Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002341.1 Hibiscus syriacus cultivar Beakdansim tig00004779_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: 1266629
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:334024 original size:31 final size:31
Alignment explanation
Indices: 333971--334078 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
333961 GTTCTACGGA
*
333971 ACATATGGATAGTTTTACCTATGTCTTTCGAG
1 ACATATGGACAG-TTTACCTATGTCTTTCGAG
* ***
334003 ACATATGGACAGTATACCTATGTTCTAAGGA-
1 ACATATGGACAGTTTACCTATG-TCTTTCGAG
*
334034 ACATATGGACAGTTTACCTATGT-TCTTCGGG
1 ACATATGGACAGTTTACCTATGTCT-TTCGAG
*
334065 ACCTATGGACAGTT
1 ACATATGGACAGTT
334079 ACCGAGGATC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.02
30 2 0.03
31 43 0.69
32 16 0.26
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTATGTCTTTCGAG
Found at i:335673 original size:23 final size:23
Alignment explanation
Indices: 335618--335683 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
335608 TCTTATATGA
* *
335618 CACTTCGGTGTATTTCTACGCGT
1 CACTTCGGTGTAATTCTACGCGG
*
335641 CACTAT-GGTGTAATTCTACGTGG
1 CACT-TCGGTGTAATTCTACGCGG
* *
335664 CACTTCGGTGCAATTATACG
1 CACTTCGGTGTAATTCTACG
335684 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
CACTTCGGTGTAATTCTACGCGG
Found at i:336414 original size:26 final size:26
Alignment explanation
Indices: 336384--336433 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
336374 GAACATCGAA
* *
336384 TGCATTTTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATACACTCAG
336410 TGCATTTGATGCATCGATACACTC
1 TGCATTTGATGCATCGATACACTC
336434 TAGCTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (26 bp):
TGCATTTGATGCATCGATACACTCAG
Found at i:337870 original size:29 final size:29
Alignment explanation
Indices: 337828--337902 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
337818 AACCCAACCA
**
337828 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
337857 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
337886 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
337903 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:337908 original size:29 final size:29
Alignment explanation
Indices: 337829--337916 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
337819 ACCCAACCAT
* * ****
337829 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
337858 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
337887 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
337916 A
1 A
337917 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:338889 original size:13 final size:13
Alignment explanation
Indices: 338867--338891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338857 ACATAAAATT
338867 AAAAAATAATTTG
1 AAAAAATAATTTG
338880 AAAAAATAATTT
1 AAAAAATAATTT
338892 ATTTTGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
AAAAAATAATTTG
Found at i:339360 original size:11 final size:12
Alignment explanation
Indices: 339336--339368 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
339326 TTTTTTTTTA
339336 TAAAATTAAAAT
1 TAAAATTAAAAT
339348 TAAAATT-AAAT
1 TAAAATTAAAAT
339359 TAAAA-TAAAA
1 TAAAATTAAAA
339369 CGCACACGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 12 0.60
12 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:339368 original size:5 final size:6
Alignment explanation
Indices: 339336--339368 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
339326 TTTTTTTTTA
339336 TAAAAT TAAAAT TAAAAT T-AAAT TAAAA- TAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAA
339369 CGCACACGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAAAT
Found at i:339745 original size:75 final size:74
Alignment explanation
Indices: 339656--339798 Score: 243
Period size: 75 Copynumber: 1.9 Consensus size: 74
339646 TGATTTAACA
*
339656 ATAAAATGACATAATTGAATATAAAATTAA-AGTTTAATTATATAATTGATAGAATCAATTTTAT
1 ATAAAATGACATAATTGAATACAAAATTAAGA-TTTAATTATATAATTGATAGAATCAATTTTAT
339720 TTATTTATTT
65 TTATTTATTT
*
339730 ATAAGAATGACATAATTGAATACAAAATTAAGATTTAATTATATGATTGATAGAATCAATTTTAT
1 ATAA-AATGACATAATTGAATACAAAATTAAGATTTAATTATATAATTGATAGAATCAATTTTAT
339795 TTAT
65 TTAT
339799 ATATAAATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
74 4 0.06
75 60 0.92
76 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (74 bp):
ATAAAATGACATAATTGAATACAAAATTAAGATTTAATTATATAATTGATAGAATCAATTTTATT
TATTTATTT
Found at i:347366 original size:32 final size:29
Alignment explanation
Indices: 347322--347388 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 29
347312 TATAAATTAT
347322 TATTATTGATATAATATTAT-TTGATATTTGTA
1 TATTATTGATATAA-ATTATATT--TATTTG-A
347354 TATTA-TGTATATAAATTATATTTATTTGA
1 TATTATTG-ATATAAATTATATTTATTTGA
347383 TATTAT
1 TATTAT
347389 AAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
29 6 0.19
30 6 0.19
31 7 0.22
32 13 0.41
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (29 bp):
TATTATTGATATAAATTATATTTATTTGA
Found at i:348015 original size:21 final size:21
Alignment explanation
Indices: 347986--348037 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
347976 CTAAACCTTG
*
347986 AACCTTAAACTCTAAATTCTA
1 AACCCTAAACTCTAAATTCTA
*
348007 AACTCTAAACTCTAAATTCTA
1 AACCCTAAACTCTAAATTCTA
348028 AACCCTAAAC
1 AACCCTAAAC
348038 CCAATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (21 bp):
AACCCTAAACTCTAAATTCTA
Found at i:348039 original size:7 final size:7
Alignment explanation
Indices: 347991--348037 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
347981 CCTTGAACCT
347991 TAAACTC
1 TAAACTC
*
347998 TAAATTC
1 TAAACTC
348005 TAAACTC
1 TAAACTC
348012 TAAACTC
1 TAAACTC
*
348019 TAAATTC
1 TAAACTC
*
348026 TAAACCC
1 TAAACTC
348033 TAAAC
1 TAAAC
348038 CCAATATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAACTC
Found at i:348496 original size:21 final size:22
Alignment explanation
Indices: 348448--348498 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
348438 TAAATAATAT
*
348448 AAAATAATGCCTAATAATTGTG
1 AAAATAATGCCTAATAATTGTA
*
348470 AAAATATATG-CTGATAA-TGTA
1 AAAATA-ATGCCTAATAATTGTA
348491 AAAATAAT
1 AAAATAAT
348499 TTACAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 9 0.35
22 12 0.46
23 3 0.12
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAATAATGCCTAATAATTGTA
Found at i:353103 original size:51 final size:51
Alignment explanation
Indices: 353020--353124 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
353010 TTGAGCTGAA
* * * *
353020 TATAGCATTTCTTTACCCATTACTCGATTCAATCTAGATTTAGTGAAATTC
1 TATAGCATTTCTATACCCATCACTAGAATCAATCTAGATTTAGTGAAATTC
353071 TATAGCATTTCTATACCCATCACTAGAATCAATCTAGATTTAGTGAAATTC
1 TATAGCATTTCTATACCCATCACTAGAATCAATCTAGATTTAGTGAAATTC
353122 TAT
1 TAT
353125 CCGACTTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (51 bp):
TATAGCATTTCTATACCCATCACTAGAATCAATCTAGATTTAGTGAAATTC
Found at i:353496 original size:2 final size:2
Alignment explanation
Indices: 353489--353531 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
353479 ATCTTATTTC
353489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
353531 A
1 A
353532 CGAATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:359396 original size:12 final size:12
Alignment explanation
Indices: 359365--359389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
359355 CATCACACTA
359365 GATAAAGAAAAG
1 GATAAAGAAAAG
359377 GATAAAGAAAAG
1 GATAAAGAAAAG
359389 G
1 G
359390 GAAAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GATAAAGAAAAG
Found at i:360306 original size:20 final size:20
Alignment explanation
Indices: 360281--360319 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
360271 TAAATTAAAT
**
360281 ATTAGATAGGATCAGTTTTA
1 ATTAGATAAAATCAGTTTTA
360301 ATTAGATAAAATCAGTTTT
1 ATTAGATAAAATCAGTTTT
360320 TATTCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTAGATAAAATCAGTTTTA
Found at i:360358 original size:20 final size:20
Alignment explanation
Indices: 360333--360425 Score: 71
Period size: 20 Copynumber: 5.0 Consensus size: 20
360323 TCTATTAGTT
360333 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
360353 ATTAGATAGAATCATTTTT-
1 ATTAGATAGAATCATTTTTA
*
360372 -TT--AT----TCTATTAGTTA
1 ATTAGATAGAATC-ATT-TTTA
*
360387 -TTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
360406 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
360426 TTTTGTTGCT
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
12 2 0.03
13 3 0.05
14 2 0.03
15 2 0.03
16 2 0.03
17 2 0.03
18 2 0.03
19 4 0.07
20 38 0.64
21 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.49
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:360399 original size:53 final size:53
Alignment explanation
Indices: 360280--360424 Score: 247
Period size: 53 Copynumber: 2.8 Consensus size: 53
360270 CTAAATTAAA
* * *
360280 TATTAGATAGGATCAGTTTTAATTAGATAAAATCA-GTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTTATTCTATTAGT
*
360332 TATTAGATATGATCATTTTTAATTAGATAGAATCATTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTTATTCTATTAGT
360385 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTT
360425 ATTTTGTTGC
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 32 0.37
53 55 0.63
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTTATTCTATTAGT
