGCCCAT
Found at i:29936880 original size:20 final size:21
Alignment explanation
Indices: 29936855--29936894 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29936845 TGGGCCCGAA
*
29936855 AGCCCATTG-GGCCCAACTTC
1 AGCCCATCGAGGCCCAACTTC
29936875 AGCCCATCGAGGCCCAACTT
1 AGCCCATCGAGGCCCAACTT
29936895 ACCGTCATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (21 bp):
AGCCCATCGAGGCCCAACTTC
Found at i:29938558 original size:3 final size:3
Alignment explanation
Indices: 29938550--29938599 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
29938540 TTACTTTATT
** *
29938550 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGGT TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
29938596 TAA T
1 TAA T
29938600 TATATATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 39 0.98
4 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:29944314 original size:22 final size:22
Alignment explanation
Indices: 29944286--29944330 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29944276 CACACACACC
29944286 TCTTTTTATAAGGCTTGGTCCT
1 TCTTTTTATAAGGCTTGGTCCT
*
29944308 TCTTTTTATCAGGCTTGGTCCT
1 TCTTTTTATAAGGCTTGGTCCT
29944330 T
1 T
29944331 TTTGTAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (22 bp):
TCTTTTTATAAGGCTTGGTCCT
Found at i:29945252 original size:17 final size:17
Alignment explanation
Indices: 29945230--29945272 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
29945220 AATGAGGAAG
29945230 GACCTAAAGTGCAAATA
1 GACCTAAAGTGCAAATA
29945247 GACCTAAAGTGCAAATA
1 GACCTAAAGTGCAAATA
*
29945264 AACCTAAAG
1 GACCTAAAG
29945273 GAGATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (17 bp):
GACCTAAAGTGCAAATA
Found at i:29951474 original size:18 final size:18
Alignment explanation
Indices: 29951425--29951477 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
29951415 ATTTATTTAG
* **
29951425 TAATAGTCAGTTATTCGG
1 TAATAATCAGTTATTCAA
* * *
29951443 TAACAATAAATTATTCAA
1 TAATAATCAGTTATTCAA
29951461 TAATAATCAGTTATTCA
1 TAATAATCAGTTATTCA
29951478 GTATCAATCA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (18 bp):
TAATAATCAGTTATTCAA
Found at i:29951486 original size:18 final size:18
Alignment explanation
Indices: 29951431--29951487 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
29951421 TTAGTAATAG
* *
29951431 TCAGTTATTCGGTAACAA
1 TCAGTTATTCAGTATCAA
* * *
29951449 TAAATTATTCAATAAT-AA
1 TCAGTTATTCAGT-ATCAA
29951467 TCAGTTATTCAGTATCAA
1 TCAGTTATTCAGTATCAA
29951485 TCA
1 TCA
29951488 ATTGATCGGT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 2 0.07
18 26 0.90
19 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (18 bp):
TCAGTTATTCAGTATCAA
Found at i:29951523 original size:18 final size:18
Alignment explanation
Indices: 29951497--29951567 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
29951487 AATTGATCGG
* * *
29951497 TTATCCAGTAACAGTCAA
1 TTATTCAGTAAAAATCAA
29951515 TTATTCAGTAAAAATCAA
1 TTATTCAGTAAAAATCAA
* * * *
29951533 ATATACAGTAATAATTAAA
1 TTATTCAGTAA-AAATCAA
*
29951552 TTATTCAGTAACAATC
1 TTATTCAGTAAAAATC
29951568 CATCTTTCTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
18 26 0.65
19 14 0.35
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (18 bp):
TTATTCAGTAAAAATCAA
Found at i:29951562 original size:19 final size:19
Alignment explanation
Indices: 29951513--29951567 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
29951503 AGTAACAGTC
29951513 AATTATTCAGTAAAAATCA
1 AATTATTCAGTAAAAATCA
* * *
29951532 AA-TATACAGTAATAATTA
1 AATTATTCAGTAAAAATCA
*
29951550 AATTATTCAGTAACAATC
1 AATTATTCAGTAAAAATC
29951568 CATCTTTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (19 bp):
AATTATTCAGTAAAAATCA
Found at i:29951771 original size:47 final size:47
Alignment explanation
Indices: 29951698--29951810 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 47
29951688 CAGTAATAGT
* * *
29951698 AACAGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
*
29951745 AACAGTAACAGTACGGTACACGGAGTACCTCATCGAAACAAATCCGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
29951792 AACAGTAACAGTAACGGTA
1 AACAGTAACAGT-ACGGTA
29951811 ATAGTAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 55 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
Found at i:29951862 original size:12 final size:12
Alignment explanation
Indices: 29951845--29951869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29951835 AGTGCCGAAT
29951845 CGGTAACAGTAA
1 CGGTAACAGTAA
29951857 CGGTAACAGTAA
1 CGGTAACAGTAA
29951869 C
1 C
29951870 AGTAGTCAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:29954184 original size:45 final size:45
Alignment explanation
Indices: 29954141--29954303 Score: 222
