Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 16 of 29
Found at i:5753674 original size:18 final size:19
Alignment explanation
Indices: 5753648--5753694 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5753638 TAGCCCAGCC
*
5753648 AAAATGAGAAAAAT-GAAA
1 AAAAGGAGAAAAATAGAAA
*
5753666 AAAAGGAGAAATATAGAAA
1 AAAAGGAGAAAAATAGAAA
*
5753685 AACAGGAGAA
1 AAAAGGAGAA
5753695 GTGGCAGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.68, C:0.02, G:0.21, T:0.09
Consensus pattern (19 bp):
AAAAGGAGAAAAATAGAAA
Found at i:5772738 original size:19 final size:20
Alignment explanation
Indices: 5772711--5772748 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5772701 GGAGTAACGC
*
5772711 ATTAAGG-AAGAACACATTT
1 ATTAAGGAAAAAACACATTT
*
5772730 ATTATGGAAAAAACACATT
1 ATTAAGGAAAAAACACATT
5772749 AGCCCATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (20 bp):
ATTAAGGAAAAAACACATTT
Found at i:5780219 original size:31 final size:32
Alignment explanation
Indices: 5780168--5780232 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
5780158 GGAGAAAGTT
*
5780168 TAAATTCTTATTATTATCTTATGTATGGAGGA
1 TAAATTCTTATTATTATCTTATATATGGAGGA
*
5780200 TAAATTCTT-TTATTTTCTTATATATGGAGGA
1 TAAATTCTTATTATTATCTTATATATGGAGGA
5780231 TA
1 TA
5780233 TTCATTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (32 bp):
TAAATTCTTATTATTATCTTATATATGGAGGA
Found at i:5789519 original size:17 final size:17
Alignment explanation
Indices: 5789490--5789522 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5789480 TAAATAATAG
5789490 CATACAATGTCATTTTC
1 CATACAATGTCATTTTC
5789507 CATACGAAT-TCATTTT
1 CATAC-AATGTCATTTT
5789523 TCAATGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (17 bp):
CATACAATGTCATTTTC
Found at i:5798926 original size:61 final size:57
Alignment explanation
Indices: 5798861--5799026 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 57
5798851 TAAATTAAAA
* *
5798861 GTTATTTTTTAATTTTAAAATTTTTAATTGAATTAAATTTATATTTTTATCCAAGTTATAT
1 GTTATTTTTTAATTTTAAAA-CTTT-A-T-AATTAAATTTATATTTTTATCAAAGTTATAT
* * *
5798922 GTTATTTTTTAATTTTGTTAAACTTTATATTTATATTTATATTTTTATCAAAGTTATAT
1 GTTATTTTTTAA-TTT-TAAAACTTTATAATTAAATTTATATTTTTATCAAAGTTATAT
* * * * *
5798981 ATTATTTTTTATTTTGTTAAACTTTATATTTATATTTATATTTTTA
1 GTTATTTTTTAATTT-TAAAACTTTATAATTAAATTTATATTTTTA
5799027 AAAAAATTAA
Statistics
Matches: 96, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
58 34 0.35
59 38 0.40
60 1 0.01
61 13 0.14
62 6 0.06
63 4 0.04
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (57 bp):
GTTATTTTTTAATTTTAAAACTTTATAATTAAATTTATATTTTTATCAAAGTTATAT
Found at i:5798937 original size:30 final size:30
Alignment explanation
Indices: 5798898--5799026 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 30
5798888 TTGAATTAAA
*
5798898 TTTATATTTTTATCCAAGTTATATGTTATTT
1 TTTATATTTTTATCAAAGTTATAT-TTATTT
* *
5798929 TTTA-ATTTTGT-T-AAACTTTATATTTA-TA
1 TTTATATTTT-TATCAAA-GTTATATTTATTT
5798957 TTTATATTTTTATCAAAGTTATATATTATTT
1 TTTATATTTTTATCAAAGTTATAT-TTATTT
** *
5798988 TTTAT-TTTGTTA--AACTTTATATTTA-TA
1 TTTATATTT-TTATCAAAGTTATATTTATTT
5799015 TTTATATTTTTA
1 TTTATATTTTTA
5799027 AAAAAATTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
27 9 0.11
28 12 0.15
29 25 0.31
30 21 0.26
31 14 0.17
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTATATTTTTATCAAAGTTATATTTATTT
Found at i:5798965 original size:29 final size:29
Alignment explanation
Indices: 5798929--5799024 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
5798919 TATGTTATTT
5798929 TTTA-ATTTTGTTAAACTTTATATTTATA
1 TTTATATTTTGTTAAACTTTATATTTATA
*
5798957 TTTATATTTT-TATCAAA-GTTATATATTAT-
1 TTTATATTTTGT-T-AAACTTTATAT-TTATA
*
5798986 TTTTTATTTTGTTAAACTTTATATTTATA
1 TTTATATTTTGTTAAACTTTATATTTATA
5799015 TTTATATTTT
1 TTTATATTTT
5799025 TAAAAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
28 12 0.21
29 37 0.65
30 8 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTATATTTTGTTAAACTTTATATTTATA
Found at i:5799017 original size:58 final size:59
Alignment explanation
Indices: 5798897--5799026 Score: 235
Period size: 58 Copynumber: 2.2 Consensus size: 59
5798887 ATTGAATTAA
* *
5798897 ATTTATATTTTTATCCAAGTTATATGTTATTTTTTAATTTTGTTAAACTTTATATTTAT
1 ATTTATATTTTTATCAAAGTTATATATTATTTTTTAATTTTGTTAAACTTTATATTTAT
5798956 ATTTATATTTTTATCAAAGTTATATATTATTTTTT-ATTTTGTTAAACTTTATATTTAT
1 ATTTATATTTTTATCAAAGTTATATATTATTTTTTAATTTTGTTAAACTTTATATTTAT
5799014 ATTTATATTTTTA
1 ATTTATATTTTTA
5799027 AAAAAATTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 36 0.52
59 33 0.48
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (59 bp):
ATTTATATTTTTATCAAAGTTATATATTATTTTTTAATTTTGTTAAACTTTATATTTAT
Found at i:5800926 original size:44 final size:44
Alignment explanation
Indices: 5800859--5801124 Score: 306
Period size: 44 Copynumber: 6.0 Consensus size: 44
5800849 TATCTATAGA
* *
5800859 ACCTAAACGAG-TCTAGTTAAGATCAACTAGATAACAAAATATAT
1 ACCTAAATGAGCT-TAGTTGAGATCAACTAGATAACAAAATATAT
* * *
5800903 ACCTAAGTGAGCTTAGTTGAGATCAGCTATAGATAACAAAATACAT
1 ACCTAAATGAGCTTAGTTGAGATCAAC--TAGATAACAAAATATAT
* * * *
5800949 ACC-AAAAGAAGCCTAGCTGAGATCAACTAGATAATAAAATATAT
1 ACCTAAATG-AGCTTAGTTGAGATCAACTAGATAACAAAATATAT
* *
5800993 ACCTAAATGAGCCTAGTTGAGATCATCTAGATAACAAAATATAT
1 ACCTAAATGAGCTTAGTTGAGATCAACTAGATAACAAAATATAT
* *
5801037 ACCTAAATGAG-TATAGTTGAGTTCAACTAGAAAACAAAATATAT
1 ACCTAAATGAGCT-TAGTTGAGATCAACTAGATAACAAAATATAT
* * *
5801081 TCCTAAATGA-ATCTAGTTGAGTTCAACTAGATAACAAAATATAT
1 ACCTAAATGAGCT-TAGTTGAGATCAACTAGATAACAAAATATAT
5801125 CTATAGAAAA
Statistics
Matches: 192, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
44 150 0.78
45 8 0.04
46 34 0.18
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (44 bp):
ACCTAAATGAGCTTAGTTGAGATCAACTAGATAACAAAATATAT
Found at i:5806119 original size:13 final size:13
Alignment explanation
Indices: 5806103--5806151 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
5806093 TCTGAACTCA
5806103 ATTATTTATATTT
1 ATTATTTATATTT
**
5806116 ATTATGAATATTT
1 ATTATTTATATTT
*
5806129 ATTTATTTATTTTT
1 A-TTATTTATATTT
5806143 GATTATTTA
1 -ATTATTTA
5806152 AGTTATTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 12 0.41
14 16 0.55
15 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (13 bp):
ATTATTTATATTT
Found at i:5807179 original size:2 final size:2
Alignment explanation
Indices: 5807172--5807201 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5807162 TTAGAAGATC
5807172 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
5807202 GCTTAAAATG
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:5814348 original size:6 final size:6
Alignment explanation
Indices: 5814315--5814356 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
5814305 AAAAAACAGA
* * *
5814315 AAAGAG -AAGAG AAAAAA AAAGAG GAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
5814357 TATGGAGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:5817021 original size:20 final size:20
Alignment explanation
Indices: 5816996--5817036 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5816986 AACATAATAG
5816996 TATCATCAGCAAATTACAAA
1 TATCATCAGCAAATTACAAA
5817016 TATCATCAGCAAATTACAAA
1 TATCATCAGCAAATTACAAA
5817036 T
1 T
5817037 GAGAAATGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (20 bp):
TATCATCAGCAAATTACAAA
Found at i:5820345 original size:15 final size:15
Alignment explanation
Indices: 5820325--5820376 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
5820315 GCATGTAAAG
5820325 TAAATAACATAAAAA
1 TAAATAACATAAAAA
* *
5820340 TAAATATCTTAAAAA
1 TAAATAACATAAAAA
5820355 CTAAATAACATAAAAA
1 -TAAATAACATAAAAA
5820371 TAAATA
1 TAAATA
5820377 TCTTAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATAACATAAAAA
Found at i:5820360 original size:31 final size:31
Alignment explanation
Indices: 5820325--5820388 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
5820315 GCATGTAAAG
5820325 TAAATAACATAAAAATAAATATCTTAAAAAC
1 TAAATAACATAAAAATAAATATCTTAAAAAC
5820356 TAAATAACATAAAAATAAATATCTTAAAAAC
1 TAAATAACATAAAAATAAATATCTTAAAAAC
5820387 TA
1 TA
5820389 GGCTTACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (31 bp):