Found at i:365020 original size:20 final size:20
Alignment explanation
Indices: 364995--365033 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
364985 TAAATTAAAT
*
364995 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
365015 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
365034 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:365072 original size:20 final size:21
Alignment explanation
Indices: 365047--365086 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
365037 TCTATTAGTT
*
365047 ATTAGATAGGATC-ATTTTTA
1 ATTAGATAGAATCAATTTTTA
365067 ATTAGATAGAATCAATTTTT
1 ATTAGATAGAATCAATTTTT
365087 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAATTTTTA
Found at i:365110 original size:53 final size:52
Alignment explanation
Indices: 364994--365138 Score: 263
Period size: 53 Copynumber: 2.8 Consensus size: 52
364984 CTAAATTAAA
* *
364994 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
365046 TATTAGATAGGATCATTTTTAATTAGATAGAATCAATTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATC-ATTTTTTATTCTATTAGT
365099 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTT
365139 ATTTTGTTGC
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
52 39 0.43
53 51 0.57
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
Found at i:365125 original size:20 final size:20
Alignment explanation
Indices: 365100--365139 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
365090 TCTATTAGTT
*
365100 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
365120 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
365140 TTTTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:368193 original size:21 final size:21
Alignment explanation
Indices: 368167--368213 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
368157 TTGGATAATG
368167 ACGACACATGTGATTTAAACA
1 ACGACACATGTGATTTAAACA
368188 ACGACACATGTGATTTAAACA
1 ACGACACATGTGATTTAAACA
368209 ACGAC
1 ACGAC
368214 TGTCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (21 bp):
ACGACACATGTGATTTAAACA
Found at i:372702 original size:23 final size:23
Alignment explanation
Indices: 372648--372713 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
372638 TATTATATGA
* *
372648 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
* *
372671 CACTACGGTGCATTTCTATGCGG
1 CACTTCGGTGCATTTCTACGCGG
* *
372694 TACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
372714 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:377807 original size:23 final size:23
Alignment explanation
Indices: 377747--377814 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
377737 ATTATTATAT
* * *
377747 GGCACTTCGATGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
377770 GGCACTACGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
*
377793 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
377815 AGATGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:381161 original size:7 final size:7
Alignment explanation
Indices: 381149--381204 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
381139 AAGAGCCCAG
381149 TCTTCAT
1 TCTTCAT
381156 TCTTCAT
1 TCTTCAT
381163 TCTTCAT
1 TCTTCAT
381170 TCTTCAT
1 TCTTCAT
381177 TCTTCAT
1 TCTTCAT
381184 TCTTCAT
1 TCTTCAT
381191 TCTTCAT
1 TCTTCAT
381198 TCTTCAT
1 TCTTCAT
381205 GCCCTCTGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (7 bp):
TCTTCAT
Found at i:388443 original size:32 final size:32
Alignment explanation
Indices: 388393--388456 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
388383 GTACTTCTGC
* *
388393 AATAGAGTTGATGAAGAAGTCTTAAAGGTTAT
1 AATAAAGTAGATGAAGAAGTCTTAAAGGTTAT
388425 AATAAAGTAGATGAAGAAGTCTTAAAGGTTAT
1 AATAAAGTAGATGAAGAAGTCTTAAAGGTTAT
388457 CCATGATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (32 bp):
AATAAAGTAGATGAAGAAGTCTTAAAGGTTAT
Found at i:393299 original size:28 final size:29
Alignment explanation
Indices: 393268--393344 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 29
393258 AAATGGGATT
393268 GGGTC-GGGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGGTTTTTTTAAGTGTGATATTC
*
393296 GGGTCGGGTCGAGTTTTTTTAAGTTTGATATTC
1 GGGTC-GG--G-GTTTTTTTAAGTGTGATATTC
393329 GGGTCGGGGTTTTTTT
1 GGGTCGGGGTTTTTTT
393345 TTAAATTCGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 5 0.12
29 8 0.19
30 2 0.05
32 3 0.07
33 25 0.58
ACGTcount: A:0.12, C:0.08, G:0.34, T:0.47
Consensus pattern (29 bp):
GGGTCGGGGTTTTTTTAAGTGTGATATTC
Found at i:393346 original size:33 final size:33
Alignment explanation
Indices: 393268--393336 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
393258 AAATGGGATT
*
393268 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
1 GGGTCGAGTTTTTTTAAGTGTGATATTCGGGTC
*
393301 GGGTCGAGTTTTTTTAAGTTTGATATTCGGGTC
1 GGGTCGAGTTTTTTTAAGTGTGATATTCGGGTC
393334 GGG
1 GGG
393337 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.09, G:0.36, T:0.42
Consensus pattern (33 bp):
GGGTCGAGTTTTTTTAAGTGTGATATTCGGGTC
Found at i:393993 original size:18 final size:17
Alignment explanation
Indices: 393958--394001 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
393948 TCAGATTCAG
393958 ATTCCAATT-CGTACAT
1 ATTCCAATTCCGTACAT
*
393974 ATTCCAATTCCTTCACAT
1 ATTCCAATTCCGT-ACAT
*
393992 ATTTCAATTC
1 ATTCCAATTC
394002 TCTCAGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTCCAATTCCGTACAT
Found at i:420845 original size:30 final size:30
Alignment explanation
Indices: 420811--420870 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
420801 AATTTCTACC
420811 ACAATGTCCTTACATCAAATGAAGAATTTA
1 ACAATGTCCTTACATCAAATGAAGAATTTA
420841 ACAATGTCCTTACATCAAATGAAGAATTTA
1 ACAATGTCCTTACATCAAATGAAGAATTTA
420871 TGGTTCGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
ACAATGTCCTTACATCAAATGAAGAATTTA
Found at i:421759 original size:22 final size:22
Alignment explanation
Indices: 421734--421775 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
421724 ATTTTTATTT
* *
421734 AAATATATATATATATTTAAAA
1 AAATAAATACATATATTTAAAA
*
421756 AAATAAATACATTTATTTAA
1 AAATAAATACATATATTTAA
421776 TTTTATAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAAATACATATATTTAAAA
Found at i:421973 original size:17 final size:17
Alignment explanation
Indices: 421951--421986 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
421941 CATTGTAAAA
*
421951 TATGATTAAAATGATTT
1 TATGATAAAAATGATTT
421968 TATGATAAAAATGATTT
1 TATGATAAAAATGATTT
421985 TA
1 TA
421987 CACAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (17 bp):
TATGATAAAAATGATTT
Found at i:424262 original size:15 final size:15
Alignment explanation
Indices: 424242--424273 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
424232 AATTTTTTCA
424242 TTCAAGATATGTTCC
1 TTCAAGATATGTTCC
424257 TTCAAGATATGTTCC
1 TTCAAGATATGTTCC
424272 TT
1 TT
424274 TTTCCAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (15 bp):
TTCAAGATATGTTCC
Found at i:433466 original size:21 final size:21
Alignment explanation
Indices: 433414--433460 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
433404 GTTTCCAGAT
433414 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
433435 TCGCAACGCGAACGTCGACTA
1 TCGCAACGCGAACATCGACTA
433456 TCGCA
1 TCGCA
433461 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:433519 original size:42 final size:42
Alignment explanation
Indices: 433456--433593 Score: 167
Period size: 42 Copynumber: 3.3 Consensus size: 42
433446 ACGTCGACTA
*
433456 TCGCATTGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
*
433496 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGC
1 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
* * *
433538 TCGCGTTGCAATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGT
433584 T--CGTTGCGAT
1 TCGCGTTGCGAT
433594 AGTCGAAGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
40 10 0.12
41 2 0.02
42 48 0.56
44 16 0.19
46 9 0.11
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (42 bp):
TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
Found at i:433565 original size:65 final size:65
Alignment explanation
Indices: 433489--433635 Score: 226
Period size: 65 Copynumber: 2.3 Consensus size: 65
433479 GTTGCGATAG
433489 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGCTCGCGTTGCAATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGCTCGCGTTGCAATTTAT
* * * *
433554 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGCTCGCGTTGCAATTTAT
* *
433619 TTCAAATT--CGTTGCGAT
1 TCCAAGTTCGCGTTGCGAT
433636 AGTCCAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
63 9 0.12
65 67 0.88
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (65 bp):
TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGCTCGCGTTGCAATTTAT
Found at i:433613 original size:42 final size:42
Alignment explanation
Indices: 433557--433639 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
433547 AATTTATTCC
*
433557 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCG
*
433599 AAGTTCGCGTTGCGATTTATTTCAAATTCGTTGCGATAGTC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
433640 CAAAATCGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCG
Found at i:433630 original size:21 final size:21
Alignment explanation
Indices: 433461--433635 Score: 132