Period size: 45 Copynumber: 3.6 Consensus size: 45
29954131 AATACCATAG
* *
29954141 TATCTTTCAA-CTATGGTATTTTCCTTTTCAATTATAATGCCATAA
1 TATCTTTCAATC-ATGGTCTTTTCCTTTTCAATTATAATGCCATGA
* *
29954186 TATCTTTTAATCATGGTCTTTTCCTTTTCAATTATAATGTCATGA
1 TATCTTTCAATCATGGTCTTTTCCTTTTCAATTATAATGCCATGA
* *
29954231 TATCTTTCAATCATGGTCTTTTCCTTTTCGATTATAATGTCATGA
1 TATCTTTCAATCATGGTCTTTTCCTTTTCAATTATAATGCCATGA
* * *
29954276 CATCTTTCAATTATGGT-TTTTGCTTTTC
1 TATCTTTCAATCATGGTCTTTTCCTTTTC
29954304 TCAAAAAAAG
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
44 10 0.09
45 97 0.90
46 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.50
Consensus pattern (45 bp):
TATCTTTCAATCATGGTCTTTTCCTTTTCAATTATAATGCCATGA
Found at i:29954288 original size:24 final size:24
Alignment explanation
Indices: 29954211--29954289 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 24
29954201 GTCTTTTCCT
*
29954211 TTTCAATTATAATGTCATGATATC
1 TTTCAATTATAATGTCATGACATC
* * * ** *
29954235 TTTCAATCAT--GGTCTTTTCCT-
1 TTTCAATTATAATGTCATGACATC
*
29954256 TTTCGATTATAATGTCATGACATC
1 TTTCAATTATAATGTCATGACATC
29954280 TTTCAATTAT
1 TTTCAATTAT
29954290 GGTTTTTGCT
Statistics
Matches: 37, Mismatches: 15, Indels: 6
0.64 0.26 0.10
Matches are distributed among these distances:
21 8 0.22
22 5 0.14
23 6 0.16
24 18 0.49
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (24 bp):
TTTCAATTATAATGTCATGACATC
Found at i:29955120 original size:15 final size:16
Alignment explanation
Indices: 29955100--29955133 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29955090 TTATTTATTC
29955100 TTTTTA-ATTATTTAA
1 TTTTTACATTATTTAA
*
29955115 TTTTTACATTATTTCA
1 TTTTTACATTATTTAA
29955131 TTT
1 TTT
29955134 GAAAACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATTATTTAA
Found at i:29958374 original size:46 final size:46
Alignment explanation
Indices: 29958307--29958454 Score: 226
Period size: 46 Copynumber: 3.2 Consensus size: 46
29958297 ATAAAATCCT
* * *
29958307 ATAATAT-CTATTAGGAATCAAATTTCTAAAAGATAATATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
*
29958352 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAGTATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
* * *
29958398 ATAATATCCTATTATGAATCAAATTGGTAAAAAATAAAATCTAATA
1 ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
29958444 ATAATATCCTA
1 ATAATATCCTA
29958455 ACAACACTAT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 7 0.07
46 87 0.93
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (46 bp):
ATAATATCCTATTAAGAATCAAATTGCTAAAAAATAATATCTAATA
Found at i:29961551 original size:14 final size:14
Alignment explanation
Indices: 29961532--29961559 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29961522 TGATAGTGAT
29961532 CTAGACACCTTGCC
1 CTAGACACCTTGCC
29961546 CTAGACACCTTGCC
1 CTAGACACCTTGCC
29961560 GTATCAGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAGACACCTTGCC
Found at i:29963241 original size:45 final size:45
Alignment explanation
Indices: 29963044--29963337 Score: 148
Period size: 45 Copynumber: 6.5 Consensus size: 45
29963034 AGGAAATGAT
* * *
29963044 TAAGACCATAGTTGAAAGACACTATGGCA-CTA-TACTAGAAACGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATC-ACGAATA-AAACGAA
* *** * ** *
29963089 TAAGACTATAGTTGAAAGATGTTATGGCATCACGATTGTATC-AA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* * * * ** ** *
29963133 GTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTTTATTGAG
1 -TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* ** ** *
29963179 TAAAATAATAGCCGAAAGACACTATGGCATCACGAATCAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
* * *
29963224 TAAGACCATAGTTGAAAGGCACTATGGCAAT-AAG-ATGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ATCACGAAT--AAAACGAA
* * * * * * *
29963270 TAAGACCAAAGTTGAAAGACACAATGACAACATGACAAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCACGA-ATAAAACGAA
* *
29963316 TAAGACCATGGCTGAAAGACAC
1 TAAGACCATAGTTGAAAGACAC
29963338 CACGGAATTA
Statistics
Matches: 190, Mismatches: 49, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
44 3 0.02
45 121 0.64
46 65 0.34
48 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.21
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCACGAATAAAACGAA
Found at i:29963283 original size:46 final size:46
Alignment explanation
Indices: 29963221--29963337 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 46
29963211 CGAATCAAAC
* * * * * ***
29963221 GAATAAGACCATAGTTGAAAGGCACTATGGCAATAAGATGGAAAAT
1 GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
*
29963267 GAATAAGACCAAAGTTGAAAGACACAATGACAACATGACAAAAAAT
1 GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
