Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008490.1 Hibiscus syriacus cultivar Beakdansim tig00111332_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: 604809
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:442773 original size:5 final size:5
Alignment explanation
Indices: 442763--442815 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
442753 AACGGTCAAC
* *
442763 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
442812 GGTC
1 GGTC
442816 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:442778 original size:17 final size:17
Alignment explanation
Indices: 442756--442816 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
442746 AACGGTCAAC
442756 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
442773 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
442795 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
442812 GGTCA
1 GGTCA
442817 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:442783 original size:7 final size:7
Alignment explanation
Indices: 442736--442766 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
442726 GTCAAAGAAA
442736 GTCAACG
1 GTCAACG
442743 GTCAACG
1 GTCAACG
442750 GTCAACG
1 GTCAACG
442757 GTCAACG
1 GTCAACG
442764 GTC
1 GTC
442767 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:442791 original size:22 final size:22
Alignment explanation
Indices: 442749--442815 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
442739 AACGGTCAAC
*
442749 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
442773 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
442795 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
442816 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:442849 original size:28 final size:27
Alignment explanation
Indices: 442812--442900 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
442802 GGTCGGGTCG
* * *
442812 GGTCAGACCGGTCAAACCGATTCAGACC
1 GGTCAAACCGGTCAAACCG-GTCAAACC
*
442840 GGTCAAACCGGTTGAAACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
*
442868 GGTCAGAACCGGTTGAAAACCGGTCAAACC
1 GGTCA-AACCGG-T-CAAACCGGTCAAACC
442898 GGT
1 GGT
442901 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
28 21 0.40
29 15 0.28
30 17 0.32
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:442857 original size:10 final size:9
Alignment explanation
Indices: 442812--442900 Score: 88
Period size: 9 Copynumber: 9.3 Consensus size: 9
442802 GGTCGGGTCG
*
442812 GGTCAGACC
1 GGTCAAACC
442821 GGTCAAACC
1 GGTCAAACC
* *
442830 GATTCAGACC
1 G-GTCAAACC
442840 GGTCAAACC
1 GGTCAAACC
*
442849 GGTTGAAACC
1 GG-TCAAACC
442859 GGTCAAACC
1 GGTCAAACC
442868 GGTCAGAACC
1 GGTCA-AACC
*
442878 GGTTGAAAACC
1 GG-T-CAAACC
442889 GGTCAAACC
1 GGTCAAACC
442898 GGT
1 GGT
442901 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
9 36 0.55
10 22 0.33
11 7 0.11
12 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:442869 original size:19 final size:19
Alignment explanation
Indices: 442818--442900 Score: 89
Period size: 19 Copynumber: 4.3 Consensus size: 19
442808 GTCGGGTCAG
* *
442818 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
442837 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAA
442856 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTCA-A
*
442875 ACCGGTTGAAAACCGG-TCAA
1 ACCGG-T-CAAACCGGTTCAA
442895 ACCGGT
1 ACCGGT
442901 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
18 2 0.04
19 37 0.66
20 7 0.12
21 10 0.18
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:442890 original size:30 final size:28
Alignment explanation
Indices: 442837--442900 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 28
442827 ACCGATTCAG
442837 ACCGGTCAAACCGGTTGAAACCGGTCAA
1 ACCGGTCAAACCGGTTGAAACCGGTCAA
442865 ACCGGTCAGAACCGGTTGAAAACCGGTCAA
1 ACCGGTCA-AACCGGTTG-AAACCGGTCAA
442895 ACCGGT
1 ACCGGT
442901 TTCCAGCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 8 0.24
29 9 0.26
30 17 0.50
ACGTcount: A:0.31, C:0.28, G:0.27, T:0.14
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTGAAACCGGTCAA
Found at i:442899 original size:20 final size:21
Alignment explanation
Indices: 442863--442901 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
442853 GAAACCGGTC
442863 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
442884 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
442902 TCCAGCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:445430 original size:2 final size:2
Alignment explanation
Indices: 445423--445452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
445413 TCGTCCACAT
445423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
445453 GTTTGCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:445591 original size:72 final size:72
Alignment explanation
Indices: 445479--445760 Score: 258
Period size: 72 Copynumber: 3.9 Consensus size: 72
445469 TGAAAATACG
* * * *
445479 TATATAATAT-GAAGTTTTCAAAACATTTTTGAAAAAATATATTATATAGTTTTTAAAACATTTT
1 TATATAATATATAATTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTTTAAAACATTTT
445543 TAAAAAT
66 TAAAAAT
* *
445550 TATATAATATATAATTTTTTAAAACATTTTTGAAAATATATATAATATATAATTTTTGAAAAAAT
1 TATATAATATATAATTTTTTAAAACATTTTTGAAAATATATAT--TATATAGTTTTT---AAAAC
445615 ATTTTTAAAAA-
61 ATTTTTAAAAAT
* * ** *
445626 CATAT-A-ATAT-A-GTTTTAAAACATTTTTGAAAACTATATAACATATAG-TTTAAAAACATTT
1 TATATAATATATAATTTTTTAAAACATTTTTGAAAA-TATATATTATATAGTTTTTAAAACATTT
*
445686 TTTAAAAT
65 TTAAAAAT
* * ** * *
445694 TTTATAATATATGATTTTAAAAAATATTTTTG-AAATGTATATTATATA-TAGTTTTAAAACAAT
1 TATATAATATATAATTTTTTAAAACATTTTTGAAAATATATATTATATAGT--TTTTAAAAC-AT
445757 TTTT
63 TTTT
445761 TAGTATATGT
Statistics
Matches: 171, Mismatches: 24, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
67 14 0.08
68 3 0.02
69 1 0.01
70 17 0.10
71 19 0.11
72 69 0.40
73 13 0.08
74 15 0.09
75 1 0.01
76 4 0.02
77 15 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (72 bp):
TATATAATATATAATTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTTTAAAACATTTT
TAAAAAT
Found at i:445774 original size:35 final size:34
Alignment explanation
Indices: 445491--445776 Score: 150
Period size: 35 Copynumber: 8.0 Consensus size: 34
445481 TATAATATGA
* * *
445491 AGTTTTCAAAACATTTTTGAAAAAATA-TATTATAT
1 AGTTTT-AAAACATTTTTTAATATATATTA-TATAT
* * *
445526 AGTTTTTAAAACATTTTTAAAAATTATATAATATAT
1 AG-TTTTAAAACATTTTTTAATA-TATATTATATAT
* * *
445562 AATTTTTTAAAACATTTTTGAAAATATATATAATATAT
1 -A-GTTTTAAAACATTTTT--TAATATATATTATATAT
* * * *
445600 AATTTTTGAAAAAATATTTTTAA-AAACA-TATAATAT
1 -AGTTTT-AAAACAT-TTTTTAATATATATTAT-ATAT
* * * *
445636 AGTTTTAAAACATTTTTGAAAACTATATAACATAT
1 AGTTTTAAAACATTTTTTAATA-TATATTATATAT
* *
445671 AGTTTAAAAACATTTTTTAA-A-ATTTTATAATAT
1 AGTTTTAAAACATTTTTTAATATATATTAT-ATAT
* *
445704 ATGATTTTAAAAAATATTTTTGAAATGTATATTATATAT
1 A-G-TTTTAAAACAT-TTTTT--AATATATATTATATAT
* *
445743 AGTTTTAAAACAATTTTTTAGTATATGTTATATA
1 AGTTTTAAAAC-ATTTTTTAATATATATTATATA
445777 GTTTTTATTT
Statistics
Matches: 199, Mismatches: 30, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
32 4 0.02
33 11 0.06
34 9 0.05
35 69 0.35
36 25 0.13
37 37 0.19
38 25 0.13
39 13 0.07
40 6 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (34 bp):
AGTTTTAAAACATTTTTTAATATATATTATATAT
Found at i:447169 original size:5 final size:5
Alignment explanation
Indices: 447154--447186 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
447144 CTCTTTAATA
447154 TTTATT TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TT
447187 CATCTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:452877 original size:249 final size:245
Alignment explanation
Indices: 452290--454640 Score: 2159
Period size: 249 Copynumber: 9.5 Consensus size: 245
452280 TTTAAGACAA
* * *
452290 CATTTGTAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGATCCTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-A-CAAAGACCCTCGAGTTCGATTAC
* * * * *
452355 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAA
63 ACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AA
* * * *
452420 AGACCTTCAAGTTCGACTACGCTCGGCTCCAAGGCATATCATTTGCAGCATAACTTAAATCGAGA
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
*
452485 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
191 AGGGTTATCTG-C--CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * *
452543 CATTTGCAGCACAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCCCCGAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACT
* *
452607 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGA
66 CAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGA
* *
452672 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGG
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* ** * * * ** *
452737 GCTATCTG-CCAAAGACCCCCAAGTTCGATTACACTCAACTTTGAGGGCACAT
194 GTTATCTGCCCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACAT
* * * * * * * *
452789 CATTTACAGCATAACTCAACTCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGAGTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAC--AAAGACCCTCGAGTTCGATTAC
* * ** * * ** * ** * * *
452854 GCTCAGCTCCAAGGCATATCATTTGTAACATAACTTAAATCGAGAAATGTTATATGCCAACTAAA
63 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAA
** * * *
452919 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTGCATCATTTGCAGTATAGCTTAAGTCGATAA
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * * * * *
452984 GGGATATCTG-CCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACAG
192 GGGTTATCTGCCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACAT
* * * * * * * * * *
453038 CATTTACAGTATAACTCAAGGCTATAAGGGTTATCTTTCACCAAAGACCATCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC-TGCA-CAAAGACCCTCGAGTTCGATTACA
* * * * * * *
453103 CTCAGCTCCAAGGCACATTATTTGCAGTA-AAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
64 CTCAGCTCCAAGGCACATCATTTACAGCATAA-CTCAAGGCTAGAAGGGTTATCTGTCACCAAAG
* * * * * * * * * *
453164 ACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
128 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* *
453229 GGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
192 GGGTTATCTG-C-CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * *
453285 CATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCCTCAAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACT
* *
453349 CAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGATATCTGTCACCAAAAGA
66 CAGCTCCAA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGA
* * *
453414 CCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAATCGAGAAGG
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * * * * **
453479 ATTATCTTCCAACTAAAGACCTTCGAGTTCGACTACGCTCTGCTCCAAAGCGTAT
194 GTTATCTGCC--C-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * *
453534 TATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCC-CAGAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCTC-GAGTTCGATTACAC
* * * * * *
453597 TCAGCTTCGAGGGCACATCATTTATAACATAACTCATGGCTAGAAGGGTTATCTGTCACTAAAAG
65 TCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC-CAAAG
* * * * *
453662 ACCTTCGAGTTTGACTACGGTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAATTGAGAAG
128 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* * *
453727 GGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGACGCAT
193 GGTTATCTGCC--C-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * *
453783 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGC-CAAAGACCCTCAAGTTTGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACT
* * * *
453847 CAGCTTCGAGGGTACATCATTTACAGCATAACTCATGGCTAGAAGGGTTATCTGTCACCAAAGAC
66 CAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGAC
* * *
453912 CTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAAAACTTAAGTCGAGAAGGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * * * *
453977 CTATCTG-CCAAAGACCCTCAAGTTCAATTACACTCAGCTTCGAGGACACAT
195 TTATCTGCCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGG-CACAT
* * * * * * * * *
454028 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGCCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CA-CAAAGACCCTCGAGTTCGATTACA
* * * * * * * * *
454093 CTCAGTTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGA
64 CTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGA
* * * * * * * * * * *
454155 CCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGAATAACTCAAGGCTAGAAG
129 CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* *
454220 GGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
193 GGTTATCTG-C-CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * * *
454276 AATTTGCTGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-A-CAAAGACCCTCGAGTTCGATTAC
* * * * * * * *
454341 GCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
63 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAG
** * * ** * * * * * *
454403 ACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATTATTTACAGCATAACTCAAGGCTAGAA
128 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* * * * * * *
454468 GGTTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGTATAG
192 GGGTTATCTG-C-CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * ** * **
454525 CATTTGCAGCATAGCTTAAGGCTAGAAGGACTATCTGC-CAAAGA-CCTCCGAGTTCGACTATGC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCT-CGAGTTCGATTACAC
* * * *
454588 TCAGCTCCAAGGCACATCATTTACAGCATAGCCCAAGGCAAGAAGGGCTATCT
65 TCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT
454641 ATCAATAAAA
Statistics
Matches: 1777, Mismatches: 283, Indels: 84
0.83 0.13 0.04
Matches are distributed among these distances:
244 113 0.06
245 239 0.13
246 45 0.03
247 73 0.04
248 268 0.15
249 976 0.55
250 30 0.02
252 1 0.00
253 32 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (245 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACAAAGACCCTCGAGTTCGATTACACT
CAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
TATCTGCCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
Found at i:453103 original size:164 final size:164
Alignment explanation
Indices: 452290--454640 Score: 2090
Period size: 164 Copynumber: 14.2 Consensus size: 164
452280 TTTAAGACAA
* * * * *
452290 CATTTGTAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGATCCTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCAAGTTCGATTAC
* * * *
452355 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AA
* * *
452420 AGACCTTCAAGTTCGACTACGCTCGGCTCCAAGGCATAT
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
452459 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCAAGTTCGATTAC
* * * * * * * * *
452524 GCTCAGCTCCAA-GGCACATCATTTGCAGCACAGCTTAAGTCGAGAAGGGCTATCTG---CCAAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
** * * * *
452585 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
127 GACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
* * * * * * * *
452624 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCAAGTTCGATTAC
* * * * * * * * *
452689 GCTCAGCTCCAA-GGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
** * * * * ** *
452750 GACCCCCAAGTTCGATTACACTCAACTTTGAGGGCACAT
127 GACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
* * * * * * * * * *
452789 CATTTACAGCATAACTCAACTCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGAGTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C-C--AAAGACCCTCAAGTTCGATTAC
* * * ** * * ** * ** * * *
452854 GCTCAGCTCCAA-GGCATATCATTTGTAACATAACTTAAATCGAGAAATGTTATATGCCAACTAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAA
**
452918 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTGCAT
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
452957 CATTTGCAGTATAGCTTAAGTCGATAAGGGATATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
* * * *
453022 AGCTTCAAGGGCACAGCATTTACAGTATAACTCAAGGCTATAAGGGTTATCTTTCACCAAAGACC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
*
453087 ATCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
453121 TATTTGCAGTA-AAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACT
1 CATTTGCAGCATAA-CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACT
*
453185 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGAC
65 CAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGAC
*
453250 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
453285 CATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
*
453350 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGATATCTGTCACCAAAAGAC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGAC
* *
453415 CTTCGAGTTCGACTACGCTCAACTCCAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* ** * * * *
453450 CATTTGCAGCATAACTTAAATCGAGAAGGATTATCTTCCAACTAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC-TGC--C-AAAGACCCTCAAGTTCGATTAC
* * * * ** * ** * * * * *
453515 GCTCTGCTCCAA-AGCGTATTATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
* * * * *
453576 GACC-CCAGAGTTCGATTACACTCAGCTTCGAGGGCACAT
127 GACCTTC-GAGTTCGACTACGCTCAGC-TCCAAGGCACAT
** * * * * * * * * * *
453615 CATTTATAACATAACTCATGGCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C-C--AAAGACCCTCAAGTTCGATTAC
** * * * * ** * *
453680 GGTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAA-ATTGAGAAGGGTTATCTGCCAACTA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGTC-ACCA
* * * *
453743 AAGACCTTCGAGTTCGACTACACTCAGCTTCAAGACGCAT
125 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
*
453783 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTTGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
* * *
453848 AGCTTCGAGGGTACATCATTTACAGCATAACTCATGGCTAGAAGGGTTATCTGTCACCAAAGACC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
* *
453913 TTTGAGTTCAACTACGCTCAGCTCCAAGGCACAT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
453947 CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCAATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
* * * *
454012 AGCTTCGAGGACACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGCC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
* *
454077 TTCGAGTTCGACTACGCTCAGTTCCAAGGCATAT
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
454111 CATTTGCACCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
* *
454176 AGCTTCGAGGGCACATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
66 AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGAC
*
454241 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * * *
454276 AATTTGCTGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCAAGTTCGATTAC
* * * * * * * * *
454341 GCTCAACTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAA
62 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
** * * ** *
454402 GACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACAT
127 GACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
* * * * * ** * * * *
454441 TATTTACAGCATAACTCAAGGCTAGAAGGTTTATATGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTCAAGTTCGATTAC
* * * * * * * **
454506 GCTCAGC-TCTAA-GGTATAGCATTTGCAGCATAGCTTAAGGCTAGAAGGACTATCTG---CCAA
62 ACTCAGCTTC-AAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAA
* *
454566 AGACCTCCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * ** * *
454605 CATTTACAGCATAGCCCAAGGCAAGAAGGGCTATCT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT
454641 ATCAATAAAA
Statistics
Matches: 1854, Mismatches: 292, Indels: 77
0.83 0.13 0.03
Matches are distributed among these distances:
163 3 0.00
164 785 0.42
165 704 0.38
166 5 0.00
167 2 0.00
168 177 0.10
169 177 0.10
170 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
AGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:454009 original size:826 final size:826
Alignment explanation
Indices: 452290--454640 Score: 3403
Period size: 826 Copynumber: 2.8 Consensus size: 826
452280 TTTAAGACAA
* * * * * *
452290 CATTTGTAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGATCCTCGAGTTCGATTAC
1 CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCAAGTTCGATTAC
* * *
452355 ACTCAGCTTCGAGGGCATATCATTTATAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAA
62 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AA
* * * * *
452420 AGACCTTCAAGTTCGACTACGCTCGGCTCCAAGGCATATCATTTGCAGCATAACTTAAATCGAGA
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGA
* * * * * * *
452485 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTG
191 AGGGCTATCTG----CCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTA
* * * * * * ** * *
452549 CAGCACAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCCCGAGTTCGATTACACTCAG
252 CAGCATAACTCAAGGCTAGAAGGGATATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * * ** * *
452610 CTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-CACCAAAAGACC
