Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006093.1 Hibiscus syriacus cultivar Beakdansim tig00014444_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: 3172561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2223822 original size:18 final size:18
Alignment explanation
Indices: 2223773--2223826 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
2223763 AAAATAGAAA
*
2223773 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
2223794 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
2223813 AATA-TAATATAAAA
1 AATAGTAATATAAAA
2223827 AAACCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:2223827 original size:18 final size:19
Alignment explanation
Indices: 2223777--2223827 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
2223767 TAGAAAAATA
*
2223777 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
2223797 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
2223816 ATAATATAAAAA
1 ATAATATAAAAA
2223828 AACCAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:2224065 original size:19 final size:19
Alignment explanation
Indices: 2224034--2224071 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2224024 AAAAGTGTAT
*
2224034 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
2224053 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
2224072 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:2224633 original size:37 final size:37
Alignment explanation
Indices: 2224584--2224676 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
2224574 GTGCTTGTGG
* * *
2224584 ATCCTATATTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
* * *
2224621 ATCTTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
2224658 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
2224677 GAATACTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCATAGCAAAACTCT
Found at i:2225603 original size:106 final size:106
Alignment explanation
Indices: 2225419--2226694 Score: 1973
Period size: 106 Copynumber: 12.0 Consensus size: 106
2225409 GCATTGTTCC
* * * * * *
2225419 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
2225483 ACCAGTC-GTCCCTTCATTGTGAGGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2225525 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
2225590 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
2225631 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
**
2225696 CCAATGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2225737 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2225802 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
2225843 GAGTTTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2225908 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
2225949 GAGCCCAATATCTTTCTCTGTGAAGTTGAAATTGTCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2226014 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2226055 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2226120 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2226161 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
2226226 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2226267 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
2226332 CCATTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTCTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2226373 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
2226438 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2226479 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
2226544 CCAGCGGTCCCTTCGTCGTGAGGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2226585 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
2226650 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2226691 GAGT
1 GAGT
2226695 GGCACGATAT
Statistics
Matches: 1076, Mismatches: 91, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
105 1 0.00
106 1073 1.00
107 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:2227508 original size:22 final size:22
Alignment explanation
Indices: 2227482--2227558 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2227472 TTATGTTTGG
2227482 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2227504 TCAAAGGTTTGGCATTTGATTC
1 TCAAAGGTTTGGCATTTGATGC
*
2227526 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
2227548 TCAACGGTTTG
1 TCAAAGGTTTG
2227559 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:2228242 original size:170 final size:171
Alignment explanation
Indices: 2227955--2228299 Score: 566
Period size: 170 Copynumber: 2.0 Consensus size: 171
2227945 TAAATAAGCC
* *
2227955 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATACCTTCAATCA----CTG
2228020 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
62 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
*
2228085 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
127 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTCATGTGCCATTT
* *
2228130 CAAACAAGTGTTTTAGGGTGTTGAACCAAGGATCAATTCATTATGATATCTTCAATCA-TGCTCA
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATACCTTCAATCACTGCTCA
* *
2228194 AAATGTTTCTCTCTTGATGCTTTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGATTG
66 AAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGATTG
* *
2228259 TGTTTGATCAATCTCATAGTTTGAAGCTTCATGTGCGATTT
131 TGCTTGATCAATCTCATAGTTTGAAGCTTCATGTGCCATTT
2228300 TTTAGGGAAT
Statistics
Matches: 161, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
170 107 0.66
175 54 0.34
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (171 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATACCTTCAATCACTGCTCA
AAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGATTG
TGCTTGATCAATCTCATAGTTTGAAGCTTCATGTGCCATTT
Found at i:2231861 original size:16 final size:18
Alignment explanation
Indices: 2231827--2231861 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2231817 TACAGATGAT
2231827 GGAATAAAATAAAAGAGA
1 GGAATAAAATAAAAGAGA
2231845 GGAA-AAAATGAAAAGAG
1 GGAATAAAAT-AAAAGAG
2231862 TTAGTAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (18 bp):
GGAATAAAATAAAAGAGA
Found at i:2233010 original size:2 final size:2
Alignment explanation
Indices: 2233003--2233032 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2232993 GAAAATATTA
2233003 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
2233033 GAGTAAAATA
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):
AT
Found at i:2233100 original size:18 final size:19
Alignment explanation
Indices: 2233051--2233100 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
2233041 TAGAAAAATA
*
2233051 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
2233071 AGT-ATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
2233089 ATAATATAAAAA
1 ATAATATAAAAA
2233101 AAAAAAACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
19 6 0.24
20 3 0.12
21 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:2233839 original size:37 final size:37
Alignment explanation
Indices: 2233798--2233902 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
2233788 GTGCTTGTGG
* *
2233798 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
2233835 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
2233872 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
2233903 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:2234496 original size:15 final size:15
Alignment explanation
Indices: 2234444--2234488 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
2234434 TTGAGACCTT
2234444 ACCCGCCCCGCATCC
1 ACCCGCCCCGCATCC
* *
2234459 ACCCGCTCTGCATCC
1 ACCCGCCCCGCATCC
2234474 ACCCGCCCCGCATCC
1 ACCCGCCCCGCATCC
2234489 GCTCGCCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.13, C:0.62, G:0.13, T:0.11
Consensus pattern (15 bp):
ACCCGCCCCGCATCC
Found at i:2234914 original size:19 final size:19
Alignment explanation
Indices: 2234886--2234924 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2234876 GTGGGTGGTT
*
2234886 GATTTGAAAATATTTAGTG
1 GATTTAAAAATATTTAGTG
2234905 GATTTAAAAATATTTAGTG
1 GATTTAAAAATATTTAGTG
2234924 G
1 G
2234925 GTATGAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (19 bp):
GATTTAAAAATATTTAGTG
Found at i:2240138 original size:30 final size:28
Alignment explanation
Indices: 2240115--2240169 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2240105 CGGTGATCGG
2240115 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
* *
2240144 TATATTTCCCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
2240170 CAGTAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:2240245 original size:19 final size:20
Alignment explanation
Indices: 2240214--2240254 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2240204 TGATTTGGCA
2240214 CCACGTGGGGGTATAGGGCG
1 CCACGTGGGGGTATAGGGCG
*
2240234 CCACGT-GGGGTATAGTGCG
1 CCACGTGGGGGTATAGGGCG
2240253 CC
1 CC
2240255 CCCTGCTCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (20 bp):
CCACGTGGGGGTATAGGGCG
Found at i:2240427 original size:12 final size:10
Alignment explanation