** *
29963313 GAATAAGACCATGGCTGAAAGACAC
1 GAATAAGACCAAAGTTGAAAGACAC
29963338 CACGGAATTA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.15
Consensus pattern (46 bp):
GAATAAGACCAAAGTTGAAAGACACAATGACAACAAGACAAAAAAT
Found at i:29963762 original size:26 final size:26
Alignment explanation
Indices: 29963726--29963776 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
29963716 AATGAAAAAG
29963726 GAACAAATTGAGTAATAGATTGAGGC
1 GAACAAATTGAGTAATAGATTGAGGC
29963752 GAACAAATTGAGTAATAGATTGAGG
1 GAACAAATTGAGTAATAGATTGAGG
29963777 AATAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.27, T:0.24
Consensus pattern (26 bp):
GAACAAATTGAGTAATAGATTGAGGC
Found at i:29966616 original size:26 final size:26
Alignment explanation
Indices: 29966587--29966694 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
29966577 TGGTACAAAT
29966587 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29966613 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29966639 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29966665 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29966691 TGAT
1 TGAT
29966695 TGAAACTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29967414 original size:131 final size:131
Alignment explanation
Indices: 29967238--29967499 Score: 461
Period size: 131 Copynumber: 2.0 Consensus size: 131
29967228 GAGTGATTTG
* * *
29967238 GTAATAAATCTGCTTGGGATAGCAACAGTAACGTGACTTTGGAAAATCACCATAAATTGTGGGAG
1 GTAATAAATCTGCTTAGGACAGCAACAGTAACGTGACTTTGGAAAATCACCATAAACTGTGGGAG
29967303 ATGAGTTAGAAGCTGCATAAATCATGTAATTAAAGCTTAATGAGTCTAGTTTCAAATGGAATAAA
66 ATGAGTTAGAAGCTGCATAAATCATGTAATTAAAGCTTAATGAGTCTAGTTTCAAATGGAATAAA
29967368 C
131 C
* * *
29967369 GTAATAAATCTGCTTAGGACAGCAATAGTAATGTGACTTTGGAAAATCACGATAAACTGTGGGAG
1 GTAATAAATCTGCTTAGGACAGCAACAGTAACGTGACTTTGGAAAATCACCATAAACTGTGGGAG
*
29967434 ATGAGTTAGAAGCTGCATAAATTATGTAATTAAAGCTTAATGAGTCTAGTTTCAAATGGAATAAA
66 ATGAGTTAGAAGCTGCATAAATCATGTAATTAAAGCTTAATGAGTCTAGTTTCAAATGGAATAAA
29967499 C
131 C
29967500 AAGAACATAT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 124 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (131 bp):
GTAATAAATCTGCTTAGGACAGCAACAGTAACGTGACTTTGGAAAATCACCATAAACTGTGGGAG
ATGAGTTAGAAGCTGCATAAATCATGTAATTAAAGCTTAATGAGTCTAGTTTCAAATGGAATAAA
C
Found at i:29967861 original size:88 final size:88
Alignment explanation
Indices: 29967712--29967887 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
29967702 AGCTCCAGTT
29967712 ATAAATAGTTTAGTGACTGTTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGTAAA
1 ATAAATAGTTTAGTGACTGTTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGTAAA
29967777 CATTGACAAAAATTTGTTAATGA
66 CATTGACAAAAATTTGTTAATGA
29967800 ATAAATAGTTTAGTGACTGTTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGTAAA
1 ATAAATAGTTTAGTGACTGTTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGTAAA
29967865 CATTGACAAAAATTTGTTAATGA
66 CATTGACAAAAATTTGTTAATGA
29967888 GTTGCTTATT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (88 bp):
ATAAATAGTTTAGTGACTGTTGCTCAGGAAGACAGCTTGCAGTGAAATTATGATTATGTGGTAAA
CATTGACAAAAATTTGTTAATGA
Found at i:29968429 original size:26 final size:26
Alignment explanation
Indices: 29968400--29968452 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
29968390 TTTACAGTTT
29968400 TACCCCTAGTAGATAAATT-ACCGAAA
1 TACCCCTAGT-GATAAATTGACCGAAA
* * *
29968426 TACCCTTAGTGTTAAATTGACCTAAA
1 TACCCCTAGTGATAAATTGACCGAAA
29968452 T
1 T
29968453 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (26 bp):
TACCCCTAGTGATAAATTGACCGAAA
Found at i:29973930 original size:31 final size:31
Alignment explanation
Indices: 29973892--29973970 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
29973882 TTGAATGGTT
29973892 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
29973923 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
29973954 ATTGGGCTGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
29973971 ACTGTAAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:29974041 original size:42 final size:42
Alignment explanation
Indices: 29973994--29974085 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
29973984 TGGCCCTTAG
* * ** *
29973994 GCCCATTTCAATATCACGTGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
29974036 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
29974078 GCCTATTT
1 GCCCATTT
29974086 AGGGAGACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:29974300 original size:26 final size:26
Alignment explanation
Indices: 29974230--29974352 Score: 205
Period size: 26 Copynumber: 4.8 Consensus size: 26
29974220 CCTCTTTAAT
29974230 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