Period size: 21 Copynumber: 8.3 Consensus size: 21
433451 GACTATCGCA
*
433461 TTGCGA-TT-TTCCAAATTCG
1 TTGCGATTTATTCCAAGTTCG
*
433480 TTGCGA--TAGTCCAAGTTCGCG
1 TTGCGATTTATTCCAAGTT--CG
*
433501 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAGTTCG
* *
433522 TTGCGA--TAGTCCAAGCTCGCG
1 TTGCGATTTATTCCAAG-T-TCG
*
433543 TTGCAATTTATTCCAAGTTCGCG
1 TTGCGATTTATTCCAAGTT--CG
433566 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
* *
433587 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAGTT--CG
* *
433608 TTGCGATTTATTTCAAATTCG
1 TTGCGATTTATTCCAAGTTCG
433629 TTGCGAT
1 TTGCGAT
433636 AGTCCAAAAT
Statistics
Matches: 124, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 29 0.23
20 1 0.01
21 48 0.39
22 1 0.01
23 44 0.35
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (21 bp):
TTGCGATTTATTCCAAGTTCG
Found at i:434502 original size:19 final size:19
Alignment explanation
Indices: 434478--434542 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
434468 TCGTTGCGAT
434478 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
434497 TTTGGATTAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* * *
434520 CTTCGACTATCGCAACAAA
1 TTTGGACTATCGCAACGAA
434539 TTTG
1 TTTG
434543 TAATAAATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 12 0.34
21 14 0.40
23 9 0.26
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:434541 original size:42 final size:42
Alignment explanation
Indices: 434482--434561 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
434472 TGCGATTTTG
* *
434482 GACTATCGCAACGAATTTGGATTAAATCGCAACGCGAACTTC
1 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
*
434524 GACTATCGCAACAAATTTGTAATAAATCGCAACGCGAA
1 GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAA
434562 TTTGTTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:434552 original size:21 final size:22
Alignment explanation
Indices: 434528--434577 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
434518 AACTTCGACT
434528 ATCGCAA-CAAATTTGTAATAA
1 ATCGCAACCAAATTTGTAATAA
* *
434549 ATCGCAACGCGAATTTGTTATAA
1 ATCGCAAC-CAAATTTGTAATAA
434572 ATCGCA
1 ATCGCA
434578 TCGCGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
23 18 0.72
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (22 bp):
ATCGCAACCAAATTTGTAATAA
Found at i:434571 original size:23 final size:23
Alignment explanation
Indices: 434537--434588 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
434527 TATCGCAACA
434537 AATTTGTAATAAATCGCAACGCG
1 AATTTGTAATAAATCGCAACGCG
* *
434560 AATTTGTTATAAATCGCATCGCG
1 AATTTGTAATAAATCGCAACGCG
434583 AATTTG
1 AATTTG
434589 GAAAATCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (23 bp):
AATTTGTAATAAATCGCAACGCG
Found at i:434596 original size:21 final size:23
Alignment explanation
Indices: 434537--434605 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
434527 TATCGCAACA
* *
434537 AATTTGTAATAAATCGCAACGCG
1 AATTTGTGATAAATCGCATCGCG
*
434560 AATTTGTTATAAATCGCATCGCG
1 AATTTGTGATAAATCGCATCGCG
434583 AATTTG-GA-AAATCGCTAT-GCG
1 AATTTGTGATAAATCGC-ATCGCG
434604 AA
1 AA
434606 CTTCGACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 12 0.29
22 3 0.07
23 27 0.64
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (23 bp):
AATTTGTGATAAATCGCATCGCG
Found at i:434617 original size:21 final size:21
Alignment explanation
Indices: 434593--434647 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
434583 AATTTGGAAA
*
434593 ATCGCTATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* * *
434614 ATCGCAACGTGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
434635 ATCACAATGCGAA
1 ATCGCAATGCGAA
434648 TATGTAAATC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:436135 original size:23 final size:23
Alignment explanation
Indices: 436108--436163 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
436098 GAATTAATCA
436108 AATTTAAAATAACT-TGAAAAAA-T
1 AATTTAAAATAA-TAT-AAAAAATT
* *
436131 AATTTTAAATGATATAAAAAATT
1 AATTTAAAATAATATAAAAAATT
436154 AATTTAAAAT
1 AATTTAAAAT
436164 CAAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
AATTTAAAATAATATAAAAAATT
Found at i:438171 original size:40 final size:40
Alignment explanation
Indices: 438127--438207 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
438117 GTAAGGACAT
438127 ATTGGAAATAGTCATCTTTAGCAGTGTCTAAACTAGACTA
1 ATTGGAAATAGTCATCTTTAGCAGTGTCTAAACTAGACTA
* *
438167 ATTGGAAATAGTCCTCTTTAGCAGTGTCTAAACTAGGCTA
1 ATTGGAAATAGTCATCTTTAGCAGTGTCTAAACTAGACTA
438207 A
1 A
438208 CTTCGGTGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (40 bp):
ATTGGAAATAGTCATCTTTAGCAGTGTCTAAACTAGACTA
Found at i:439428 original size:125 final size:125
Alignment explanation
Indices: 439202--439452 Score: 475
Period size: 125 Copynumber: 2.0 Consensus size: 125
439192 ACGAAGAACT
439202 ATCGGAAACTGAAGATGACTCAAAAGGTGACAACTTATCGATGAGAGGATCAGATTCTGAATACG
1 ATCGGAAACTGAAGATGACTCAAAAGGTGACAACTTATCGATGAGAGGATCAGATTCTGAATACG
* *
439267 AAGTTTCGTATCTTGATGAAGAAAGTGAAGGTAGCTCATCCGGGTTGCACAAGAGTGACA
66 AAGTTTCGTATCTTGATGAAGAAAATGAAGGAAGCTCATCCGGGTTGCACAAGAGTGACA
439327 ATCGGAAACTGAAGATGACTCAAAAGGTGACAACTTATCGATGAGAGGATCAGATTCTGAATACG
1 ATCGGAAACTGAAGATGACTCAAAAGGTGACAACTTATCGATGAGAGGATCAGATTCTGAATACG
*
439392 AAGTTTCTTATCTTGATGAAGAAAATGAAGGAAGCTCATCCGGGTTGCACAAGAGTGACA
66 AAGTTTCGTATCTTGATGAAGAAAATGAAGGAAGCTCATCCGGGTTGCACAAGAGTGACA
439452 A
1 A
439453 AGATGATTTA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (125 bp):
ATCGGAAACTGAAGATGACTCAAAAGGTGACAACTTATCGATGAGAGGATCAGATTCTGAATACG
AAGTTTCGTATCTTGATGAAGAAAATGAAGGAAGCTCATCCGGGTTGCACAAGAGTGACA
Found at i:442784 original size:21 final size:20
Alignment explanation
Indices: 442698--442855 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
442688 AAATGACAAA
**
442698 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
442717 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
442737 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
442757 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
442778 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
442799 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
442819 CCAAAATCGTAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
442840 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
442856 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:442865 original size:20 final size:20
Alignment explanation
Indices: 442842--442974 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
442832 GCGAATATGA
* *
442842 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
442862 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
442882 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
442902 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
442922 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
442942 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
442962 AAATCGCAACGCG
1 AAATCGCAACGCG
442975 ATATTTAAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
20 98 0.98
21 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:442873 original size:40 final size:40
Alignment explanation
Indices: 442822--442974 Score: 119
Period size: 40 Copynumber: 3.8 Consensus size: 40
442812 CGATTTTCCA
* *
442822 AAATCGTAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CAT
* * * * * *
442862 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
* ** * * * *
442902 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
* * * *
442942 ATATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACGAAAATCGCAACGCG
442975 ATATTTAAAG
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 94 0.98
41 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
Found at i:443395 original size:33 final size:33
Alignment explanation
Indices: 443356--443426 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
443346 TTCACTTAGA
*
443356 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
443389 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
443422 TTTCA
1 TTTCA
443427 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:443549 original size:20 final size:20
Alignment explanation
Indices: 443505--443613 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
443495 TGCAGAAGAG
*
443505 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
443526 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
443546 TCGCAACGAGAGAATGAAAA
1 TCGCAACGAGAGAATGAAAA
443566 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
443580 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
443599 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
443614 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
18 3 0.04
19 12 0.16
20 32 0.44
21 11 0.15
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:443569 original size:40 final size:36
Alignment explanation
Indices: 443498--443613 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 36
443488 TTCAATTTGC
*
443498 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAG--AAATGAAAATCGCAACGAG
443536 AGAATGACTGTCGCAACGAGAGAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGA-AATGAAAATCGCAACGAG
*
443576 AG-A-A-TCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
443609 AGAAT