Indices: 2240395--2240425 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2240385 TTCATCACAC
2240395 CAAATTCTCT
1 CAAATTCTCT
2240405 CAAATTCTCT
1 CAAATTCTCT
*
2240415 CAAATACTCT
1 CAAATTCTCT
2240425 C
1 C
2240426 TCGTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2240501 original size:17 final size:18
Alignment explanation
Indices: 2240466--2240507 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2240456 ATATTCTATA
*
2240466 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2240484 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2240501 TTTACTT
1 TTTACTT
2240508 ATATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2241912 original size:65 final size:65
Alignment explanation
Indices: 2241836--2241958 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
2241826 TAGCGCGGTA
* * *
2241836 CAGGGGGCGCGCTAAACCCCACATGGCGCCAAATCAACGTATAACGTGGGTCAGGGGGTGCGGGT
1 CAGGGGGCGCGCTAAACACCACATGGCACCAAATCAACGTATAACGCGGGTCAGGGGGTGCGGGT
* ** * *
2241901 CAGGGGGCGCGCTATACACCATGTGGCACCAAATCAGCGTATAGCGCGGGTCAGGGGG
1 CAGGGGGCGCGCTAAACACCACATGGCACCAAATCAACGTATAACGCGGGTCAGGGGG
2241959 CGCGCTTTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (65 bp):
CAGGGGGCGCGCTAAACACCACATGGCACCAAATCAACGTATAACGCGGGTCAGGGGGTGCGGGT
Found at i:2243628 original size:23 final size:24
Alignment explanation
Indices: 2243592--2243640 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2243582 TTGTAGTCAA
2243592 AACTGCCACATAGAAT-TGCACCG
1 AACTGCCACATAGAATATGCACCG
* *
2243615 AACTGCCGCGTAGAATATGCACCG
1 AACTGCCACATAGAATATGCACCG
2243639 AA
1 AA
2243641 GTTCCACGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16
Consensus pattern (24 bp):
AACTGCCACATAGAATATGCACCG
Found at i:2243650 original size:24 final size:23
Alignment explanation
Indices: 2243592--2243653 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
2243582 TTGTAGTCAA
*
2243592 AACTGCCACATAGAATTGCACCG
1 AACTGCCACGTAGAATTGCACCG
*
2243615 AACTGCCGCGTAGAATATGCACCG
1 AACTGCCACGTAGAAT-TGCACCG
* *
2243639 AAGTTCCACGTAGAA
1 AACTGCCACGTAGAA
2243654 ATTATCCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (23 bp):
AACTGCCACGTAGAATTGCACCG
Found at i:2243699 original size:23 final size:23
Alignment explanation
Indices: 2243673--2243746 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
2243663 AATGACCACA
2243673 TAGAAATGTCCCGAAAGACCGCG
1 TAGAAATGTCCCGAAAGACCGCG
**
2243696 TAGAAATGTCCC-AAATGACTACG
1 TAGAAATGTCCCGAAA-GACCGCG
* *
2243719 TAGAATTG-CCCTGAAGGACCGCG
1 TAGAAATGTCCC-GAAAGACCGCG
2243742 TAGAA
1 TAGAA
2243747 CCCTTGACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 6 0.14
23 34 0.81
24 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (23 bp):
TAGAAATGTCCCGAAAGACCGCG
Found at i:2246203 original size:21 final size:21
Alignment explanation
Indices: 2246178--2246219 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2246168 AATTTAAAAT
2246178 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
2246199 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
2246220 ATAACCGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:2246912 original size:61 final size:61
Alignment explanation
Indices: 2246796--2246912 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
2246786 GCTAAATCTG
* * *
2246796 CACTAAGCTTACGCCATAGTGCTAATCCGGATATGACACATAAGGTCGTGCCCACCACCTA
1 CACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCATACCCACCACCTA
* * * *
2246857 CACTAAGCTTATGCTATAGTGCTAATCCGGACATGATACATAAGGTCATATCCACC
1 CACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCATACCCACC
2246913 TTCCCGCACT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (61 bp):
CACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCATACCCACCACCTA
Found at i:2250800 original size:28 final size:26
Alignment explanation
Indices: 2250764--2250848 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 26
2250754 CATTTTTTTC
*
2250764 TTTTTTTCTTTCTGTTTTCTGTTTTATA
1 TTTTCTTCTTTCT-TTTTCT-TTTTATA
* *
2250792 TTTTCTTCTTTCTTCTTTCTTTTTCTT
1 TTTTCTTCTTTCTT-TTTCTTTTTATA
*
2250819 TTCTTCTT-TTTCTTTTTCTTTTTTTA
1 TT-TTCTTCTTTCTTTTTCTTTTTATA
2250845 TTTT
1 TTTT
2250849 TTAGCTCTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 2 0.04
26 12 0.24
27 14 0.28
28 22 0.44
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (26 bp):
TTTTCTTCTTTCTTTTTCTTTTTATA
Found at i:2250810 original size:14 final size:14
Alignment explanation
Indices: 2250793--2250839 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 14
2250783 TGTTTTATAT
2250793 TTTCTTCTTTCTTC
1 TTTCTTCTTTCTTC
2250807 TTTCTT-TTTC-T-
1 TTTCTTCTTTCTTC
2250818 TTTCTTCTTT-TTC
1 TTTCTTCTTTCTTC
2250831 TTT-TTCTTT
1 TTTCTTCTTT
2250840 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.20
12 11 0.37
13 7 0.23
14 6 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTCTTTCTTC
Found at i:2250817 original size:20 final size:20
Alignment explanation
Indices: 2250792--2250838 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2250782 CTGTTTTATA
2250792 TTTTCTTCT-TTCTTCTTTCT
1 TTTTCTTCTCTTCTT-TTTCT
*
2250812 TTTTCTTTTCTTCTTTTTCT
1 TTTTCTTCTCTTCTTTTTCT
2250832 TTTTCTT
1 TTTTCTT
2250839 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTCTTCTTTTTCT
Found at i:2250818 original size:6 final size:6
Alignment explanation
Indices: 2250758--2250841 Score: 80
Period size: 7 Copynumber: 12.8 Consensus size: 6
2250748 ATCTCTCATT
*
2250758 TTTTTC TTTTT- TTCTTTC TGTTTTC TGTTTTA TATTTTC TTCTTTC TTCTTTC
1 TTTTTC TTTTTC TT-TTTC T-TTTTC T-TTTTC T-TTTTC TT-TTTC TT-TTTC
2250811 TTTTTC TTTTCTTC TTTTTC TTTTTC TTTTT
1 TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTT
2250842 TTATTTTTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
5 2 0.03
6 27 0.39
7 36 0.52
8 4 0.06
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:2250842 original size:14 final size:14
Alignment explanation
Indices: 2250758--2250849 Score: 66
Period size: 15 Copynumber: 6.4 Consensus size: 14
2250748 ATCTCTCATT
2250758 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
*
2250772 --TTTC-TGTTTTC
1 TTTTTCTTTTTTTC
*
2250783 TGTTTTATATTTTCTTC
1 T-TTTTCT-TTTT-TTC
2250800 TTTCTTCTTTCTTTT-
1 TTT-TTCTTT-TTTTC
2250815 TCTTTTCTTCTTTTTC
1 T-TTTTCTT-TTTTTC
*
2250831 TTTTTCTTTTTTTA
1 TTTTTCTTTTTTTC
2250845 TTTTT
1 TTTTT
2250850 TAGCTCTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
11 6 0.10
12 4 0.06
14 13 0.21
15 17 0.27
16 13 0.21
17 9 0.15
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:2250848 original size:20 final size:20
Alignment explanation
Indices: 2250807--2250849 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2250797 TTCTTTCTTC
*
2250807 TTTCTTTTTCTTTTCTTCTT
1 TTTCTTTTTCTTTTCTTATT
*
2250827 TTTCTTTTTCTTTTTTTATT
1 TTTCTTTTTCTTTTCTTATT
2250847 TTT
1 TTT
2250850 TAGCTCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTCTTTTCTTATT
Found at i:2253627 original size:61 final size:61
Alignment explanation
Indices: 2253542--2253656 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
2253532 GTAGTGCTAA
* * *
2253542 ACCTGCACTAAGCTTAAGCCATAGTGCTAATATGGATATGACAAATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTAAGCCATAGTGCTAATACGGACATGACAAATAAGGTCGTGCCCACC
* * * * *
2253603 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGACATGATACATAAGGTCGT
1 ACCTACACTAAGCTTAAGCCATAGTGCTAATACGGACATGACAAATAAGGTCGT
2253657 ATCCACCTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (61 bp):
ACCTACACTAAGCTTAAGCCATAGTGCTAATACGGACATGACAAATAAGGTCGTGCCCACC
Found at i:2260664 original size:23 final size:23
Alignment explanation
Indices: 2260625--2260699 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
2260615 AAGTTCCACG
*
2260625 TAGAAATTATCCCGAAGGATCACA
1 TAGAAA-TGTCCCGAAGGATCACA
* *
2260649 TAGAAATGTCCCGAAGGATCGCG
1 TAGAAATGTCCCGAAGGATCACA
* * *
2260672 TAGAAGTGTCTCGAAGGACCACA
1 TAGAAATGTCCCGAAGGATCACA
*
2260695 CAGAA
1 TAGAA
2260700 TTATCCTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 36 0.86
24 6 0.14
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGATCACA
Found at i:2262388 original size:20 final size:21
Alignment explanation
Indices: 2262363--2262401 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2262353 TGTTTGGAAA
2262363 ATTACCCTAG-TATCGATAAT
1 ATTACCCTAGATATCGATAAT
*
2262383 ATTACCCTCGATATCGATA
1 ATTACCCTAGATATCGATA
2262402 CCAAGATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTACCCTAGATATCGATAAT
Found at i:2264378 original size:24 final size:24
Alignment explanation
Indices: 2264346--2264393 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2264336 CTAGTAGTCC
2264346 TTTTGGTTGTAAGTTTTTAGCCCA
1 TTTTGGTTGTAAGTTTTTAGCCCA
2264370 TTTTGGTTGTAAGTTTTTAGCCCA
1 TTTTGGTTGTAAGTTTTTAGCCCA
2264394 ACTCATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (24 bp):
TTTTGGTTGTAAGTTTTTAGCCCA
Found at i:2270574 original size:75 final size:75
Alignment explanation
Indices: 2270485--2270648 Score: 213
Period size: 76 Copynumber: 2.2 Consensus size: 75
2270475 TAAACTCAAG
* ** *