317 C-TCCAAGGCATATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCT-TCCAACAAAAGACC
452674 TTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
380 TTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
*
452739 TATCTGCCAAAGACCCCCA-AGTTCGATTACACTCAACTTTGAGGGCACATCATTTACAGCATAA
445 TATCTGCCAAAGA-CCCCAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAA
** * *
452803 CTCAACTCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGAGTATGCTCAGCTCCAAGG
509 CTCAAGGCTAGAAGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGG
* * * ** *
452868 CATATCATTTGTAACATAACTTAAATCGAGAAATGTTATATGCCAACTAAAGACCTTCGAGTTCG
574 CATATCATTTGCAGCATAACTTAAATTGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCG
* * * *
452933 ACTACGCTCAGCTCCAAGGTGCATCATTTGCAGTATAGCTTAAGTCGATAAGGGATATCTGCCAA
639 ACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
* *
452998 AGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACAGCATTTACAGTATAACTCAAGGCTAT
704 AGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACAGCATTTACAGCATAACTCAAGGCTAG
* *
453063 AAGGGTTATCTTTCACCAAAGACCATCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
769 AAGGGTTATCTGTCACCAAAGACCATCGAGTTCAACTACGCTCAGCTCCAAGGCACAT
* * *
453121 TATTTGCAGTAAAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
453186 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
66 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
453251 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGC
453316 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
196 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
*
453381 TCAAGGCTAGAAGGGATATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGC
261 TCAAGGCTAGAAGGGATATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* *
453446 ATATCATTTGCAGCATAACTTAAATCGAGAAGGATTATCTTCCAACTAAAGACCTTCGAGTTCGA
326 ATATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGA
* * * * *
453511 CTACGCTCTGCTCCAAAGCGTATTATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
391 CTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
* * * *
453576 GACCCCAGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAACATAACTCATGGCTAGA
456 GACCCCAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGA
*
453641 AGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTACGGTCAGCTCCAAGGCATATCATTTGC
521 AGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGC
*
453706 AGCATAACTTAAATTGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACACTCAGC
586 AGCATAACTTAAATTGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGC
* * *
453771 TTCAAGACGCATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGT
651 TCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGT
* * * * *
453836 TTGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCATGGCTAGAAGGGTTATCTG
716 TCGATTACACTCAGCTTCAAGGGCACAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
* *
453901 TCACCAAAGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACAT
781 TCACCAAAGACCATCGAGTTCAACTACGCTCAGCTCCAAGGCACAT
*
453947 CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCAATTACACTC
1 CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
* * *
454012 AGCTTCGAGGACACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGCC
66 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
*
454077 TTCGAGTTCGACTACGCTCAGTTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGC
* *
454142 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGAATAAC
196 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
*
454207 TCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
261 TCAAGGCTAGAAGGGATATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * *
454272 ATATAATTTGCTGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
326 ATATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGA
* *
454337 CTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
391 CTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
* *
454402 GACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATTATTTACAGCATAACTCAAGGCTAGA
456 GACCCCAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGA
* * * * * * *
454467 AGGTTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGTATAGCATTTGC
521 AGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGC
* ** ** * *
454532 AGCATAGCTTAAGGCT-AGAAGGACTATCTG-C--C-AAAGACCTCCGAGTTCGACTATGCTCAG
586 AGCATAACTTAA-ATTGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAG
* * ** * *
454592 CTCCAAGGCACATCATTTACAGCATAGCCCAAGGCAAGAAGGGCTATCT
650 CTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
454641 ATCAATAAAA
Statistics
Matches: 1371, Mismatches: 141, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
822 96 0.07
823 38 0.03
825 7 0.01
826 1094 0.80
827 106 0.08
831 30 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (826 bp):
CATTTGCAGCAAAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCACCATAGCTTAAGTCGAGAAGGGC
TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAAC
TCAAGGCTAGAAGGGATATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ATATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
GACCCCAGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGA
AGGGTTATCTGTCACTAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGC
AGCATAACTTAAATTGAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGT
TCGATTACACTCAGCTTCAAGGGCACAGCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
TCACCAAAGACCATCGAGTTCAACTACGCTCAGCTCCAAGGCACAT
Found at i:455208 original size:35 final size:34
Alignment explanation
Indices: 455159--455442 Score: 173
Period size: 35 Copynumber: 7.9 Consensus size: 34
455149 GAAAATAAGT
* * *
455159 ATATAATATGTAGTTTTCAAAACATTTTTGACAAA
1 ATATATTATATAGTTTTAAAAACATTTTTGA-AAA
*
455194 ATATATTATATAGTTTTTAAAACATTTTT-AAAA
1 ATATATTATATAGTTTTAAAAACATTTTTGAAAA
* *
455227 ATTATATAATATATAATTTTTTAAAACATTTTTGAAAA
1 A-TATAT--TATAT-AGTTTTAAAAACATTTTTGAAAA
*
455265 TATATATAATATATAATTTTTGAAAAAAAACATTTTT-AAAA
1 -ATATAT--TATAT-AGTTTT----AAAAACATTTTTGAAAA
* *
455306 ACATATAATATAGTTTT-AAAACATTTTTGAAAA
1 ATATATTATATAGTTTTAAAAACATTTTTGAAAA
** *
455339 CTATATAACATATAG-TTTAAAAACATTTTTTTAAAA
1 --ATATATTATATAGTTTTAAAAACA-TTTTTGAAAA
* * * * *
455375 TTTTATAATATATGATTTTAAAAAATATTTTTGAAAT
1 ATATATTATATA-G-TTTT-AAAAACATTTTTGAAAA
*
455412 GTATATTATATATAGTTTT-AAAACAATTTTT
1 ATATA-T-TATATAGTTTTAAAAAC-ATTTTT
455443 TTAGTATATG
Statistics
Matches: 204, Mismatches: 23, Indels: 43
0.76 0.09 0.16
Matches are distributed among these distances:
32 11 0.05
33 8 0.04
34 17 0.08
35 47 0.23
36 20 0.10
37 40 0.20
38 35 0.17
39 6 0.03
40 5 0.02
41 4 0.02
42 11 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (34 bp):
ATATATTATATAGTTTTAAAAACATTTTTGAAAA
Found at i:455241 original size:36 final size:36
Alignment explanation
Indices: 455158--455442 Score: 230
Period size: 37 Copynumber: 7.8 Consensus size: 36
455148 TGAAAATAAG
* *
455158 TATATAATATGTAGTTTTCAAAACATTTTTGACAAAA-
1 TATATAATATATAGTTTTTAAAACATTTTT-A-AAAAT
455195 TATAT--TATATAGTTTTTAAAACATTTTTAAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAT
* *
455229 TATATAATATATAATTTTTTAAAACATTTTTGAAAAT
1 TATATAATATAT-AGTTTTTAAAACATTTTTAAAAAT
*
455266 ATATATAATATATAATTTTTGAAAAAAAACATTTTTAAAAA-
1 -TATATAATATATAGTTTTT-----AAAACATTTTTAAAAAT
* * *
455307 CATAT-A-ATATAG-TTTTAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAT
* * *
455340 TATATAACATATAG-TTTAAAAACATTTTTTTAAAAT
1 TATATAATATATAGTTTTTAAAACA-TTTTTAAAAAT
* * * **
455376 TTTATAATATAT-GATTTTAAAAAATATTTTTGAAAT
1 TATATAATATATAGTTTTTAAAACAT-TTTTAAAAAT
*
455412 GTATATTATATATAG-TTTTAAAACAATTTTT
1 -TATATAATATATAGTTTTTAAAAC-ATTTTT
455443 TTAGTATATG
Statistics
Matches: 208, Mismatches: 21, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
32 15 0.07
33 8 0.04
34 7 0.03
35 38 0.18
36 41 0.20
37 59 0.28
38 20 0.10
39 1 0.00
40 4 0.02
42 15 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTAAAAAT
Found at i:455265 original size:111 final size:106
Alignment explanation
Indices: 455144--455442 Score: 282
Period size: 111 Copynumber: 2.7 Consensus size: 106
455134 TTGCAAATGG
* * * *
455144 TTTTTGAAAATAAGTATATAATATGT-AGTTTT-CAAAACATTTTTGACAAAATATATTATATAG
1 TTTTTGAAAAT-A-TATATAATATATAAGTTTTAAAAAACATTTTT-A-AAAACATATAATATAG
* * * *
455207 TTTTTAAAACATTTTTAAAAATTATATAATATATAATTTTTTAAAACA
62 -TTTTAAAACATTTTTAAAAACTATATAACATAT-A-GTTTAAAAACA
*
455255 TTTTTGAAAATATATATAATATATAATTTTTGAAAAAAAACATTTTTAAAAACATATAATATAGT
1 TTTTTGAAAATATATATAATATATAAGTTTT---AAAAAACATTTTTAAAAACATATAATATAGT
*
455320 TTTAAAACATTTTTGAAAACTATATAACATATAGTTTAAAAACA
63 TTTAAAACATTTTTAAAAACTATATAACATATAGTTTAAAAACA
* * * * ***
455364 TTTTTTTAAAAT-TTTATAATATATGA-TTTTAAAAAATATTTTTGAAATGTATATTATATATAG
1 -TTTTTGAAAATATATATAATATATAAGTTTTAAAAAACATTTTT-AAAAACATA-TA-ATATAG
455427 TTTTAAAACAATTTTT
62 TTTTAAAAC-ATTTTT
455443 TTAGTATATG
Statistics
Matches: 161, Mismatches: 17, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
105 12 0.07
106 6 0.04
107 2 0.01
108 19 0.12
109 38 0.24
110 17 0.11
111 41 0.25
112 14 0.09
113 1 0.01
114 11 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (106 bp):
TTTTTGAAAATATATATAATATATAAGTTTTAAAAAACATTTTTAAAAACATATAATATAGTTTT
AAAACATTTTTAAAAACTATATAACATATAGTTTAAAAACA
Found at i:455312 original size:40 final size:36
Alignment explanation
Indices: 455158--455442 Score: 189
Period size: 36 Copynumber: 7.9 Consensus size: 36
455148 TGAAAATAAG
* * *
455158 TATATAATATGT-AGTTTTCAAAACATTTTTGACAAAA
1 TATATAATATATAATTTTTAAAAACATTTTT-A-AAAA
*
455195 TATAT--TATATAGTTTTT-AAAACATTTTTAAAAA
1 TATATAATATATAATTTTTAAAAACATTTTTAAAAA
*
455228 TTATATAATATATAATTTTTTAAAACATTTTTGAAAATA
1 -TATATAATATATAATTTTTAAAAACATTTTT-AAAA-A
455267 TATATAATATATAATTTTTGAAAAAAAACATTTTTAAAAA
1 TATATAATATATAATTTTT----AAAAACATTTTTAAAAA
* * *
455307 CATAT-A-ATAT-AGTTTT-AAAACATTTTTGAAAAC
1 TATATAATATATAATTTTTAAAAACATTTTT-AAAAA
* * *
455340 TATATAACATAT-A-GTTTAAAAACATTTTTTTAAAAT
1 TATATAATATATAATTTTTAAAAACA--TTTTTAAAAA
* * * * *
455376 TTTATAATATATGATTTTAAAAAATATTTTT-GAAA
1 TATATAATATATAATTTTTAAAAACATTTTTAAAAA
* * *
455411 TGTATATTATATATAGTTTT-AAAACAATTTTT
1 TATATAATATATA-ATTTTTAAAAAC-ATTTTT
455443 TTAGTATATG
Statistics
Matches: 203, Mismatches: 24, Indels: 43
0.75 0.09 0.16
Matches are distributed among these distances:
32 11 0.05
33 12 0.06
34 10 0.05
35 42 0.21
36 44 0.22