1 AGAAT
443614 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
33 20 0.29
34 11 0.16
37 1 0.01
38 4 0.06
39 3 0.04
40 20 0.29
41 11 0.16
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (36 bp):
AGAATAGTCGCAACGAGAAATGAAAATCGCAACGAG
Found at i:443583 original size:14 final size:14
Alignment explanation
Indices: 443564--443620 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
443554 AGAGAATGAA
443564 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
443578 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
443597 AATCGCAACGAGAG
1 AATCGCAACGAGAG
443611 AATCGCAACG
1 AATCGCAACG
443621 CGAAACCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:443598 original size:33 final size:33
Alignment explanation
Indices: 443517--443625 Score: 146
Period size: 33 Copynumber: 3.1 Consensus size: 33
443507 GCAACGAGAT
*
443517 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
443556 AGAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 A-AATGAAAATCGCAACGAGAGAATCGCAACGCG
443590 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
443623 AAA
1 AAA
443626 CCGTAATCGC
Statistics
Matches: 68, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
33 35 0.51
34 10 0.15
37 1 0.01
39 2 0.03
40 20 0.29
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:443654 original size:19 final size:19
Alignment explanation
Indices: 443632--443729 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
443622 GAAACCGTAA
*
443632 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
443651 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
443665 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
443684 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* *
443698 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
443717 TCGCGTTGCGATT
1 TCGCGTTGCGATT
443730 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:443673 original size:14 final size:14
Alignment explanation
Indices: 443654--443743 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
443644 TTTCATTTCG
443654 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
443668 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
443687 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
*
443701 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
443720 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
443734 CGTTGCGATT
1 CGTTGCGATT
443744 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 1 0.02
16 4 0.07
17 4 0.07
18 1 0.02
19 20 0.33
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:443679 original size:33 final size:33
Alignment explanation
Indices: 443637--443751 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
443627 CGTAATCGCA
443637 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
443670 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
443703 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
443736 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
443752 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:445604 original size:93 final size:93
Alignment explanation
Indices: 445445--445913 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
445435 TAGATTGCTT
*
445445 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
445510 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
445538 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
445603 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
445631 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
445696 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
445724 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
445789 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
445817 AGTAAATTTGTTCGGTTGGTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
445882 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
445909 AGTAA
1 AGTAA
445914 TGCAATCCAT
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 368 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:446001 original size:19 final size:19
Alignment explanation
Indices: 445961--446089 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
445951 TAGTTTACTT
* *
445961 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
445981 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
446000 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
446019 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
446033 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
446052 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
446066 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
446085 TCGCA
1 TCGCA
446090 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:446040 original size:33 final size:32
Alignment explanation
Indices: 445997--446089 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
445987 CGCGAAACCA
**
445997 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
446029 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
446062 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
446090 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:446087 original size:52 final size:52
Alignment explanation
Indices: 445961--446089 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
445951 TAGTTTACTT
** *
445961 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
446013 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
446066 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
446090 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:446107 original size:19 final size:19
Alignment explanation
Indices: 446085--446219 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
446075 GAAACCAAAA
*
446085 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
446104 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
446120 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
446137 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
446153 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
446170 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
446189 TCGCGTTGTGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
446209 TCGTGTTGCGA
1 TCGCGTTGCGA
446220 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 11 0.12
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:446126 original size:14 final size:14
Alignment explanation
Indices: 446107--446163 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
446097 TTTCATTTCG
446107 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
446121 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
446138 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
446154 CGTTGCGATT
1 CGTTGCGATT
446164 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:446132 original size:33 final size:33
Alignment explanation
Indices: 446090--446182 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
446080 CAAAATCGCA
*
446090 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
446123 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
446156 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
446183 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:448149 original size:14 final size:14
Alignment explanation
Indices: 448130--448165 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
448120 ATTGTTTAAT
448130 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
448144 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
448158 TGATTTGT
1 TGATTTGT
448166 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:448288 original size:19 final size:18
Alignment explanation
Indices: 448272--448368 Score: 121
Period size: 19 Copynumber: 5.4 Consensus size: 18
448262 AAAAATGACT
448272 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
448290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
448309 ATCGCAA--CGAGAT--A
1 ATCGCAATGCGAAATGAA
448323 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
448342 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
448362 ATCGCAA
1 ATCGCAA
448369 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 5 0.07
18 16 0.23
19 20 0.29
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:448400 original size:53 final size:53
Alignment explanation
Indices: 448272--448386 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 53
448262 AAAAATGACT
*
448272 ATCGCAATGCGAAATG-AAATCGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
448323 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
448376 ATCGCAATGCG
1 ATCGCAATGCG
448387 TTTATAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 16 0.26
52 12 0.20
53 33 0.54
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:448420 original size:14 final size:16
Alignment explanation
Indices: 448400--448544 Score: 77
Period size: 19 Copynumber: 8.6 Consensus size: 16
448390 ATAATTTCGC
448400 ATTGCGATTC-TCTCG
1 ATTGCGATTCATCTCG
*
448415 -TTGCGATTTCATTTCG
1 ATTGCGA-TTCATCTCG
*
448431 CATTGCGATTTTCATTTCG
1 -ATTGCGA--TTCATCTCG
448450 CATTGCGATTC-TCTCG
1 -ATTGCGATTCATCTCG
*
448466 -TTGCGATTTTCATTTCG
1 ATTGCGA--TTCATCTCG
*
448483 CATTGCGATTTTCATTTCG
1 -ATTGCGA--TTCATCTCG
*
448502 CATTGCGATTTTCATTTCG
1 -ATTGCGA--TTCATCTCG
448521 CATTGCGATTC-TCTCG
1 -ATTGCGATTCATCTCG