2270485 TTTAGGATAATATTTTAAACATTATATTT-TTTCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATATTATTTTAAACATTATATTTGTTT-TAGGTATTTTAATTTAAATAGGTTTTAGTAT
*
2270549 TTTAATTAAGT
65 TTTAATTAAGA
* **
2270560 TTTAGGATATTATTTTTATATTTTATATTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTAT
1 TTTAGGATATTA-TTTTAAACATTATATTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTAT
*
2270625 TTTAATTAGGA
65 TTTAATTAAGA
*
2270636 TTTAGAATATTAT
1 TTTAGGATATTAT
2270649 ATGATTTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 12 0.16
76 62 0.81
77 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (75 bp):
TTTAGGATATTATTTTAAACATTATATTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTATT
TTAATTAAGA
Found at i:2270583 original size:32 final size:32
Alignment explanation
Indices: 2270540--2270601 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
2270530 TTTAAATAGG
2270540 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
2270573 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
2270602 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:2270629 original size:24 final size:24
Alignment explanation
Indices: 2270521--2270631 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 24
2270511 TTTTTTCTTT
*
2270521 GTATTTTAGTTTAAATAGGTTTTA
1 GTATTTTAATTTAAATAGGTTTTA
* *
2270545 GTATTTTAA-TTAAGTTTTAGGATATTA
1 GTATTTTAATTTAA---ATAGG-TTTTA
* **
2270572 -T-TTTTATATTTTATATTTGTTTTA
1 GTATTTTA-A-TTTAAATAGGTTTTA
2270596 GGTATTTTAATTTAAATAGGTTTTA
1 -GTATTTTAATTTAAATAGGTTTTA
2270621 GTATTTTAATT
1 GTATTTTAATT
2270632 AGGATTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
23 4 0.06
24 23 0.35
25 19 0.29
26 8 0.12
27 9 0.14
28 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.59
Consensus pattern (24 bp):
GTATTTTAATTTAAATAGGTTTTA
Found at i:2270634 original size:19 final size:19
Alignment explanation
Indices: 2270530--2270640 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
2270520 TGTATTTTAG
*
2270530 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
2270549 TTTAATTAAGTTTTAGGATAT
1 TTTAATTAGGTTTTA-G-TAT
* **
2270570 TATT-TTTATATTTTA-TAT
1 T-TTAATTAGGTTTTAGTAT
* *
2270588 TTGT-TTTAGGTATTT--TAA
1 TT-TAATTAGGT-TTTAGTAT
*
2270606 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
2270625 TTTAATTAGGATTTAG
1 TTTAATTAGGTTTTAG
2270641 AATATTATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 32 0.45
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:2270649 original size:63 final size:62
Alignment explanation
Indices: 2270582--2270702 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 62
2270572 TTTTTATATT
*
2270582 TTATAT-TTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATA
1 TTATATATT-TTTTAGGTATTTTAATTTAAATA-GTTTAAGTATTTTAATTAGGATTTAGAATA
* * *
2270645 TTATATGATTTTTTAGGTATTTTAGTTTAAATAGTTTAAGTGTTTTACTTAGGATTTA
1 TTATAT-ATTTTTTAGGTATTTTAATTTAAATAGTTTAAGTATTTTAATTAGGATTTA
2270703 AGATGTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
63 28 0.54
64 22 0.42
65 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.55
Consensus pattern (62 bp):
TTATATATTTTTTAGGTATTTTAATTTAAATAGTTTAAGTATTTTAATTAGGATTTAGAATA
Found at i:2271232 original size:20 final size:20
Alignment explanation
Indices: 2271187--2271239 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2271177 ATTCTCTTTA
2271187 ATTTGTTTATTT--AATTATT
1 ATTT-TTTATTTAAAATTATT
*
2271206 A-TTTTTATTTAAAATTCTT
1 ATTTTTTATTTAAAATTATT
2271225 ATTTTTTATTTAAAA
1 ATTTTTTATTTAAAA
2271240 AAAAACTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.23
18 2 0.07
19 8 0.27
20 13 0.43
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTTATTTAAAATTATT
Found at i:2271312 original size:17 final size:15
Alignment explanation
Indices: 2271284--2271330 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
2271274 CTATTAATAT
*
2271284 TTATTATTT-TATTA
1 TTATTATTTATTTTA
*
2271298 TTATCATTT-TTTTA
1 TTATTATTTATTTTA
*
2271312 TAATTATTTATTTTA
1 TTATTATTTATTTTA
2271327 TTAT
1 TTAT
2271331 ACCTTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTATTTATTTTA
Found at i:2271643 original size:5 final size:5
Alignment explanation
Indices: 2271628--2271685 Score: 62
Period size: 5 Copynumber: 10.6 Consensus size: 5
2271618 GATGAAATTG
2271628 CTTTCT CTTTT CTTTT CTTTTT CTTTTCT CTTTCT CTTTT CTTTT CTTTT
1 CTTT-T CTTTT CTTTT C-TTTT C-TTT-T CTTT-T CTTTT CTTTT CTTTT
*
2271678 GTTTT CTT
1 CTTTT CTT
2271686 GATTTGGCAC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
5 24 0.50
6 22 0.46
7 2 0.04
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:2271649 original size:11 final size:11
Alignment explanation
Indices: 2271629--2271682 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
2271619 ATGAAATTGC
2271629 TTTCTCTTTTCT
1 TTTCT-TTTTCT
2271641 TTTCTTTTTCT
1 TTTCTTTTTCT
2271652 TTTCTCTTTCTCT
1 TTTCT-TTT-TCT
2271665 TTTC-TTTTCT
1 TTTCTTTTTCT
*
2271675 TTTGTTTT
1 TTTCTTTT
2271683 CTTGATTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.16
11 17 0.45
12 8 0.21
13 7 0.18
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:2271659 original size:18 final size:18
Alignment explanation
Indices: 2271628--2271674 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2271618 GATGAAATTG
2271628 CTTTCTCTTTTCT-TTTCT
1 CTTT-TCTTTTCTCTTTCT
2271646 -TTTTCTTTTCTCTTTCT
1 CTTTTCTTTTCTCTTTCT
2271663 CTTTTCTTTTCT
1 CTTTTCTTTTCT
2271675 TTTGTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
18 11 0.41
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTCTTTTCTCTTTCT
Found at i:2280128 original size:18 final size:20
Alignment explanation
Indices: 2280105--2280143 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2280095 TATTGTAACC
2280105 CCTTGT-AAA-GTCACCTAG
1 CCTTGTCAAATGTCACCTAG
2280123 CCTTGTCGAAATGTCACCTAG
1 CCTTGTC-AAATGTCACCTAG
2280144 TTATTCGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (20 bp):
CCTTGTCAAATGTCACCTAG
Found at i:2283240 original size:33 final size:33
Alignment explanation
Indices: 2283197--2283268 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
2283187 ACCAAGTGAC
*
2283197 ACCTTCCATCAAATTGAAAGATTAAGAGACATG
1 ACCTTTCATCAAATTGAAAGATTAAGAGACATG
2283230 ACCTTTCATCAAATTGAAAGATTAAGAGACATG
1 ACCTTTCATCAAATTGAAAGATTAAGAGACATG
2283263 ACCTTT
1 ACCTTT
2283269 GAAAATCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (33 bp):
ACCTTTCATCAAATTGAAAGATTAAGAGACATG
Found at i:2286503 original size:21 final size:21
Alignment explanation
Indices: 2286455--2286508 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2286445 GGTATTGAAA
* *
2286455 TGACAGTTCATGGTGTTGACG
1 TGACAGTCCATGGCGTTGACG
*
2286476 T-AGCAGTCCATGGCGTTGATG
1 TGA-CAGTCCATGGCGTTGACG
2286497 TGACAGTCCATG
1 TGACAGTCCATG
2286509 ATGGCTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (21 bp):
TGACAGTCCATGGCGTTGACG
Found at i:2286876 original size:25 final size:25
Alignment explanation
Indices: 2286826--2286893 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 25
2286816 ACTAGATGAA
* * *
2286826 TCGAGACTTATAAAATTTAAATTTG
1 TCGAGACTTATAATATTTTAAGTTG
*** *
2286851 TTTTGACTTATAATATTTTTAGTTG
1 TCGAGACTTATAATATTTTAAGTTG
2286876 TCGAGACTTATAAT-TTTT
1 TCGAGACTTATAATATTTT
2286894 GGATTAGTCG
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (25 bp):
TCGAGACTTATAATATTTTAAGTTG
Found at i:2290093 original size:27 final size:26
Alignment explanation
Indices: 2290042--2290093 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
2290032 CACTCAAAAA
*
2290042 AATATTTTATACATTTAATATTAAATT
1 AATATTTTATACATTT-ATAATAAATT
2290069 AATATTTTAATATCATTT-TAATAAA
1 AATATTTT-ATA-CATTTATAATAAA
2290094 ATATTAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 14 0.64
28 3 0.14
29 5 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATTTTATACATTTATAATAAATT
Found at i:2290904 original size:40 final size:40
Alignment explanation
Indices: 2290860--2291095 Score: 160
Period size: 40 Copynumber: 5.8 Consensus size: 40
2290850 AAAAATAATG
*
2290860 TACTTTAGTGGCATTTTTATAAAAACGCCGCTAAATTCTC
1 TACTTTAGTGGCATTTTTATACAAACGCCGCTAAATTCTC
** * *
2290900 TACTTTAGTGGTGTTTTTATACAAACGCCGCTAAAGGTC-A
1 TACTTTAGTGGCATTTTTATACAAACGCCGCTAAA-TTCTC
* * * * *
2290940 TACTTTAGTGGCGTTTTAAGCACAAATGCCGCT-AATTACAC
1 TACTTTAGTGGCATTTTTA-TACAAACGCCGCTAAATT-CTC
* * * *
2290981 GCACTTTAGTGGCA-TTTTACGCACAAACACTGCT-AATTACATGC
1 -TACTTTAGTGGCATTTTTA--TACAAACGCCGCTAAATT-C-T-C
* * * * * *
2291025 -ACTATAATGGCATTTTTATATAAACACCGATAAATAT-TG
1 TACTTTAGTGGCATTTTTATACAAACGCCGCTAAAT-TCTC
2291064 TACTTTAGTGGCATTTTTATACAAACGCCGCT
1 TACTTTAGTGGCATTTTTATACAAACGCCGCT
2291096 CAACCCTGCA
Statistics
Matches: 154, Mismatches: 30, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
39 1 0.01
40 79 0.51
41 26 0.17
42 41 0.27
43 6 0.04
44 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (40 bp):
TACTTTAGTGGCATTTTTATACAAACGCCGCTAAATTCTC
Found at i:2290999 original size:42 final size:42
Alignment explanation
Indices: 2290941--2291040 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
2290931 TAAAGGTCAT
* **