37 27 0.13
38 35 0.17
39 2 0.01
40 5 0.02
41 4 0.02
42 11 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATAATATATAATTTTTAAAAACATTTTTAAAAA
Found at i:455382 original size:147 final size:147
Alignment explanation
Indices: 455159--455430 Score: 363
Period size: 147 Copynumber: 1.8 Consensus size: 147
455149 GAAAATAAGT
** *
455159 ATATAATATGTAGTTTTCAAAACATTTTTGACAAAATATATTATATAGTTTTTAAAACATTTTTA
1 ATATAATA-GTAGTTTTCAAAACATTTTTGACAAAATATAACATATAGTTTTAAAAACATTTTTA
**
455224 AAAATTATATAATATATAATTTTTTAAAACATTTTTGAAAATATATATAATATATAATTTTTGAA
65 AAAATTATATAATATATAATTTTAAAAAACATTTTTG-AAATATATATAATATATAATTTTTGAA
455289 AAAAAACATTTTTAAAAAC
129 AAAAAACATTTTTAAAAAC
455308 ATATAATA-TAGTTTT-AAAACATTTTTGA-AAACTATATAACATATAG-TTTAAAAACATTTTT
1 ATATAATAGTAGTTTTCAAAACATTTTTGACAAA--ATATAACATATAGTTTTAAAAACA-TTTT
* * * * * * *
455369 TTAAAATTTTATAATATATGATTTTAAAAAATATTTTTGAAATGTATATTATATATAGTTTT
63 TAAAAATTATATAATATATAATTTTAAAAAACATTTTTGAAATATATATAATATATAATTTT
455431 AAAACAATTT
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
145 3 0.03
146 42 0.39
147 55 0.51
149 8 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (147 bp):
ATATAATAGTAGTTTTCAAAACATTTTTGACAAAATATAACATATAGTTTTAAAAACATTTTTAA
AAATTATATAATATATAATTTTAAAAAACATTTTTGAAATATATATAATATATAATTTTTGAAAA
AAAACATTTTTAAAAAC
Found at i:455457 original size:36 final size:35
Alignment explanation
Indices: 455313--455459 Score: 95
Period size: 35 Copynumber: 4.1 Consensus size: 35
455303 AAAACATATA
** * * *
455313 ATATAGTTTTAAAAC-ATTTTTGAAAACTATATAAC
1 ATATAGTTTTAAAACAATTTTTTTATA-TATATTAT
* * *
455348 ATATAGTTTAAAAAC-ATTTTTTTA-AAATTTTAT
1 ATATAGTTTTAAAACAATTTTTTTATATATATTAT
* *
455381 AATATATGATTTTAAAA-AATATTTTTGAAATGTATATTAT
1 -ATATA-G-TTTTAAAACAAT-TTTTT--TATATATATTAT
*
455421 ATATAGTTTTAAAACAATTTTTTTAGTATATGTTAT
1 ATATAGTTTTAAAACAATTTTTTTA-TATATATTAT
455457 ATA
1 ATA
455460 GTTTTTATTC
Statistics
Matches: 87, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
33 4 0.05
34 6 0.07
35 23 0.26
36 20 0.23
37 18 0.21
38 4 0.05
39 6 0.07
40 6 0.07
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (35 bp):
ATATAGTTTTAAAACAATTTTTTTATATATATTAT
Found at i:455459 original size:73 final size:73
Alignment explanation
Indices: 455177--455445 Score: 201
Period size: 73 Copynumber: 3.7 Consensus size: 73
455167 TGTAGTTTTC
** * * *
455177 AAAACATTTTTGACAAA--ATATATTATATAGTTTTTAAAACA-TTTTTAAAAATTATATAATAT
1 AAAACATTTTTGA-AAACTATATAACATATAG-TTTAAAAACATTTTTTTAAAATTGTATAATAT
* **
455239 ATAATTTTTT
64 ATGATTTTAA
* * * * ** ***
455249 AAAACATTTTTGAAAATATATATAATATATAATTTTTGAAAAAAAACATTTTTAAAAACATATAA
1 AAAACATTTTTGAAAA-CTATATAACATAT-A-GTTT--AAAAACATTTTTTTAAAATTGTATAA
455314 TATA-G-TTTT--
61 TATATGATTTTAA
*
455323 AAAACATTTTTGAAAACTATATAACATATAGTTTAAAAACATTTTTTTAAAATTTTATAATATAT
1 AAAACATTTTTGAAAACTATATAACATATAGTTTAAAAACATTTTTTTAAAATTGTATAATATAT
455388 GATTTTAA
66 GATTTTAA
* ** * * *
455396 AAAATATTTTTGAAATGTATATTATATATAGTTTTAAAACAATTTTTTTA
1 AAAACATTTTTGAAAACTATATAACATATAGTTTAAAAAC-ATTTTTTTA
455446 GTATATGTTA
Statistics
Matches: 160, Mismatches: 24, Indels: 24
0.77 0.12 0.12
Matches are distributed among these distances:
69 24 0.15
70 1 0.01
71 10 0.06
72 14 0.09
73 45 0.28
74 35 0.22
75 4 0.03
76 4 0.03
77 5 0.03
78 18 0.11
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (73 bp):
AAAACATTTTTGAAAACTATATAACATATAGTTTAAAAACATTTTTTTAAAATTGTATAATATAT
GATTTTAA
Found at i:455825 original size:44 final size:44
Alignment explanation
Indices: 455762--455856 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
455752 AAACGGGGAT
*
455762 CATCGAGAGATATCAACAGTACCAAAACACCCTCAATGAGGAAC
1 CATCGAGAGATATCAACAGTACCAAAACACCCTCAACGAGGAAC
*
455806 CATCGAGAGATATCAACAGTACCAAAACACCCTCAACGGGGAAC
1 CATCGAGAGATATCAACAGTACCAAAACACCCTCAACGAGGAAC
455850 CATCGAG
1 CATCGAG
455857 CCACACAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.41, C:0.28, G:0.18, T:0.13
Consensus pattern (44 bp):
CATCGAGAGATATCAACAGTACCAAAACACCCTCAACGAGGAAC
Found at i:456748 original size:5 final size:5
Alignment explanation
Indices: 456738--456769 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
456728 TAATATTCAT
456738 TTTTA TTTTA TTTTA TTTT- TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
456770 CGTCTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:456762 original size:14 final size:15
Alignment explanation
Indices: 456738--456769 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
456728 TAATATTCAT
456738 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
456753 TTTT-TTTTATTTTA
1 TTTTATTTTATTTTA
456767 TTT
1 TTT
456770 CGTCTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:461874 original size:36 final size:36
Alignment explanation
Indices: 461832--461907 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
461822 TTATAGCTAA
*
461832 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
461868 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
461904 AAAA
1 AAAA
461908 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:466387 original size:15 final size:15
Alignment explanation
Indices: 466369--466398 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
466359 CCACGGTGCT
466369 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
466384 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
466399 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:466862 original size:36 final size:36
Alignment explanation
Indices: 466820--466895 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
466810 TTATAGCTAA
*
466820 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
466856 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
466892 AAAA
1 AAAA
466896 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:475264 original size:20 final size:20
Alignment explanation
Indices: 475205--475265 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
475195 TTTCGCATTG
* *
475205 CGAATCTGTAAATCGCAACG
1 CGAATTTGTAAATCGCAACA
475225 CGAATTTGTAAATCGCAACA
1 CGAATTTGTAAATCGCAACA
*
475245 CGAATTTGTAAATCACAACA
1 CGAATTTGTAAATCGCAACA
475265 C
1 C
475266 AGAAGTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CGAATTTGTAAATCGCAACA
Found at i:475424 original size:22 final size:22
Alignment explanation
Indices: 475399--475449 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
475389 CTACGGCGAC
475399 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
475421 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
475443 ATCCGTC
1 ATCCGTC
475450 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:475846 original size:14 final size:14
Alignment explanation
Indices: 475807--475847 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
475797 CACGAAAATG
* *
475807 AAAATCGCAACACC
1 AAAATCGCAACGCA
475821 AAAATCGCAACGCA
1 AAAATCGCAACGCA
*
475835 AAAATGGCAACGC
1 AAAATCGCAACGC
475848 GATTTTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.49, C:0.29, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGCA
Found at i:478106 original size:21 final size:21
Alignment explanation
Indices: 478082--478152 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
478072 TTCATCATCG
478082 AAGAAGCCCCTCCCACCGTTC
1 AAGAAGCCCCTCCCACCGTTC
* ** *
478103 AAGAGGCCCCTGTCATCGTTC
1 AAGAAGCCCCTCCCACCGTTC
* * * *
478124 AAGAGGTCCCACCCGCCGTTC
1 AAGAAGCCCCTCCCACCGTTC
478145 AAG-AGCCC
1 AAGAAGCCC
478153 GATTCATATG
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
20 3 0.08
21 35 0.92
ACGTcount: A:0.23, C:0.41, G:0.21, T:0.15
Consensus pattern (21 bp):
AAGAAGCCCCTCCCACCGTTC
Found at i:478143 original size:42 final size:42
Alignment explanation
Indices: 478056--478149 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
478046 CGCCTCCTAT
* *
478056 CGTTCAAGAGGCCCCTTTCATCATCGAAGAAGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTGTCATCATCGAAGAAGCCCCACCCAC
* * * *
478098 CGTTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCACCCGC
1 CGTTCAAGAGGCCCCTGTCATC-ATCGAAGAAGCCCCACCCAC
478140 CGTTCAAGAG
1 CGTTCAAGAG
478150 CCCGATTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.19
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTGTCATCATCGAAGAAGCCCCACCCAC
Found at i:479557 original size:69 final size:65
Alignment explanation
Indices: 479477--479647 Score: 213
Period size: 65 Copynumber: 2.6 Consensus size: 65
479467 GGTGTACACT
479477 TTTTTTGCTTGTTTAACTAAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATG-AGGAAATA
1 TTTTTTGCTTGTTTAA-TAAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGTA-GAAATA
479539 AGAATTA
59 AGAATTA
** *
479546 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTATAAATAAGAATTA
1 TTTTTTGCTTGTTTAATAAATTTGTAAAAGTTGATTTGTTTAATTTGATGTAGAAATAAGAATTA
**
479611 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTT
1 TTTTTTGCTTGTTTAATAAATTTGTAAAAGTTGATTT
479648 TTTGTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
64 17 0.18
65 55 0.57
66 1 0.01
67 1 0.01
68 5 0.05
69 17 0.18
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (65 bp):
TTTTTTGCTTGTTTAATAAATTTGTAAAAGTTGATTTGTTTAATTTGATGTAGAAATAAGAATTA
Found at i:479587 original size:64 final size:65
Alignment explanation
Indices: 479508--479647 Score: 248
Period size: 65 Copynumber: 2.2 Consensus size: 65
479498 TTTTACATTG
479508 AAAGTTGATTTGTTTAA-TTGATG-AGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAATTTGATGTA-GAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGT
479571 A
65 A
*
479572 AAAGTTGATTTGTTTAATTTGATGTATAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTTGATGTAGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
479637 AAAGTTGATTT
1 AAAGTTGATTT
479648 TTTGTTTTAA
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
64 17 0.23
65 55 0.75
66 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTTGATGTAGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
Found at i:479802 original size:14 final size:13
Alignment explanation
Indices: 479758--479803 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
479748 GTGAAAGTCA
479758 AATTTGCGTTGCG
1 AATTTGCGTTGCG
479771 ATATTTG-GTTTGCG
1 A-ATTTGCG-TTGCG
479785 -ATTTCGCGTTGCG
1 AATTT-GCGTTGCG
479798 AATTTG
1 AATTTG
479804 ACTTTCGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.14
13 9 0.32
14 15 0.54
ACGTcount: A:0.15, C:0.13, G:0.28, T:0.43
Consensus pattern (13 bp):
AATTTGCGTTGCG