TAAATAACATAAAAATAAATATCTTAAAAAC
Found at i:5820383 original size:15 final size:15
Alignment explanation
Indices: 5820334--5820385 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
5820324 GTAAATAACA
5820334 TAAAAATAAATATCT
1 TAAAAATAAATATCT
* *
5820349 TAAAAACTAAATAACA
1 TAAAAA-TAAATATCT
5820365 TAAAAATAAATATCT
1 TAAAAATAAATATCT
5820380 TAAAAA
1 TAAAAA
5820386 CTAGGCTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAATAAATATCT
Found at i:5833541 original size:60 final size:59
Alignment explanation
Indices: 5833461--5833578 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
5833451 GCCCAATCCA
* ** * *
5833461 ATTTAATAAATCAAAGGACAAAATGTGATACATACTACATTATAGCAAATTCAATATTTT
1 ATTTAACAAATCAAAGGACAAAAAATAATACATACTACATGATAGCAAATTC-ATATTTT
*
5833521 ATTTAACAAATCCAAA-GACAAAAAATAATACATACTACATGATAGTAAATTCATATTT
1 ATTTAACAAAT-CAAAGGACAAAAAATAATACATACTACATGATAGCAAATTCATATTT
5833579 AAGTTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 6 0.12
60 41 0.80
61 4 0.08
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (59 bp):
ATTTAACAAATCAAAGGACAAAAAATAATACATACTACATGATAGCAAATTCATATTTT
Found at i:5845253 original size:32 final size:32
Alignment explanation
Indices: 5845217--5845321 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
5845207 AACAATGACA
5845217 GCTTAAACTTGATGAGCACTTTGATAAATGGC
1 GCTTAAACTTGATGAGCACTTTGATAAATGGC
** * * *
5845249 GCTTAAGTTTGATTAG-A---AGA-ACAATGAC
1 GCTTAAACTTGATGAGCACTTTGATA-AATGGC
5845277 AGCTTAAACTTGATGAGCACTTTGATAAATGGC
1 -GCTTAAACTTGATGAGCACTTTGATAAATGGC
*
5845310 GCTTAAGCTTGA
1 GCTTAAACTTGA
5845322 CATGGCTTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 13 0.24
30 1 0.02
31 1 0.02
32 24 0.44
33 7 0.13
34 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (32 bp):
GCTTAAACTTGATGAGCACTTTGATAAATGGC
Found at i:5845285 original size:61 final size:61
Alignment explanation
Indices: 5845190--5845321 Score: 255
Period size: 61 Copynumber: 2.2 Consensus size: 61
5845180 AAGCATAAAT
5845190 TTAAGTTTGATTAGAAGAACAATGACAGCTTAAACTTGATGAGCACTTTGATAAATGGCGC
1 TTAAGTTTGATTAGAAGAACAATGACAGCTTAAACTTGATGAGCACTTTGATAAATGGCGC
5845251 TTAAGTTTGATTAGAAGAACAATGACAGCTTAAACTTGATGAGCACTTTGATAAATGGCGC
1 TTAAGTTTGATTAGAAGAACAATGACAGCTTAAACTTGATGAGCACTTTGATAAATGGCGC
*
5845312 TTAAGCTTGA
1 TTAAGTTTGA
5845322 CATGGCTTGT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (61 bp):
TTAAGTTTGATTAGAAGAACAATGACAGCTTAAACTTGATGAGCACTTTGATAAATGGCGC
Found at i:5845289 original size:29 final size:29
Alignment explanation
Indices: 5845196--5845290 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
5845186 AAATTTAAGT
5845196 TTGATTAGAAGAACAATGACAGCTTAAAC
1 TTGATTAGAAGAACAATGACAGCTTAAAC
* * * **
5845225 TTGATGAGCACTTTGATA-AATGGC-GCTTAAGT
1 TTGATTAG-A---AGA-ACAATGACAGCTTAAAC
5845257 TTGATTAGAAGAACAATGACAGCTTAAAC
1 TTGATTAGAAGAACAATGACAGCTTAAAC
5845286 TTGAT
1 TTGAT
5845291 GAGCACTTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
27 1 0.02
28 7 0.14
29 18 0.37
30 1 0.02
31 1 0.02
32 13 0.27
33 7 0.14
34 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (29 bp):
TTGATTAGAAGAACAATGACAGCTTAAAC
Found at i:5850729 original size:2 final size:2
Alignment explanation
Indices: 5850722--5850756 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5850712 TAAAAATGAC
*
5850722 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5850757 GATTTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5853039 original size:3 final size:3
Alignment explanation
Indices: 5853031--5853058 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5853021 CGTCCTATGG
5853031 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5853059 TTGAAAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5857852 original size:41 final size:42
Alignment explanation
Indices: 5857789--5857875 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
5857779 TTTTCATTTT
5857789 TTATCTCTCTTCAACCCCATCATCTTCTTCTCCTC-TTCTTCCA
1 TTATCTCTC-TCAACCCCATCATCTTCTTCTCCTCTTTCTT-CA
* *
5857832 TTATCTCTC-CAACTCTATCATCTTCTTCTCCTCTTTCTTCA
1 TTATCTCTCTCAACCCCATCATCTTCTTCTCCTCTTTCTTCA
5857873 TTA
1 TTA
5857876 AAATTAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 27 0.66
42 5 0.12
43 9 0.22
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (42 bp):
TTATCTCTCTCAACCCCATCATCTTCTTCTCCTCTTTCTTCA
Found at i:5859825 original size:24 final size:24
Alignment explanation
Indices: 5859798--5859853 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5859788 GCATTGCTTG
* *
5859798 GGAGGTGGGGGTGGTTCAGGATCA
1 GGAGCTGGGGCTGGTTCAGGATCA
* *
5859822 GGAGCTGGGGCTGGTTCCGGTTCA
1 GGAGCTGGGGCTGGTTCAGGATCA
*
5859846 GGATCTGG
1 GGAGCTGG
5859854 AGGTTCAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.50, T:0.23
Consensus pattern (24 bp):
GGAGCTGGGGCTGGTTCAGGATCA
Found at i:5860018 original size:60 final size:60
Alignment explanation
Indices: 5859916--5860028 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
5859906 GCGGCAGGTC
*
5859916 GGTGCAGGTTCTGAGCTGTTCATTGCTGCAGGGTCCTATGCTGGGTCTCGAGCCGGCTCT
1 GGTGCAGGTTCTGAGCTGTTCATTGCTGCAGGGTCCTATGCTGGCTCTCGAGCCGGCTCT
* * *
5859976 GGTGCAGGTTCTGAAGCTGGTTCA-T-CTGCTGGTTCCTCTGCTGGCTCTCGAGC
1 GGTGCAGGTTCTG-AGCT-GTTCATTGCTGCAGGGTCCTATGCTGGCTCTCGAGC
5860029 TGGGTCAGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 37 0.79
61 5 0.11
62 5 0.11
ACGTcount: A:0.10, C:0.26, G:0.34, T:0.31
Consensus pattern (60 bp):
GGTGCAGGTTCTGAGCTGTTCATTGCTGCAGGGTCCTATGCTGGCTCTCGAGCCGGCTCT
Found at i:5867132 original size:30 final size:30
Alignment explanation
Indices: 5867098--5867159 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5867088 TCTCCAGTGG
5867098 TCGCTGCTCTTGCCTTAATTTGTACTATTA
1 TCGCTGCTCTTGCCTTAATTTGTACTATTA
5867128 TCGCTGCTCTTGCCTTAATTTGTACTATTA
1 TCGCTGCTCTTGCCTTAATTTGTACTATTA
5867158 TC
1 TC
5867160 CGCAATCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (30 bp):
TCGCTGCTCTTGCCTTAATTTGTACTATTA
Found at i:5870537 original size:25 final size:26
Alignment explanation
Indices: 5870493--5870542 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
5870483 TTTAAATTAT
5870493 TTAGTTAGAGTTATAATATAATACTG
1 TTAGTTAGAGTTATAATATAATACTG
*
5870519 TTAGTTAGA-TTATATTATAATACT
1 TTAGTTAGAGTTATAATATAATACT
5870543 ATTAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAGTTAGAGTTATAATATAATACTG
Found at i:5874736 original size:30 final size:30
Alignment explanation
Indices: 5874687--5874758 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5874677 TATTAAGTTT
* *
5874687 AATAAATTTTATATATTTTTATTTTAAGTCA
1 AATAAATTTT-TGTATTTTTATTTTAAATCA
* *
5874718 AGTAAGTTTTTGTATTTTTATTTTAAATCA
1 AATAAATTTTTGTATTTTTATTTTAAATCA
5874748 AATAAATTTTT
1 AATAAATTTTT
5874759 ATAATTAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 27 0.77
31 8 0.23
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (30 bp):
AATAAATTTTTGTATTTTTATTTTAAATCA
Found at i:5874933 original size:22 final size:20
Alignment explanation
Indices: 5874895--5874934 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
5874885 GTGATTTTTT
*
5874895 TATTATGTATATCAATATTA
1 TATTATGTATATAAATATTA
5874915 TATTAGTGTCATATAAATAT
1 TATTA-TGT-ATATAAATAT
5874935 AAAATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (20 bp):
TATTATGTATATAAATATTA
Found at i:5886979 original size:29 final size:28
Alignment explanation
Indices: 5886940--5886994 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
5886930 TCTATTAATG
5886940 AAAATAATTATATCGTTAGCAAAAAAAA
1 AAAATAATTATATCGTTAGCAAAAAAAA
5886968 AAAATTAATTATATCGTTAGCAAAAAA
1 AAAA-TAATTATATCGTTAGCAAAAAA
5886995 TAGATGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.27
Consensus pattern (28 bp):
AAAATAATTATATCGTTAGCAAAAAAAA
Found at i:5905448 original size:2 final size:2
Alignment explanation
Indices: 5905435--5905466 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5905425 AGTTTTGAGT
*
5905435 TA TA TA TT 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
5905467 AGATTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5907751 original size:41 final size:41
Alignment explanation
Indices: 5907694--5907779 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