2290941 ACTTTAGTGGCGTTTTAAGCACAAATGCCGCTAATTACACGC
1 ACTTTAGTGGCATTTTAAGCACAAACACCGCTAATTACACGC
* * *
2290983 ACTTTAGTGGCATTTTACGCACAAACACTGCTAATTACATGC
1 ACTTTAGTGGCATTTTAAGCACAAACACCGCTAATTACACGC
* *
2291025 ACTATAATGGCATTTT
1 ACTTTAGTGGCATTTT
2291041 TATATAAACA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (42 bp):
ACTTTAGTGGCATTTTAAGCACAAACACCGCTAATTACACGC
Found at i:2293503 original size:20 final size:21
Alignment explanation
Indices: 2293465--2293503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2293455 TTTCTGGTCC
2293465 TATCCTATAAACACGACTGTG
1 TATCCTATAAACACGACTGTG
*
2293486 TATCTTATAAAC-CGACTG
1 TATCCTATAAACACGACTG
2293504 CCTACTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
TATCCTATAAACACGACTGTG
Found at i:2295061 original size:21 final size:21
Alignment explanation
Indices: 2295028--2295068 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2295018 TTCTACGTGC
2295028 TCCTTCGGGACATATATGTAA
1 TCCTTCGGGACATATATGTAA
2295049 TCCTT-GGGAACATATATGTA
1 TCCTTCGGG-ACATATATGTA
2295069 GTTATTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (21 bp):
TCCTTCGGGACATATATGTAA
Found at i:2295112 original size:21 final size:21
Alignment explanation
Indices: 2295058--2295112 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2295048 ATCCTTGGGA
*
2295058 ACATATATGTAGTTATTTGGAAT
1 ACATATATG--GTCATTTGGAAT
* *
2295081 ACCTATTTGGTCATTTGGAAT
1 ACATATATGGTCATTTGGAAT
*
2295102 ATATATATGGT
1 ACATATATGGT
2295113 TATTAAGGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 19 0.73
23 7 0.27
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (21 bp):
ACATATATGGTCATTTGGAAT
Found at i:2295194 original size:45 final size:46
Alignment explanation
Indices: 2295122--2295209 Score: 112
Period size: 45 Copynumber: 1.9 Consensus size: 46
2295112 TTATTAAGGA
2295122 GATATTTATGTGGTCCTTCGGGACATTTTATATG-G-CACTTCGATG
1 GATATTTATGTGGTCCTTCGGGACATTTT-TATGTGACACTTCGATG
*
2295167 GATATTTATGTGG-CACTTTGGTG-CATTTTTATGTGACACTTCG
1 GATATTTATGTGGTC-CTTCGG-GACATTTTTATGTGACACTTCG
2295210 GTGCATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
44 5 0.13
45 25 0.66
46 8 0.21
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (46 bp):
GATATTTATGTGGTCCTTCGGGACATTTTTATGTGACACTTCGATG
Found at i:2295212 original size:23 final size:23
Alignment explanation
Indices: 2295126--2295218 Score: 93
Period size: 23 Copynumber: 4.1 Consensus size: 23
2295116 TAAGGAGATA
2295126 TTTATGTGGTC-CTTCGG-GACA-T
1 TTTATGTGG-CACTTCGGTG-CATT
* * * *
2295148 TTTATATGGCACTTCGATGGATA
1 TTTATGTGGCACTTCGGTGCATT
*
2295171 TTTATGTGGCACTTTGGTGCATT
1 TTTATGTGGCACTTCGGTGCATT
*
2295194 TTTATGTGACACTTCGGTGCATT
1 TTTATGTGGCACTTCGGTGCATT
2295217 TT
1 TT
2295219 ATACAAGCTT
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.02
22 14 0.25
23 42 0.74
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (23 bp):
TTTATGTGGCACTTCGGTGCATT
Found at i:2308589 original size:10 final size:11
Alignment explanation
Indices: 2308569--2308594 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2308559 AATTTTGGCG
2308569 TTTTTGTTTTT
1 TTTTTGTTTTT
2308580 TTTTTGTTTTT
1 TTTTTGTTTTT
2308591 TTTT
1 TTTT
2308595 AAATAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:2309341 original size:42 final size:43
Alignment explanation
Indices: 2309260--2309357 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
2309250 ATAACTAATG
* **
2309260 AATAAAATAATAATAAACTAAACATATCTTAACTCTAATTCCT
1 AATAAAATAATAATAAACTAAACATAACCCAACTCTAATTCCT
*
2309303 AATAAAATAATAAT-AACTAAAGATAACCCAAC-CTTAATTCCT
1 AATAAAATAATAATAAACTAAACATAACCCAACTC-TAATTCCT
2309345 AATAAAATAATAA
1 AATAAAATAATAA
2309358 ATCTAATCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.02
42 35 0.70
43 14 0.28
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (43 bp):
AATAAAATAATAATAAACTAAACATAACCCAACTCTAATTCCT
Found at i:2326383 original size:40 final size:40
Alignment explanation
Indices: 2326328--2326460 Score: 194
Period size: 40 Copynumber: 3.3 Consensus size: 40
2326318 CTTGCACATA
* * * *
2326328 CATATGCACCGAAGTGCATTACAAATAAGATTGTTCCCAC
1 CATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCAC
*
2326368 CATATGCATCGAAGTGCATTACACATAAGGTCGTGCCCAC
1 CATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCAC
* * *
2326408 CATATACATCGAAGTGCATTACACATAAGGTCGTGCCAAC
1 CATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCAC
2326448 CATATGCACCGAA
1 CATATGCACCGAA
2326461 CTACTTAATC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
CATATGCACCGAAGTGCATTACACATAAGGTCGTGCCCAC
Found at i:2338948 original size:198 final size:198
Alignment explanation
Indices: 2338610--2339006 Score: 794
Period size: 198 Copynumber: 2.0 Consensus size: 198
2338600 TATACAATTG
2338610 TGTCATCTTTGTTACCTCGATGATTTTGTTTATTTAGTCTAAGTATCATAGAACATGTTAGACGA
1 TGTCATCTTTGTTACCTCGATGATTTTGTTTATTTAGTCTAAGTATCATAGAACATGTTAGACGA
2338675 ATGTTCATATATCAAAGATTTTGCTTGCCTTAATTTGATAAATTTGGACAAGTATATCTAAATAT
66 ATGTTCATATATCAAAGATTTTGCTTGCCTTAATTTGATAAATTTGGACAAGTATATCTAAATAT
2338740 CTCATAAATTTGTAGCTCCATTGTAAAAGAGAAAAATCCTTACCATTTTAATAACCTTTTCATCA
131 CTCATAAATTTGTAGCTCCATTGTAAAAGAGAAAAATCCTTACCATTTTAATAACCTTTTCATCA
2338805 TTT
196 TTT
2338808 TGTCATCTTTGTTACCTCGATGATTTTGTTTATTTAGTCTAAGTATCATAGAACATGTTAGACGA
1 TGTCATCTTTGTTACCTCGATGATTTTGTTTATTTAGTCTAAGTATCATAGAACATGTTAGACGA
2338873 ATGTTCATATATCAAAGATTTTGCTTGCCTTAATTTGATAAATTTGGACAAGTATATCTAAATAT
66 ATGTTCATATATCAAAGATTTTGCTTGCCTTAATTTGATAAATTTGGACAAGTATATCTAAATAT
2338938 CTCATAAATTTGTAGCTCCATTGTAAAAGAGAAAAATCCTTACCATTTTAATAACCTTTTCATCA
131 CTCATAAATTTGTAGCTCCATTGTAAAAGAGAAAAATCCTTACCATTTTAATAACCTTTTCATCA
2339003 TTT
196 TTT
2339006 T
1 T
2339007 TCCTTGTTGA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 199 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (198 bp):
TGTCATCTTTGTTACCTCGATGATTTTGTTTATTTAGTCTAAGTATCATAGAACATGTTAGACGA
ATGTTCATATATCAAAGATTTTGCTTGCCTTAATTTGATAAATTTGGACAAGTATATCTAAATAT
CTCATAAATTTGTAGCTCCATTGTAAAAGAGAAAAATCCTTACCATTTTAATAACCTTTTCATCA
TTT
Found at i:2349628 original size:21 final size:21
Alignment explanation
Indices: 2349604--2349651 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2349594 TAGGCTGGTG
*
2349604 TCCATACCAGATAAATTGATA
1 TCCATACCAGATAAACTGATA
* * *
2349625 TCCACATCAGATAAACTGGTA
1 TCCATACCAGATAAACTGATA
2349646 TCCATA
1 TCCATA
2349652 TAGGATGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (21 bp):
TCCATACCAGATAAACTGATA
Found at i:2352130 original size:27 final size:27
Alignment explanation
Indices: 2352099--2352151 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2352089 TCCTATAACC
*
2352099 GAATTAACTGGTTAAGCCGTCTAAACT
1 GAATTAACTGGTTAAGCCATCTAAACT
2352126 GAATTAACTGGTTAAGCCATCTAAAC
1 GAATTAACTGGTTAAGCCATCTAAAC
2352152 CGAGTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (27 bp):
GAATTAACTGGTTAAGCCATCTAAACT
Found at i:2354089 original size:13 final size:13
Alignment explanation
Indices: 2354066--2354107 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2354056 AATGACGCGC
*
2354066 AATGAGCGTCAAA
1 AATGCGCGTCAAA
* *
2354079 AATGCGTGTCATA
1 AATGCGCGTCAAA
2354092 AATGCGCGTCAAA
1 AATGCGCGTCAAA
2354105 AAT
1 AAT
2354108 TTATGATGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (13 bp):
AATGCGCGTCAAA
Found at i:2358682 original size:19 final size:20
Alignment explanation
Indices: 2358639--2358684 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2358629 GACTATGATG
* *
2358639 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
2358659 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
2358678 GAAATTG
1 GAAATTG
2358685 GATTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:2370813 original size:34 final size:35
Alignment explanation
Indices: 2370770--2370845 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
2370760 CCTATAAATA
*
2370770 TATATATAACAATATAAGATAAGAATGCACTC-CT
1 TATATATAACAATATAAGATAAGAACGCACTCACT
* *
2370804 TATATATAACAATATAGGGTAAGAACGCACTCACT
1 TATATATAACAATATAAGATAAGAACGCACTCACT
2370839 TAGTATA
1 TA-TATA
2370846 CTTCACTAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 29 0.78
35 4 0.11
36 4 0.11
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (35 bp):
TATATATAACAATATAAGATAAGAACGCACTCACT
Found at i:2371752 original size:6 final size:6
Alignment explanation
Indices: 2371738--2371770 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2371728 GACTCGTGAC
*
2371738 AAAAA- AAAAAG AAAAAG AAAAAG AAAAAT AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
2371771 GATGATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:2371758 original size:12 final size:11
Alignment explanation
Indices: 2371738--2371772 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2371728 GACTCGTGAC
2371738 AAAAAAAAAAG
1 AAAAAAAAAAG
2371749 AAAAAGAAAAAG
1 AAAAA-AAAAAG
*
2371761 AAAAATAAAAG
1 AAAAAAAAAAG
2371772 A
1 A
2371773 TGATAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2374328 original size:23 final size:23
Alignment explanation