Found at i:480124 original size:18 final size:18
Alignment explanation
Indices: 480101--480136 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
480091 AACTCGGTTG
*
480101 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
480119 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
480137 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:481540 original size:25 final size:25
Alignment explanation
Indices: 481512--481561 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
481502 CATTATTTTC
*
481512 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
481537 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
481562 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:481660 original size:20 final size:21
Alignment explanation
Indices: 481622--481665 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
481612 AGACCTATTG
481622 AAGGTAAACTTTCGCAACGCGA
1 AAGGTAAAC-TTCGCAACGCGA
*
481644 AAGGTAAA-TTCGTAACGCGA
1 AAGGTAAACTTCGCAACGCGA
481664 AA
1 AA
481666 TAAGAGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
AAGGTAAACTTCGCAACGCGA
Found at i:481762 original size:14 final size:14
Alignment explanation
Indices: 481712--481762 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
481702 CAAATTCTCG
*
481712 TTGCGATTTTCGAT
1 TTGCGAATTTCGAT
** *
481726 TTGCGGTTTTCGGT
1 TTGCGAATTTCGAT
*
481740 TTGCG-ATTTCGCT
1 TTGCGAATTTCGAT
481753 TTGCGAATTT
1 TTGCGAATTT
481763 GACTTTCGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.49
Consensus pattern (14 bp):
TTGCGAATTTCGAT
Found at i:481851 original size:14 final size:15
Alignment explanation
Indices: 481815--481852 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
481805 AACATAATTG
481815 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
481830 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
481845 AAAAATTA
1 AAAAATTA
481853 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:482096 original size:20 final size:20
Alignment explanation
Indices: 482068--482134 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
482058 GAAATTCCGC
*
482068 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
482088 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
482108 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
482128 GTTGCGA
1 GTTGCGA
482135 TTTATAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:482109 original size:40 final size:41
Alignment explanation
Indices: 482047--482154 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 41
482037 TTGAAATTCA
* *
482047 GTTGCGAATTTGAAATTCCGCGTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTCTGT
*
482088 GTTGCGAATTTG-ACTAT-CGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAAAT-TCCGCGTTGCGAATTTGACTTCTGT
*
482128 GTTGCG-ATTTATAAATT-CGCGTTGCGA
1 GTTGCGAATTT-GAAATTCCGCGTTGCGA
482155 TTTACAGATT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.07
40 40 0.68
41 15 0.25
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTCTGT
Found at i:482151 original size:20 final size:20
Alignment explanation
Indices: 482128--482174 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
482118 TGACTTCTGT
*
482128 GTTGCGATTTATAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
482148 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
482168 GTTGCGA
1 GTTGCGA
482175 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:487228 original size:18 final size:18
Alignment explanation
Indices: 487205--487252 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
487195 AAATTGCCCT
*
487205 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
487223 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
487240 TATTTATATATTT
1 TA-TTATATATTT
487253 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:509660 original size:15 final size:15
Alignment explanation
Indices: 509640--509671 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
509630 AAAATCTTTC
*
509640 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTAGAT
509655 TTTCCCGTTCTAGAT
1 TTTCCCGTTCTAGAT
509670 TT
1 TT
509672 GGATATGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.25, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTAGAT
Found at i:519007 original size:57 final size:56
Alignment explanation
Indices: 518935--519162 Score: 339
Period size: 57 Copynumber: 4.0 Consensus size: 56
518925 TATAACCATA
* * * * *
518935 CAACCCTGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACTTGCAAGTAAT
1 CAACCC-GTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
518992 CAACCTCATCACGAACAGTAAGGCTCTCAGCACAAAACCGAGGAACCTGCAAGTATT
1 CAACC-CGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
519049 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGTAAGTATT
1 CAA-CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
**
519106 CTTCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
519162 C
1 C
519163 TTCCTCCAAC
Statistics
Matches: 156, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
56 53 0.34
57 100 0.64
58 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (56 bp):
CAACCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:523965 original size:57 final size:57
Alignment explanation
Indices: 523735--523962 Score: 323
Period size: 57 Copynumber: 4.0 Consensus size: 57
523725 TAACCATACA
* * * * *
523735 ACCCCGTCACGAACAGTAAGGCCCTGAACACAAAGCAAAGGAACCTGCAAGTAATCT
1 ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCAGAGGAACCTGCAAGTATTCT
* * * * *
523792 ACCGCATCACGAACAGTAAGGCTCTCAGCACAAAGCTGATGAACCTGCAAGTATTCA
1 ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCAGAGGAACCTGCAAGTATTCT
* *
523849 ACCCCGTCACGAATAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATTCT
1 ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCAGAGGAACCTGCAAGTATTCT
*
523906 TCCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGTC-GAGGAACCTGCAAGTATTCT
1 ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAG-CAGAGGAACCTGCAAGTATTCT
523963 TCCTCCAACT
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
57 151 0.99
58 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (57 bp):
ACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCAGAGGAACCTGCAAGTATTCT
Found at i:527092 original size:23 final size:23
Alignment explanation
Indices: 527062--527115 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
527052 TCGGTTTGTC
*
527062 GATCGGAGCTCGGATGACATGTA
1 GATCGGAGCTCGGACGACATGTA
* *
527085 GATCGGAGGTCGGACGACGTGTA
1 GATCGGAGCTCGGACGACATGTA
527108 GATCGGAG
1 GATCGGAG
527116 TTGAAAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.19
Consensus pattern (23 bp):
GATCGGAGCTCGGACGACATGTA
Found at i:528261 original size:2 final size:2
Alignment explanation
Indices: 528254--528285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
528244 AACGATTATT
528254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
528286 CACGTGCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:528368 original size:2 final size:2
Alignment explanation
Indices: 528361--528424 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
528351 TATCTAATTG
528361 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
*
528403 AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
528425 TATTGTATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528431 original size:10 final size:12
Alignment explanation
Indices: 528361--528432 Score: 94
Period size: 12 Copynumber: 6.2 Consensus size: 12
528351 TATCTAATTG
*
528361 ATATATATATAT
1 ATATATATATGT
*
528373 ATATATATATAT
1 ATATATATATGT
*
528385 ATATATATATAT
1 ATATATATATGT
*
528397 ATATATATATAT
1 ATATATATATGT
528409 ATATATATATGT
1 ATATATATATGT
528421 ATAT-TAT-TGT
1 ATATATATATGT
528431 AT
1 AT
528433 TATCACGATG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
10 5 0.08
11 3 0.05
12 51 0.86
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
ATATATATATGT
Found at i:536704 original size:20 final size:20
Alignment explanation
Indices: 536678--536753 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
536668 GAAAGCTGGA
*
536678 AACCGGTTTTAACTGGTTTTG
1 AACCGG-TTTAACCGGTTTTG
536699 -ACCGGTTTAACCGGTTTTG
1 AACCGGTTTAACCGGTTTTG
*
536718 AACCGGTTTGACCGGTTTTG
1 AACCGGTTTAACCGGTTTTG
*
536738 AACCGGTTTGACCGGT
1 AACCGGTTTAACCGGT
536754 CACGACCCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 13 0.25
20 39 0.75
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTG
Found at i:536727 original size:29 final size:31
Alignment explanation
Indices: 536678--536753 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 31
536668 GAAAGCTGGA
*
536678 AACCGGTTTT-AACTGGTTTTGACCGG-TTT-
1 AACCGGTTTTGAACCGG-TTTGACCGGTTTTG
536707 AACCGGTTTTGAACCGGTTTGACCGGTTTTG
1 AACCGGTTTTGAACCGGTTTGACCGGTTTTG
536738 AACCGG-TTTG-ACCGGT
1 AACCGGTTTTGAACCGGT
536754 CACGACCCGA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 25 0.58
30 12 0.28
31 6 0.14
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (31 bp):
AACCGGTTTTGAACCGGTTTGACCGGTTTTG
Found at i:536747 original size:10 final size:10
Alignment explanation
Indices: 536678--536753 Score: 79
Period size: 10 Copynumber: 7.7 Consensus size: 10
536668 GAAAGCTGGA
*
536678 AACCGGTTTT
1 AACCGGTTTG
*
536688 AACTGGTTTTG
1 AACCGG-TTTG
536699 -ACCGGTTT-
1 AACCGGTTTG
536707 AACCGGTTTTG
1 AACCGG-TTTG
536718 AACCGGTTTG
1 AACCGGTTTG
536728 -ACCGGTTTTG
1 AACCGG-TTTG
536738 AACCGGTTTG
1 AACCGGTTTG
536748 -ACCGGT
1 AACCGGT
536754 CACGACCCGA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
9 19 0.33
10 24 0.42
11 14 0.25
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.36
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:536787 original size:17 final size:18
Alignment explanation
Indices: 536756--536832 Score: 131
Period size: 17 Copynumber: 4.4 Consensus size: 18
536746 TGACCGGTCA
536756 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
536774 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
*
536791 CAACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
536809 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
536826 CGACCCG
1 CGACCCG
536833 TTGACCGGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
17 32 0.57
18 24 0.43
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:536797 original size:35 final size:35
Alignment explanation
Indices: 536758--536832 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