5907684 TGCCTGTTGC
* *
5907694 CATTATGGGATAAAAATGTAAAAAGTAAAAGTTTTTTCTTT
1 CATTATGGGATAAAAATGTAAAAAGCAAAAGATTTTTCTTT
*
5907735 CATTATGGTATAAAAATGTAAAAAGCAAAAGATTTTTCTTT
1 CATTATGGGATAAAAATGTAAAAAGCAAAAGATTTTTCTTT
5907776 CATT
1 CATT
5907780 TACATGTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (41 bp):
CATTATGGGATAAAAATGTAAAAAGCAAAAGATTTTTCTTT
Found at i:5911769 original size:8 final size:8
Alignment explanation
Indices: 5911743--5911784 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
5911733 AAATTATGAA
5911743 TAAAATAT
1 TAAAATAT
* *
5911751 TAATATTT
1 TAAAATAT
5911759 TAAAATAT
1 TAAAATAT
5911767 TAAAAT-T
1 TAAAATAT
*
5911774 TAAATTAT
1 TAAAATAT
5911782 TAA
1 TAA
5911785 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TAAAATAT
Found at i:5911777 original size:15 final size:16
Alignment explanation
Indices: 5911743--5911784 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
5911733 AAATTATGAA
*
5911743 TAAAATATTAATATTT
1 TAAAATATTAATAATT
5911759 TAAAATATTAA-AATT
1 TAAAATATTAATAATT
*
5911774 TAAATTATTAA
1 TAAAATATTAA
5911785 GAAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATATTAATAATT
Found at i:5912075 original size:22 final size:22
Alignment explanation
Indices: 5912050--5912127 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
5912040 AAGATTTAAA
5912050 TTATAAATAAAATATTAGTATT
1 TTATAAATAAAATATTAGTATT
*
5912072 TTAT-AATATTAATGATTAG-A--
1 TTATAAATA-AAAT-ATTAGTATT
*
5912092 TTATAAATAAAATATTAATATT
1 TTATAAATAAAATATTAGTATT
* *
5912114 TAAAAAATAAAATA
1 TTATAAATAAAATA
5912128 AAATATATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 4 0.09
20 8 0.18
21 8 0.18
22 20 0.44
23 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TTATAAATAAAATATTAGTATT
Found at i:5933181 original size:26 final size:26
Alignment explanation
Indices: 5933135--5933184 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5933125 TATAATTCAC
* *
5933135 TAATTATTTAAATCAATTTAAAATTT
1 TAATTATGTAAATAAATTTAAAATTT
5933161 TAATTATGTAAA-AAATATTAAAAT
1 TAATTATGTAAATAAAT-TTAAAAT
5933185 ACACTTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTATGTAAATAAATTTAAAATTT
Found at i:5933632 original size:14 final size:14
Alignment explanation
Indices: 5933613--5933648 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5933603 AATTAACACA
5933613 ATATATAAAAAAAT
1 ATATATAAAAAAAT
*
5933627 ATATATTAAAAAAT
1 ATATATAAAAAAAT
5933641 AT-TATAAA
1 ATATATAAA
5933649 TTAATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATATAAAAAAAT
Found at i:5933687 original size:22 final size:24
Alignment explanation
Indices: 5933638--5933698 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
5933628 TATATTAAAA
5933638 AATATTATAAATTAATTAATAATTTT
1 AATATTATAAATTAATT-ATAA-TTT
*
5933664 AATTTTATAAATTAATT-TAA-TT
1 AATATTATAAATTAATTATAATTT
*
5933686 AATAATATAAATT
1 AATATTATAAATT
5933699 TGTATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 13 0.41
24 3 0.09
26 16 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTATAAATTAATTATAATTT
Found at i:5935155 original size:18 final size:19
Alignment explanation
Indices: 5935132--5935174 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5935122 GTTTTTTATT
5935132 TATTTTAAATA-ATAATTA
1 TATTTTAAATATATAATTA
*
5935150 TATTTTAAATATATAGTTA
1 TATTTTAAATATATAATTA
*
5935169 CATTTT
1 TATTTT
5935175 TTATTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTTAAATATATAATTA
Found at i:5935468 original size:22 final size:22
Alignment explanation
Indices: 5935421--5935471 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5935411 TTTTTAATTC
*
5935421 AAAAAATAACAAGTAGAAAATGA
1 AAAAAATAACAAGTA-AAAATAA
*
5935444 AAAAAATAGACAAGT-AATATAA
1 AAAAAATA-ACAAGTAAAAATAA
5935466 AAAAAA
1 AAAAAA
5935472 GGAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAAATAACAAGTAAAAATAA
Found at i:5937433 original size:24 final size:25
Alignment explanation
Indices: 5937393--5937439 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
5937383 ATAACAACTT
*
5937393 TTTGTATATTATGTAAAAAGTTATC
1 TTTGTACATTATGTAAAAAGTTATC
*
5937418 TTTGTACA-TATGTAAAAGGTTA
1 TTTGTACATTATGTAAAAAGTTA
5937440 ATTAACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (25 bp):
TTTGTACATTATGTAAAAAGTTATC
Found at i:5937813 original size:22 final size:20
Alignment explanation
Indices: 5937776--5937816 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
5937766 TTGAATTTTA
*
5937776 TTAAATATATAATAAAAAAT
1 TTAAAAATATAATAAAAAAT
*
5937796 TTAAAAATGATAATTAAAAAT
1 TTAAAAAT-ATAATAAAAAAT
5937817 ATAATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAAATATAATAAAAAAT
Found at i:5937820 original size:12 final size:12
Alignment explanation
Indices: 5937775--5937827 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
5937765 ATTGAATTTT
*
5937775 ATTAAATATATA
1 ATTAAAAATATA
5937787 A-TAAAAA-AT-
1 ATTAAAAATATA
5937796 -TTAAAAATGATA
1 ATTAAAAAT-ATA
5937808 ATTAAAAATATA
1 ATTAAAAATATA
5937820 ATTAAAAA
1 ATTAAAAA
5937828 AGAATATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 7 0.20
12 12 0.34
13 8 0.23
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATTAAAAATATA
Found at i:5938007 original size:17 final size:16
Alignment explanation
Indices: 5937985--5938030 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5937975 ATTTTTCATT
5937985 TATTTTTAAAGAATATA
1 TATTTTTAAA-AATATA
5938002 TATTTTTTAAAAATATA
1 TA-TTTTTAAAAATATA
* *
5938019 AAATTTTAAAAA
1 TATTTTTAAAAA
5938031 ATAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 9 0.35
18 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TATTTTTAAAAATATA
Found at i:5938025 original size:16 final size:15
Alignment explanation
Indices: 5938006--5938038 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5937996 AATATATATT
5938006 TTTTAAAAATATAAAA
1 TTTTAAAAA-ATAAAA
5938022 TTTTAAAAAATAAAA
1 TTTTAAAAAATAAAA
5938037 TT
1 TT
5938039 ATTCATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTTAAAAAATAAAA
Found at i:5938029 original size:15 final size:16
Alignment explanation
Indices: 5938006--5938038 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5937996 AATATATATT
*
5938006 TTTTAAAAATATAAAA
1 TTTTAAAAAAATAAAA
5938022 TTTT-AAAAAATAAAA
1 TTTTAAAAAAATAAAA
5938037 TT
1 TT
5938039 ATTCATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTAAAAAAATAAAA
Found at i:5938031 original size:17 final size:17
Alignment explanation
Indices: 5937988--5938033 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5937978 TTTCATTTAT
* * *
5937988 TTTTAAAGAATATATAT
1 TTTTAAAAAATATAAAA
*
5938005 TTTTTAAAAATATAAAA
1 TTTTAAAAAATATAAAA
5938022 TTTTAAAAAATA
1 TTTTAAAAAATA
5938034 AAATTATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTTAAAAAATATAAAA
Found at i:5940101 original size:12 final size:13
Alignment explanation
Indices: 5940084--5940116 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
5940074 ATATATTTTT
5940084 AATAATTTTTA-A
1 AATAATTTTTATA
5940096 AATAATTTTTATTA
1 AATAATTTTTA-TA
5940110 AATAATT
1 AATAATT
5940117 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAATTTTTATA
Found at i:5940284 original size:23 final size:23
Alignment explanation
Indices: 5940258--5940310 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
5940248 AGTAAAGTTA
*
5940258 TTATTTAATTTTTTTATTTATAT
1 TTATTTAATTTTTTTAATTATAT
*
5940281 TTATTT-ATTTTTTTAATTCTAT
1 TTATTTAATTTTTTTAATTATAT
5940303 TCTATTTA
1 T-TATTTA
5940311 CTTATATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTAATTTTTTTAATTATAT
Found at i:5940451 original size:16 final size:16
Alignment explanation
Indices: 5940432--5940464 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5940422 GTTATGTGGA
*
5940432 TTTTATTTTTAATAAT
1 TTTTATTTTTAAAAAT
5940448 TTTTATTTTTAAAAAT
1 TTTTATTTTTAAAAAT
5940464 T
1 T
5940465 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTTTTAAAAAT
Found at i:5940695 original size:14 final size:13
Alignment explanation
Indices: 5940678--5940725 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
5940668 TTTGTATATC
5940678 ATATTTAACTATTT
1 ATATTTAA-TATTT
*
5940692 ATATTTTATATATT