Indices: 2374293--2374348 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2374283 GTTGTCCCAT
* *
2374293 TCTCATAAATTATTGCGAACTCA
1 TCTCATCAATTATTGCGAAATCA
*
2374316 TCTCATCAGTTATTGCGAAATCA
1 TCTCATCAATTATTGCGAAATCA
2374339 TCTCATCAAT
1 TCTCATCAAT
2374349 CCGGTATACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (23 bp):
TCTCATCAATTATTGCGAAATCA
Found at i:2380561 original size:30 final size:29
Alignment explanation
Indices: 2380527--2380599 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
2380517 TGCTTCACTG
**
2380527 AGTGTCCTTACACACTACAATGTTGTACTA
1 AGTGTCCTTA-ACACTACAATACTGTACTA
* *
2380557 AGTGTCC-TAACACTATAGTACTGTACTA
1 AGTGTCCTTAACACTACAATACTGTACTA
*
2380585 AATGTCCTTATACAC
1 AGTGTCCTTA-ACAC
2380600 CATAGTACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.58
29 4 0.11
30 11 0.31
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (29 bp):
AGTGTCCTTAACACTACAATACTGTACTA
Found at i:2380607 original size:30 final size:28
Alignment explanation
Indices: 2380550--2380607 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2380540 ACTACAATGT
* *
2380550 TGTACTAAGTGTCCTAACACTATAGTAC
1 TGTACTAAATGTCCTAACACCATAGTAC
2380578 TGTACTAAATGTCCTTATACACCATAGTAC
1 TGTACTAAATGTCC-TA-ACACCATAGTAC
2380608 CAAATGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 13 0.50
29 2 0.08
30 11 0.42
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (28 bp):
TGTACTAAATGTCCTAACACCATAGTAC
Found at i:2386874 original size:30 final size:30
Alignment explanation
Indices: 2386840--2387037 Score: 184
Period size: 30 Copynumber: 6.5 Consensus size: 30
2386830 ATATAGACTG
* * *
2386840 AGTGTCCTTACACACCATAGTGTTGCATTG
1 AGTGTCCTTACACACCATAGTGTTGTACTA
*
2386870 AGTGTCCTTACACA--TTACGATGTTGTACTA
1 AGTGTCCTTACACACCATA-G-TGTTGTACTA
* * *
2386900 AGTGTCCTTACACACCATAGTGTTGCATTG
1 AGTGTCCTTACACACCATAGTGTTGTACTA
** *
2386930 AGTGTCCTTACACATTACAGTGTTGTACTA
1 AGTGTCCTTACACACCATAGTGTTGTACTA
* * *
2386960 AGTGTCCTTACACACTATAATATTGTACTA
1 AGTGTCCTTACACACCATAGTGTTGTACTA
* * *
2386990 AATGTCCTTACACACCATAGTATCATATGCACTA
1 AGTGTCCTTACACACCATAG--T-GT-TGTACTA
2387024 AGTGTCCTTACACA
1 AGTGTCCTTACACA
2387038 TTATAGCGGT
Statistics
Matches: 137, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.01
29 1 0.01
30 109 0.80
31 1 0.01
32 3 0.02
33 2 0.01
34 19 0.14
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (30 bp):
AGTGTCCTTACACACCATAGTGTTGTACTA
Found at i:2386996 original size:90 final size:90
Alignment explanation
Indices: 2386838--2387010 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 90
2386828 CTATATAGAC
* * * * * * *
2386838 TGAGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTACGATGTTGTACTAAGT
1 TGAGTGTCCTTACACACCACAGTGTTGCACTAAGTGTCCTTACACACTACAATATTGTACTAAAT
2386903 GTCCTTACACACCATAGTGTTGCAT
66 GTCCTTACACACCATAGTGTTGCAT
** * *
2386928 TGAGTGTCCTTACACATTACAGTGTTGTACTAAGTGTCCTTACACACTATAATATTGTACTAAAT
1 TGAGTGTCCTTACACACCACAGTGTTGCACTAAGTGTCCTTACACACTACAATATTGTACTAAAT
2386993 GTCCTTACACACCATAGT
66 GTCCTTACACACCATAGT
2387011 ATCATATGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (90 bp):
TGAGTGTCCTTACACACCACAGTGTTGCACTAAGTGTCCTTACACACTACAATATTGTACTAAAT
GTCCTTACACACCATAGTGTTGCAT
Found at i:2387003 original size:60 final size:60
Alignment explanation
Indices: 2386840--2386974 Score: 254
Period size: 60 Copynumber: 2.2 Consensus size: 60
2386830 ATATAGACTG
2386840 AGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTACGATGTTGTACTA
1 AGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTACGATGTTGTACTA
2386900 AGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTAC-AGTGTTGTACTA
1 AGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTACGA-TGTTGTACTA
2386960 AGTGTCCTTACACAC
1 AGTGTCCTTACACAC
2386975 TATAATATTG
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 1 0.01
60 73 0.99
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (60 bp):
AGTGTCCTTACACACCATAGTGTTGCATTGAGTGTCCTTACACATTACGATGTTGTACTA
Found at i:2394867 original size:7 final size:7
Alignment explanation
Indices: 2394855--2394885 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2394845 AGATTTTTTA
2394855 TGAATAG
1 TGAATAG
2394862 TGAATAG
1 TGAATAG
2394869 TGAATAG
1 TGAATAG
2394876 T-AATAG
1 TGAATAG
2394882 TGAA
1 TGAA
2394886 CAATACCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (7 bp):
TGAATAG
Found at i:2394882 original size:13 final size:14
Alignment explanation
Indices: 2394855--2394885 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2394845 AGATTTTTTA
2394855 TGAATAGTGAATAG
1 TGAATAGTGAATAG
2394869 TGAATAGT-AATAG
1 TGAATAGTGAATAG
2394882 TGAA
1 TGAA
2394886 CAATACCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (14 bp):
TGAATAGTGAATAG
Found at i:2395446 original size:22 final size:22
Alignment explanation
Indices: 2395421--2395493 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
2395411 AAGCTTATTT
2395421 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
*
2395443 TACC-ATA-AGCTCGTAAGCTTATTT--
1 TACCAATATA-CT--T-A-C-CATTTAA
2395467 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
2395489 TACCA
1 TACCA
2395494 TAAGCTTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
20 5 0.13
21 6 0.15
22 10 0.26
23 2 0.05
24 5 0.13
25 6 0.15
26 5 0.13
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (22 bp):
TACCAATATACTTACCATTTAA
Found at i:2395459 original size:46 final size:46
Alignment explanation
Indices: 2395387--2395531 Score: 247
Period size: 46 Copynumber: 3.2 Consensus size: 46
2395377 ATAAAATCTT
*
2395387 TTACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATAC
1 TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATATAC
*
2395432 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATATAC
*
2395478 TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATACAC
1 TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATATAC
*
2395524 TTGCCATT
1 TTACCATT
2395532 ATTCCATAAC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 9 0.10
46 85 0.90
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (46 bp):
TTACCATTTAATACCATAAGCTTGTAAGCTTATTTTACCAATATAC
Found at i:2395562 original size:20 final size:20
Alignment explanation
Indices: 2395537--2395579 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2395527 CCATTATTCC
* *
2395537 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
2395557 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
2395577 ATA
1 ATA
2395580 GCCCAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:2395695 original size:40 final size:40
Alignment explanation
Indices: 2395637--2395785 Score: 219
Period size: 40 Copynumber: 3.8 Consensus size: 40
2395627 ACCGTAGTGC
* *
2395637 TACATATAGGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
* * *
2395677 TACACATAAGGTCGTGCCCACCATATACAACAAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
*
2395717 TACATATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
* *
2395757 TACACATAAGGTCGTACCCACCAT-TACAC
1 TACACATAAGGTCATGCCCACCATATACAC
2395786 AAAAATGTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 5 0.05
40 92 0.95
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
Found at i:2395770 original size:80 final size:79
Alignment explanation
Indices: 2395637--2395797 Score: 270
Period size: 80 Copynumber: 2.0 Consensus size: 79
2395627 ACCGTAGTGC
* *
2395637 TACATATAGGGTCATGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTGCCCACCATA
1 TACATATAAGGTCATGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTACCCACCAT-
*
2395702 TACA-ACAAAGTGTAT
65 TACACA-AAAATGTAT
2395717 TACATATAAGGTCATGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTACCCACCATT
1 TACATATAAGGTCATGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTACCCACCATT
2395782 ACACAAAAATGTAT
66 ACACAAAAATGTAT
2395796 TA
1 TA
2395798 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
79 14 0.18
80 63 0.82
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (79 bp):
TACATATAAGGTCATGCCCACCATATACACCGAAGTGTATTACACATAAGGTCGTACCCACCATT
ACACAAAAATGTAT
Found at i:2402944 original size:44 final size:45
Alignment explanation
Indices: 2402894--2403000 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 45
2402884 ATAAAATCTT
* *
2402894 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAA-ATAC
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACAC
2402938 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATACAC
* *
2402984 TTGCCA-TTATTCCATAA
1 TTACCATTTATACCATAA
2403001 CCATATACCA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 17 0.30
45 32 0.56
46 8 0.14
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACAC
Found at i:2403022 original size:20 final size:20
Alignment explanation
Indices: 2402997--2403039 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2402987 CCATTATTCC
* *
2402997 ATAACCATATACCATAGACA
1 ATAACCATAAACAATAGACA
2403017 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
2403037 ATA
1 ATA
2403040 GCCCAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:2403152 original size:40 final size:40