29974255 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
29974280 AACTGGTGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
29974306 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
29974332 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
29974353 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 32 0.35
26 59 0.65
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:29975226 original size:27 final size:27
Alignment explanation
Indices: 29975153--29975217 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29975143 AGGCATATTC
* * *
29975153 GTCATTTTACCATACAAGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
29975180 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
*
29975207 GTCTCTTTACC
1 GTCACTTTACC
29975218 TAATAGGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:29975352 original size:27 final size:25
Alignment explanation
Indices: 29975308--29975612 Score: 119
Period size: 27 Copynumber: 11.4 Consensus size: 25
29975298 TTTTAGAAAG
29975308 TCAAGGGTATTTCT-GTAACTTTGTAAA
1 TCAAGGGTATTT-TGGTAA-TTT-TAAA
29975335 TCAAGGGTATTTTGGTAATTTTACAAA
1 TCAAGGGTATTTTGGTAATTTT--AAA
** * * *
29975362 TTGAGAGTATTTCGGTAATTTCACAA
1 TCAAGGGTATTTTGGTAATTTTA-AA
* *
29975388 ACCAGTGGTATTTTGGTAATTTTACAA
1 TCAAG-GGTATTTTGGTAATTTTA-AA
* * * *
29975415 ACTAGGGGTATTTTGATTATTTTACAAA
1 TC-AAGGGTATTTTGGTAATTTT--AAA
** *
29975443 TTGAGGGTATTTCGGTAATTTTACAAA
1 TCAAGGGTATTTTGGTAATTTT--AAA
* * * *
29975470 CCAGGGGTATTTTAGCAATTTTACAGA
1 TCAAGGGTATTTTGGTAATTTTA-A-A
* *
29975497 -CTAGGGTATTTTGGTAATTTTACTGA
1 TCAAGGGTATTTTGGTAATTTTA--AA
* *
29975523 TCGAGGGTATTTTGATAATTTTGTAAA
1 TCAAGGGTATTTTGGTAA-TTT-TAAA
* * *
29975550 CCAATGGTATTTTAGTAATTTTGTAAA
1 TCAAGGGTATTTTGGTAA-TTT-TAAA
* *** *
29975577 TCGAGGGTAAAATAGTAATTCTGTAAA
1 TCAAGGGTATTTTGGTAATT-T-TAAA
29975604 TCAAGGGTA
1 TCAAGGGTA
29975613 AAACAGTAAT
Statistics
Matches: 213, Mismatches: 50, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.01
26 30 0.14
27 171 0.80
28 6 0.03
29 3 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (25 bp):
TCAAGGGTATTTTGGTAATTTTAAA
Found at i:29975437 original size:81 final size:80
Alignment explanation
Indices: 29975338--29975571 Score: 315
Period size: 81 Copynumber: 2.9 Consensus size: 80
29975328 TTGTAAATCA
* * *
29975338 AGGGTATTTTGGTAATTTTACAAATTGAGAGTATTTCGGTAATTTCACAAACCAGTGGTATTTTG
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTTA
29975403 GTAATTTTACAAACT
66 GTAATTTTACAAACT
* * *
29975418 AGGGGTATTTTGATTATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTT
1 A-GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTT
* *
29975483 AGCAATTTTACAGACT
65 AGTAATTTTACAAACT
** * * * ** *
29975499 AGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGATAATTTTGTAAACCAATGGTATTTTA
1 AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTTA
29975564 GTAATTTT
66 GTAATTTT
29975572 GTAAATCGAG
Statistics
Matches: 133, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
80 61 0.46
81 72 0.54
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (80 bp):
AGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTTA
GTAATTTTACAAACT
Found at i:29975580 original size:54 final size:54
Alignment explanation
Indices: 29975336--29975585 Score: 222
Period size: 54 Copynumber: 4.6 Consensus size: 54
29975326 CTTTGTAAAT
* * * * *
29975336 CAAGGGTATTTTGGTAATTTTACAAATTGAGAGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAAC
* * *
29975390 C-AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGATTATTTTACAAAT
1 CAAG-GGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGATAATTTTACAAAC
** * * * *
29975444 TGAGGGTATTTCGGTAATTTTACAAA-CCAGGGGTATTTT-AGCAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGA-TAATTTTACAAAC
* ** **
29975497 CTAGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGATAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAAC
* * **
29975551 CAATGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTA
29975586 AAATAGTAAT
Statistics
Matches: 158, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
53 42 0.27
54 114 0.72
55 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAAC
Found at i:29975596 original size:54 final size:54
Alignment explanation
Indices: 29975536--29975693 Score: 165
Period size: 54 Copynumber: 2.9 Consensus size: 54
29975526 AGGGTATTTT
* **** * *
29975536 GATAATTTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATA
1 GATAATTTTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAA-A
* * *
29975591 G-TAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAC
1 GATAATTTTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAA
* * * * *
29975644 GATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGTA
1 GATAATTTTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTA
29975694 CTTCGGTAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 85 0.98
55 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (54 bp):
GATAATTTTGTAAACCAAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAA
Found at i:29975613 original size:27 final size:27
Alignment explanation
Indices: 29975563--29975693 Score: 165
Period size: 27 Copynumber: 4.9 Consensus size: 27
29975553 ATGGTATTTT
* *
29975563 AGTAATTTTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
29975590 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
29975617 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
29975644 -GATAATTTTGTAAATCGAGAGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
29975671 GGTAATTCTATAAATCGATGGTA
1 AGTAATTCTGTAAATCGAGGGTA
29975694 CTTCGGTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 88 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:29975879 original size:27 final size:27
Alignment explanation
Indices: 29975839--29975976 Score: 163
Period size: 27 Copynumber: 5.1 Consensus size: 27
29975829 GCCCAAATCT
*
29975839 TAATTTTACTAATT-GAGGGTATTTTGG
1 TAATTTTACAAATTAG-GGGTATTTTGG
*
29975866 TAATTTCACAAATTAGGGGTATTTTGG
1 TAATTTTACAAATTAGGGGTATTTTGG
* *
29975893 TAATTTTACAAACTAGGGGGATTTTGG
1 TAATTTTACAAATTAGGGGTATTTTGG
**
29975920 TAA-TTTAGCAAACAAGGGGTATTTTGG
1 TAATTTTA-CAAATTAGGGGTATTTTGG
** *
29975947 TAATTTTACAAACAAGGGGTATTTTAG
1 TAATTTTACAAATTAGGGGTATTTTGG
29975974 TAA
1 TAA
29975977 ATCGAGGGTA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
26 4 0.04
27 91 0.91
28 5 0.05
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (27 bp):
TAATTTTACAAATTAGGGGTATTTTGG
Found at i:29976011 original size:27 final size:27
Alignment explanation
Indices: 29975973--29976094 Score: 156
Period size: 27 Copynumber: 4.5 Consensus size: 27
29975963 GGGTATTTTA
*
29975973 GTAAATCGAGGGTAAAATAGTAATTCT
1 GTAAATCGAGGGTAAAACAGTAATTCT
*
29976000 GTAAATCAAGGGTAAAACAGTAATTCT
1 GTAAATCGAGGGTAAAACAGTAATTCT
* *
29976027 ATAAATCGAGGGTAAAAC-GATAATTTT
1 GTAAATCGAGGGTAAAACAG-TAATTCT
* *
29976054 GTAAATCGAGAGTAAAACGGTAATTCT
1 GTAAATCGAGGGTAAAACAGTAATTCT
* *
29976081 ATAAATCGATGGTA
1 GTAAATCGAGGGTA
29976095 CTTCGGTAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 80 0.98
28 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (27 bp):
GTAAATCGAGGGTAAAACAGTAATTCT
Found at i:29976042 original size:54 final size:54
Alignment explanation
Indices: 29975974--29976094 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
29975964 GGTATTTTAG
*
29975974 TAAATCGAGGGTAAAATAG-TAATTCTGTAAATCAAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAA-AGATAATTCTGTAAATCAAGAGTAAAACAGTAATTCTA
* * * *
29976028 TAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAAAGATAATTCTGTAAATCAAGAGTAAAACAGTAATTCTA
*
29976082 TAAATCGATGGTA
1 TAAATCGAGGGTA
29976095 CTTCGGTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.02
54 59 0.98
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (54 bp):
TAAATCGAGGGTAAAAAGATAATTCTGTAAATCAAGAGTAAAACAGTAATTCTA
Found at i:29976183 original size:401 final size:404
Alignment explanation
Indices: 29975433--29976239 Score: 1349
Period size: 401 Copynumber: 2.0 Consensus size: 404
29975423 TATTTTGATT
* *
29975433 ATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAGAC
1 ATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTAGCAATTTTACAAAC
* * * * ** *
29975498 TAGGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGATAATTTTGTAAACCAATGGTATTTT
66 TAGGGGATTTTGGTAATTTTACTAAACAAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTT
29975563 AGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTAT
131 A-TAA---TGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTAT
29975628 AAATCGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGT
192 AAATCGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGT
29975693 ACTTCGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAACTAAAGTATTCTAAACAAG
257 ACTTCGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAACTAAAGTATTCTAAACAAG
29975758 GATAACAATACGAATGGGCCTAAAGCCTATTCTCGGCCCAAATGGGCCCACACGCTCGTGTGGCC
322 GATAACAATACGAATGGGCCTAAAGCCTATTCTCGGCCCAAATGGGCCCACACGCTCGTGTGGCC
29975823 CTTTTAGCCCAAATCTTA
387 CTTTTAGCCCAAATCTTA
* * ** * *
29975841 ATTTTACTAATTGAGGGTATTTTGGTAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAAC
1 ATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTAGCAATTTTACAAAC
*
29975906 TAGGGGGATTTTGGTAA-TTTAGC-AAACAAGGGGTATTTTGGTAATTTTACAAA-CAAGGGGTA