448537 -TTGCGATT
1 ATTGCGATT
448545 TTCATTTCCG
Statistics
Matches: 116, Mismatches: 4, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
14 20 0.17
15 3 0.03
16 15 0.13
17 10 0.09
18 6 0.05
19 62 0.53
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (16 bp):
ATTGCGATTCATCTCG
Found at i:448445 original size:19 final size:19
Alignment explanation
Indices: 448415--448597 Score: 218
Period size: 19 Copynumber: 10.4 Consensus size: 19
448405 GATTCTCTCG
448415 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
448433 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
448452 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
448466 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
448485 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
448504 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
448523 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
448537 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
448557 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
448571 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
448590 TTGCGATT
1 TTGCGATT
448598 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 6, Indels: 33
0.78 0.03 0.18
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 13 0.09
18 9 0.06
19 69 0.49
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:448505 original size:71 final size:72
Alignment explanation
Indices: 448415--448630 Score: 338
Period size: 71 Copynumber: 3.1 Consensus size: 72
448405 GATTCTCTCG
448415 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
448479 TT-CGCA
66 TTCCGCA
448485 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
448550 TTCCGCA
66 TTCCGCA
* * *
448557 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
**
448617 TTCCGTG
66 TTCCGCA
448624 TTGCGAT
1 TTGCGAT
448631 AGTCAAATGC
Statistics
Matches: 139, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
67 55 0.40
69 1 0.01
70 7 0.05
71 60 0.43
72 16 0.12
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCCGCA
Found at i:448619 original size:33 final size:33
Alignment explanation
Indices: 448433--448611 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
448423 TCATTTCGCA
448433 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
448466 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
448502 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
448537 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
448571 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
448604 TTGCGATT
1 TTGCGATT
448612 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.01
33 62 0.47
34 29 0.22
35 8 0.06
36 7 0.05
38 25 0.19
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:450908 original size:12 final size:12
Alignment explanation
Indices: 450891--450915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
450881 TTCTTCGGGA
450891 CTTTTTCTTCTT
1 CTTTTTCTTCTT
450903 CTTTTTCTTCTT
1 CTTTTTCTTCTT
450915 C
1 C
450916 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:451124 original size:24 final size:24
Alignment explanation
Indices: 451090--451136 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
451080 CTGAAACATC
451090 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
451114 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
451137 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:451845 original size:20 final size:20
Alignment explanation
Indices: 451817--452046 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
451807 AAATTTCAGT
* * *
451817 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
451837 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
451857 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
451877 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
451897 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
451917 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
451937 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
451957 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
451977 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
451997 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
452017 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
452037 GTTGCGATTT
1 GTTGCGATTT
452047 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:452063 original size:21 final size:21
Alignment explanation
Indices: 452033--452115 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
452023 ATTTTCATAT
*
452033 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
452054 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
452075 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
452096 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
452116 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:452106 original size:42 final size:43
Alignment explanation
Indices: 452013--452111 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
452003 ATTTATGTGT
* *
452013 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
452054 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
452096 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
452112 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:458382 original size:20 final size:20
Alignment explanation
Indices: 458359--458396 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
458349 TTAGCGTGAT
458359 TTTAATTCTTTTGGAGTGGA
1 TTTAATTCTTTTGGAGTGGA
458379 TTTAATTCTTTTGGAGTG
1 TTTAATTCTTTTGGAGTG
458397 AATCACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.24, T:0.53
Consensus pattern (20 bp):
TTTAATTCTTTTGGAGTGGA
Found at i:458826 original size:60 final size:60
Alignment explanation
Indices: 458726--458884 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 60
458716 ATGAATTTAG
* * * * * * * * * *
458726 GGATTAAATTGGAAGATTTTAAAGTTTGGGGACCATTTTAGAATGGGTCTCATATTTTGA
1 GGATAAAATTGGAATATTTAAAATTTTAGGGACTAATTTAGAATGAGTATCATAGTTTGA
* *
458786 GGATAAAATTGGAATATTTAAAATTTTAAGGACTAATTTAGAATGAGTATTATAGTTTGA
1 GGATAAAATTGGAATATTTAAAATTTTAGGGACTAATTTAGAATGAGTATCATAGTTTGA
*
458846 GGATAAAATTAGAATA-TTAAAATATTTAGGGA-TAATTTA
1 GGATAAAATTGGAATATTTAAAAT-TTTAGGGACTAATTTA
458885 TAATAAGAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 14 0.17
60 70 0.83
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (60 bp):
GGATAAAATTGGAATATTTAAAATTTTAGGGACTAATTTAGAATGAGTATCATAGTTTGA
Found at i:469439 original size:22 final size:22
Alignment explanation
Indices: 469411--469455 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
469401 TATCCCATAT
*
469411 TGTAATACTCTTGTCTGGAGAG
1 TGTAATAATCTTGTCTGGAGAG
469433 TGTAATAATCTTGTCTGGAGAG
1 TGTAATAATCTTGTCTGGAGAG
469455 T
1 T
469456 ATAACTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TGTAATAATCTTGTCTGGAGAG
Found at i:473462 original size:21 final size:22
Alignment explanation
Indices: 473432--473472 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
473422 ATCCACGCCA
473432 ACTCAAAATATATG-CAACTAC
1 ACTCAAAATATATGCCAACTAC
*
473453 ACTCATAATATATGCCAACT
1 ACTCAAAATATATGCCAACT
473473 CAAAACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (22 bp):
ACTCAAAATATATGCCAACTAC
Found at i:486608 original size:23 final size:23
Alignment explanation
Indices: 486561--486608 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
486551 GATAACATAT
**
486561 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
486584 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
486607 TA
1 TA
486609 AATATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:486671 original size:87 final size:87
Alignment explanation
Indices: 486525--486686 Score: 297
Period size: 87 Copynumber: 1.9 Consensus size: 87
486515 ATATTATATC
* *
486525 ATTTAATCGAAAATATTATCAAGTACGATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
486590 GCGCTTATATAATAAAATAAAT
66 GCGCTTATATAATAAAATAAAT
*
486612 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
486677 GCGCTTATAT
66 GCGCTTATAT
486687 TGACCTATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAAAT
Found at i:487179 original size:200 final size:199
Alignment explanation
Indices: 486703--487402 Score: 896
Period size: 200 Copynumber: 3.5 Consensus size: 199
486693 ATTTTTAACT
** * * * * *
486703 AAACCGGTTTATTTATACCGGTAACATTGCAAATTTACCTATTACAGTATAATTATCGGTTTCGA
1 AAACCGGTAAATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* ** * * * * * *
486768 TTTTTTTAGGATCGATA-TAATTGTAAATATATCGACACTTTATGCATGCACCTCGTTGGGTATT
66 TGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATT
* * *
486832 CATTATGGAAAAAAGTATCGACATAAACTTAAA-AAGTGTCGATACATTATGGAGA-ACTATTTT
131 CATTATGGAAAAAAGTATCGACA-CAAGTTAAACAAGTGTCGATACATTATGTAGATA-TATTTT
486895 CTCATA
194 CTCATA
* * *
486901 AAACCGGT-AATTTCTA-TCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTTG
1 AAACCGGTAAATTTCTACT-GGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCG
* *
486964 ATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCAT
65 ATGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCAT
*
487029 TCATTCTGGATAAAAAGTATCGACACAAGTTAAACAAGTGTCGATACATTATGTAGATATATTTT
130 TCATTATGGA-AAAAAGTATCGACACAAGTTAAACAAGTGTCGATACATTATGTAGATATATTTT
*
487094 TTCATA
194 CTCATA