Alignment explanation
Indices: 2403097--2403258 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
2403087 ACCGTAGTGC
* *
2403097 TACACATAAGGTCGTGCCCGCCATTTACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2403137 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
2403177 TACACATAAGGTCGTGTCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
2403217 TACACATAAGGTCGTGCCCACCATATACACAAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2403257 TA
1 TA
2403259 TAAACCTGCA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:2409692 original size:24 final size:24
Alignment explanation
Indices: 2409664--2409720 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
2409654 TTATTGCACA
2409664 TAATCAATATTAATTTCTTTCACT
1 TAATCAATATTAATTTCTTTCACT
2409688 TAATCAATATTAATTTCTTTCACT
1 TAATCAATATTAATTTCTTTCACT
2409712 TAATCAATA
1 TAATCAATA
2409721 CTACTTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATCAATATTAATTTCTTTCACT
Found at i:2413462 original size:23 final size:21
Alignment explanation
Indices: 2413435--2413481 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 21
2413425 AGAATTATCG
2413435 ATGCATCGCATATTTATATTTT
1 ATGCAT-GCATATTTATATTTT
2413457 AT---TGCATATTTATATTTT
1 ATGCATGCATATTTATATTTT
2413475 ATTGCAT
1 A-TGCAT
2413482 TTTATCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
18 16 0.76
19 2 0.10
22 3 0.14
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (21 bp):
ATGCATGCATATTTATATTTT
Found at i:2413491 original size:16 final size:18
Alignment explanation
Indices: 2413442--2413493 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
2413432 TCGATGCATC
*
2413442 GCATATTTATATTTTATT
1 GCATATTTATACTTTATT
*
2413460 GCATATTTATATTTTATT
1 GCATATTTATACTTTATT
2413478 GCAT-TTTAT-CTTTATT
1 GCATATTTATACTTTATT
2413494 TTCTCCTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
16 6 0.18
17 5 0.15
18 22 0.67
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (18 bp):
GCATATTTATACTTTATT
Found at i:2413492 original size:23 final size:18
Alignment explanation
Indices: 2413442--2413486 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2413432 TCGATGCATC
2413442 GCATATTTATATTTTATT
1 GCATATTTATATTTTATT
2413460 GCATATTTATATTTTATT
1 GCATATTTATATTTTATT
2413478 GCAT-TTTAT
1 GCATATTTAT
2413487 CTTTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (18 bp):
GCATATTTATATTTTATT
Found at i:2417976 original size:46 final size:46
Alignment explanation
Indices: 2417919--2418136 Score: 307
Period size: 46 Copynumber: 4.7 Consensus size: 46
2417909 TTAAAATATG
* *
2417919 GCATCCATTCATGCCCTAATGCATCCTTTCATGCATTTTAATTATA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATA
* *
2417965 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATA
*
2418011 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATA
* * *
2418057 G--TCCTTTCATGCCTTAATGCATCATTTAATGCATTTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCA-TTTTAATTATA
*
2418102 GAATCC-TTCATGCCTTAAATAGCATCCTTTCATGC
1 GCATCCTTTCATGCCTT-AAT-GCATCCTTTCATGC
2418137 CTTAATGCAT
Statistics
Matches: 154, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
44 30 0.19
45 10 0.06
46 96 0.62
47 6 0.04
48 12 0.08
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATA
Found at i:2418112 original size:90 final size:91
Alignment explanation
Indices: 2417906--2418136 Score: 349
Period size: 92 Copynumber: 2.5 Consensus size: 91
2417896 TCAATTTATA
* * * *
2417906 CATTTAAAATATGGCATCCATTCATGCCCTAATGCATCCTTTCATGCATTTTAATTATAGCATCC
1 CATTTTAATTATGGCATCCATTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATAG-ATCC
*
2417971 TTTCATGCCTTAATGCATCATTTCATG
65 TTTCATGCCTTAATGCATCATTTAATG
*
2417998 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATAG-TCCT
1 CATTTTAATTATGGCATCCATTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATAGATCCT
2418062 TTCATGCCTTAATGCATCATTTAATG
66 TTCATGCCTTAATGCATCATTTAATG
*
2418088 CATTTTTAATTATGGAATCC-TTCATGCCTTAAATAGCATCCTTTCATGC
1 CA-TTTTAATTATGGCATCCATTCATGCCTT-AAT-GCATCCTTTCATGC
2418137 CTTAATGCAT
Statistics
Matches: 129, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
90 41 0.32
91 19 0.15
92 69 0.53
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (91 bp):
CATTTTAATTATGGCATCCATTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATAGATCCT
TTCATGCCTTAATGCATCATTTAATG
Found at i:2418135 original size:68 final size:66
Alignment explanation
Indices: 2417919--2418202 Score: 249
Period size: 68 Copynumber: 4.2 Consensus size: 66
2417909 TTAAAATATG
* * * * * *
2417919 GCATCCATTCATGCCCTAATGCATCCTTTCATGCATTTTAATTATAGCATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGAATCCTTTCATGCCTTAA
2417984 T
66 T
* * * * * *
2417985 GCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATG
1 GCATCCTTTCATGC--CTT-A--AT-GCATCATTTAATGCATTTTAATTATGGAATCCTTTCATG
*
2418044 CATTTTAAGT
60 C--CTTAA-T
**
2418054 ATAGTCCTTTCATGCCTTAATGCATCATTTAATGCATTTTTAATTATGGAATCC-TTCATGCCTT
1 GCA-TCCTTTCATGCCTTAATGCATCATTTAATGCA-TTTTAATTATGGAATCCTTTCATGCCTT
2418118 AAAT
64 -AAT
* *
2418122 AGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTA
1 -GCATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGAATCCTTTCATGCCTTA
2418187 AT
65 AT
2418189 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2418203 ATTTTAAGTA
Statistics
Matches: 179, Mismatches: 19, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
64 12 0.07
65 2 0.01
66 40 0.22
67 24 0.13
68 52 0.29
69 7 0.04
70 21 0.12
71 7 0.04
72 14 0.08
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (66 bp):
GCATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGAATCCTTTCATGCCTTAA
T
Found at i:2418170 original size:158 final size:159
Alignment explanation
Indices: 2417962--2418372 Score: 668
Period size: 158 Copynumber: 2.6 Consensus size: 159
2417952 CATTTTAATT
2417962 ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
1 ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
2418027 TAATGCATCCTTTCATGCATTTTAAGTATAG-TCCTTTCATGCCTTAATGCATCATTTAATGCAT
66 TAATGCATCCTTTCATGCATTTTAAGTATAGATCCTTTCATGCCTTAATGCATCATTTAATGCAT
2418091 TTTTAATTATGGAATCC-TTCATGCCTTAA
131 TTTTAATTATGGAATCCTTTCATGCCTT-A
2418120 ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
1 ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
2418185 TAATGCATCCTTTCATGCATTTTAAGTATAGTATCCTTTCATGCCTTAATGCATCATTTAATGCA
66 TAATGCATCCTTTCATGCATTTTAAGTATAG-ATCCTTTCATGCCTTAATGCATCATTTAATGCA
2418250 TTTTTAATTATGGAATCCTTTCATGCCTTA
130 TTTTTAATTATGGAATCCTTTCATGCCTTA
* * * *
2418280 AT-GCATTCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGTAT-CTTTC
1 ATAGCATCCTTTCATGC--CTT-A--AT-GCATCATTTCATGCATTTTAATTATGGCATCCTTTC
* *
2418343 ATGCATTAATACATCCTTTCATGCATTTTA
60 ATGCCTTAATGCATCCTTTCATGCATTTTA
2418373 CATACTCTAT
Statistics
Matches: 238, Mismatches: 6, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
158 96 0.40
159 13 0.05
160 53 0.22
161 12 0.05
162 1 0.00
164 35 0.15
165 28 0.12
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (159 bp):
ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
TAATGCATCCTTTCATGCATTTTAAGTATAGATCCTTTCATGCCTTAATGCATCATTTAATGCAT
TTTTAATTATGGAATCCTTTCATGCCTTA
Found at i:2418175 original size:46 final size:46
Alignment explanation
Indices: 2418123--2418321 Score: 319
Period size: 46 Copynumber: 4.3 Consensus size: 46
2418113 GCCTTAAATA
2418123 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
* * *
2418169 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAGTATA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
* *
2418215 GTATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTTTAATTATG
*
2418262 GAATCCTTTCATGCCTTAATGCATTC-TTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCA-TCATTTCATGCATTTTAATTATG
2418308 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2418322 ATTTTAATTA
Statistics
Matches: 140, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
46 99 0.71
47 39 0.28
48 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
Found at i:2418291 original size:93 final size:92
Alignment explanation
Indices: 2418120--2418321 Score: 341
Period size: 93 Copynumber: 2.2 Consensus size: 92
2418110 CATGCCTTAA
* *
2418120 ATAGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCT
1 ATAGCATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGAATCCTTTCATGCCT
2418185 TAATGCATCCTTTCATGCATTTTAAGT
66 TAATGCATCCTTTCATGCATTTTAAGT
*
2418212 ATAGTATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTTAATTATGGAATCCTTTCATGCC
1 ATAGCATCCTTTCATGCCTTAATGCATCATTTAATGCA-TTTTAATTATGGAATCCTTTCATGCC
* *
2418277 TTAATGCATTCTTTCATGCATTTTAATT
65 TTAATGCATCCTTTCATGCATTTTAAGT
*
2418305 ATGGCATCCTTTCATGC
1 ATAGCATCCTTTCATGC
2418322 ATTTTAATTA
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
92 36 0.35
93 66 0.65
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (92 bp):
ATAGCATCCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGAATCCTTTCATGCCT
TAATGCATCCTTTCATGCATTTTAAGT
Found at i:2418347 original size:25 final size:25
Alignment explanation