1 ATATTTAATAT-TT
5940706 ATAATTTAATATTT
1 AT-ATTTAATATTT
5940720 AATATT
1 -ATATT
5940726 ATAAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 10 0.34
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:5940718 original size:28 final size:29
Alignment explanation
Indices: 5940666--5940725 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
5940656 GAAATTCTTA
*
5940666 ATTTTGTATATCATATTTAACTATTT-AT
1 ATTTTATATATCATATTTAACTATTTAAT
*
5940694 ATTTTATATATTATAATTTAA-TATTTAAT
1 ATTTTATATATCAT-ATTTAACTATTTAAT
5940723 ATT
1 ATT
5940726 ATAAGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTTATATATCATATTTAACTATTTAAT
Found at i:5940726 original size:20 final size:22
Alignment explanation
Indices: 5940696--5940735 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5940686 CTATTTATAT
5940696 TTTATATATTATAA-TTTAATA
1 TTTATATATTATAAGTTTAATA
5940717 TTTA-ATATTATAAGTTTAA
1 TTTATATATTATAAGTTTAA
5940736 ATATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTATATATTATAAGTTTAATA
Found at i:5940742 original size:20 final size:20
Alignment explanation
Indices: 5940701--5940743 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5940691 TATATTTTAT
*
5940701 ATATTATAATTTAATATTTA
1 ATATTATAATTTAATATATA
5940721 ATATTATAAGTTTAA-ATATA
1 ATATTATAA-TTTAATATATA
5940741 ATA
1 ATA
5940744 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTATAATTTAATATATA
Found at i:5952039 original size:92 final size:92
Alignment explanation
Indices: 5951842--5952029 Score: 306
Period size: 92 Copynumber: 2.1 Consensus size: 92
5951832 ATATATATAT
** * * *
5951842 GAATGGACTAAGAAAGGTAGGCAAGCAAAATTGCCTAGGAATAAATGAACATTGAATATTCAAAG
1 GAATGGACTGGGAACGGTGGGCAAGCAAAATTGCCTAGGAATAAATGAACATTGAATACTCAAAG
*
5951907 AACTAAAGATCATGAGCGGCAAAAAGA
66 AACTAAAGATCATGAGCAGCAAAAAGA
*
5951934 GAATGGACTGGGAACGGTGGGCAAGCAAATTTGCCTAGGAATAAATGAACATTGAATACTCAAA-
1 GAATGGACTGGGAACGGTGGGCAAGCAAAATTGCCTAGGAATAAATGAACATTGAATACTCAAAG
5951998 AACTAAAGATCATGAGCAGCAAAAAGA
66 AACTAAAGATCATGAGCAGCAAAAAGA
5952025 GAATG
1 GAATG
5952030 TGGTTGGGAA
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 31 0.35
92 58 0.65
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.18
Consensus pattern (92 bp):
GAATGGACTGGGAACGGTGGGCAAGCAAAATTGCCTAGGAATAAATGAACATTGAATACTCAAAG
AACTAAAGATCATGAGCAGCAAAAAGA
Found at i:5953800 original size:47 final size:46
Alignment explanation
Indices: 5953693--5953800 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 46
5953683 TTACTATATA
*
5953693 ATACTAATATTAATATAAATTAATTTAATAATATAAGTTATATTACT
1 ATACT-ATATTAATATAAATTAATTTAATAATATAAGCTATATTACT
* * *
5953740 ATAGTATACTAATATTAA-TAATTTAAT-ATAAGTAATGCTATATTACT
1 ATACTATATTAATATAAATTAATTTAATAAT-A-TAA-GCTATATTACT
*
5953787 ATACTTTATTAATA
1 ATACTATATTAATA
5953801 ACTTATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 2 0.04
45 10 0.20
46 14 0.27
47 25 0.49
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (46 bp):
ATACTATATTAATATAAATTAATTTAATAATATAAGCTATATTACT
Found at i:5957882 original size:35 final size:35
Alignment explanation
Indices: 5957836--5957904 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
5957826 TATGGAATAG
5957836 GCAAATACACTTCATCAGTCAGTCCTCTAGGAGTT
1 GCAAATACACTTCATCAGTCAGTCCTCTAGGAGTT
5957871 GCAAATACACTTCATCAGTCAGTCCTCTAGGAGT
1 GCAAATACACTTCATCAGTCAGTCCTCTAGGAGT
5957905 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (35 bp):
GCAAATACACTTCATCAGTCAGTCCTCTAGGAGTT
Found at i:5962287 original size:22 final size:22
Alignment explanation
Indices: 5962262--5962310 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5962252 ATTTTGTTAA
*
5962262 TATATAATTTTTGACTAATTAG
1 TATATAATTATTGACTAATTAG
** *
5962284 TATATTGTTATTGGCTAATTAG
1 TATATAATTATTGACTAATTAG
5962306 TATAT
1 TATAT
5962311 TAATAAGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (22 bp):
TATATAATTATTGACTAATTAG
Found at i:5968328 original size:3 final size:3
Alignment explanation
Indices: 5968320--5968350 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5968310 CTGAACTAAC
5968320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5968351 CATATATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5974723 original size:59 final size:59
Alignment explanation
Indices: 5974623--5974734 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
5974613 CTGTTTTTAT
5974623 ATATATACACAATAATCCTAATGCATTAATTCTCAGAACTAGGGGTTTTGTTCTAACTC
1 ATATATACACAATAATCCTAATGCATTAATTCTCAGAACTAGGGGTTTTGTTCTAACTC
* * * *
5974682 ATATGTACACAATAATCCTAGTGCATTAATTC-CTAGCACTAGGGTTTTTGTTC
1 ATATATACACAATAATCCTAATGCATTAATTCTC-AGAACTAGGGGTTTTGTTC
5974735 CTCTATTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (59 bp):
ATATATACACAATAATCCTAATGCATTAATTCTCAGAACTAGGGGTTTTGTTCTAACTC
Found at i:5975690 original size:77 final size:76
Alignment explanation
Indices: 5975538--5975691 Score: 195
Period size: 77 Copynumber: 2.0 Consensus size: 76
5975528 AAAAGTTTAA
* * *
5975538 ATATGAAAAATTATCTTTTCATATTAAAGCTTAAAGTTATGTCTTATAAAATAAGTGATTATCCT
1 ATATGAAAAATTATCTTTTCATATTAAAGCTTAAAATTATGTCTTATAAAATAAATGATTAGCCT
5975603 GTTATAAGGTG
66 GTTATAAGGTG
* * * * *
5975614 ATATGAAAAGTTATCTTTTCATATTATA-TTTCAAAAATTATGTCTTATAGAATAAATGGTTAGC
1 ATATGAAAAATTATCTTTTCATATTAAAGCTT--AAAATTATGTCTTATAAAATAAATGATTAGC
5975678 CT-TTGATAAGGTG
64 CTGTT-ATAAGGTG
5975691 A
1 A
5975692 CTGTTAAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
75 2 0.03
76 28 0.42
77 37 0.55
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (76 bp):
ATATGAAAAATTATCTTTTCATATTAAAGCTTAAAATTATGTCTTATAAAATAAATGATTAGCCT
GTTATAAGGTG
Found at i:5992860 original size:22 final size:22
Alignment explanation
Indices: 5992817--5992862 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5992807 ATTATATGAT
**
5992817 TAATTTTTAAGCAGTGCTTTAC
1 TAATTTTTAAGCAGTGAGTTAC
* *
5992839 TAATTTTTAAGTATTGAGTTAC
1 TAATTTTTAAGCAGTGAGTTAC
5992861 TA
1 TA
5992863 GTTGATATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (22 bp):
TAATTTTTAAGCAGTGAGTTAC
Found at i:5992958 original size:23 final size:23
Alignment explanation
Indices: 5992901--5993011 Score: 100
Period size: 23 Copynumber: 4.9 Consensus size: 23
5992891 TAGGTATTAT
* *
5992901 GTGACTGATTAGTAAGACATTGC
1 GTGACTAATTAGTAAGGCATTGC
5992924 GTGACTAATTAGTAAGGCATTGC
1 GTGACTAATTAGTAAGGCATTGC
* ** * *
5992947 GTGATTGGTTAGTAAGGTATTGT
1 GTGACTAATTAGTAAGGCATTGC
* * *
5992970 ATAACTAATTTGTAAGGCATT--
1 GTGACTAATTAGTAAGGCATTGC
* *
5992991 GTAACTAGTTAGTAAGGCATT
1 GTGACTAATTAGTAAGGCATT
5993012 ATGTGTCCAG
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 18 0.25
23 53 0.75
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.35
Consensus pattern (23 bp):
GTGACTAATTAGTAAGGCATTGC
Found at i:5993113 original size:21 final size:21
Alignment explanation
Indices: 5993052--5993114 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 21
5993042 TATGTATTAC
* *
5993052 CTTAAAATCAGTCACACAATG
1 CTTAAAAACAGTCACGCAATG
* ** *
5993073 CCTAAAAACTAACCATGCAATG
1 CTTAAAAAC-AGTCACGCAATG
5993095 CTTAAAAACAGTCACGCAAT
1 CTTAAAAACAGTCACGCAAT
5993115 AACTAAAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (21 bp):
CTTAAAAACAGTCACGCAATG
Found at i:5995145 original size:21 final size:21
Alignment explanation
Indices: 5995092--5995152 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
5995082 TGAAAGGAAG
* *
5995092 AATAATGTAATTGTAAG-AGT
1 AATAATGTAATTGTATGAAAT
*
5995112 AAAAATGTAATTGTATGAAAT
1 AATAATGTAATTGTATGAAAT
* *
5995133 AATAATGTGATTGAATGAAA
1 AATAATGTAATTGTATGAAA
5995153 GAAGATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (21 bp):
AATAATGTAATTGTATGAAAT
Found at i:6006143 original size:22 final size:22
Alignment explanation
Indices: 6006113--6006158 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6006103 TTTTATAATT
6006113 TAATAATAAAATAATATT-TATA
1 TAATAATAAAATAA-ATTATATA
* *
6006135 TAATCATAATATAAATTATATA
1 TAATAATAAAATAAATTATATA
6006157 TA
1 TA
6006159 TTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATAATAAAATAAATTATATA
Found at i:6006308 original size:14 final size:16
Alignment explanation
Indices: 6006279--6006310 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