* * *
487100 AAACCGATAAATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCAA
1 AAACCGGTAAATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * *
487165 TGTTATTT-GGATCGATACTTTTTGTAAATGTATCGACACTTTATGCGT-AAACCCTTTTGAGCA
66 TGTT-TTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTG-GCA
* * *
487228 TTCATTATGGAGAACAAGTATTGACACAAGTTACACAAGTGTCGATACATTATGTAGACT-TATT
129 TTCATTATGGA-AAAAAGTATCGACACAAGTTAAACAAGTGTCGATACATTATGTAGA-TATATT
487292 TTCTCATA
192 TTCTCATA
** * *
487300 AAACCGGTAAATTAATACTGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTAAATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
487365 TGATTTT-GGATCGATACTTTTTATAAATGTATCGACAC
66 TGTTTTTAGGATCGATACTTTTTATAAATGTATCGACAC
487403 ATATTTAGGT
Statistics
Matches: 443, Mismatches: 49, Indels: 19
0.87 0.10 0.04
Matches are distributed among these distances:
197 61 0.14
198 61 0.14
199 94 0.21
200 222 0.50
201 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
AAACCGGTAAATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATT
CATTATGGAAAAAAGTATCGACACAAGTTAAACAAGTGTCGATACATTATGTAGATATATTTTCT
CATA
Found at i:488766 original size:199 final size:198
Alignment explanation
Indices: 488415--488778 Score: 523
Period size: 199 Copynumber: 1.8 Consensus size: 198
488405 GTCAATCATC
* * * *
488415 ACAAATGTATCGACACAAATTCCACAAGTGTCGATACGTTATGTAGACCTGTTTTCTCATAAAAC
1 ACAAATGTATCGACACAAATTACACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
** * * **
488480 CGATAAATTTATACCGGTTACATTGTTAATTTACCTATTACATTAAAATTATCAGTTTTTATATT
66 CGATAAATTTATACCGGTTACATTGCAAAATTACCTATAACATTAAAATTATCAGTTTCGATATT
* *
488545 TTTGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCTTGCACCCTTTTGGGTATTTATC
131 TTTGGAATCAATACGTTTTATAAATGTATCGACACTTTATGCTTGCACCCTTTTGGGTATTTATC
488610 TGG
196 TGG
* *
488613 ACAAATTGTATCGACACAAATTACACATGTGTTGATACATTATGTAGACCTATTCTCTCATAAAA
1 ACAAA-TGTATCGACACAAATTACACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAA
* ** * *
488678 CCGATATATTTATACCGGTTACATTGCAAAATTACCTATAACATTAAAATTATGGGTTTCGGTGT
65 CCGATAAATTTATACCGGTTACATTGCAAAATTACCTATAACATTAAAATTATCAGTTTCGATAT
*
488743 TTTTGGAATCAATA-TTGTTTATAAATGTATCGACAC
130 TTTTGGAATCAATACGT-TTTATAAATGTATCGACAC
488779 ATATGTTTAC
Statistics
Matches: 144, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
198 6 0.04
199 138 0.96
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
ACAAATGTATCGACACAAATTACACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
CGATAAATTTATACCGGTTACATTGCAAAATTACCTATAACATTAAAATTATCAGTTTCGATATT
TTTGGAATCAATACGTTTTATAAATGTATCGACACTTTATGCTTGCACCCTTTTGGGTATTTATC
TGG
Found at i:489215 original size:19 final size:19
Alignment explanation
Indices: 489187--489234 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
489177 TTACATTCAC
489187 ATAC-AAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
489205 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
489224 ATACAAAATTA
1 ATACAAAATTA
489235 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:493970 original size:181 final size:182
Alignment explanation
Indices: 493266--494248 Score: 1345
Period size: 181 Copynumber: 5.4 Consensus size: 182
493256 TACGCATACT
*
493266 TATTAATGTATCGACACTTTCAACATATCCGGTAGCGC-TTACCGGTTTTGTCATTTATAGACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
* * * *
493330 ATTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATTGACACT
66 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * *
493395 TTATAGGCGCTATTATTGTTCCTC-TTTAAATTCCAAAAGTATCGATACTTA
131 TTATAGGCGCTATTATTGCTCCACTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
493446 TATTAATGTATCGACACCTTAAACATATCCGATAGCGCTTTATCGGTTTTTTCATTTATAGACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
* * * *
493511 GTTTTTTTAATTTTTTTTACATGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACA
66 G-TTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
* * *
493576 CTTTATAGGCG-TCATTACTGCTCCTCTTTTAAATTCCAAAGGTGTCGATACTTA
129 CTTTATAGGCGCT-ATTATTGCTCCACTTTTAAATTCCAAAAGTGTCGATACTTA
* ** * *
493630 TATTAATGTATCGACACTTTCAACATATCTAGTAGCGCTTTGCCGGTTTTGTCATTTATAAACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
* * *
493695 G--TTGACATTTTTTTACCTGTTATATTATTATGGATCAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * * * *
493758 TTATAAGCGCTATTACTGCTCTTA-TTTTAAATTCTAAAAGTGTCAATATTTA
131 TTATAGGCGCTATTATTGCTC-CACTTTTAAATTCCAAAAGTGTCGATACTTA
* ***
493810 TATTAATGTATCGACACCTTCAACATATCCGGTAGTGCTTTATTAGTTTTGTCATTTATAGACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
*
493875 GTTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATTGACACT
66 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
493939 TTATAGGCG-TCATTATTGCTCCACCTTTAAATTCCAAAGGTGTCGATACTTA
131 TTATAGGCGCT-ATTATTGCTCCACTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
493991 TATTAATGTATCGACACTTTCAACATATCTGGTAGCGCTTTGCTGGTTTTGTCATTTATATACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
* * * *
494056 GTTTTGGCA-TTTTTTACCTATTATATTGTTATGGATCGATATATTTTTATAAAATATCGACACT
66 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* ** *
494120 TTATAAGCGCTATTATTGCTCTTCTTTTAAATTCTAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTATTGCTCCACTTTTAAATTCCAAAAGTGTCGATACTTA
* * **
494172 TATTAATGTATCGACACCTTTAACATATCCGATAGTACTTTACCGGTTTTGTCATTTATAGACCG
1 TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
494237 GTTTTGTCATTT
66 GTTTTGTCATTT
494249 ATAGACTGGT
Statistics
Matches: 702, Mismatches: 88, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
180 188 0.27
181 345 0.49
182 15 0.02
183 72 0.10
184 82 0.12
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAATGTATCGACACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTATAGACCG
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTATTGCTCCACTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:494238 original size:20 final size:20
Alignment explanation
Indices: 494213--494268 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
494203 ATAGTACTTT
494213 ACCGGTTTTGTCATTTATAG
1 ACCGGTTTTGTCATTTATAG
494233 ACCGGTTTTGTCATTTATAG
1 ACCGGTTTTGTCATTTATAG
*
494253 ACTGGTTTTGTCATTT
1 ACCGGTTTTGTCATTT
494269 TTTTTACTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (20 bp):
ACCGGTTTTGTCATTTATAG
Found at i:499052 original size:25 final size:25
Alignment explanation
Indices: 499027--499075 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
499017 TATCTTCTAT
*
499027 TTAAAATGATTTTTTA-ATTTATTA
1 TTAAAATGATTTTTAAGATTTATTA
* *
499051 TTATAATTATTTTTAAGATTTATTA
1 TTAAAATGATTTTTAAGATTTATTA
499076 ATGCACATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TTAAAATGATTTTTAAGATTTATTA
Found at i:501660 original size:2 final size:2
Alignment explanation
Indices: 501653--501683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
501643 TAGACTGCAT
501653 TA TA 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 TA TA T
501684 TAATGCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:501894 original size:54 final size:54
Alignment explanation
Indices: 501829--501932 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
501819 ACGGAATTGG
* *
501829 GGAGAGTTAATTAAGATCAATTAATAATTGCCTAATT-TATATTTGACAAATGCC
1 GGAGAGCTAATTAAGATCAATTAAGAATTGCCTAATTAT-TATTTGACAAATGCC
501883 GGAGAGCTAATTAAGATCAATTAAGAATTGCCTAATTATTATTTGACAAA
1 GGAGAGCTAATTAAGATCAATTAAGAATTGCCTAATTATTATTTGACAAA
501933 CGTAAGACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (54 bp):
GGAGAGCTAATTAAGATCAATTAAGAATTGCCTAATTATTATTTGACAAATGCC
Found at i:503493 original size:30 final size:30
Alignment explanation
Indices: 503457--503530 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
503447 TGGGATGATT
503457 TTGAAGCTAAATGAGCTAGGGTATTTATAG
1 TTGAAGCTAAATGAGCTAGGGTATTTATAG
503487 TTGAAGCTAAATGAGCTAGGGTATTTATAG
1 TTGAAGCTAAATGAGCTAGGGTATTTATAG
*
503517 TTGAAGCTTAATGA
1 TTGAAGCTAAATGA
503531 CTAATCTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.34
Consensus pattern (30 bp):
TTGAAGCTAAATGAGCTAGGGTATTTATAG
Found at i:503666 original size:20 final size:21
Alignment explanation
Indices: 503641--503682 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
503631 CCAACTTACA
503641 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
503661 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
503682 A
1 A
503683 GTTGCATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Found at i:509915 original size:40 final size:40
Alignment explanation
Indices: 509854--509974 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 40
509844 ATCTGAGCAG
* *
509854 AAGCCACCGAAAAGGACGAATGTGTTGTCAAGTGTTTTAC
1 AAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
*
509894 AAGCCACAGAAAATGATGAATGTGTTGTCAAGTGTTTTAC
1 AAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
**
509934 ATCCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
1 AAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
509974 A
1 A
509975 TCTGAGCTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (40 bp):
AAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC
Found at i:510059 original size:54 final size:54
Alignment explanation
Indices: 509944--510081 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 54