66 TA-GGGGATTTTGGTAATTTTA-CTAAACAA-GGGTATTTTGATAATTTTACAAACCAA-GGGTA
29975968 -TTT-T-A-GTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTAT
127 TTTTATAATGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTAT
29976029 AAATCGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGT
192 AAATCGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGT
29976094 ACTTCGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAACTAAAGTATTCTAAACAAG
257 ACTTCGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAACTAAAGTATTCTAAACAAG
29976159 GATAACAATACGAATGGGCCTAAAGCCTATTCTCGGCCCAAATGGGCCCACACGCTCGTGTGGCC
322 GATAACAATACGAATGGGCCTAAAGCCTATTCTCGGCCCAAATGGGCCCACACGCTCGTGTGGCC
29976224 CTTTTAGCCCAAATCT
387 CTTTTAGCCCAAATCT
29976240 AGACACAGAT
Statistics
Matches: 379, Mismatches: 16, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
401 267 0.70
405 1 0.00
406 1 0.00
408 72 0.19
409 38 0.10
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (404 bp):
ATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTAGCAATTTTACAAAC
TAGGGGATTTTGGTAATTTTACTAAACAAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTT
ATAATGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATAAAT
CGAGGGTAAAACGATAATTTTGTAAATCGAGAGTAAAACGGTAATTCTATAAATCGATGGTACTT
CGGTAATTTTACAATTTGAGGGCATTTCAGTAATTTGGTAAACTAAAGTATTCTAAACAAGGATA
ACAATACGAATGGGCCTAAAGCCTATTCTCGGCCCAAATGGGCCCACACGCTCGTGTGGCCCTTT
TAGCCCAAATCTTA
Found at i:29986379 original size:23 final size:23
Alignment explanation
Indices: 29986353--29986399 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
29986343 TATGTGTTAG
29986353 ACTTATGGATTAAATTGAGTTGC
1 ACTTATGGATTAAATTGAGTTGC
29986376 ACTTATGGATTAAATTGAGTTGC
1 ACTTATGGATTAAATTGAGTTGC
29986399 A
1 A
29986400 TTAAGCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (23 bp):
ACTTATGGATTAAATTGAGTTGC
Found at i:29997397 original size:16 final size:16
Alignment explanation
Indices: 29997370--29997411 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
29997360 AGAAAAAACT
*
29997370 AGGAGGAGGAAAGGGAA
1 AGGAGAAGGAAA-GGAA
29997387 AGGA-AAGGAAAGGAA
1 AGGAGAAGGAAAGGAA
29997402 AGGAGAAGGA
1 AGGAGAAGGA
29997412 GGATACACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 11 0.48
17 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (16 bp):
AGGAGAAGGAAAGGAA
Found at i:29997410 original size:11 final size:11
Alignment explanation
Indices: 29997370--29997411 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
29997360 AGAAAAAACT
*
29997370 AGGAGGAGGAA
1 AGGAGAAGGAA
29997381 AGG-GAAAGGAA
1 AGGAG-AAGGAA
29997392 AGGA-AAGGAA
1 AGGAGAAGGAA
29997402 AGGAGAAGGA
1 AGGAGAAGGA
29997412 GGATACACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 11 0.41
11 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (11 bp):
AGGAGAAGGAA
Found at i:29997412 original size:6 final size:5
Alignment explanation
Indices: 29997376--29997411 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
29997366 AACTAGGAGG
29997376 AGGAA AGGGAA AGGAA AGGAA AGGAA AGGAGA AGGA
1 AGGAA A-GGAA AGGAA AGGAA AGGAA AGGA-A AGGA
29997412 GGATACACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:29998117 original size:34 final size:32
Alignment explanation
Indices: 29998072--29998138 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
29998062 TTATACTATA
* * *
29998072 AAATATTTATTATTTATATATTTATAATTGTAAT
1 AAATATCTATTATTAAAATATTTAT-ATTG-AAT
29998106 AAATATCTATTATTAAAATATTTATATTGAAT
1 AAATATCTATTATTAAAATATTTATATTGAAT
29998138 A
1 A
29998139 TTTTCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 4 0.13
34 22 0.73
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
AAATATCTATTATTAAAATATTTATATTGAAT
Found at i:29998191 original size:16 final size:16
Alignment explanation
Indices: 29998160--29998196 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29998150 ATGTGAAGAA
29998160 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
29998176 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
29998192 TATTA
1 TATTA
29998197 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:30002941 original size:29 final size:30
Alignment explanation
Indices: 30002879--30002947 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
30002869 ACTACCAAAA
** *
30002879 TAGTCACTTTTGTTTGTCTCAAGTTATATTT
1 TAGTCACTTTTGTTTG-CAAAAGTTACATTT
*
30002910 TAGTCACTTTTGTTTG-AAAAGTTACGTTT
1 TAGTCACTTTTGTTTGCAAAAGTTACATTT
30002939 TAGTCACTT
1 TAGTCACTT
30002948 ACGTTATCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (30 bp):
TAGTCACTTTTGTTTGCAAAAGTTACATTT
Found at i:30003353 original size:9 final size:9
Alignment explanation