536748 ACCGGTCACG
536758 ACCCGACCCGTTGACCCGACCCGACCGTTGACCCA
1 ACCCGACCCGTTGACCCGACCCGACCGTTGACCCA
*
536793 ACCCGACCCGTTGACCCGACCCGACCGTTGACCCG
1 ACCCGACCCGTTGACCCGACCCGACCGTTGACCCA
536828 ACCCG
1 ACCCG
536833 TTGACCGGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.11
Consensus pattern (35 bp):
ACCCGACCCGTTGACCCGACCCGACCGTTGACCCA
Found at i:536827 original size:12 final size:13
Alignment explanation
Indices: 536793--536838 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 13
536783 CGTTGACCCA
536793 ACCCGACCCGTTG
1 ACCCGACCCGTTG
536806 ACCCGACCCGACCGTTG
1 ACCCGA--C--CCGTTG
536823 ACCCGACCCGTTG
1 ACCCGACCCGTTG
536836 ACC
1 ACC
536839 GGTGCTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 15 0.52
15 2 0.07
17 12 0.41
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:536900 original size:29 final size:29
Alignment explanation
Indices: 536868--536935 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
536858 ATTTGGTTTT
536868 GGTGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * *
536897 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
536926 GGTGCTATTT
1 GGTGCTATTT
536936 GTATAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:537673 original size:24 final size:24
Alignment explanation
Indices: 537641--537709 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
537631 ATAGTTTATC
*
537641 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
** * *
537665 TGATATTTGACCTAAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
537689 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
537710 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:543954 original size:10 final size:10
Alignment explanation
Indices: 543939--543981 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
543929 AACGCTGGAA
543939 ACCGGTTTTG
1 ACCGGTTTTG
*
543949 ACCGG-TTTA
1 ACCGGTTTTG
543958 ACCGGTTTTG
1 ACCGGTTTTG
543968 AACCGGTTTTG
1 -ACCGGTTTTG
543979 ACC
1 ACC
543982 AATTTGACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 10 0.34
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:543962 original size:19 final size:20
Alignment explanation
Indices: 543938--543976 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
543928 GAACGCTGGA
543938 AACCGGTTTTG-ACCGGTTT
1 AACCGGTTTTGAACCGGTTT
543957 AACCGGTTTTGAACCGGTTT
1 AACCGGTTTTGAACCGGTTT
543977 TGACCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
AACCGGTTTTGAACCGGTTT
Found at i:543973 original size:11 final size:11
Alignment explanation
Indices: 543938--543979 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
543928 GAACGCTGGA
543938 AACCGGTTTTG
1 AACCGGTTTTG
543949 -ACCGG-TTT-
1 AACCGGTTTTG
543957 AACCGGTTTTG
1 AACCGGTTTTG
543968 AACCGGTTTTG
1 AACCGGTTTTG
543979 A
1 A
543980 CCAATTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.29
10 8 0.29
11 12 0.43
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:544023 original size:17 final size:17
Alignment explanation
Indices: 543997--544059 Score: 108
Period size: 17 Copynumber: 3.6 Consensus size: 17
543987 GACCGGTCAC
543997 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
544014 GACCCAACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
544032 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
544049 GACCCGACCCG
1 GACCCGACCCG
544060 TTGACCGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 27 0.63
18 16 0.37
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.10
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:544054 original size:12 final size:13
Alignment explanation
Indices: 544020--544065 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 13
544010 CGTTGACCCA
544020 ACCCGACCCGTTG
1 ACCCGACCCGTTG
544033 ACCCGACCCGACCGTTG
1 ACCCGA--C--CCGTTG
544050 ACCCGACCCGTTG
1 ACCCGACCCGTTG
544063 ACC
1 ACC
544066 GGTGCTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 15 0.52
15 2 0.07
17 12 0.41
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:544127 original size:29 final size:29
Alignment explanation
Indices: 544095--544162 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
544085 ATTTGGTTTT
544095 GGTGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * *
544124 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
544153 GGTGCTATTT
1 GGTGCTATTT
544163 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:544914 original size:24 final size:24
Alignment explanation
Indices: 544860--544924 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
544850 ATATAAATAG
* * **
544860 TTTATCTGATTTTTGACCTGGATT
1 TTTATATGATATTTGACCTAAATT
* *
544884 CTGATATGATATTTGACCTAAATT
1 TTTATATGATATTTGACCTAAATT
*
544908 TTTATATGATACTTGAC
1 TTTATATGATATTTGAC
544925 ATAGACTCTG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (24 bp):
TTTATATGATATTTGACCTAAATT
Found at i:552133 original size:18 final size:18
Alignment explanation
Indices: 552110--552144 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
552100 AGGGATTATC
*
552110 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGGGACAT
552128 AGTGGTCCTACGGGACA
1 AGTGGTCCTACGGGACA
552145 AATTTCTATG
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:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:557374 original size:19 final size:19
Alignment explanation
Indices: 557346--557391 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
557336 AACTTATACA
557346 TGCT-GAAGGGAGAGACTT
1 TGCTAGAAGGGAGAGACTT
557364 TGCTAGAAGGGAGAGACTT
1 TGCTAGAAGGGAGAGACTT
557383 TGCTAGAAG
1 TGCTAGAAG
557392 CAGAAGCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.30, C:0.11, G:0.37, T:0.22
Consensus pattern (19 bp):
TGCTAGAAGGGAGAGACTT
Found at i:557801 original size:35 final size:37
Alignment explanation
Indices: 557734--557805 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 37
557724 CTTTTTCGTC
557734 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
*
557771 CTACTAGGATTC-AACTC-CTAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
557806 TTGCTATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 17 0.50
36 5 0.15
37 12 0.35
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCTCAAAAATAGGATAGAATT
Found at i:558517 original size:16 final size:16
Alignment explanation
Indices: 558496--558529 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
558486 CATGTATTTA
558496 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
558512 TATTATTTTACTTTAT
1 TATTATATTACATTAT
558528 TA
1 TA
558530 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:558534 original size:21 final size:22
Alignment explanation
Indices: 558510--558560 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
558500 ATATTACATT
*
558510 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
558531 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
558553 TTTATTAT
1 ATTATTAT
558561 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:563092 original size:155 final size:155
Alignment explanation
Indices: 562805--563113 Score: 555
Period size: 155 Copynumber: 2.0 Consensus size: 155
562795 ATTAAACCCG
562805 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
562870 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACAATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
562935 TTGTCAGGCCAAAGACTTTGTGATC
131 TTGTCAGGCCAAAGACTTTGTGATC
*
562960 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
563025 ATAGATTACATTCAAACAATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTACATTCAAACAATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
563090 TTGTCAGGCCAAAGACTTTGTGAT
131 TTGTCAGGCCAAAGACTTTGTGAT
563114 GAGATGAACC
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
155 147 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (155 bp):
TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACAATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATC
Found at i:564477 original size:37 final size:37
Alignment explanation
Indices: 564410--564496 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
564400 ATTGAAAACA
** * *
564410 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
564446 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
564483 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
564497 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:564503 original size:102 final size:102
Alignment explanation
Indices: 564323--564903 Score: 988
Period size: 102 Copynumber: 5.7 Consensus size: 102
564313 TTAAAACAAG
* * * *
564323 ATTTTTTCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAG-TTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAGTTTCT
*
564387 CTTTAAACAT-AACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
564425 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
564490 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *** *
564527 GTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCATCTCCATTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
564592 TGAAACATAAACATTGGAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
564629 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
564694 TAAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
564731 ATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
564796 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
564833 ATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
564897 TGAAACA
66 TGAAACA
564904 CAAAACCTTT
Statistics
Matches: 455, Mismatches: 22, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
100 19 0.04
101 53 0.12
102 383 0.84
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:564661 original size:36 final size:37
Alignment explanation
Indices: 564614--564903 Score: 157
Period size: 36 Copynumber: 8.4 Consensus size: 37
564604 ATTGGAAACA
** *
564614 TTTCCCTTGAAA-TGAATTTTGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
564650 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
* * *
564687 TTTCTCTTAAAACATAAA---------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTGTCTCCATTG-AGACAG
** *
564716 TTTCCCTTGAAA-TGAATTTTGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
* *
564752 TTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
* *
564789 TTTCTCTTGAAACATAAA---------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTGTCTCCATTG-AGACAG