6006269 TTTCATGATC
6006279 AAAAGTGTTTATTTAT
1 AAAAGTGTTTATTTAT
6006295 AAAAGT-TTTA-TTAT
1 AAAAGTGTTTATTTAT
6006309 AA
1 AA
6006311 TTTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (16 bp):
AAAAGTGTTTATTTAT
Found at i:6014965 original size:13 final size:13
Alignment explanation
Indices: 6014947--6014975 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6014937 ATCAAACATC
6014947 ATAATACAATCAA
1 ATAATACAATCAA
6014960 ATAATACAATCAA
1 ATAATACAATCAA
6014973 ATA
1 ATA
6014976 TAACCCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATACAATCAA
Found at i:6016822 original size:3 final size:3
Alignment explanation
Indices: 6016814--6016851 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6016804 TTTTAAATGG
6016814 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6016852 TGTTTTATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6018400 original size:78 final size:79
Alignment explanation
Indices: 6018300--6018450 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 79
6018290 TTATTGTTTC
*
6018300 TTTTTTGTAGAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTTTA
1 TTTTTTGTAGAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATA
6018365 AAATTTAGTGGTTA
66 AAATTTAGTGGTTA
*
6018379 TTTTTTGT-GAAAAAAATATTGTTAACACTATATTAAAAAATATAGTATTACACATCATGTTATA
1 TTTTTTGTAGAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATA
6018443 AAATTTAG
66 AAATTTAG
6018451 CTATTATACG
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 62 0.89
79 8 0.11
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (79 bp):
TTTTTTGTAGAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATA
AAATTTAGTGGTTA
Found at i:6018456 original size:28 final size:27
Alignment explanation
Indices: 6018411--6018477 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
6018401 TAACACTATA
6018411 TTAAAAAATATAGTATTACACATCATG
1 TTAAAAAATATAGTATTACACATCATG
* * * *
6018438 TTATAAAATTTAGCTATTATACGTCATG
1 TTAAAAAATATAG-TATTACACATCATG
6018466 TTAAAAAATATA
1 TTAAAAAATATA
6018478 ATTATTATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.37
Consensus pattern (27 bp):
TTAAAAAATATAGTATTACACATCATG
Found at i:6018472 original size:78 final size:78
Alignment explanation
Indices: 6018309--6018476 Score: 230
Period size: 78 Copynumber: 2.1 Consensus size: 78
6018299 CTTTTTTGTA
*
6018309 GAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTTTAAAATTTAGT
1 GAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATAAAATTTAGT
* *** **
6018374 GGTTATTTTTTGT
66 GATTATACGTCAT
*
6018387 GAAAAAAATATTGTTAACACTATATTAAAAAATATAGTATTACACATCATGTTATAAAATTTAGC
1 GAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATAAAATTTAG-
6018452 T-ATTATACGTCAT
65 TGATTATACGTCAT
*
6018465 GTTAAAAAATAT
1 G-AAAAAAATAT
6018477 AATTATTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
78 69 0.87
79 10 0.13
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (78 bp):
GAAAAAAATATTGTTAACACCATATTAAAAAATATAGTATTACACATCATGTTATAAAATTTAGT
GATTATACGTCAT
Found at i:6018483 original size:28 final size:28
Alignment explanation
Indices: 6018411--6018492 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
6018401 TAACACTATA
* *
6018411 TTAAAAAATAT-AGTATTACACATCATG
1 TTAAAAAATATAACTATTATACATCATG
* * * *
6018438 TTATAAAATTTAGCTATTATACGTCATG
1 TTAAAAAATATAACTATTATACATCATG
* *
6018466 TTAAAAAATATAATTATTATATATCAT
1 TTAAAAAATATAACTATTATACATCAT
6018493 ATTGAAAATT
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 9 0.21
28 33 0.79
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (28 bp):
TTAAAAAATATAACTATTATACATCATG
Found at i:6018501 original size:55 final size:54
Alignment explanation
Indices: 6018408--6018557 Score: 151
Period size: 55 Copynumber: 2.7 Consensus size: 54
6018398 TGTTAACACT
* * * *
6018408 ATATTAAAAAATAT-AGTATTACACATCATGTTATAAAATTTA-GCTATTATACGTC
1 ATATTAAAAAATATAATTATTACATATCAT-AT-TAAAATTTAGGC-ATTACACGTC
* * * * *
6018463 ATGTTAAAAAATATAATTATTATATATCATATTGAAAATTTAGGCGTTACAGGTT
1 ATATTAAAAAATATAATTATTACATATCATATT-AAAATTTAGGCATTACACGTC
* *
6018518 ATATTAAAAAATATAATTGTTACATGTCATATTAAAATTT
1 ATATTAAAAAATATAATTATTACATATCATATTAAAATTT
6018558 TAATTATTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
54 8 0.10
55 57 0.72
56 14 0.18
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (54 bp):
ATATTAAAAAATATAATTATTACATATCATATTAAAATTTAGGCATTACACGTC
Found at i:6026287 original size:33 final size:32
Alignment explanation
Indices: 6026211--6026287 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
6026201 CCAAACTTCC
* *
6026211 ATTATTCATTTTAATCTTGGTTATATAAGTTA
1 ATTATTAATTTTAATCTTGGTTATATAAGTCA
*
6026243 ATTATTCATTTTAATCTTGGTTA-AGGTAAGTCA
1 ATTATTAATTTTAATCTTGGTTATA--TAAGTCA
6026276 ATCT-TTAATTTT
1 AT-TATTAATTTT
6026288 TTTGAAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 1 0.03
32 23 0.57
33 15 0.38
34 1 0.03
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTATTAATTTTAATCTTGGTTATATAAGTCA
Found at i:6044743 original size:21 final size:21
Alignment explanation
Indices: 6044683--6044747 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
6044673 GTATCAATAA
6044683 TTTATTCAAAGGTATTGATACC
1 TTTATTCAAAGGTATTGATA-C
** * *
6044705 TGCA-TGAAA-GTATCGATAC
1 TTTATTCAAAGGTATTGATAC
*
6044724 TTTATTTAAAGGTATTGATAC
1 TTTATTCAAAGGTATTGATAC
6044745 TTT
1 TTT
6044748 CAACATAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 16 0.48
22 2 0.06
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTATTCAAAGGTATTGATAC
Found at i:6049729 original size:2 final size:2
Alignment explanation
Indices: 6049722--6049747 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6049712 ATGGATATTC
6049722 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
6049748 TCATAACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6053882 original size:20 final size:20
Alignment explanation
Indices: 6053857--6053902 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
6053847 AAATAAAAAA
6053857 ATATTAACACATAATATTTG
1 ATATTAACACATAATATTTG
*
6053877 ATATT-A-ACATAATTTTTG
1 ATATTAACACATAATATTTG
6053895 ATA-TAACA
1 ATATTAACA
6053903 ATTAGTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 2 0.09
20 5 0.22
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (20 bp):
ATATTAACACATAATATTTG
Found at i:6064455 original size:4 final size:4
Alignment explanation
Indices: 6064433--6064490 Score: 53
Period size: 4 Copynumber: 14.5 Consensus size: 4
6064423 CAAGAAAACT
* * * * * * *
6064433 ATAC ATGC ATGC ATGC ATAC ATAC ATAC ACAC ATAG ACAC ATAA ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
6064481 ATAC ATAC AT
1 ATAC ATAC AT
6064491 TTATATAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:6069017 original size:2 final size:2
Alignment explanation
Indices: 6069010--6069036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6069000 CCTACTTACC
6069010 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6069037 TCAACTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6071984 original size:30 final size:29
Alignment explanation
Indices: 6071907--6071998 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
6071897 AAGCATTAAA
* * *
6071907 GTGTAATAA-AAT-GTTTTTGAATATGGC
1 GTGTAATAACAATATTTTTTCAACATGGC
6071934 GTGTAATAACAATATTTTTTCAACATGGC
1 GTGTAATAACAATATTTTTTCAACATGGC
* * **
6071963 GTGTAATAATAGTATTTTTTTCAACATAAC
1 GTGTAATAACAATA-TTTTTTCAACATGGC
6071993 GTGTAA
1 GTGTAA
6071999 CAATCTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
27 9 0.16
28 3 0.05
29 24 0.44
30 19 0.35
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (29 bp):
GTGTAATAACAATATTTTTTCAACATGGC
Found at i:6072033 original size:26 final size:26
Alignment explanation
Indices: 6071940--6072026 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
6071930 TGGCGTGTAA
* **
6071940 TAACAATATTTTTTCAACATGGCGTG
1 TAACAATTTTTTTTCAACATAACGTG
*
6071966 TAATAATAGTATTTTTTTCAACATAACGTG
1 TAA-CA-A-T-TTTTTTTCAACATAACGTG
* *
6071996 TAACAATCTTTTTT-AACCATGACGTG
1 TAACAATTTTTTTTCAA-CATAACGTG
6072022 TAACA
1 TAACA
6072027 TGTTTTTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.04