Indices: 30003339--30003363 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30003329 GAAAATAGAG
30003339 GAAGAAGTA
1 GAAGAAGTA
30003348 GAAGAAGTA
1 GAAGAAGTA
30003357 GAAGAAG
1 GAAGAAG
30003364 ATTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (9 bp):
GAAGAAGTA
Found at i:30005851 original size:10 final size:10
Alignment explanation
Indices: 30005833--30005871 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
30005823 TACAACTATT
*
30005833 TTCTTTTCTC
1 TTCTCTTCTC
30005843 TTCTCTTCTC
1 TTCTCTTCTC
*
30005853 TTCTCTTTTC
1 TTCTCTTCTC
30005863 TTCTCTTCT
1 TTCTCTTCT
30005872 TCTACTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTCTTCTC
Found at i:30005856 original size:15 final size:15
Alignment explanation
Indices: 30005833--30005871 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
30005823 TACAACTATT
*
30005833 TTCTTTTCTCTTCTC
1 TTCTCTTCTCTTCTC
*
30005848 TTCTCTTCTCTTTTC
1 TTCTCTTCTCTTCTC
30005863 TTCTCTTCT
1 TTCTCTTCT
30005872 TCTACTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTCTTCTCTTCTC
Found at i:30010882 original size:16 final size:16
Alignment explanation
Indices: 30010861--30010897 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
30010851 ATCACAATAC
30010861 ATAATCTTTTTAACAT
1 ATAATCTTTTTAACAT
30010877 ATAATCTTTTTAACAT
1 ATAATCTTTTTAACAT
30010893 ATAAT
1 ATAAT
30010898 AATATTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATCTTTTTAACAT
Found at i:30013292 original size:34 final size:34
Alignment explanation
Indices: 30013254--30013324 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
30013244 TACAATGTGT
30013254 AAATTTACAACACGAGCAACTTTCTCAATACTAA
1 AAATTTACAACACGAGCAACTTTCTCAATACTAA
30013288 AAATTTACAACACGAGCAACTTTCTCAATACTAA
1 AAATTTACAACACGAGCAACTTTCTCAATACTAA
30013322 AAA
1 AAA
30013325 AAAAAATTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (34 bp):
AAATTTACAACACGAGCAACTTTCTCAATACTAA
Found at i:30018409 original size:46 final size:45
Alignment explanation
Indices: 30018337--30018427 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 45
30018327 GGAGAGGGAA
* *
30018337 AGAGGCTTTATTTTACCATTTTCAACTGAAGTTTTCAGGGGAGCT
1 AGAGACTTTATTTTACCATTTTCAACTGAAGCTTTCAGGGGAGCT
30018382 NAGAGACTTTATTTTACCATTTTCAACTGAAGCTTTCAGGGGAGCT
1 -AGAGACTTTATTTTACCATTTTCAACTGAAGCTTTCAGGGGAGCT
30018428 TCCTCACTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.36
Consensus pattern (45 bp):
AGAGACTTTATTTTACCATTTTCAACTGAAGCTTTCAGGGGAGCT
Found at i:30022653 original size:27 final size:27
Alignment explanation
Indices: 30022619--30022673 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
30022609 AATAACATGC
30022619 ATAATTTTTACTTAGTTTTCTTAGCAT
1 ATAATTTTTACTTAGTTTTCTTAGCAT
30022646 ATAATTTTTACTTAGTTTTCTTAGCAT
1 ATAATTTTTACTTAGTTTTCTTAGCAT
30022673 A
1 A
30022674 CCAATGAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (27 bp):
ATAATTTTTACTTAGTTTTCTTAGCAT
Found at i:30035068 original size:27 final size:27
Alignment explanation
Indices: 30035038--30035137 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 27
30035028 GCAATCTAAT
* *
30035038 CAGAGTACGCTACAAAGGTGATCCATA
1 CAGAGTACACCACAAAGGTGATCCATA
* * * *
30035065 CAGAGTACGCCAGAAATGG-CATCTATA
1 CAGAGTACACCACAAA-GGTGATCCATA
* * * * *
30035092 TAGAGTACACTATAAAGGTGATTCATT
1 CAGAGTACACCACAAAGGTGATCCATA
30035119 CAGAGTACACCACAAAGGT
1 CAGAGTACACCACAAAGGT
30035138 TGACAGGATG
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
26 2 0.04
27 52 0.93
28 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (27 bp):
CAGAGTACACCACAAAGGTGATCCATA
Found at i:30036884 original size:6 final size:6
Alignment explanation
Indices: 30036867--30036896 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30036857 TGTACCTAAA
*
30036867 TGTTAC TATTAC TGTTAC TGTTAC TGTTAC
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC
30036897 CCTACGGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
TGTTAC
Found at i:30040089 original size:19 final size:18
Alignment explanation
Indices: 30040048--30040083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30040038 AAAGGATTGG
*
30040048 GAAATGGAAATGAGATGT
1 GAAATGGAAATGAAATGT
30040066 GAAATGGAATATGAAATG
1 GAAATGGAA-ATGAAATG
30040084 GTAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (18 bp):
GAAATGGAAATGAAATGT
Found at i:30041309 original size:27 final size:27
Alignment explanation
Indices: 30041278--30041331 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
30041268 ACATTTAACC
30041278 AATTCATAATACTCATACAACAAATAA
1 AATTCATAATACTCATACAACAAATAA
30041305 AATTCATAATACTCATACAACAAATAA
1 AATTCATAATACTCATACAACAAATAA
30041332 CTAAGTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (27 bp):