** * *
564818 TTTCCCTTGAAA-TGAATTTCGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
*
564854 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
*
564890 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
564904 CAAAACCTTT
Statistics
Matches: 192, Mismatches: 29, Indels: 65
0.67 0.10 0.23
Matches are distributed among these distances:
27 4 0.02
29 30 0.16
30 8 0.04
35 7 0.04
36 73 0.38
37 64 0.33
38 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
Found at i:564682 original size:37 final size:37
Alignment explanation
Indices: 564614--564700 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
564604 ATTGGAAACA
** *
564614 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
564650 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCTC-TTGAGACAG
* *
564687 TTTCTCTTAAAACA
1 TTTCCCTTGAAACA
564701 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 13 0.30
37 31 0.70
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
Found at i:564773 original size:37 final size:37
Alignment explanation
Indices: 564730--564802 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
564720 CCTTGAAATG
* *
564730 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
* *
564767 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACA
564803 TAAACATTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
Found at i:564926 original size:67 final size:67
Alignment explanation
Indices: 564845--565003 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
564835 TTCGTCTCTC
* * *
564845 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
564910 CT
66 CT
* *
564912 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
564977 CT
66 CT
*
564979 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
565004 ATTTCGTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 78 0.94
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
CT
Found at i:565943 original size:106 final size:104
Alignment explanation
Indices: 565584--566104 Score: 491
Period size: 109 Copynumber: 4.9 Consensus size: 104
565574 TAGCTATAGT
* * * * *
565584 CAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTT-TCAATTTCAGAACCAA
* * *
565649 TTTCAACTCCACGATG-G-AGGATATCGTGCTACCCGAGACAACA
65 TTTCAACTTCAC-A-GCGAAGGATAT--TG-GACTCGAGACAACA
* * **
565692 CAAGATCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-TTTTCAATTTCAGAAC-C
* * * *
565756 GATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACA
63 AATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACA
* * *
565801 CAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTC-AATTTCAGAACCA
*
565866 ATTTCAACTTCACAGCGAAGGATATTGGACTCGATACAACA
64 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* * **
565907 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GA-TTTC-A-TTCAGAGTCAAT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTTCAATTTCAGAACCAAT
*
565968 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACA
66 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* * * ** * * * ** *
566007 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAATAAATAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTT-TCAATTTCAGAACCA
* *
566072 ATTTCAACTTCACAACGGAGGATATTGGACTCG
64 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
566105 GAACAATATT
Statistics
Matches: 355, Mismatches: 43, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
100 83 0.23
101 3 0.01
102 1 0.00
103 6 0.02
104 1 0.00
105 2 0.01
106 88 0.25
107 2 0.01
108 44 0.12
109 120 0.34
110 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (104 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTTCAATTTCAGAACCAAT
TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
Found at i:566077 original size:206 final size:211
Alignment explanation
Indices: 565584--566104 Score: 511
Period size: 206 Copynumber: 2.5 Consensus size: 211
565574 TAGCTATAGT
* * * ** * * * * *
565584 CAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGCTCAACTTCACAACGAAGGGACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCA
* * * * * * *
565648 ATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGATCAACTTCACAACGAA
66 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCGATACAACACAAGATCAACTTCACAACGAA
* * * *
565713 GGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCCGCGATTTCAACTCCACGACGGAGG
128 GGGACGGCTGATTGTCAACGAACAAC-TTTCAG-TTCATCAGCAATTTCAACTCCACGACGAAGG
565778 ATATCGTGCCACTCGAGACAACA
191 ATATC-TG-CACTCGAGACAACA
* ** * * * *
565801 CAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGCTCAACTTCACAACGAAGGGACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCA
* *
565866 ATTTCAACTTCACAGCGAAGGATATTGGACTCGATACAACACAAGTTCAACTTCACAACGAAGGG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCGATACAACACAAGATCAACTTCACAACGAAGGG
* * *
565931 ACGGCTGATTGTCAAC-AA-GA-TTTCA-TTCA-GAGTCAATTTCAACTTCAC-AGCGAAGGATA
131 ACGGCTGATTGTCAACGAACAACTTTCAGTTCATCAG-CAATTTCAACTCCACGA-CGAAGGATA
565990 T-TAG-ACTCGAGACAACA
194 TCT-GCACTCGAGACAACA
* * * * * ***
566007 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAATAAATAATTTCCCGGTTCCAGAACCA
1 CAAGCTCAACTTCACAACGAAGGGACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCA
*
566072 ATTTCAACTTCACAACGGAGGATATTGGACTCG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCG
566105 GAACAATATT
Statistics
Matches: 258, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
206 94 0.36
207 1 0.00
208 3 0.01
209 26 0.10
211 5 0.02
213 1 0.00
214 2 0.01
215 49 0.19
216 2 0.01
217 37 0.14
218 38 0.15
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (211 bp):
CAAGCTCAACTTCACAACGAAGGGACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCA
ATTTCAACTTCACAACGAAGGATATTGGACTCGATACAACACAAGATCAACTTCACAACGAAGGG
ACGGCTGATTGTCAACGAACAACTTTCAGTTCATCAGCAATTTCAACTCCACGACGAAGGATATC
TGCACTCGAGACAACA
Found at i:566629 original size:35 final size:35
Alignment explanation
Indices: 566565--566664 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
566555 TTTCGTCCTA
* *
566565 CTAGGATTCAAACTCTCAAAAATATGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
566602 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
566637 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
566665 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:567325 original size:16 final size:16
Alignment explanation
Indices: 567304--567337 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
567294 CATGTATTTA
567304 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
567320 TATTATTTTACTTTAT
1 TATTATATTACATTAT
567336 TA
1 TA
567338 AATTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:570932 original size:18 final size:20
Alignment explanation
Indices: 570904--570959 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
570894 CACTGAATAT
*
570904 TTGTCCAGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
570923 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
570942 TTGTTCCGAATGACCACT
1 TTGTCCCGAAGGACCACT
570960 CCTTAAGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.50
19 1 0.03
20 15 0.47
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:571703 original size:19 final size:19
Alignment explanation
Indices: 571679--571730 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
571669 TTTAAGTAGG
571679 TGCATCGATGCACTCCCCA
1 TGCATCGATGCACTCCCCA
*
571698 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCCCA
571717 TGCATCGATGCACT
1 TGCATCGATGCACT
571731 AATTGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCACTCCCCA
Found at i:582925 original size:46 final size:48
Alignment explanation
Indices: 582799--583005 Score: 316
Period size: 46 Copynumber: 4.3 Consensus size: 48
582789 GTGAGTTTAA
*
582799 AAAATATATTTTTTATTAAAATTTATCAAATCGAGATAAAAATTTTGAAT
1 AAAA-ATA-TTTTTATTAAAATTTATCAAATCGAGATAAAAAATTTGAAT
582849 AAAAATATTTTTTTATTAAAATTTATCAAAT-GAGATAAAAAATTTGAAT
1 AAAAATA--TTTTTATTAAAATTTATCAAATCGAGATAAAAAATTTGAAT
582898 -AAAATATTTTTATTAAAATTTATCAAAT-GAGAT-AAAAATTTGAAT
1 AAAAATATTTTTATTAAAATTTATCAAATCGAGATAAAAAATTTGAAT
* *
582943 AAAAATATTTTTATTAAAATTTATCAAATCGAGACAAAAATTTTGAAT
1 AAAAATATTTTTATTAAAATTTATCAAATCGAGATAAAAAATTTGAAT
582991 AAAAATA-TTTTATTA
1 AAAAATATTTTTATTA
583006 GAACTCATCA
Statistics
Matches: 150, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
45 12 0.08
46 55 0.37
47 12 0.08
48 24 0.16
49 20 0.13
50 27 0.18
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (48 bp):
AAAAATATTTTTATTAAAATTTATCAAATCGAGATAAAAAATTTGAAT
Found at i:586962 original size:21 final size:21
Alignment explanation
Indices: 586923--586962 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
586913 TTTTCAGAAA
*
586923 TTTAATTTATATAATTTTAAT
1 TTTAATTTATAAAATTTTAAT
586944 TTTAATTT-TAAAATATTTA
1 TTTAATTTATAAAAT-TTTA
586963 TATTCATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTTATAAAATTTTAAT
Found at i:589447 original size:30 final size:29
Alignment explanation
Indices: 589411--589479 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 29
589401 TTAGGCAGTA
589411 CTCGACTCTGCACT-TTAAAAAAAATTATTG
1 CTCGACTC-GCACTCTT-AAAAAAATTATTG
*
589441 CTCGACTCGTACTCGTTAAAAAAATTATTG
1 CTCGACTCGCACTC-TTAAAAAAATTATTG
589471 CTCGACTCG
1 CTCGACTCG
589480 TGCTCGTTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 4 0.11
30 30 0.83
31 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (29 bp):
CTCGACTCGCACTCTTAAAAAAATTATTG
Found at i:589480 original size:30 final size:30
Alignment explanation
Indices: 589428--589487 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
589418 CTGCACTTTA
589428 AAAAAAATTATTGCTCGACTCGTACTCGTT
1 AAAAAAATTATTGCTCGACTCGTACTCGTT
*
589458 AAAAAAATTATTGCTCGACTCGTGCTCGTT
1 AAAAAAATTATTGCTCGACTCGTACTCGTT
589488 GCTCGTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAAAAATTATTGCTCGACTCGTACTCGTT
Found at i:589705 original size:24 final size:24
Alignment explanation
Indices: 589678--589735 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
589668 ATATTAAAAG
* *
589678 CAAAGTAACAATCCATAAATTCAC
1 CAAAGTAACAATCCACAAATACAC
*
589702 CAAAGTAACAATCCACAAATACAT
1 CAAAGTAACAATCCACAAATACAC
*
589726 CAAACTAACA
1 CAAAGTAACA
589736 TATTAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.17
Consensus pattern (24 bp):
CAAAGTAACAATCCACAAATACAC
Found at i:593195 original size:13 final size:14
Alignment explanation
Indices: 593171--593206 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