26 22 0.45
27 2 0.04
28 2 0.04
29 2 0.04
30 19 0.39
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (26 bp):
TAACAATTTTTTTTCAACATAACGTG
Found at i:6072124 original size:75 final size:76
Alignment explanation
Indices: 6071956--6072126 Score: 191
Period size: 80 Copynumber: 2.2 Consensus size: 76
6071946 TATTTTTTCA
* * * *
6071956 ACATGGCGTGTAATAATAGTATTTTTTTCAACATAACGTGTAACAATCTTTTTTAACCATGACGT
1 ACATGACGTGTAACAATAGTATTTTTTTCAACATAACGTATAACAATC----TTAACCATAACGT
6072021 GTAACATGTTTTTGT
62 GTAACATGTTTTTGT
*** * * * *
6072036 ACATGATACGTAACAATAGTATTTTTTTTAACATGACGTATAACAGTC-TAACTATAACGTGTAA
1 ACATGACGTGTAACAATAGTATTTTTTTCAACATAACGTATAACAATCTTAACCATAACGTGTAA
*
6072100 TATGTTTTTGT
66 CATGTTTTTGT
6072111 ACATGACGTGTAACAA
1 ACATGACGTGTAACAA
6072127 CCTAATCATG
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
75 37 0.49
80 39 0.51
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (76 bp):
ACATGACGTGTAACAATAGTATTTTTTTCAACATAACGTATAACAATCTTAACCATAACGTGTAA
CATGTTTTTGT
Found at i:6072142 original size:45 final size:45
Alignment explanation
Indices: 6072066--6072215 Score: 135
Period size: 45 Copynumber: 3.3 Consensus size: 45
6072056 ATTTTTTTTA
* ** * **
6072066 ACATGACGTATAACAGTCTAACTATAACGTGTAATATGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGGCGTGTAATATGTTTTTGT
* *
6072111 ACATGACGTGTAACAACCTAATCATGGCGTGTCACACAT-TTTTATGT
1 ACATGACGTGTAACAACCTAACCATGGCGTGT-A-ATATGTTTT-TGT
* * * *
6072158 --ATGGCATGTAACAACCTAACCATGGCGTATAATATGTTTCTGT
1 ACATGACGTGTAACAACCTAACCATGGCGTGTAATATGTTTTTGT
*
6072201 ACATGATGTGTAACA
1 ACATGACGTGTAACA
6072216 TTATGACGTG
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
43 6 0.07
44 4 0.05
45 61 0.74
46 5 0.06
47 6 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (45 bp):
ACATGACGTGTAACAACCTAACCATGGCGTGTAATATGTTTTTGT
Found at i:6075438 original size:18 final size:19
Alignment explanation
Indices: 6075405--6075456 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
6075395 CAGTCAAATT
6075405 TATAATAAAAATTTAT-AAA
1 TATAAT-AAAATTTATCAAA
* *
6075424 TATCATAATATTTATCAAA
1 TATAATAAAATTTATCAAA
6075443 TATAATAAAATTTA
1 TATAATAAAATTTA
6075457 ACATCAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAATAAAATTTATCAAA
Found at i:6076350 original size:27 final size:27
Alignment explanation
Indices: 6076306--6076357 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
6076296 TGCCGTGTTT
*
6076306 AAAAAATATTATTGCACACCATGTTAA
1 AAAAAATATTATTACACACCATGTTAA
* *
6076333 AAAAAATGTTGTTACACACCATGTT
1 AAAAAATATTATTACACACCATGTT
6076358 TAAGTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAAAATATTATTACACACCATGTTAA
Found at i:6076741 original size:28 final size:28
Alignment explanation
Indices: 6076678--6076741 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
6076668 AGTCACATGC
* *
6076678 CATGTTGAAAAAAAAAATTATTACACGT
1 CATGTTTAAAAAAAAAATTATTACACAT
** * *
6076706 CGCG-TTAAAAATAAAATTATTATACAT
1 CATGTTTAAAAAAAAAATTATTACACAT
6076733 CATGTTTAA
1 CATGTTTAA
6076742 GGTGTTTAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (28 bp):
CATGTTTAAAAAAAAAATTATTACACAT
Found at i:6076776 original size:126 final size:127
Alignment explanation
Indices: 6076331--6076809 Score: 452
Period size: 126 Copynumber: 3.8 Consensus size: 127
6076321 ACACCATGTT
* * * * * * * * *
6076331 AAAAAAAATGTTGTTACACACCATGTTTAAGTTGTTTAATTCTAAGAGTATAAGTCTTAGA-GAA
1 AAAAAAAAAGTTATTATACATCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCTTA-ATGAA
* * * *
6076395 ATACAAAGATAGAGACCAAGTTACATGCCATGTT-TAAAAAAAAATTATTACACGTCATTTTGAA
65 ATACAAAGATAAAGATCAAGTTACATGCCATGTTGAAAAAAAAAATTATTACACGTCATATT---
6076459 G
127 G
* * * * * *
6076460 AAAAAAAAAGTTATTACACATCATATTTAA-GTGTTTAACTCCAAGATTTTTTCTCTTAGTGAAA
1 AAAAAAAAAGTTATTATACATCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCTTAATGAAA
* * * * * * * * * *
6076524 AATAAATACAAAGATCAAGTTATATGCCATGTTGAAAATAAAAGTTGTTACAAGCCATATTG
66 TACAAAGATAAAGATCAAGTTACATGCCATGTTGAAAAAAAAAATTATTACACGTCATATTG
* * * * * *
6076586 AAAAAAAAAGTTATTAT--ATGCTATGTTTAAGATATTTAACTCTAACAGTTTATATCTTAGTGA
1 AAAAAAAAAGTTATTATACAT-C-ATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCTTAATGA
* ***
6076649 AATACAAAGATAAAGATCAAGTCACATGCCATGTTGAAAAAAAAAATTATTACACGTCGCGTT-
64 AATACAAAGATAAAGATCAAGTTACATGCCATGTTGAAAAAAAAAATTATTACACGTCATATTG
6076712 AAAAATAAAA-TTATTATACATCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGT-TATAATGA
1 AAAAA-AAAAGTTATTATACATCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCT-TAATGA
* * *
6076775 AATAAAAAAATAAAGGTCAAGTTACATGCCATGTT
64 AATACAAAGATAAAGATCAAGTTACATGCCATGTT
6076810 TAAACTATGT
Statistics
Matches: 281, Mismatches: 60, Indels: 21
0.78 0.17 0.06
Matches are distributed among these distances:
124 2 0.01
125 2 0.01
126 100 0.36
127 79 0.28
128 52 0.19
129 46 0.16
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (127 bp):
AAAAAAAAAGTTATTATACATCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCTTAATGAAA
TACAAAGATAAAGATCAAGTTACATGCCATGTTGAAAAAAAAAATTATTACACGTCATATTG
Found at i:6077639 original size:29 final size:27
Alignment explanation
Indices: 6077607--6077684 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
6077597 AGAGACTAAG
*
6077607 TTACATAACATATTTAAAAAATATGGTTA
1 TTACATAACATATTGAAAAAA-AT-GTTA
**
6077636 TTACATGCCATATTGAAAAAAATGTTA
1 TTACATAACATATTGAAAAAAATGTTA
* ** *
6077663 TAACATGCCATGTTGAAAAAAA
1 TTACATAACATATTGAAAAAAA
6077685 AAAGTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 24 0.55
28 2 0.05
29 18 0.41
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (27 bp):
TTACATAACATATTGAAAAAAATGTTA
Found at i:6077662 original size:27 final size:27
Alignment explanation
Indices: 6077615--6077705 Score: 101
Period size: 29 Copynumber: 3.2 Consensus size: 27
6077605 AGTTACATAA
*
6077615 CATATTTAAAAAATATGGTTATTACATGC
1 CATATTGAAAAAA-AT-GTTATTACATGC
*
6077644 CATATTGAAAAAAATGTTATAACATGC
1 CATATTGAAAAAAATGTTATTACATGC
* * *
6077671 CATGTTGAAAAAAAAAAGTTATTACATGT
1 CATATTG--AAAAAAATGTTATTACATGC
6077700 CATATT
1 CATATT
6077706 TAAGGTGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 17 0.32
28 2 0.04
29 34 0.64
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (27 bp):
CATATTGAAAAAAATGTTATTACATGC
Found at i:6078813 original size:28 final size:28
Alignment explanation
Indices: 6078781--6078836 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
6078771 ATGTGACGTA
6078781 CTTCAGCAAAAAATGTTACACACCAAAG
1 CTTCAGCAAAAAATGTTACACACCAAAG
** *
6078809 CTTCAGCAACTAATGTTACACGCCAAAG
1 CTTCAGCAAAAAATGTTACACACCAAAG
6078837 TCAAAACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (28 bp):
CTTCAGCAAAAAATGTTACACACCAAAG
Found at i:6078896 original size:34 final size:34
Alignment explanation
Indices: 6078820--6078896 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 34
6078810 TTCAGCAACT
* * *
6078820 AATGTTACACGCCAAAGTCAAAACTTTAACACTA
1 AATGTTACACACCAAAGCCAAAACTTTAACACCA
* * * * *
6078854 GATATTACACATCAAGGCCAAAACTTTAGCACCA
1 AATGTTACACACCAAAGCCAAAACTTTAACACCA
6078888 AATGTTACA
1 AATGTTACA
6078897 TGTTAAGGCC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (34 bp):
AATGTTACACACCAAAGCCAAAACTTTAACACCA
Found at i:6081853 original size:30 final size:30
Alignment explanation
Indices: 6081832--6081889 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6081822 AAGGGATTAT
6081832 TTGATTCAAAATAAAAATATAAACACTTAC
1 TTGATTCAAAATAAAAATATAAACACTTAC
* *
6081862 TTGATTCAAAATAAAAGTATAAAGACTT
1 TTGATTCAAAATAAAAATATAAACACTT
6081890 GAACGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (30 bp):
TTGATTCAAAATAAAAATATAAACACTTAC
Found at i:6084514 original size:35 final size:35
Alignment explanation
Indices: 6084475--6084634 Score: 108
Period size: 35 Copynumber: 4.5 Consensus size: 35
6084465 TACTTGATTA
*
6084475 AAATTATTTAATTAAGTTATT-GAGCTTAATTAATT
1 AAATTATTTAATTAAGTTATTGGA-CCTAATTAATT
* * *
6084510 AAATTGTTTAATTAAGTCATTGGACCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGACCTAATTAATT
* * * * ** *
6084545 AAAATTGTTTAAGTAAATTATTATG-TTTAATTAGTT
1 -AAATTATTTAATTAAGTTATT-GGACCTAATTAATT
* * * * * *