Indices: 2417939--2418349 Score: 135
Period size: 26 Copynumber: 17.6 Consensus size: 25
2417929 ATGCCCTAAT
*
2417939 GCATCCTTTCATGCATTTTAATTATA
1 GCAT-CTTTCATGCATTTTAATTATG
*
2417965 GCATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
2417985 GCATCATTTCATGCATTTTAATTATG
1 GCATC-TTTCATGCATTTTAATTATG
*
2418011 GCATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
* *
2418031 GCATCCTTTCATGCATTTTAAGTATA
1 GCAT-CTTTCATGCATTTTAATTATG
*
2418057 G--TCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
*
2418075 GCATCATTTAATGCATTTTTAATTATG
1 GCATC-TTTCATGCA-TTTTAATTATG
* * * *
2418102 GAATCCTTCATGC--CTTAA--ATA
1 GCATCTTTCATGCATTTTAATTATG
*
2418123 GCATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
2418143 GCATCATTTCATGCATTTTAATTATG
1 GCATC-TTTCATGCATTTTAATTATG
*
2418169 GCATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
* *
2418189 GCATCCTTTCATGCATTTTAAGTATA
1 GCAT-CTTTCATGCATTTTAATTATG
* *
2418215 GTATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
*
2418235 GCATCATTTAATGCATTTTTAATTATG
1 GCATC-TTTCATGCA-TTTTAATTATG
* *
2418262 GAATCCTTTCATGC--CTT-A--AT-
1 GCAT-CTTTCATGCATTTTAATTATG
2418282 GCATTCTTTCATGCATTTTAATTATG
1 GCA-TCTTTCATGCATTTTAATTATG
2418308 GCATCCTTTCATGCATTTTAATTATG
1 GCAT-CTTTCATGCATTTTAATTATG
*
2418334 GTATCTTTCATGCATT
1 GCATCTTTCATGCATT
2418350 AATACATCCT
Statistics
Matches: 301, Mismatches: 28, Indels: 113
0.68 0.06 0.26
Matches are distributed among these distances:
18 1 0.00
19 6 0.02
20 81 0.27
21 20 0.07
22 23 0.08
23 18 0.06
24 23 0.08
25 23 0.08
26 89 0.30
27 16 0.05
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.44
Consensus pattern (25 bp):
GCATCTTTCATGCATTTTAATTATG
Found at i:2418878 original size:22 final size:23
Alignment explanation
Indices: 2418841--2418893 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
2418831 CTGGTATCGA
*
2418841 TACCCTTACCATGGTACTGATAC
1 TACCCTTACCATGGTACTAATAC
*
2418864 TACCC-TACTATGGTACTAATAC
1 TACCCTTACCATGGTACTAATAC
*
2418886 -CCCCTTAC
1 TACCCTTAC
2418894 GACATTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.30
Consensus pattern (23 bp):
TACCCTTACCATGGTACTAATAC
Found at i:2423988 original size:17 final size:17
Alignment explanation
Indices: 2423966--2424086 Score: 64
Period size: 17 Copynumber: 7.1 Consensus size: 17
2423956 AATTAAGAGT
2423966 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* **
2423983 TAGTTTGATGGATGAAC
1 TAGTTTAATAAATGAAC
* *
2424000 AAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * * *
2424017 TAACTTTATTCAATGAAA
1 T-AGTTTAATAAATGAAC
** * * *
2424035 TAAATGAATGAATGAAA
1 TAGTTTAATAAATGAAC
*
2424052 TAGTTTATTAAAT-AAC
1 TAGTTTAATAAATGAAC
* **
2424068 TAGATGCATAAATGAAC
1 TAGTTTAATAAATGAAC
2424085 TA
1 TA
2424087 CTTCCCTAAA
Statistics
Matches: 75, Mismatches: 27, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
16 11 0.15
17 51 0.68
18 13 0.17
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2427936 original size:17 final size:17
Alignment explanation
Indices: 2427889--2427941 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2427879 AATTAAGAGT
2427889 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * * *
2427906 AAATTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
2427923 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
2427940 TA
1 TA
2427942 ACTTTATTCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:2427954 original size:18 final size:17
Alignment explanation
Indices: 2427892--2427956 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2427882 TAAGAGTTAG
* * *
2427892 TTTAATAAATGAACAAA
1 TTTAATTAATGAACTAC
* * *
2427909 TTTGATGAATGAACTAG
1 TTTAATTAATGAACTAC
2427926 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACT-AC
2427944 TTT-ATTCAATGAA
1 TTTAATT-AATGAA
2427957 ATAAATGCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 29 0.74
18 10 0.26
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (17 bp):
TTTAATTAATGAACTAC
Found at i:2434142 original size:14 final size:14
Alignment explanation
Indices: 2434123--2434164 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
2434113 TTTCAATTTT
2434123 GAGTTATTCGAGTC
1 GAGTTATTCGAGTC
2434137 GAGTTATTCGAGTC
1 GAGTTATTCGAGTC
*
2434151 GAGTTATTCAAGTC
1 GAGTTATTCGAGTC
2434165 AACTTGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (14 bp):
GAGTTATTCGAGTC
Found at i:2434514 original size:153 final size:160
Alignment explanation
Indices: 2434293--2434628 Score: 429
Period size: 153 Copynumber: 2.1 Consensus size: 160
2434283 ATTTCATTAT
* * * * * * *
2434293 TTCTTCAATTCCTCCTTCA-TTTAAGTCCATTGTTTTTCCCAAAATTGAACTACGTGCTCTTAAA
1 TTCTTCAATTCGTCATTTATTTTAAGTCCATTGTTTTTACCAAAATTGAACCACATGCTCCTAAA
* *
2434357 CCATAGTAGAATACATGTGTACTTTCAATTCC-TCTTTTTGAT-A-ATA-TTTT-TTTTTCAATT
66 CCATAGAAGAATACATGTGTACTTTCAATTCCAT-TTTTTGATAACAAATTTTTATTTTTCAATT
* * **
2434417 TAGTCTTTTAA-TTTTTCATAATCTTTTTAA
130 TAGTCCTTCAATTTTTTCATAATCTCCTTAA
* * *
2434447 TTCTTCAATTCGTCATTTATTTTAAGTCCA-T-TTTTTACTAAATTTGAACCACATGCTCCTAAG
1 TTCTTCAATTCGTCATTTATTTTAAGTCCATTGTTTTTACCAAAATTGAACCACATGCTCCTAAA
2434510 CCATAGAAGAATACATGTGTACTTTCAATTCCATTTTTTGATAACAAATTTTTATTTTTCAATTT
66 CCATAGAAGAATACATGTGTACTTTCAATTCCATTTTTTGATAACAAATTTTTATTTTTCAATTT
*
2434575 AGTCCTTCAATTTTTTCATAATCTCCTTAT
131 AGTCCTTCAATTTTTTCATAATCTCCTTAA
* *
2434605 TTCTTCAATTTGTGATTTATTTTA
1 TTCTTCAATTCGTCATTTATTTTA
2434629 GAGAAAATAA
Statistics
Matches: 156, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
153 64 0.41
154 19 0.12
155 12 0.08
156 4 0.03
157 19 0.12
158 38 0.24
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (160 bp):
TTCTTCAATTCGTCATTTATTTTAAGTCCATTGTTTTTACCAAAATTGAACCACATGCTCCTAAA
CCATAGAAGAATACATGTGTACTTTCAATTCCATTTTTTGATAACAAATTTTTATTTTTCAATTT
AGTCCTTCAATTTTTTCATAATCTCCTTAA
Found at i:2434823 original size:21 final size:21
Alignment explanation
Indices: 2434794--2434846 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2434784 ATTTTGACTA
2434794 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
2434815 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2434836 TCGCAATGCGA
1 TCGCATTGCGA
2434847 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2434861 original size:20 final size:20
Alignment explanation
Indices: 2434836--2434989 Score: 227
Period size: 20 Copynumber: 7.7 Consensus size: 20
2434826 TTTTCCTAAT
2434836 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2434856 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2434877 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2434897 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
2434917 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2434937 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2434957 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2434977 TCGCAACGCGAAT
1 TCGCAATGCGAAT
2434990 CTGACTATCG
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
20 105 0.88
21 15 0.12
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2434966 original size:60 final size:60
Alignment explanation
Indices: 2434836--2435007 Score: 238
Period size: 60 Copynumber: 2.9 Consensus size: 60
2434826 TTTTCCTAAT
** *
2434836 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAATCGCAATGCGAATACGTAAA
* * * *
2434897 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAATCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCGCAATGCGAATACGTAAA
**
2434957 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTGACTATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATAC-GAAAATCGCAATGCGA
2435008 TTTACATAGA
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
59 1 0.01
60 66 0.68
61 30 0.31
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAATCGCAATGCGAATACGTAAA
Found at i:2435000 original size:40 final size:40
Alignment explanation
Indices: 2434836--2435007 Score: 199
Period size: 40 Copynumber: 4.3 Consensus size: 40
2434826 TTTTCCTAAT
* *
2434836 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GACAA
* * *
2434877 TCGCAATGCGATTACGTAAATCGCAATGCGATTAC-GTA-AA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACAA
* *
2434917 TCGCAATGCGAATACGTAAATCGTAATGCGAATAC-GTA-AA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-ACAA
*
2434957 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACAA
2434997 TCGCAATGCGA
1 TCGCAATGCGA
2435008 TTTACATAGA
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.02
40 84 0.72
41 31 0.26
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACAA
Found at i:2435213 original size:22 final size:22
Alignment explanation
Indices: 2435187--2435252 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
2435177 GGCGACATCC
*
2435187 GTCCCCATCTCTGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2435209 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
2435231 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
2435253 TTAATGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2435686 original size:20 final size:20
Alignment explanation