509934 ATCCCACAGA
* * *
509944 AAAGGATGAATGTGTTGTCAAGTGTTTT----ACATCTGAGCTGAAACCACATG
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACACG
* * * *
509994 AGATGAAGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAGCCACACG
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACACG
* *
510048 AAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
510082 CTGCTATTCT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
50 24 0.33
54 48 0.67
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (54 bp):
AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACACG
Found at i:510472 original size:22 final size:22
Alignment explanation
Indices: 510446--510525 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
510436 TACATCTACA
*
510446 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAAATTCT
510468 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAAATTCT
* * *
510490 CTTTTTAAAGATGATATATTCT
1 CTCTTCAAAGATGATAAATTCT
* *
510512 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
510526 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAAATTCT
Found at i:511108 original size:113 final size:113
Alignment explanation
Indices: 510910--512410 Score: 2404
Period size: 113 Copynumber: 13.3 Consensus size: 113
510900 TTCCAGGTCG
* *
510910 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
* *
510975 CCAGGTCGATTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
511023 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
* *
511088 CCAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAAAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
511136 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAGCATTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
511201 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
511249 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCAATA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
511314 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
511362 AGTTCATAATGAAAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGAATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
* *
511427 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAAAATGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
511475 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
* *
511540 CCAGGTCGAGTTCACAATGAGAAGAACTCATCTGAAGAATGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
511588 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCGATGGATCAGCATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
511653 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
511701 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTCGATGGATCAACATTA
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
* * *
511766 CCAGGTCGAGTTCATAATAAGAAGAACTTATCTGAAGAATGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * * * *
511814 AGTTCATAATGAGAAGAACTTGTTCAAGTTTTCGCTTAAATTCATCATTCAATGGATCAACATTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
511879 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
511927 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
*
511992 CCAGAG-CGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGA
66 CCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
512040 AGTTCATAATGAGAA-AACTTGTTCAACTTTTTGCTCGAATTCATCACTT-GATGGATCAACTTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCA-TTCGATGGATCAACATT
* * * *
512103 TCCAAAG-AGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGA
65 ACC-AGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
512152 AGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
512217 CCAGAG-CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
66 CCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
512265 AGTTCATAATGAGAATAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAA-ATTT
1 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACA-TT
* * * *
512329 TCCAAAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATA
65 ACC-AGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
512378 AGTTCATAATGAGAAGAACTTGTTCAATCTTTT
1 AGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
512411 GCATGATTCT
Statistics
Matches: 1307, Mismatches: 72, Indels: 17
0.94 0.05 0.01
Matches are distributed among these distances:
112 104 0.08
113 1196 0.92
114 7 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
CCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
Found at i:512693 original size:3 final size:3
Alignment explanation
Indices: 512687--512769 Score: 112
Period size: 3 Copynumber: 26.7 Consensus size: 3
512677 TTTTTATATA
* *
512687 TAT TAT TAT TTT TTT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
512733 TAT TAT TAT TAT TAA TAT TAT TATT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TA
512770 CAGGCTTAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
3 64 0.88
4 9 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:514093 original size:3 final size:3
Alignment explanation
Indices: 514085--514183 Score: 75
Period size: 3 Copynumber: 34.0 Consensus size: 3
514075 TTTATTTTTG
* *
514085 ATT ATT ATT ATT ATT -TT A-T ATT -TT AAT ATT A-T ATT TTT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* * *
514127 ATT ATT -TGC AAT ATT ATT -TT ATT ATT ATT ATT ACTT TTT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
514172 ATT CTT ATT ATT
1 ATT ATT ATT ATT
514184 TATATAAATA
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
2 11 0.15
3 60 0.80
4 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:514106 original size:13 final size:13
Alignment explanation
Indices: 514085--514183 Score: 57
Period size: 13 Copynumber: 7.5 Consensus size: 13
514075 TTTATTTTTG
514085 ATTATTATTATTAT
1 ATTATTATT-TTAT
*
514099 TTTA-TATTTTAAT
1 ATTATTATTTT-AT
514112 ATTA-TATTTT-T
1 ATTATTATTTTAT
*
514123 AATTATTATTTGCAAT
1 -ATTATTATTT--TAT
514139 ATTATT-TTATTATT
1 ATTATTATT-TTA-T
514153 ATTATTACTTTT-T
1 ATTATTA-TTTTAT
*
514166 ATTATTATTCT-T
1 ATTATTATTTTAT
514178 ATTATT
1 ATTATT
514184 TATATAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.01
12 16 0.23
13 29 0.41
14 12 0.17
15 9 0.13
16 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (13 bp):
ATTATTATTTTAT
Found at i:514122 original size:21 final size:21
Alignment explanation
Indices: 514046--514123 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 21
514036 TACTCTAGTT
514046 TTATAATTTTATATTTTAATCA
1 TTATAATTTTATATTTTAAT-A
514068 TTCA-AATTTTAT-TTTTGATTATTA
1 TT-ATAATTTTATATTTT-A--A-TA
*
514092 TTATTATTTTATATTTTAATA
1 TTATAATTTTATATTTTAATA
*
514113 TTATATTTTTA
1 TTATAATTTTA
514124 ATTATTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
21 15 0.33
22 12 0.26
23 2 0.04
24 12 0.26
25 5 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATAATTTTATATTTTAATA
Found at i:514401 original size:20 final size:19
Alignment explanation
Indices: 514376--514417 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
514366 TTATTTTATA
514376 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
514396 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
514415 AAT
1 AAT
514418 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:514403 original size:119 final size:120
Alignment explanation
Indices: 514280--514509 Score: 295
Period size: 120 Copynumber: 1.9 Consensus size: 120
514270 TTTTAATATA
* * * * *
514280 TATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAATAACTGGATGTCCATTTTCTG
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CATTTTCTG
* *
514343 ATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAATTGTTTTAAT
65 ATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAATTGTTTTAAT
* * ** * *
514399 TATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTTA
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGA
*
514464 TATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
66 TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAAT
514510 ATATATTTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
119 29 0.31
120 50 0.53
121 15 0.16
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (120 bp):
TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGA
TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAATTGTTTTAAT
Found at i:528398 original size:31 final size:31
Alignment explanation
Indices: 528362--528421 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
528352 AACTTAAAAG
* *
528362 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
528393 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
528422 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:528476 original size:22 final size:21
Alignment explanation
Indices: 528443--528509 Score: 107
Period size: 22 Copynumber: 3.1 Consensus size: 21
528433 AATAATAAAT
*
528443 TATTTAAAATAAATCAATTCA
1 TATTTAAAATAAATCAATCCA
528464 TATTTAAAAATAAATCAATCCA
1 TATTT-AAAATAAATCAATCCA
528486 TATTTTAAAATAAATCAATCCA
1 TA-TTTAAAATAAATCAATCCA
528508 TA
1 TA
528510 CTAATAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
21 5 0.12
22 35 0.81
23 3 0.07
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:528518 original size:22 final size:21
Alignment explanation