6084581 GAATCATTTAATTAAATTATTGGCCCTGATTGATT
1 AAATTATTTAATTAAGTTATTGGACCTAATTAATT
**
6084616 AAATTAAATAATTAAGTTA
1 AAATTATTTAATTAAGTTA
6084635 ATTAAATTTT
Statistics
Matches: 94, Mismatches: 27, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
34 1 0.01
35 65 0.69
36 27 0.29
37 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGACCTAATTAATT
Found at i:6084548 original size:71 final size:71
Alignment explanation
Indices: 6084468--6084634 Score: 185
Period size: 71 Copynumber: 2.4 Consensus size: 71
6084458 TCTCAAATAC
** *
6084468 TTGATTAAAATTATTTAATTAAGTTATTGA-GCTTAATTAATTAAATTGTTTAATTAAGTCATTG
1 TTGATTAAAATTATTTAATTAAGTTATT-ATGCTTAATTAATTAAATCATTTAATTAAATCATTG
6084532 GACCTAA
65 GACCTAA
* * * * * * *
6084539 TTGATTAAAATTGTTTAAGTAAATTATTATGTTTAATTAGTTGAATCATTTAATTAAATTATTGG
1 TTGATTAAAATTATTTAATTAAGTTATTATGCTTAATTAATTAAATCATTTAATTAAATCATTGG
* *
6084604 CCCTGA
66 ACCTAA
**
6084610 TTGATT-AAATTAAATAATTAAGTTA
1 TTGATTAAAATTATTTAATTAAGTTA
6084635 ATTAAATTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
70 15 0.19
71 63 0.81
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (71 bp):
TTGATTAAAATTATTTAATTAAGTTATTATGCTTAATTAATTAAATCATTTAATTAAATCATTGG
ACCTAA
Found at i:6084680 original size:21 final size:22
Alignment explanation
Indices: 6084613--6084685 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
6084603 GCCCTGATTG
** *
6084613 ATTAAATTAAATAATTAAGTTA
1 ATTAAATTATTTAATTAAATTA
*
6084635 ATTAAATTTTTTAA--AAACTTA
1 ATTAAATTATTTAATTAAA-TTA
6084656 ATTAAATTATTTAATTAAATT-
1 ATTAAATTATTTAATTAAATTA
*
6084677 ATTAGATTA
1 ATTAAATTA
6084686 ATTAGTAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.05
21 24 0.57
22 13 0.31
23 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTAAATTATTTAATTAAATTA
Found at i:6084686 original size:13 final size:13
Alignment explanation
Indices: 6084653--6084679 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6084643 TTTTAAAAAC
6084653 TTAATTAAATTAT
1 TTAATTAAATTAT
6084666 TTAATTAAATTAT
1 TTAATTAAATTAT
6084679 T
1 T
6084680 AGATTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTAAATTAT
Found at i:6087788 original size:28 final size:28
Alignment explanation
Indices: 6087723--6087928 Score: 132
Period size: 28 Copynumber: 7.5 Consensus size: 28
6087713 TGGTACATAA
* **
6087723 TATATTG-AAAATGTAGTTGTTATTTGT
1 TATATTGAAAAATATAGTTGTTATACGT
* * * * *
6087750 CATGTTAAAAAATACAGTTGTTATATGT
1 TATATTGAAAAATATAGTTGTTATACGT
* * * **
6087778 TATATTG-AAAATTTAGTTATTAAATAT
1 TATATTGAAAAATATAGTTGTTATACGT
* * * *
6087805 CATGTTAAAAAATATAATTGTT-TCACGT
1 TATATTGAAAAATATAGTTGTTAT-ACGT
* * * *
6087833 TATGTTGAAAATTTTAGTTGTTATACAT
1 TATATTGAAAAATATAGTTGTTATACGT
*
6087861 TATATTGAAAAATATAGTTGTTACACGT
1 TATATTGAAAAATATAGTTGTTATACGT
* * * * *
6087889 TATGTT-AAATATTTAATTATTATACGT
1 TATATTGAAAAATATAGTTGTTATACGT
6087916 TATATTGAAAAAT
1 TATATTGAAAAAT
6087929 TTAATTATTA
Statistics
Matches: 132, Mismatches: 42, Indels: 9
0.72 0.23 0.05
Matches are distributed among these distances:
27 44 0.33
28 87 0.66
29 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.45
Consensus pattern (28 bp):
TATATTGAAAAATATAGTTGTTATACGT
Found at i:6087795 original size:55 final size:55
Alignment explanation
Indices: 6087723--6087891 Score: 169
Period size: 55 Copynumber: 3.1 Consensus size: 55
6087713 TGGTACATAA
* * * * *
6087723 TATATTGAAAATGTAGTTGTTATTTGTCATGTTAAAAAATACAGTTGTTAT-ATGT
1 TATATTGAAAATTTAGTTGTTATATATCATGTTAAAAAATACAATTGTT-TCACGT
* * *
6087778 TATATTGAAAATTTAGTTATTAAATATCATGTTAAAAAATATAATTGTTTCACGT
1 TATATTGAAAATTTAGTTGTTATATATCATGTTAAAAAATACAATTGTTTCACGT
* * * * * * * *
6087833 TATGTTGAAAATTTTAGTTGTTATACATTATATTGAAAAATATAGTTGTTACACGT
1 TATATTGAAAA-TTTAGTTGTTATATATCATGTTAAAAAATACAATTGTTTCACGT
6087889 TAT
1 TAT
6087892 GTTAAATATT
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
54 1 0.01
55 55 0.58
56 39 0.41
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (55 bp):
TATATTGAAAATTTAGTTGTTATATATCATGTTAAAAAATACAATTGTTTCACGT
Found at i:6087882 original size:56 final size:56
Alignment explanation
Indices: 6087757--6087928 Score: 181
Period size: 55 Copynumber: 3.1 Consensus size: 56
6087747 TGTCATGTTA
* * * * * * * *
6087757 AAAAATACAGTTGTTAT-ATGTTATATTGAAAA-TTTAGTTATTAAATATCATGTTA
1 AAAAATATAGTTGTT-TCACGTTATGTTGAAAATTTTAGTTATTATACATTATATTG
* *
6087812 AAAAATATAATTGTTTCACGTTATGTTGAAAATTTTAGTTGTTATACATTATATTG
1 AAAAATATAGTTGTTTCACGTTATGTTGAAAATTTTAGTTATTATACATTATATTG
* * *
6087868 AAAAATATAGTTGTTACACGTTATGTT--AAATATTTAATTATTATACGTTATATTG
1 AAAAATATAGTTGTTTCACGTTATGTTGAAAAT-TTTAGTTATTATACATTATATTG
6087923 AAAAAT
1 AAAAAT
6087929 TTAATTATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
54 5 0.05
55 52 0.53
56 42 0.42
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (56 bp):
AAAAATATAGTTGTTTCACGTTATGTTGAAAATTTTAGTTATTATACATTATATTG
Found at i:6087906 original size:83 final size:83
Alignment explanation
Indices: 6087765--6087931 Score: 185
Period size: 83 Copynumber: 2.0 Consensus size: 83
6087755 TAAAAAATAC
** * * *
6087765 AGTTGTTATATGTTATATTGAAAATTTAGTTATTAAATATCATGTTAAAAAATATAATTGTT-TC
1 AGTTGTTATACATTATATTGAAAATATAGTTATTAAACATCATGTTAAAAAATATAATTATTAT-
* *
6087829 ACGTTATGTTGAAAATTTT
65 ACGTTATATTGAAAAATTT
* * * * * *
6087848 AGTTGTTATACATTATATTGAAAAATATAGTTGTTACACGTTATGTT-AAATATTTAATTATTAT
1 AGTTGTTATACATTATATTG-AAAATATAGTTATTAAACATCATGTTAAAAAATATAATTATTAT
6087912 ACGTTATATTGAAAAATTT
65 ACGTTATATTGAAAAATTT
6087931 A
1 A
6087932 ATTATTACAC
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
83 48 0.70
84 21 0.30
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.46
Consensus pattern (83 bp):
AGTTGTTATACATTATATTGAAAATATAGTTATTAAACATCATGTTAAAAAATATAATTATTATA
CGTTATATTGAAAAATTT
Found at i:6098870 original size:12 final size:12
Alignment explanation
Indices: 6098853--6098878 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6098843 ATATCTACAC
6098853 TTGCAAAAGGCA
1 TTGCAAAAGGCA
6098865 TTGCAAAAGGCA
1 TTGCAAAAGGCA
6098877 TT
1 TT
6098879 ACTGATACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (12 bp):
TTGCAAAAGGCA
Found at i:6105853 original size:2 final size:2
Alignment explanation
Indices: 6105846--6105870 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6105836 ATATTTTCCC
6105846 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6105871 CCTTCTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6110513 original size:164 final size:164
Alignment explanation
Indices: 6110242--6110569 Score: 638
Period size: 164 Copynumber: 2.0 Consensus size: 164
6110232 ATATGTTTCG
*
6110242 GAATTATGACAGTAGTTGGACAAATTCTATAATTTATATGATATTAGTCGGATAATTTGATGATC
1 GAATTATGACAGTAGTTGGACAAATTCTATAATTTATATGATATTAGTAGGATAATTTGATGATC
6110307 TGAAAAATGGAGGCTCCATTGTCCATTGGTGTCTTTTGATGCTCATAAGGATTGTCTATGTGAAT
66 TGAAAAATGGAGGCTCCATTGTCCATTGGTGTCTTTTGATGCTCATAAGGATTGTCTATGTGAAT
*
6110372 TGTAACACCACAGTGTTAACTGAGAGATTTATCA
131 TGTAACACCACAGTGTAAACTGAGAGATTTATCA
6110406 GAATTATGACAGTAGTTGGACAAATTCTATAATTTATATGATATTAGTAGGATAATTTGATGATC
1 GAATTATGACAGTAGTTGGACAAATTCTATAATTTATATGATATTAGTAGGATAATTTGATGATC
6110471 TGAAAAATGGAGGCTCCATTGTCCATTGGTGTCTTTTGATGCTCATAAGGATTGTCTATGTGAAT
66 TGAAAAATGGAGGCTCCATTGTCCATTGGTGTCTTTTGATGCTCATAAGGATTGTCTATGTGAAT
6110536 TGTAACACCACAGTGTAAACTGAGAGATTTATCA
131 TGTAACACCACAGTGTAAACTGAGAGATTTATCA
6110570 AAAGCATTTT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 162 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (164 bp):
GAATTATGACAGTAGTTGGACAAATTCTATAATTTATATGATATTAGTAGGATAATTTGATGATC
TGAAAAATGGAGGCTCCATTGTCCATTGGTGTCTTTTGATGCTCATAAGGATTGTCTATGTGAAT
TGTAACACCACAGTGTAAACTGAGAGATTTATCA
Found at i:6124853 original size:19 final size:20
Alignment explanation
Indices: 6124828--6124885 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
6124818 TTGATGTATA
**
6124828 AATTAATAAATTATTAATTT
1 AATTAATAAATTAAAAATTT
6124848 -ATTAATTAAA-TAAAAATTT
1 AATTAA-TAAATTAAAAATTT
6124867 AATTAATAAA-T-AAAATTT
1 AATTAATAAATTAAAAATTT
6124885 A
1 A
6124886 TGATCTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.24
19 17 0.50
20 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTAATAAATTAAAAATTT
Found at i:6126437 original size:14 final size:14
Alignment explanation
Indices: 6126418--6126448 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6126408 GGTATAATCT
*
6126418 TCTCTGTTTCTCTC
1 TCTCTGTCTCTCTC
6126432 TCTCTGTCTCTCTC
1 TCTCTGTCTCTCTC
6126446 TCT
1 TCT
6126449 TCTTCTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.06, T:0.55
Consensus pattern (14 bp):
TCTCTGTCTCTCTC
Found at i:6128767 original size:26 final size:27
Alignment explanation
Indices: 6128710--6128767 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 27
6128700 AAATAAAAAG
*
6128710 TTTGTAATTAATGATAGTGATAAGACTCGC
1 TTTGTAATTAATGACAGTGATAAG---CGC
6128740 TTTGTAATTAATGACAGTGATAAG-GC
1 TTTGTAATTAATGACAGTGATAAGCGC
6128766 TT
1 TT
6128768 CCTTTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
30 23 0.85
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
TTTGTAATTAATGACAGTGATAAGCGC
Found at i:6151777 original size:15 final size:15
Alignment explanation
Indices: 6151757--6151796 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6151747 GCCGATGCGT
* *
6151757 GGCACGCAGATATGC
1 GGCACGAAGATACGC
*
6151772 GGCACGAAGGTACGC
1 GGCACGAAGATACGC
6151787 GGCACGAAGA
1 GGCACGAAGA
6151797 ATGGCTCTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.25, G:0.38, T:0.07
Consensus pattern (15 bp):
GGCACGAAGATACGC
Found at i:6152047 original size:15 final size:15
Alignment explanation
Indices: 6152012--6152054 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
6152002 CTCCTAAATA
*
6152012 TTTTGGAGGGAAATC
1 TTTTGGAGGGAAAAC
**
6152027 CATTGGAGGGAAAAC
1 TTTTGGAGGGAAAAC
*
6152042 TTTTGGAAGGAAA
1 TTTTGGAGGGAAA
6152055 TGTGGGGGGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.26
Consensus pattern (15 bp):
TTTTGGAGGGAAAAC
Found at i:6158478 original size:26 final size:26
Alignment explanation
Indices: 6158378--6158479 Score: 98
Period size: 26 Copynumber: 4.0 Consensus size: 26
6158368 TTACGACATT
6158378 CATCCACTTCTGATGGTAAAATTATC
1 CATCCACTTCTGATGGTAAAATTATC
* * * **
6158404 TATCTATTTCTGGCGGTAAAATTATC
1 CATCCACTTCTGATGGTAAAATTATC
* ** **
6158430 CTTAGA-TTCCAATGGTAAAATTATC
1 CATCCACTTCTGATGGTAAAATTATC
*
6158455 CATCCACTTCTGGTGGTAAAATTAT
1 CATCCACTTCTGATGGTAAAATTAT
6158480 AATTAAAATA
Statistics
Matches: 56, Mismatches: 19, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
25 18 0.32
26 38 0.68
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (26 bp):
CATCCACTTCTGATGGTAAAATTATC
Found at i:6171455 original size:14 final size:14
Alignment explanation
Indices: 6171436--6171470 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
6171426 AATACACATG
6171436 CACACACA-GCCATA
1 CACACACACGCCA-A
6171450 CACACACACGCCAA
1 CACACACACGCCAA
6171464 CACACAC
1 CACACAC
6171471 CAAAGAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.43, C:0.49, G:0.06, T:0.03
Consensus pattern (14 bp):
CACACACACGCCAA
Found at i:6190105 original size:53 final size:52
Alignment explanation
Indices: 6190025--6190131 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 52
6190015 CAATCAACCC
* * *
6190025 TACAAATATTTCCACTAAGAGGTTCTAGTTCATGAAGTA-CTATACATCCCCA
1 TACAAATATTTCCACTAAGAGGTTCTAGTCCATGAAGAAGC-ATACAACCCCA
6190077 TACAAATATTTCCATCTAAGAGGTTCTAGTCCATGAAGAAGCATACAACCCCA
1 TACAAATATTTCCA-CTAAGAGGTTCTAGTCCATGAAGAAGCATACAACCCCA
6190130 TA
1 TA
6190132 TGCTTTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 14 0.28
53 35 0.70
54 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (52 bp):
TACAAATATTTCCACTAAGAGGTTCTAGTCCATGAAGAAGCATACAACCCCA
Found at i:6194662 original size:98 final size:98
Alignment explanation
Indices: 6194553--6194755 Score: 361
Period size: 98 Copynumber: 2.1 Consensus size: 98
6194543 CATTAACTAC
* *
6194553 AATTTTTTTTTATTTGTGCTTTCGATTTCTCTCTCGCACCATTCAACTTTCTTTAATTTTATCAA
1 AATTTCTTTTTATTTGTACTTTCGATTTCTCTCTCGCACCATTCAACTTTCTTTAATTTTATCAA
6194618 TTTCTCTTTTCGACATTCATCTACTATATTCCT
66 TTTCTCTTTTCGACATTCATCTACTATATTCCT
* *
6194651 AATTTCTTTTTATTTGTACTTTCGATTTCTTTCTCGCACCATTTAACTTTCTTTAATTTTATCAA
1 AATTTCTTTTTATTTGTACTTTCGATTTCTCTCTCGCACCATTCAACTTTCTTTAATTTTATCAA
*
6194716 TTTCTCTTTTCGAGATTCATCTACTATATTCCT
66 TTTCTCTTTTCGACATTCATCTACTATATTCCT
6194749 AATTTCT
1 AATTTCT
6194756 CTCTTTTGCG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (98 bp):
AATTTCTTTTTATTTGTACTTTCGATTTCTCTCTCGCACCATTCAACTTTCTTTAATTTTATCAA
TTTCTCTTTTCGACATTCATCTACTATATTCCT
Found at i:6195194 original size:29 final size:29
Alignment explanation
Indices: 6195162--6195246 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
6195152 GTAACAAAAT
6195162 TTTTTTTAATATGACGTGTAATAATAATA
1 TTTTTTTAATATGACGTGTAATAATAATA
*
6195191 TTTTTTTAACATGAC--GT-ATAAT-AT-
1 TTTTTTTAATATGACGTGTAATAATAATA
* * *
6195215 GTTTTTGAATATGACGTGTAACAATAATA
1 TTTTTTTAATATGACGTGTAATAATAATA
6195244 TTT
1 TTT
6195247 GTTTGCAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 12 0.27
25 2 0.04
26 7 0.16
27 6 0.13
28 2 0.04
29 16 0.36
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTTTTAATATGACGTGTAATAATAATA
Found at i:6195211 original size:23 final size:24
Alignment explanation
Indices: 6195185--6195231 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6195175 ACGTGTAATA
*
6195185 ATAATAT-TTTTTTAACATGACGT
1 ATAATATGTTTTTGAACATGACGT
*
6195208 ATAATATGTTTTTGAATATGACGT
1 ATAATATGTTTTTGAACATGACGT
6195232 GTAACAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
ATAATATGTTTTTGAACATGACGT
Found at i:6195269 original size:31 final size:30
Alignment explanation
Indices: 6195208--6195269 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
6195198 AACATGACGT
* * *
6195208 ATAATATGTTTTTGAATATGACGTGTAACA
1 ATAATATGTTTTTGAACATGACATGCAACA
6195238 ATAATAT-TTGTTTGCAACATGACATGCAACA
1 ATAATATGTT-TTTG-AACATGACATGCAACA
6195269 A
1 A
6195270 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 11 0.41
31 14 0.52
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (30 bp):
ATAATATGTTTTTGAACATGACATGCAACA
Found at i:6195468 original size:29 final size:28
Alignment explanation
Indices: 6195436--6195511 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 28
6195426 TGTAGCAATC
6195436 TTTTTAACCATAACGTGTAATAATAATATT
1 TTTTTAA-CATAACGTGTAATAATAAT-TT
* *
6195466 TTTTTAACATGAC-T-T-GTAATAA-TT
1 TTTTTAACATAACGTGTAATAATAATTT
*
6195490 TTTTTAATCATAAAGTGTAATA
1 TTTTTAA-CATAACGTGTAATA
6195512 TAGTTTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
24 9 0.24
25 4 0.11
26 7 0.19
27 2 0.05
28 3 0.08
29 5 0.14
30 7 0.19
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (28 bp):
TTTTTAACATAACGTGTAATAATAATTT
Found at i:6195494 original size:54 final size:56
Alignment explanation
Indices: 6195389--6195511 Score: 169
Period size: 54 Copynumber: 2.2 Consensus size: 56
6195379 ATTTTTGTAT
* * *
6195389 ATAATGTGTAATAATAATATTTTTTTTCAATATGACTTGTAGCAATCTTTTTAACC
1 ATAAAGTGTAATAATAATATTTTTTTTCAACATGACTTGTAACAATCTTTTTAACC
* * * *
6195445 ATAACGTGTAATAATAATA-TTTTTTT-AACATGACTTGTAATAATTTTTTTAATC
1 ATAAAGTGTAATAATAATATTTTTTTTCAACATGACTTGTAACAATCTTTTTAACC
6195499 ATAAAGTGTAATA
1 ATAAAGTGTAATA
6195512 TAGTTTTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 35 0.58
55 7 0.12
56 18 0.30
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (56 bp):
ATAAAGTGTAATAATAATATTTTTTTTCAACATGACTTGTAACAATCTTTTTAACC
Found at i:6195508 original size:25 final size:24
Alignment explanation
Indices: 6195459--6195511 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
6195449 CGTGTAATAA
* **
6195459 TAAT-ATTTTTTTAACATGACTTG
1 TAATAATTTTTTTAACATAAAGTG
6195482 TAATAATTTTTTTAATCATAAAGTG
1 TAATAATTTTTTTAA-CATAAAGTG
6195507 TAATA
1 TAATA
6195512 TAGTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 10 0.40
25 11 0.44
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (24 bp):
TAATAATTTTTTTAACATAAAGTG
Found at i:6201887 original size:1 final size:1
Alignment explanation
Indices: 6201883--6201908 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6201873 AAGAAAAGGA
6201883 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
6201909 AGTATGACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.