593161 AGAGATGAAA
593171 TTGTGATTTGTGAT
1 TTGTGATTTGTGAT
593185 TTGTG-TTTGTGAT
1 TTGTGATTTGTGAT
593198 TTGTGATTT
1 TTGTGATTT
593207 TGAGATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.11, C:0.00, G:0.28, T:0.61
Consensus pattern (14 bp):
TTGTGATTTGTGAT
Found at i:593218 original size:7 final size:7
Alignment explanation
Indices: 593171--593206 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
593161 AGAGATGAAA
593171 TTGTGAT
1 TTGTGAT
593178 TTGTGAT
1 TTGTGAT
593185 TTGTG-T
1 TTGTGAT
593191 TTGTGAT
1 TTGTGAT
593198 TTGTGAT
1 TTGTGAT
593205 TT
1 TT
593207 TGAGATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.11, C:0.00, G:0.28, T:0.61
Consensus pattern (7 bp):
TTGTGAT
Found at i:593358 original size:37 final size:37
Alignment explanation
Indices: 593317--593393 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
593307 TATTGTATAA
593317 TAAAATAATATTA-TAAATTAAT-AATATTATTATTTAT
1 TAAAAT-ATATTAGT-AATTAATCAATATTATTATTTAT
* * *
593354 TAAAATATATTAGTAATTTATCATTATTATTATTTGT
1 TAAAATATATTAGTAATTAATCAATATTATTATTTAT
593391 TAA
1 TAA
593394 CAAATTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
TAAAATATATTAGTAATTAATCAATATTATTATTTAT
Found at i:595660 original size:44 final size:43
Alignment explanation
Indices: 595612--595710 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
595602 AGAAAAGACA
* *
595612 AATAAATAAATAAAATACACTAAAATTAAAAGAGAAAAAAAATG
1 AATAACTAAATAAAAAACACTAAAATTAAAA-AGAAAAAAAATG
* *
595656 AATAACTAAAATAAAAAATACTAAAATTAAAAAGGAAAAAAATG
1 AATAACT-AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATG
595700 AATAACTAAAT
1 AATAACTAAAT
595711 TGAAATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.08
44 24 0.48
45 22 0.44
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (43 bp):
AATAACTAAATAAAAAACACTAAAATTAAAAAGAAAAAAAATG
Found at i:595666 original size:40 final size:40
Alignment explanation
Indices: 595601--595709 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
595591 AAATAAAAAT
* *
595601 AAGAAAAGACAAATAAATAAATAAAAT-ACACTAAAATTAAA
1 AAGAAAA-A-AAATGAATAACTAAAATAACACTAAAATTAAA
*
595642 AGAGAAAAAAAATGAATAACTAAAATAAAAAATACTAAAATTAAA
1 A-AGAAAAAAAATGAATAACTAAAAT----AACACTAAAATTAAA
*
595687 AAGGAAAAAAATGAATAACTAAA
1 AAGAAAAAAAATGAATAACTAAA
595710 TTGAAATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
40 15 0.26
41 2 0.03
42 6 0.10
44 21 0.36
45 14 0.24
ACGTcount: A:0.71, C:0.06, G:0.07, T:0.17
Consensus pattern (40 bp):
AAGAAAAAAAATGAATAACTAAAATAACACTAAAATTAAA
Found at i:595679 original size:45 final size:44
Alignment explanation
Indices: 595619--595709 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
595609 ACAAATAAAT
*
595619 AAATAAAATACACTAAAATTAAAAGAGAAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAA-AGAAAAAAAATGAATAACTA
* *
595664 AAATAAAAAATACTAAAATTAAAAAGGAAAAAAATGAATAACTA
1 AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATGAATAACTA
595708 AA
1 AA
595710 TTGAAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
44 21 0.49
45 22 0.51
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (44 bp):
AAATAAAAAACACTAAAATTAAAAAGAAAAAAAATGAATAACTA
Found at i:595715 original size:22 final size:22
Alignment explanation
Indices: 595647--595720 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
595637 TTAAAAGAGA
595647 AAAAAAATGAATAACTAAAAT-
1 AAAAAAATGAATAACTAAAATG
* *
595668 AAAAAATACT-AA-AATTAAAAAGG
1 AAAAAA-A-TGAATAACT-AAAATG
*
595691 AAAAAAATGAATAACTAAATTG
1 AAAAAAATGAATAACTAAAATG
*
595713 AAATAAAT
1 AAAAAAAT
595721 TAAAATTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 10 0.24
22 21 0.51
23 10 0.24
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAATGAATAACTAAAATG
Found at i:595725 original size:44 final size:44
Alignment explanation
Indices: 595632--595727 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
595622 TAAAATACAC
595632 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
1 TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
* *
595676 CTAAAATTAAAA-AGGAAAAAAATGAATAACTAAATTGAAATAAAT-
1 -TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAAT-AAA-AAATA
595721 TAAAATT
1 TAAAATT
595728 GATGGATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (44 bp):
TAAAATTAAAAGAGAAAAAAAATGAATAACTAAAATAAAAAATA
Found at i:598149 original size:106 final size:106
Alignment explanation
Indices: 597947--599041 Score: 1526
Period size: 106 Copynumber: 10.6 Consensus size: 106
597937 TATTGTTCCA
* * * * * *
597947 AGTCCAATATCCTCCG-CGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
598011 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
598052 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *
598117 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
598158 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAGATTGAGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
*
598223 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
598264 AATCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCAGAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
598329 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
598370 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *
598435 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
598476 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* **
598541 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
598582 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
598646 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
598687 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA--G----TTGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* *** *
598745 CAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
598786 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G----T---AAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
598839 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
598880 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAG-AA--G----TTGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
* * *** *
598938 CAGCAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
598979 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
599042 GACAACTTTT
Statistics
Matches: 891, Mismatches: 72, Indels: 53
0.88 0.07 0.05
Matches are distributed among these distances:
88 2 0.00
90 2 0.00
94 75 0.08
95 1 0.00
98 1 0.00
99 160 0.18
100 1 0.00
102 2 0.00
103 2 0.00
104 1 0.00
105 112 0.13
106 532 0.60
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:598967 original size:193 final size:192
Alignment explanation
Indices: 598619--599011 Score: 723
Period size: 193 Copynumber: 2.0 Consensus size: 192
598609 AAATTGGCTC
* *
598619 TGAAATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGGGAAATTGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
598684 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGACAGTCAGC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAGC
*
598749 GGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
131 AGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
*
598811 TGAAATTGGTAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTG-TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
598876 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAG
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAG
598941 CAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
130 CAGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
599004 TGAAATTG
1 TGAAATTG
599012 ACTCTGAAAT
Statistics
Matches: 194, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
192 14 0.07
193 180 0.93
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (192 bp):
TGAAATTGGGAAATTGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTAAGAAGTTGACAGTCAGC
AGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:599056 original size:99 final size:99
Alignment explanation
Indices: 598655--599031 Score: 460
Period size: 99 Copynumber: 3.9 Consensus size: 99
598645 CCAGCGGTCC
* **
598655 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* * * * *
598720 GCTCTGAAATTGAGAAGTTGACAGTCAGCGGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* *
598754 CTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
**** ** * * *
598819 G---T-AAATTGTTTA-TTGACAACCAGCGGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* **
598848 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* *
598913 GATCTGAAATTAAGAAGTTGACAGTCAGCAGTCC
66 GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
* *
598947 CTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-
1 CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
*
599011 GACTCTGAAATTGAGAAGTTG
66 GA-TCTGAAATTAAGAAGTTG
599032 TTTGTTGACA
Statistics
Matches: 244, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
94 76 0.31
95 7 0.03
96 1 0.00
97 1 0.00
98 8 0.03
99 151 0.62
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (99 bp):
CTTCGTCTTGAAGTTGAACTTGCACTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
GATCTGAAATTAAGAAGTTGACAGTCAGCAGACA
Found at i:601176 original size:27 final size:26
Alignment explanation
Indices: 601124--601177 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
601114 TGAGACATGT
*
601124 GAATGTAAAAAAAAGGAAAAATAATGC
1 GAATGTAAAAAAAA-GAAAAAAAATGC
601151 GAATGTAAAAAAAA-AATAACAAAATGC
1 GAATGTAAAAAAAAGAA-AA-AAAATGC
601178 ACAATATGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 2 0.08
27 20 0.83
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (26 bp):
GAATGTAAAAAAAAGAAAAAAAATGC
Found at i:602337 original size:21 final size:21
Alignment explanation
Indices: 602311--602355 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
602301 GATTTCTGGG
* *
602311 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
602332 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
602353 CAA
1 CAA
602356 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:604057 original size:22 final size:22
Alignment explanation
Indices: 604029--604094 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
604019 TATGGACATC
*
604029 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
604051 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
604073 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
604095 TTATATACGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Done.