Indices: 2435589--2435679 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
2435579 GCGATTCTGT
2435589 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** * **
2435608 CGTTGCGATAGTAAAATTCG
1 CGTTGCGATTTTCATTTTCG
*
2435628 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2435648 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
2435668 TGTTGCGATTTT
1 CGTTGCGATTTT
2435680 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:2437537 original size:20 final size:20
Alignment explanation
Indices: 2437512--2437690 Score: 78
Period size: 20 Copynumber: 9.6 Consensus size: 20
2437502 AGAATAGTTT
* **
2437512 ACTATCGCAATGTGAAAATG
1 ACTATCGCAACGCAAAAATG
2437532 ACTATCGCAACGCAAAAATG
1 ACTATCGCAACGCAAAAATG
*
2437552 ACTATCGCAACG---AGA-G
1 ACTATCGCAACGCAAAAATG
*
2437568 A--ATCGCAATGC-AAAATG
1 ACTATCGCAACGCAAAAATG
** *
2437585 AAAATCGCAA--CAACAA--
1 ACTATCGCAACGCAAAAATG
*
2437601 A--ATCGCAACGCGAAAATG
1 ACTATCGCAACGCAAAAATG
* * **
2437619 ACTATCACAATGCGGAAATG
1 ACTATCGCAACGCAAAAATG
* ** *
2437639 ACTATTGCAATACGAAAATG
1 ACTATCGCAACGCAAAAATG
* * **
2437659 ACTATCACAATGCAAATTTG
1 ACTATCGCAACGCAAAAATG
2437679 ACTATCGCAACG
1 ACTATCGCAACG
2437691 AAAGAATCAC
Statistics
Matches: 123, Mismatches: 24, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
14 15 0.12
16 9 0.07
17 5 0.04
18 4 0.03
19 7 0.06
20 83 0.67
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCAAAAATG
Found at i:2437592 original size:33 final size:34
Alignment explanation
Indices: 2437535--2437619 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
2437525 GAAAATGACT
** * * *
2437535 ATCGCAACGCAAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCAAAAATGAAAATCGCAACAACAAA
*
2437569 ATCGCAATGC-AAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCAAAAATGAAAATCGCAACAACAAA
*
2437602 ATCGCAACGCGAAAATGA
1 ATCGCAACGCAAAAATGA
2437620 CTATCACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 27 0.63
34 16 0.37
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (34 bp):
ATCGCAACGCAAAAATGAAAATCGCAACAACAAA
Found at i:2437681 original size:40 final size:39
Alignment explanation
Indices: 2437602--2437726 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 39
2437592 CAACAACAAA
**
2437602 ATCGCAACGCGAAAATGACTATCACAATGCGGAAATGACT
1 ATCGCAATACGAAAATGACTATCACAATGC-GAAATGACT
*
2437642 ATTGCAATACGAAAATGACTATCACAATGC-AAATTTGACT
1 ATCGCAATACGAAAATGACTATCACAATGCGAAA--TGACT
**
2437682 ATCGC-A-ACG-AAA-GA--ATCACAATGCGAAATGAAA
1 ATCGCAATACGAAAATGACTATCACAATGCGAAATGACT
*
2437715 ATCGCATTACGA
1 ATCGCAATACGA
2437727 TTCTCTCGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
33 8 0.11
34 10 0.14
35 6 0.08
36 2 0.03
37 3 0.04
38 6 0.08
39 1 0.01
40 36 0.50
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (39 bp):
ATCGCAATACGAAAATGACTATCACAATGCGAAATGACT
Found at i:2437831 original size:20 final size:20
Alignment explanation
Indices: 2437733--2437821 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
2437723 ACGATTCTCT
* *
2437733 CGTTACGATAGTCAAATTT-G
1 CGTTGCGATAGTC-ATTTTCG
*
2437753 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2437773 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2437793 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2437813 CGTTGCGAT
1 CGTTGCGAT
2437822 TTTAAGTTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.06
20 60 0.94
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2439934 original size:33 final size:33
Alignment explanation
Indices: 2439884--2439979 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
2439874 AAAACAGACT
* **
2439884 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* * *
2439918 ATCGCAATGCGAAATGAAAATCTCTACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2439951 ATCGCAATGCGAAAATCAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2439980 CGAAATTAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 29 0.56
34 23 0.44
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2440014 original size:20 final size:20
Alignment explanation
Indices: 2439989--2440116 Score: 133
Period size: 20 Copynumber: 6.7 Consensus size: 20
2439979 GCGAAATTAG
**
2439989 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
*
2440009 TTTCGCATTGCGAT--TC--
1 TTTCGCGTTGCGATAGTCAT
*
2440025 TCTC--GTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* *
2440043 TTCCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
2440063 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* *
2440083 TTCCGTGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
*
2440103 ATTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2440117 TTCTGCGTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
18 4 0.04
20 73 0.82
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:2440083 original size:40 final size:40
Alignment explanation
Indices: 2440028--2440116 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
2440018 GCGATTCTCT
2440028 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATA-TTCG
*
2440068 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
2440108 CGTTGCGAT
1 CGTTGCGAT
2440117 TTCTGCGTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 46 0.98
41 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:2442608 original size:24 final size:24
Alignment explanation
Indices: 2442541--2442600 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2442531 CTGAAAAATC
2442541 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
2442565 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
2442589 ATCAAATTTCGA
1 ATCAAAATTCGA
2442601 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:2443479 original size:20 final size:20
Alignment explanation
Indices: 2443435--2443482 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2443425 GAAATTCAGT
*
2443435 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
2443455 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
2443475 ATTGCGAT
1 ATTGCGAT
2443483 TTACGTATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:2443492 original size:20 final size:20
Alignment explanation
Indices: 2443469--2443580 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
2443459 CGATAGTCAG
*
2443469 ATTCGCATTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
2443489 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
* *
2443509 ATTCACGTTACGATTTACGT
1 ATTCGCGTTGCGATTTACGT
* * **
2443529 ATTCACGTTGCGATTTTCCAA
1 ATTCGCGTTGCGA-TTTACGT
*
2443550 ATTCGTGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
2443570 ATTCGCATTGC
1 ATTCGCGTTGC
2443581 AAATTAGGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 62 0.81
21 15 0.19
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACGT
Found at i:2443498 original size:40 final size:38
Alignment explanation
Indices: 2443454--2443580 Score: 119
Period size: 40 Copynumber: 3.2 Consensus size: 38
2443444 GTCAGAATCT
*
2443454 CGTTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCG
* * * *
2443494 CGTTGCGATTTACGTATTCACGTTACGATTTACGTATTCA
1 CGTTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCG
* *
2443534 CGTTGCGATTTTCCAAATTCGTGTTGCGATTTACGTATTCG
1 CGTTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCG
*
2443575 CATTGC
1 CGTTGC
2443581 AAATTAGGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 38 0.54
41 26 0.37
42 2 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (38 bp):
CGTTGCGATTCAGATTCGCGTTGCGATTTACGTATTCG
Found at i:2443624 original size:21 final size:21
Alignment explanation
Indices: 2443572--2443624 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2443562 ATTTACGTAT
* *
2443572 TCGCATTGCAAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
2443593 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
2443614 TCGCAATGCGA
1 TCGCAATGCGA
2443625 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:2444220 original size:15 final size:14
Alignment explanation
Indices: 2444197--2444238 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
2444187 TCCTCAAAAT
2444197 TATTTTGAAATATAA
1 TATTTTGAAATAT-A
*
2444212 TATTATG-AATAT-
1 TATTTTGAAATATA
2444224 TATTTTGAAATATA
1 TATTTTGAAATATA
2444238 T
1 T
2444239 CAACAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 6 0.26
15 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATTTTGAAATATA
Found at i:2444319 original size:21 final size:21
Alignment explanation
Indices: 2444290--2444330 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2444280 TAATTGGAAC
* * *
2444290 AAATCATTATCATAATATTAT
1 AAATAATTATAATAAAATTAT
2444311 AAATAATTATAATAAAATTA
1 AAATAATTATAATAAAATTA
2444331 GTATAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATAATTATAATAAAATTAT
Found at i:2445531 original size:17 final size:17
Alignment explanation
Indices: 2445502--2445542 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2445492 GTGAATTGAT
*
2445502 TATTTAATAATAACTAA
1 TATTTAATAATAAATAA
2445519 TATTATAAT-ATAAATAA
1 TATT-TAATAATAAATAA
2445536 TATTTAA
1 TATTTAA
2445543 CATATTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTAATAATAAATAA
Done.