Indices: 528449--528518 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
528439 AAATTATTTA
*
528449 AAATAAATCAATTCATATTTAA-
1 AAATAAATCAATCCATA--TAAT
**
528471 AAATAAATCAATCCATATTTT
1 AAATAAATCAATCCATATAAT
528492 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATA-TAAT
528515 AAAT
1 AAAT
528519 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
22 37 0.93
23 2 0.05
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATCAATCCATATAAT
Found at i:528525 original size:32 final size:32
Alignment explanation
Indices: 528489--528892 Score: 249
Period size: 32 Copynumber: 14.2 Consensus size: 32
528479 CAATCCATAT
528489 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * *
528521 TTTAAAATAAATCAATCAAT-C-CATACAACTA
1 TTTAAAATAAATCAATCCATACTAATA-AATTA
*
528552 --CAATAATAAATCAAT---T-C--AT--A-T-
1 TTTAA-AATAAATCAATCCATACTAATAAATTA
528573 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
528605 TTTAAAATAAATC-A---ATA-T-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
528627 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
528659 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
528689 --T--AATAAATCAATTCACATACTAATAAATTA
1 TTTAAAATAAATCAA-TC-CATACTAATAAATTA
*
528719 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
528751 TTTAAAATAAATCAATTCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
528781 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
528799 TTTAAAATAAATCAATCTATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
528831 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
528853 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
528885 TTTAAAAT
1 TTTAAAAT
528893 TAATTATTTT
Statistics
Matches: 296, Mismatches: 16, Indels: 120
0.69 0.04 0.28
Matches are distributed among these distances:
20 1 0.00
22 54 0.18
23 7 0.02
24 4 0.01
25 2 0.01
26 35 0.12
27 6 0.02
28 19 0.06
29 4 0.01
30 20 0.07
31 13 0.04
32 119 0.40
33 2 0.01
34 10 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:528621 original size:22 final size:22
Alignment explanation
Indices: 528596--528642 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
528586 AATCCATACT
528596 AATAAAT-TATTTAAAATAAATC
1 AATAAATAT-TTTAAAATAAATC
*
528618 AATATATATTTTAAAATAAATC
1 AATAAATATTTTAAAATAAATC
528640 AAT
1 AAT
528643 CCATACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATATTTTAAAATAAATC
Found at i:528628 original size:54 final size:54
Alignment explanation
Indices: 528435--528892 Score: 345
Period size: 54 Copynumber: 8.3 Consensus size: 54
528425 ACAACTACAA
*
528435 TAATAAATTATTTAAAATAAATCAAT-TCATATTTAAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATAT-ATATTTTAAAATAAATCAATCCATAC
** * ** * ** * *
528488 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCAAT-C
1 TAATAAATTATTTAAAATAAAT-C-AATATATAT-TTTAAAATAAATCAATCCATAC
* * *
528542 -CATACAACTA--CAATAATAAATCAAT-TCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATAT-ATATTTTAAAATAAATCAATCCATAC
528595 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
* * **
528649 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCACATAC
1 TAATAAATTATTTAAAATAAATCAAT--ATA-TATTTTAA-AATAAATCAA-TC-CATAC
*
528709 TAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATC-A---ATA-T-AT--A-T-TTTAAAATAAATCAATCCATAC
* ** * *
528773 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
1 TAA-TAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
** *
528821 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
528875 TAATAAATTATTTAAAAT
1 TAATAAATTATTTAAAAT
528893 TAATTATTTT
Statistics
Matches: 326, Mismatches: 40, Indels: 77
0.74 0.09 0.17
Matches are distributed among these distances:
48 22 0.07
49 3 0.01
50 2 0.01
52 32 0.10
53 19 0.06
54 156 0.48
55 3 0.01
56 3 0.01
57 5 0.02
58 18 0.06
59 2 0.01
60 29 0.09
61 1 0.00
62 2 0.01
63 3 0.01
64 11 0.03
65 2 0.01
66 10 0.03
67 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCCATAC
Found at i:528729 original size:14 final size:14
Alignment explanation
Indices: 528710--528762 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
528700 TTCACATACT
528710 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
528724 AATAAATCAATCTATACT
1 AATAAAT-TAT-T-TA-A
528742 AATAAATTATTTAA
1 AATAAATTATTTAA
528756 AATAAAT
1 AATAAAT
528763 CAATTCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 2 0.06
17 4 0.13
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:528741 original size:92 final size:90
Alignment explanation
Indices: 528627--528892 Score: 353
Period size: 92 Copynumber: 3.1 Consensus size: 90
528617 CAATATATAT
*
528627 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
528692 TAAATCAATTCACATACTAATAAATTA
66 TAAATCAA-TC-CATACTAATAAATTA
*
528719 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
528784 TAAATCAAT-C---C--AT--A-T-
66 TAAATCAATCCATACTAATAAATTA
* * **
528799 TTTAAAATAAATCAATCTATATTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
*
528860 TAAATCAATCTATACTAATAAATTA
66 TAAATCAATCCATACTAATAAATTA
528885 TTTAAAAT
1 TTTAAAAT
528893 TAATTATTTT
Statistics
Matches: 156, Mismatches: 8, Indels: 26
0.82 0.04 0.14
Matches are distributed among these distances:
76 11 0.07
77 4 0.03
80 51 0.33
81 1 0.01
82 3 0.02
84 3 0.02
85 1 0.01
86 9 0.06
89 1 0.01
91 1 0.01
92 71 0.46
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (90 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCCATACTAATAAATTA
Found at i:528828 original size:22 final size:22
Alignment explanation
Indices: 528782--528827 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
528772 CAACTACAAT
*
528782 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTATAA
*
528804 AATAAATCAATCTATATTAATAA
1 AATAAATCAATCCATATT-ATAA
528827 A
1 A
528828 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAATCCATATTATAA
Found at i:528882 original size:22 final size:22
Alignment explanation
Indices: 528833--528881 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
528823 ATAAATTATT
**
528833 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
528855 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
528878 TAAA
1 TAAA
528882 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:528968 original size:45 final size:45
Alignment explanation
Indices: 528850--529007 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 45
528840 AATCAATCCA
* * *
528850 TATTTTAAAATAAATCAATCTATACTAATAAATTA-TTTAAAATTAAT
1 TATTTTAAAATAAATC-AT-TTTA-AAATAAATTATTTTAAAATAAAT
* * *
528897 TATTTTAAAATAATTAATTCATATTTTATAATAATTTATTTTAAAATAATT
1 TATTTTAAAAT-A--AA-TC--ATTTTAAAATAAATTATTTTAAAATAAAT
*
528948 TATTTTATAATAAATCATTTTAAAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCATTTTAAAATAAATTATTTTAAAATAAAT
528993 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
529008 AACCTTATTA
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
45 40 0.42
47 13 0.14
48 3 0.03
50 12 0.13
51 25 0.26
52 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (45 bp):
TATTTTAAAATAAATCATTTTAAAATAAATTATTTTAAAATAAAT
Found at i:529004 original size:15 final size:15
Alignment explanation
Indices: 528876--529007 Score: 149
Period size: 15 Copynumber: 8.5 Consensus size: 15
528866 AATCTATACT
528876 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
528890 AATTAATTATTTTAA
1 AATAAATTATTTTAA
*
528905 AATAATTAATTCATATTTTAT
1 AAT-A--AA-T--TATTTTAA
*
528926 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
528941 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
528956 AATAAATCATTTTAA
1 AATAAATTATTTTAA
528971 AATAAATTATTTTAA
1 AATAAATTATTTTAA
528986 AATAAATTATTTTAA
1 AATAAATTATTTTAA
529001 AATAAAT
1 AATAAAT
529008 AACCTTATTA
Statistics
Matches: 101, Mismatches: 10, Indels: 13
0.81 0.08 0.10
Matches are distributed among these distances:
14 8 0.08
15 77 0.76
17 1 0.01
18 3 0.03
19 1 0.01
20 1 0.01
21 10 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:529680 original size:2 final size:2
Alignment explanation
Indices: 529673--529698 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
529663 CAATAACACA
529673 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
529699 GTGTGTGTAT
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:535596 original size:15 final size:15
Alignment explanation
Indices: 535542--535600 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
535532 CTCACAGATC
535542 TGCTTCTCC-ACGGGT
1 TGCTTCTCCTA-GGGT
* * *
535557 TCCTTCTCCAAGGAT
1 TGCTTCTCCTAGGGT
*
535572 TGCCTCTCCTAGGGT
1 TGCTTCTCCTAGGGT
535587 TGCTTCTCCTAGGG
1 TGCTTCTCCTAGGG
535601 CAGCTTTCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 35 0.97
16 1 0.03
ACGTcount: A:0.10, C:0.32, G:0.24, T:0.34
Consensus pattern (15 bp):
TGCTTCTCCTAGGGT
Found at i:535606 original size:15 final size:15
Alignment explanation
Indices: 535576--535628 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
535566 AAGGATTGCC
**
535576 TCTCCTAGGGTTGCT
1 TCTCCTAGGGCAGCT
535591 TCTCCTAGGGCAGCTT
1 TCTCCTAGGGCAGC-T
*
535607 TCCTCCCTAGAGCAGCT
1 T-CT-CCTAGGGCAGCT
535624 TCTCC
1 TCTCC
535629 AAGAACTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 14 0.44
16 4 0.12
17 4 0.12
18 10 0.31
ACGTcount: A:0.11, C:0.36, G:0.21, T:0.32
Consensus pattern (15 bp):
TCTCCTAGGGCAGCT
Done.