AATTCATAATACTCATACAACAAATAA
Found at i:30042852 original size:26 final size:26
Alignment explanation
Indices: 30042816--30042868 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
30042806 CTATTCCTAA
30042816 GGTTCAAACGAGATTCTTTCTCACAT
1 GGTTCAAACGAGATTCTTTCTCACAT
30042842 GGTTCAAACGAGATTCTTTCTCACAT
1 GGTTCAAACGAGATTCTTTCTCACAT
30042868 G
1 G
30042869 TACATAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (26 bp):
GGTTCAAACGAGATTCTTTCTCACAT
Found at i:30044950 original size:32 final size:31
Alignment explanation
Indices: 30044874--30044936 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
30044864 TAAGGTCCCA
30044874 TAAATTCATTTTAAGGGTTGTAAAAGTATTT
1 TAAATTCATTTTAAGGGTTGTAAAAGTATTT
30044905 TAAATTCATTTTAAGGGTTGTAAAAGTATTT
1 TAAATTCATTTTAAGGGTTGTAAAAGTATTT
30044936 T
1 T
30044937 TACTCTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (31 bp):
TAAATTCATTTTAAGGGTTGTAAAAGTATTT
Found at i:30048570 original size:141 final size:141
Alignment explanation
Indices: 30048316--30048595 Score: 488
Period size: 141 Copynumber: 2.0 Consensus size: 141
30048306 ACTATTAGTT
* * *
30048316 TGTCGAAACCATTCTTTTGAAAACGGGGATCAACTTTGTTTGAAAGTGAAAATTAAAACGGGAGT
1 TGTCGAAACCATTCTGTTGAAAACAGGGATCAACTTTGTTTGAAAGTGAAAATTAAAACAGGAGT
*
30048381 CGCCACCAATCTTTTATCAGGTGTGATCGGATCACCTTTGTTTTAATAAATCAATTTTAGTTTAC
66 CACCACCAATCTTTTATCAGGTGTGATCGGATCACCTTTGTTTTAATAAATCAATTTTAGTTTAC
30048446 TAAAACAGGAC
131 TAAAACAGGAC
* *
30048457 TGTCGAAACCATTCTGTTGAAAACAGGGATCGACTTTGTTTGAAAGTGAAAATTAAAATAGGAGT
1 TGTCGAAACCATTCTGTTGAAAACAGGGATCAACTTTGTTTGAAAGTGAAAATTAAAACAGGAGT
* *
30048522 CACCACCAATCTTTTATCAGGTGTGATCGGATCACCTTTGTTTTAATAAATCAATTTTCGTTTCC
66 CACCACCAATCTTTTATCAGGTGTGATCGGATCACCTTTGTTTTAATAAATCAATTTTAGTTTAC
30048587 TAAAACAGG
131 TAAAACAGG
30048596 GCCTTTGGTC
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 131 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (141 bp):
TGTCGAAACCATTCTGTTGAAAACAGGGATCAACTTTGTTTGAAAGTGAAAATTAAAACAGGAGT
CACCACCAATCTTTTATCAGGTGTGATCGGATCACCTTTGTTTTAATAAATCAATTTTAGTTTAC
TAAAACAGGAC
Found at i:30049344 original size:25 final size:23
Alignment explanation
Indices: 30049292--30049346 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
30049282 TATAAATAGT
30049292 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
30049315 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
30049340 AATAGTG
1 AATAGTG
30049347 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:30049526 original size:25 final size:25
Alignment explanation
Indices: 30049412--30049621 Score: 100
Period size: 25 Copynumber: 8.6 Consensus size: 25
30049402 ATATAAAAAA
* * * *
30049412 ATATGTACATAATATAGTGTAAAAA
1 ATATATACATAATATAGTATTAAAG
*
30049437 ATACATACATAATATA--ATTAAA-
1 ATATATACATAATATAGTATTAAAG
* ** *
30049459 ATATATACATAAGATAACATGTAAAAAAAAT
1 ATATATACAT-A-AT-ATA-GT--ATTAAAG
*
30049490 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
30049515 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
30049540 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
30049564 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
30049586 A-ATATATATAATATAATATTAAA-
1 ATATATACATAATATAGTATTAAAG
*
30049609 AAATATA-ATAATA
1 ATATATACATAATA
30049622 ACAAAAAAAA
Statistics
Matches: 142, Mismatches: 28, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
21 1 0.01
22 24 0.17
23 26 0.18
24 16 0.11
25 54 0.38
26 1 0.01
27 2 0.01
28 2 0.01
29 2 0.01
30 5 0.04
31 9 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:30049603 original size:50 final size:50
Alignment explanation
Indices: 30049483--30049604 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 50
30049473 TAACATGTAA
*
30049483 AAAAAATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGT
1 AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
* * ** * * * *
30049533 ATAATATATATATACGTAATATAGAATT-TAGA-ATATACCTAATATATT
1 AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
30049581 AAAAGAATATATATAATATAATAT
1 AAAA-AATATATATAA-ATAATAT
30049605 TAAAAAATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
48 16 0.28
49 12 0.21
50 29 0.51
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (50 bp):
AAAAAATATATATAAATAATATAGAATTAAAGATATATACATAAAATAGT
Found at i:30049899 original size:16 final size:16
Alignment explanation
Indices: 30049861--30049899 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30049851 TCTCCAAAAA
*
30049861 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
30049877 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
30049893 AATAACT
1 AAAAACT
30049900 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Done.